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clinicalnlplab

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PubmedSumm_train

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[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: although great progress has been made in breast cancer therapy , the treatments are often unsuccessful once metastases to vital organs occur . after removal of the primary breast tumor , the disease can be dormant over several years . as of today we are unable to predict reliably if or when the cancer will progress . il - 17 is a proinflammatory cytokine family with a documented association with poor prognosis in breast cancer . in our reviewwe also attempt to discern the context in which il - 17 has the opposite role and mediates antitumor reactions during cancer therapies . the il - 17 family is comprised of 6 cytokines , including il - 17a to il - 17f . among them , il - 17a and il - 17f share the highest sequence homology and have similar biological functions . il - 17 is primarily secreted by t helper ( th ) 17 cells and innate lymphocytes ( t cells , natural killer ( nk ) cells , and innate lymphoid cells ) . the prototypic il - 17a induces a signaling cascade in its target cells by binding to its receptor il - 17ra / rc . these receptor chains are broadly expressed in many cell types accounting for the pleiotropic effects of il - 17a on epithelial cells ( including transformed tumor cells ) , endothelial cells , osteoblasts , fibroblasts , and various myeloid cells . downstream of the il - 17 receptor , nfb activator 1 ( act1 ) and tnf receptor associated factor ( traf ) 4 are important adaptor proteins that transmit the intracellular signal cascade to activate transcription factors such as nuclear factor kappa b ( nfb ) and activator protein ( ap ) 1 in cell and tissue - specific manner . in turnil - 17 induces expression of certain chemokines and vascular endothelial growth factor ( vegf ) that lead to the recruitment of specific subsets of immune cells to the site of inflammation and the induction of angiogenesis , respectively . loss of control in il - 17 signaling is a common pathogenic mechanism in chronic inflammatory diseases / autoimmune diseases such as rheumatoid arthritis , psoriasis , and inflammatory bowel disease . in rheumatoid arthritis , il - 17 induces the expression of receptor activator of nuclear factor kappa b ligand ( rankl ) in osteoblasts which leads to the activation of osteoclasts . in addition among other il - 17 target genes , matrix metalloproteinases ( mmps ) and il - 6 play important roles in bone resorption and pathogenesis of the disease . although il - 17a / f is typically associated with destructive tissue damage in autoimmune disease and pathogen infections , it is also involved in protective immunity . for example , il - 17a acts as a potent inducer of t cell mediated immune responses by activating and recruiting dendritic cells ( dcs ) , monocytes , and neutrophils in various tissues . the recruitment and modulation of neutrophils are critical in host defense . however , beyond certain pathogen infection , il - 17 has an almost ubiquitous role as coordinator of neutrophil - dominated inflammation . furthermore , il - 17 stimulates dendritic cells ( dcs ) to produce il - 12 , while inhibiting il - 10 to augment th1 differentiation . studies on tumor infiltrating lymphocytes ( tils ) of breast cancer patients revealed the presence of th17 cells and pointed out the role of tumor microenvironmental factors including chemokine ( c - c motif ) ligand 5 and monocyte chemoattractant protein 1 in generating and attracting these cells into the tumors . il - 17 immune cells ( either lymphocytes or macrophages ) were also detected by cochaud et al . in tils of 8 of 40 breast cancer patients . . found a correlation between large numbers of il - 17 cells and high histological grade of the tumors , triple negative molecular subtype , and shorter disease - free survival . another study showed that three single nucleotide polymorphisms ( snps ) in the il - 17a gene are associated with increased breast cancer risk in a chinese patient population . determined an association between coordinately upregulated treg and th17 cells and aggressiveness of the disease . these and other findings discussed below in sections 3.2 to 3.5 are in support of il - 17 as a marker of poor prognosis and risk in breast cancer . however , it was also recognized that the blood of metastatic breast cancer patients contains a higher frequency of treg cells associated with risk . and in the her2 subtype of breast cancer very low levels of th17 cellsanti - her2 ( trastuzumab ) treatment increased th17 cell numbers to restore a balance between treg and th17 cells . similarly , other il - 17 family members have been correlated to pro- and antibreast cancer activities . therefore it is necessary to investigate the detailed mechanisms to decipher il - 17 's multiple roles in breast cancer . due to the high frequency of expression of il - 17 receptor chains on tumor cells , il - 17 family members can have direct effects on tumor cells . in a mouse breast cancer model , tumor - induced transforming growth factor beta ( tgf - ) induced cd8 t cells to produce il - 17 . in vitro , il - 17 in turn suppressed apoptosis of 4t1 mouse mammary carcinoma , ct26 mouse colon carcinoma , and mda - mb231 human breast carcinoma cell lines . furthermore , il - 17r knockdown in 4t1 breast cancer cells enhanced apoptosis and decreased tumor growth in vivo . treatment with endothelin - 1 receptor dual antagonist decreased il - 17a levels and caused slower 4t1 tumor growth . in another study , il - 17a via activation of tumor progression locus 2 ( tpl2 ) induced mitogen activated protein kinase ( mapk ) , c - jun n - terminal kinase ( jnk ) , and signal transducer and activator of transcription ( stat ) 3 signaling and cellular transformation in jb6 ci41 mouse epidermal cells and promoted mcf7 ( human breast cancer cell line ) tumorigenicity . this interaction increased tgf - production and consequently induced il - 17 expression , which enhanced mda - mb231 proliferation through stat3 activation . furthermore , il - 17a and il - 17e ( il - 25 ) were involved in proliferation and survival of human breast cancer cell lines t47d and mcf7 as well as primary breast cancer biopsy cells ijg1731 and thereby promoted their resistance to the antimitotic chemotherapy agent docetaxel . interestingly , under some circumstances , il - 17e ( il - 25 ) produced by nonmalignant mammary epithelial cells also displays antitumor function by targeting adjacent tumor cells , which express high levels of il - 25r and inducing apoptosis . similar to tnf - receptor , a death domain ( dd ) portion in the il - 25r may be linked to apoptosis inducing adaptor molecules fas - associated protein with death domain ( fadd ) and tnf - r1 - associated death domain protein ( tradd ) under certain conditions . for example , cells in the peritumoral area expressed il - 17 in 8 of 19 breast cancer patients studied . in vitro , the human breast cancer cell lines mda - mb231 and mda - mb435 were examined in a matrigel invasion assay by plating them on matrigel invasion chambers . added il - 17 greatly induced invasion of these cells into matrigel . it has been found that the tumor - promoting il - 17 : tumor angiogenesis axis causes resistance to anti - vegf therapy . tumor infiltrating th17 cells and il - 17 induced the expression of granulocyte - colony stimulating factor ( g - csf ) leading to immature myeloid cell recruitment into the tumor microenvironment and anti - vegf therapy resistance through the production of proangiogenic bv8 by these myeloid cells . in patients with invasive ductal carcinoma ( idc ) , tumor aggressiveness was reported to be enhanced by il - 17 via induction of angiogenic factors , such as chemokine cxcl8 , mmp - 2 , mmp - 9 , and vegf . similarly , injection of recombinant il - 17 in the murine breast cancer model 4t1 was shown to increase microvascular density , a parameter for tumor angiogenesis . in an attempt to produce a specific antihuman cancer vaccine by combining one of the most specific cancer - associated structures , the tn antigen ( alpha - galnac - o - ser / thr ) with mucin ( muc ) 6 , it was noted that tn strongly diminished immunogenicity compared to muc6 alone via a partial abrogation of th1 response and promotion of il - 17 responses . middle t - ( pymt - ) induced breast cancer models , il - 17 induced the secretion of cxcl1 and cxcl5 from mammary carcinoma cells and increased the suppressive function of myeloid derived suppressor cells ( mdscs ) on t cells by upregulating arginase ( arg ) , indoleamine 2,3 - dioxygenase ( ido ) , and prostaglandin - endoperoxide synthase - ( cox - ) 2 expression . the connection between breast cancer cells , il - 17 , and mdscs was further elucidated by coffelt et al . while studying a different model of breast cancer ( tissue - specific cadherin ( cdh ) 1 / p53 double knockout ) . the tumor - derived il - 1 induced il - 17 expression by t cells , which resulted in g - csf - dependent expansion and polarization of neutrophils into cells with mdsc characteristics . thus , the collaboration of il - 17 t cells with mdscs is important for tumor escape from host immune reactions and metastasis formation in distant organs . in an attempt to understand the interactions of t cells and mdscs in breast cancer models ( welte et al . , submitted ) , we confirmed the immunosuppressive activities of breast tumor - induced mdscs ( welte et al . , submitted ) in the in vitro coculture assay . mdscs isolated from blood of breast tumor bearing mice were admixed with nave splenic t cells . cocultures were stimulated with combination of plate - bound anti - cd3 and il - 2 and t cell proliferation was assessed by the cfse - labeling method . furthermore , cytokine secretion was compared to that of t cells activated in the absence of mdscs . it was noted that the regulatory cytokine il - 10 was diminished in the presence of mdscs ( figure 1 ( a ) ) , suggesting an il - 10 - independent inhibition on t cell proliferation . interestingly , t cells cocultured with large numbers of mdscs produced higher levels of il - 6 , il - 1 , and il - 17 , which indicates mdscs promote th17 cell differentiation ( figure 1 ( b ) ) . in addition to th17 cells , t cells serve as one main resource for il - 17 . in breast cancer mdscspromoted the tumor - infiltration of v4ccr6 t cells ( welte et al . , unpublished ) , subsets phenotypically related to il - 17 producers in previous studies . overall , these findings suggest a complex reciprocal interaction between mdscs and il - 17 producing t cells . in addition to the enhancement of metastasis via suppression of antitumor immunity , il - 17 may also promote metastasis through its inflammatory activities . found a link between intratumoral mmp - 11 mononuclear inflammatory cells and metastasis . il - 17 was among the proinflammatory factors associated with mmp - 11 cells , although its function in these cells still needs to be demonstrated . a very recent report analyzed the pathogenesis mechanism of metastasis in invasive ductal carcinoma ( ida ) and found that il - 17a affected different steps of metastasis such as migration of tumorigenic neutrophils and tumor cells to distant metastatic sites and production of il - 6 and ccl20 in metastatic tumor cells . a previous study also found that the metastasis promoting interaction of human bone marrow - derived stem cells with breast cancer tumor cells could be mediated by il - 17b / il - 17br signaling . the role of il - 17 in breast cancer metastasis to bone is also demonstrated by studies in mukherjee 's lab . mukherjee 's group generated arthritic mouse models and found enhanced bone and lung metastasis of breast cancer line 4t1 and pymt mouse breast cancer model upon arthritis induction . combination therapy of anti - il - 17 and anti - inflammatory celecoxib abrogated metastasis . a severe side effect of cancer treatment with aromatase inhibitor is arthralgia mediated by il - 17 . based on these findings , it is an attractive hypothesis that bone - destructive events in autoimmune arthritis and at late stage bone metastasis could both be caused by an il -17-dependent mechanism . since the discoveries that identified il - 17 as a central proinflammatory mediator , it has garnered a lot of attention and our knowledge on il - 17 is expanding quickly . in the biology of many tumors , il - 17 cytokines have a protumor role either directly on tumor cells or indirectly by having detrimental effects on the patient 's antitumor response and by causing microenvironmental changes that worsen the disease towards more invasive and metastatic phenotype . furthermore , il -17-induced changes in rheumatoid arthritis resemble the bone destruction phenotypes observed at late stage bone metastasis . therefore , treatment with anti - il - 17 holds a promise as anticancer therapy and in ameliorating the effects of bone metastasis . one concern in this treatment is that it could make patients more vulnerable to infections normally held in check by il - 17 . , it is less clear whether il - 17 could have beneficial effects in the immunotherapy of cancer . recent studies by zitvogel and colleagues described how certain chemotherapy drugs such as doxorubicin induce immunogenic tumor cell death . the immune response mounted to the dying tumor cells is critical for the efficacy of these chemotherapeutic drugs in preventing tumor progression . il - 17 expressed by t17 cells is important for initiating this immune reaction and eventually leads to activation of protective tumor - specific ifn expressing cd8 t cells . the challenge in future studies will be to understand how to restrict il - 17 's role to the promotion of cd8 / ifn antitumor activity without unleashing its other pathogenic protumor functions described above .\noutput:\n" }, { "from": "agent", "value": "metastatic disease accounts for more than 90 % of deaths from breast cancer . yet the factors that trigger metastasis , often years after primary tumor removal , are not understood well . recently the proinflammatory cytokine interleukin - ( il - ) 17 family has been associated with poor prognosis in breast cancer . here we review current literature on the pathogenic mechanisms driven by il - 17 during breast cancer progression and connect these findings to metastasis . these include ( 1 ) direct effects of il - 17 on tumor cells promoting tumor cell survival and invasiveness , ( 2 ) regulation of tumor angiogenesis , and ( 3 ) interaction with myeloid derived suppressor cells ( mdscs ) to inhibit antitumor immune response and collaborate at the distant metastatic site . furthermore , il - 17 might also be a culprit in bone destruction caused by late stage bone metastasis . interestingly , in addition to these potential prometastasis functions , there is also evidence for an opposite , antitumor role of il - 17 during cancer therapies . we hypothesize that these contradictory roles may be due to chronic , imbalanced versus acute transient nature of the immune reactions , as well as differences in the cells that interact with il - 17 + cells under different circumstances ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: mandibular canines usually have one root and one root canal however , approximately 15 % may have two canals or may have two roots . a previous study of sikri and kumar on permanent human mandibular canines showed anatomic variation in the root canal system . type i ( 70 % ) , type ii ( 4 - 12 % ) , type iii ( 4 - 6 % ) , type iv ( 4 - 10 % ) , type v ( 2 % ) , straight canals ( 53.84 - 60.71 % ) , curved canals ( 46 - 39 % ) , apical foramen centrally located ( 34.61 - 57.14 % ) , and apical foramen laterally located ( 65.38 - 42.85 % ) . various clinical cases has been reported in the literature involving anatomical variation in mandibular canines . a review of literature on previous studies of mandibular canines was shown in table 1 ( percentage of canals with type ii morphology ) , [ table 2 ] ( bilateral presence of two canals in a single root [ case reports ] ) , [ table 3 ] ( type ii canal configuration in a single root [ case reports ] ) . percentage of type ii canal configuration in the mandibular canines in different studies mandibular canine with bilateral two canals in a single root ( case reports ) mandibular canine with type ii canal configuration in single root ( case reports ) it was found that only one study was reported with bilateral type ii morphology in mandibular canine till date . the present case report describes the bilateral mandibular canine with two canals joining short of the apex with one canal and one foramina in a single root . a 54 - year - old woman reported to the department with discolored bilateral mandibular canines . both the canines were carious [ figure 1 ] . radiographic examination revealed bilateral mandibular canine with two canals without any periapical changes [ figures 2 and 3 ] . as the carious lesion was on the mesio buccal surface , the carious lesion was removed and the access was made from the buccal aspect [ figure 4 ] . the buccal and lingual orifices were identified and negotiated with no 8 and 10 k files . the buccal canal was having a straight path and the lingual canal was curved . the gg drill no 1 , 2 were used in crown down method under dental operating microscope to enlarge the orifices and to have the straight line access . the working length was measured with the help of an apex locator and verified with radiograph [ figures 2 and 3 ] . the lingual canal was merged with the buccal canal forming single canal at the apical third . the ca ( oh ) 2 dressing were placed in the canals and the patient was called after 1 week . the patient was asymptomatic after a week and the canals were irrigated with 3 % naocl and saline , dried with paper points and were obturated with gutta - percha of respective size and ah plus sealer using lateral condensation . the access preparation was thereafter restored with composite resin [ figures 2 and 3 ] . clinical photograph of bilateral mandibular canine preoperative working length and final obturation radiograph of 33 preoperative working length and final obturation radiograph of 43 access preparation showing two canals in 43 and 33the root canal morphology can be complex and should be thoroughly understood prior to the endodontic treatment . endodontic exploration using magnification tools such as dental operating microscope helps in the identification of an extra canal . additional root canals if not detected , are a major reason for failure of the treatment . mandibular canines usually have a single root with one canal ; however , variation in the number of roots and root canals has been reported . previous studies reported that 15 % of mandibular canines possess two canals with one or two foramen . mandibular canine with two roots and two canals , two roots and three canals with two foramina have also been described . all these cases show complex nature of the root canal , morphology of mandibular canines . the case reported was also of complex nature showing bilateral presentation of type ii canal morphology in mandibular canines within the same patient . root canal in a mandibular canine with a single root and single canal usually does not cause procedural errors during instrumentation . however , mandibular canines presenting with two roots or two canals poses difficulty during biomechanical preparation as the long axis of the canal meets the crown surface at the incisal edge or on the labial surface . therefore modifications in the access preparation were needed to avoid procedural error particularly on the buccal side of the canal . in addition , in cases of two canals and two canal orifices , the closer the orifices to each other , the greater the chance of the two canals joining at some point within the body of the root . in the present case , since there was carious lesion on the mesial aspect with wide buccal embrasure on both the mandibular canines , access preparation was made from the bucco - mesial aspect thereby preserving the tooth structure and making the straight line access and instrumentation of both the canals convenient and predictable . type ii canal configuration where two canals merge into a single canal short of the apex requires meticulous adherence to technicalities . blockage of canal may occur as the pulp tissue or organic debris may be pushed from one canal into the adjoining canal . manual exploration of these canals should be done carefully with radiographs before the use of larger or rotary instruments to avoid procedural error . coronal pulpal tissue removal with hand instruments should be done as much as possible prior to going down into the canal . the use of rotary instrument in such canal configuration requires precaution to avoid instrument separation as the instrument would be penetrating the joined part at a very acute angle or at a right angle , when it reaches the canal confluence . therefore in the present case , hyflex cm files with 4 % taper were used for enlargement . schilder suggested alternative preparation of such canals to prevent apical hourglass preparation which otherwise makes obturation difficult . castellucci suggested the cleaning and shaping of the straight canal first till the apex followed by curved canal till the point of merging . during obturation also , the main canal should be first obturated and thereafter the second canal was obturated to the point of merging . the knowledge of the morphologic variation is of paramount importance for the clinician for diagnosing and treating such complicated cases . radiographs and magnification devices such as dental operating microscope are also important tools in identification and management of extra canals .\noutput:\n" }, { "from": "agent", "value": "successful endodontic treatment depends upon the clinician 's knowledge and ability to manage aberrant anatomy . the mandibular canine normally comprises one canal and one root but 15 % may have two canals with one or two foramina and even less frequent may have two roots . this paper presents a case report of bilateral mandibular canine having two root canals which merge into one canal and one foramina ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: moderate alcohol consumption can transiently improve movement - associated symptoms such as essential tremors , dystonias , and tics . however , chronic alcohol consumption can trigger or aggravate hyperkinetic conditions such as akathisia , chorea , and myoclonus . delirium tremens is a severe form of alcohol withdrawal with symptoms of tremors , restlessness , agitation , and altered mental function , peaking around 72 hours after the last drink . the fda has approved quetiapine ( seroquel ) for the treatment of schizophrenia , bipolar disorder , and depression . most clinical trials conducted so far have shown efficacy of quetiapine to alleviate symptoms of depression , anxiety , and insomnia . additionally , quetiapine improved symptoms of akathisia , dyskinesia , and other preexisting involuntary motor movements when used in clinical trials for treating psychotic syndromes , dementia , and parkinson 's disease . when compared to risperidone and olanzapine in treatment of parkinson 's disease with or without dementia , quetiapine treatment was just as effective and additionally did not worsen patients ' motor symptoms . compared to a typical antipsychotic such as chlorpromazine , quetiapine treated patients showed lower incidence of parkinsonian symptoms ( 32 % versus 5 % ) . patients with concomitant alcohol dependence and depression share a common underlying molecular neuropathology and therefore have similar clinical phenotypic presentation . alcohol abuse and clinical depression have been individually associated with movement disorders such as akathisia . fornazzari and carlen reported development of akathisia in patients during alcohol withdrawal . a large study by baynes et al . involving 120 subjects reported an association approaching significance ( p = 0.007 ) between depression measures and development of akathisia . however , treatment of akathisia in the heavy drinking population with clinically significant depression remains an understudied area . this gap in our knowledge could limit our ability to treat movement disorders in alcoholics who are likely to have symptoms of depression . using the global assessment item of the bars scale , we also studied effects of history of drinking and active drinking during the treatment course of quetiapine xr . this study is one of the investigational arms of a larger protocol ( clinicaltrials.gov : nct # 00498628 ) that was supported by national institute on alcohol abuse and alcoholism . this investigation evaluated the efficacy of quetiapine xr in reducing akathisia in alcohol dependent patients with high and low depression scores . the inclusion criteria used in this study were diagnosis of alcohol dependence ( using diagnostic and statistical manual of mental disorders , fourth edition ) and age between 18 and 64 years . men consumed 10 or more drinks per day while women consumed 8 or more drinks per day for at least 40 % of the last 60 days of the 90 - day drinking assessment ( timeline followback , tlfb ) , and all subjects had 0.00 breath alcohol level at the time of consent . major exclusions included other psychoactive drug dependence within the last year , positive urine screen for drugs , participation in other pharmacological / behavioral studies within the last three months , lifetime diagnosis of major depression or eating disorder , use of antidepressants ( last 30 days ) and / or antipsychotics ( last 14 days ) before randomization , and a score 10 on the clinical institute withdrawal assessment of alcohol . study participants received quetiapine xr ( seroquel xr astrazeneca , wilmington , de ) for three months in 50 and 200 mg tablets . clinical and subjective assessments from baseline ( 0 w ) , week six ( 6 w ) , and end of week 12 ( or during week 13 , 12 w ) were evaluated . the dose of the medication was titrated in the first two weeks up to a target dose of 400 mg / d , which continued through week 12 followed by one week of tapering dose . all individuals received medical management ( mm ) that included assessment of medication side effects , participant education , and advice on drinking . individual demographics were collected including age ( years ) , sex ( male or female ) , weight ( lbs . ) , and drinking ( tlfb ) history . age , weight , and recent drinking were included as covariates as needed . we used the following recent tlfb measures : total drinks ( td90 ) ; average drinks per drinking day in last 90 days ( avgdpd90 ) ; number of drinking days in last 90 days ( ndd90 ) ; and heavy drinking days in last 90 days ( hdd90 ) . further , there was a 1 - month period during the recruitment phase when similar drinking history measures were also collected for 30 days ( td30 , hdd30 , ndd30 , and avgdpd30 ) . six - week and twelve - week assessment of drinking history were collected using tlfb for the 2 - week interval prior to the visit . patients were categorized by their madrs scores at baseline ( high madrs or clinically significant if seven ; and low madrs or clinically nonsignificant level if seven ) . we compared the prevalence of akathisia as the primary study outcome in patients with clinically significant and clinically nonsignificant depression and used the barnes akathisia rating scale ( bars ) instrument for collecting data on akathisia . bars was designed to rate the severity of drug - induced or parkinson 's disease - based akathisia and has been used regularly since its adoption in 1989 in clinical studies involving assessment of akathisia . quantitative assessment of akathisia is possible when both the subjective experience and the objective signs and features are taken into account . to test the effect of time , we evaluated prevalence of akathisia during the treatment period using chi - square analysis . we used univariate analysis of variance ( uanova ) to characterize recent drinking at each time point between the two depression groups ( used as a factor ) and further with the prevalence of reported akathisia within each madrs group . we also report corresponding clinical institute withdrawal assessment of alcohol ( ciwa ) scores for these patients . we also performed repeated analysis of variance between baseline , week 6 , and end of the study assessment of akathisia between low madrs and high madrs groups . data analysis platforms used in this study were spss 22.0 version ( ibm , chicago , il ) , ms office excel 2013 ( ms corp . , redmond , wa ) , and graphpad prism 6 ( graphpad software , inc . , la jolla , ca ) . there were three times as many men as women in this study , but since this occurred in all groups evenly , it did not restrain the analysis ; however between sex analysis could not be performed . there were a few dropouts during the course of the study and 4 - 5 % of the total data points could not be included from this study due to missing values . statistical analysis data were not conclusive at week 12 due to lowered prevalence of akathisia since by then their symptoms most likely got better with treatment . out of 108 enrolled patients , 31 patients showed clinically significant level of depression using the madrs scale . demographic measures were comparatively similar in all subgroups differentiated by madrs group ( table 1 ) . patients consuming at least 10 drinks per day matched the profile of very heavy drinkers . there was no significant main effect of any of the demographic or drinking history markers between the two madrs groups , and these patients also roughly matched in age and drinking history . we found that quetiapine reduced the occurrence of akathisia in very heavy drinking patient population in the group having clinically significant depression ( high madrs scores ) . ciwa scores for the assessment of alcohol withdrawal severity did not show any clinical significance throughout the study period ( table 1 ) . at baseline , there was a statistically significant elevation of ciwa scores found in patients with high madrs ; however numerically this elevation was not clinically significant . we performed repeated analysis of variance to measure severity of akathisia using bars assessment at week 6 and week 12 comparing from baseline values to identify if there is any significant contrast existing between the timelines due to madrs reporting . this finding supports our assessment that time course of treatment has a significant effect on improvement of akathisia , demonstrated by gradual lowering of extent of reporting of akathisia in both madrs groups . notably , there was also a trending level of contrast effect in time and madrs severity for akathisia reporting , p = 0.105 . however , there was a trending difference between the two groups , for which assessment of prevalence of akathisia at each time point was tested further . we performed chi - square analysis to separate this effect of quetiapine treatment on occurrence of akathisia between the two groups . also , there was no change in the significance observed when drinking history markers were included . other studies that have studied the efficacy of propranolol and lorazepam for treatment of akathisia have also reported time - course dependent alleviation of akathisia symptoms . there is substantial evidence that 5 - ht2a antagonists are successful in treating akathisia symptoms , exclusively neuroleptic - induced akathisia . a part of the subject population in this study reported symptoms of akathisia from alcohol withdrawal regardless of baseline level of madrs . our data suggest that continued treatment with quetiapine xr improved symptoms of akathisia especially in patients with clinically significant depression ( high madrs ) , when there was simultaneous lowering of alcohol intake . thereafter , we conducted chi - square tests to evaluate significance of occurrence of akathisia during quetiapine treatment course by depression level ( table 2 ) . at baseline , patients in both madrs groups experienced akathisia symptoms ; however , there were no significant differences between the two groups . the occurrence of akathisia more than doubled at 6 w from baseline reporting ( 0 w ) in the high madrs group . interestingly , akathisia incidence ( 44.4 % ) in high madrs group at week 6 was also four times higher than the corresponding occurrence of akathisia in low madrs group ( table 2 ) . our data are consistent with a recently published study , investigating efficacy of quetiapine in treating alcohol dependence in patients diagnosed with bipolar disorder . the authors found that although quetiapine treatment did not yield anticipated lowering of alcohol intake , patients experienced an increase in akathisia symptoms at 6 weeks ( bars score , p = 0.04 ) , but not at 12 weeks . at baseline , the likelihood of akathisia incidence in high madrs group compared to low madrs group was low . however , at week 6 , this likelihood increased to significant moderate levels of occurrence in the same comparison that was also statistically significant ( table 2 ) . at baseline and at 12 w , the likelihood ratio between the two groups remained low , tested by chi - square analyses . at 12 weeks , the incidence of akathisia in high madrs group dropped to 9 % , a ~ 5-fold decrease from 6 w and 2-fold decrease from baseline . patients , who exhibited lowering of akathisia scores after 6 weeks of treatment , also had correspondingly lowered madrs scores . this finding could be explained by the lowered levels of the heavy drinking markers ( figure 1 ( c ) ) . in the low madrs group , the occurrence of akathisia continuously dropped during the entire treatment course with a 5-fold lowering at 12 w from the baseline occurrence ( 0 w ) , which also supports the role of quetiapine in reducing akathisia in heavy drinking alcoholic patients without any ongoing clinically significant depression , who were actively drinking . thus , the primary aim of this study was to determine if quetiapine xr reduces akathisia in alcohol dependent patients . akathisia is generally associated with the sense of inner restlessness , mental uneasiness , unrest , or dysphonia , which can be intense . the occurrence and reduction in akathisia have also been evaluated in several studies that have used atypical antipsychotics including clozapine , olanzapine , quetiapine , ziprasidone , and others . based on our findings , we also report that there was an increase in akathisia in high madrs group at 6 weeks of treatment , and it was important to identify the cause for such an increase . akathisia has also been reported to be either primary or secondary to drug use . we found an increase in akathisia reported at 6 weeks and evaluated recent drinking amount and drinking pattern at baseline , 6 w , and 12 w time points to identify whether this increase was due to a direct adverse effect of quetiapine treatment , a change in drinking pattern , or interaction of quetiapine with drinking in the high madrs group . total drinks ( marker of heavy drinking ) recorded at all time points were higher in patients who exhibited akathisia in the high madrs group . we did not find any significant differences in drinking either at baseline ( 0 w ) or at the end of the study ( 12 w ) between patients that exhibited akathisia and those that did not ( figures 1 ( a ) and 1 ( c ) ) . however , at 6 weeks of treatment , total drinks reported were approximately four times more in patients who exhibited akathisia symptoms in the high madrs group ( figure 1 ( b ) ) and were highly statistically significant . the amount of drinking potentially influenced the incidence of akathisia at 6 w in high madrs group . a sizeable proportion of patients with depression and related disease conditions reported higher susceptibility to heavy alcohol drinking . interestingly , in the patient group with low madrs scores , total drinks decreased over time , and patients who exhibited akathisia did not show significant differences in total drinks compared to those who did not have akathisia , asserting the role of drinking and clinically relevant level of madrs in the appearance of akathisia symptoms at 6 weeks in the high madrs group . heavy drinking days ( another marker of heavy drinking from tlfb questionnaire , hdd30 ) at baseline were higher in patients with akathisia in the high madrs group . however , they were higher at both 6 - week and 12 - week assessments ( figures 2 ( a ) and 2 ( c ) ) . hdd at 6 weeks showed a significant elevation in patients who exhibited akathisia ( figure 2 ( b ) ) compared to those who did not , within the high madrs group . within the low madrs group , total number of heavy drinking days progressively lowered as treatment continued and frequency of heavy drinking days was similar in patients with akathisia compared to those without akathisia . both the amount and pattern of heavy drinkingwere influential in increasing the incidence of akathisia in the high madrs group at six weeks . the amount and pattern of heavy drinking were lower in this group both at baseline and at 12 weeks of treatment . on the other hand , in the low madrs group , we did not find any significant increase in patterns of heavy drinking during treatment , and the occurrence of akathisia progressively decreased over time . thus , we did not observe any influence of drinking alone or its interaction with quetiapine in patients who did not have clinically significant symptoms of depression . quetiapine xr seemed to alleviate akathisia symptoms in very heavy drinking alcohol dependent ( ad ) patients who did not have clinically significant symptoms of depression . in alcoholdependent patients with clinically significant symptoms of depression , the effects of quetiapine xr in reducing akathisia do not seem to begin until after the first six weeks of treatment . increases in the amount and pattern of heavy drinking potentially played a significant role in exacerbation of akathisia symptoms in heavy drinking ad patients . however , with continued treatment of quetiapine xr , ad patients showed a significant lowering of the incidence of akathisia . results from the present study extend our understanding of the interplay between heavy drinking , presence of clinically significant symptoms of depression , and the efficacy of quetiapine xr in alleviating symptoms of akathisia in very heavy drinking alcohol dependent patients . akathisia has been reported to either worsen or emerge as a new symptom during alcohol withdrawal in chronic alcoholics . results from our study show that an antidepressant drug such as quetiapine xr may reduce akathisia potentially resulting from alcohol withdrawal .\noutput:\n" }, { "from": "agent", "value": "heavy drinking contributes to involuntary body movements such as akathisia . quetiapine has been shown to alleviate symptoms of akathisia ; however , its efficacy in the alcohol dependent population is not well established . thus , we aimed to identify efficacy of quetiapine in treating akathisia in very heavy drinking alcohol dependent patients . 108 male and female heavy alcohol consuming study participants received 13 weeks of quetiapine xr . drinking history ( timeline followback , tlfb ) , depression ( montgomery - asberg depression rating scale , madrs ) , and movement ( barnes akathisia scale , bars ) measures were collected at baseline ( 0 w ) , week 6 ( 6 w ) , and week 12 ( 12 w ) . the role of drinking , symptoms of depression , and efficacy of quetiapine for treating akathisia were assessed . in patients with no symptoms of depression ( low madrs ) , quetiapine treatment decreased symptoms of akathisia . patients with clinically significant depression ( high madrs ) reported a significant increase in akathisia measures at 6 w which eventually decreased at 12 w to below baseline levels . the increase in akathisia at 6 w corresponded with a significant increase in the patients ' total drinks and heavy drinking pattern . treatment with quetiapine progressively lowered the occurrence of akathisia in alcohol dependent patients who do not show symptoms of depression . quetiapine treatment lowered akathisia over time in heavy drinkers who had clinically significant symptoms of depression ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: nasal polyps are polypoidal masses arising mainly from the mucous membranes of the nose and paranasal sinuses . when they extend to the choana , they are called choanal polyps , which constitute 36 % of all nasal polyps . nasal choanal polyps occur in three different forms , which produce similar symptoms : sphenochoanal , antrochoanal , and ethmoido - choanal polyps . sphenochoanal polyps are rare , while antrochoanal polyps are the most frequent and originate from the inflamed sinus mucosa . the etiology of sphenochoanal polyps is not clear . most nasal polyps produce the same symptoms : nasal obstruction , nasal discharge , and headache . nasal polyps are seen in anterior rhinoscopy , while an endoscopic examination or computed tomography ( ct ) is needed to differentiate sphenochoanal polyps . nasal polyps can be removed via endoscopic sinus surgery , but the site of origin is very important , especially for polyps originating from the sphenoid sinus because the carotid artery and optic nerve are located near the sphenoid sinus . any uncontrolled maneuver in endoscopic sinus surgery can damage these essential structures , so a preoperative diagnosis of the polyp origin is essential . a 16 - year - old boy presented to our outpatient clinic with a 1 - year history of bilateral nasal obstruction and discharge . the nasal cavity was filled with a nasal polyp and there was right septal deviation . at nasal endoscopy , the origin of the nasal polyp was not clear ; it seemed to originate posteriorly , occupying the left choana . paranasal coronal images showed a homogeneously opacified maxillary sinus , totally opacified left sphenoid sinus , and obliterated choanal passage . figure 1paranasal sinus computed tomography shows homogeneously opacified maxillary sinus walls , a totally opacified left sphenoid sinus , and an obliterated choanal passage . paranasal sinus computed tomography shows homogeneously opacified maxillary sinus walls , a totally opacified left sphenoid sinus , and an obliterated choanal passage . after decongestion , the polyp was seen to originate from the sphenoethmoidal recess , not the maxillary sinus . using nasal forceps , the polyp originated from the posterior wall of the sphenoid sinus . while attempting to excise the polyp stalk , dehiscence in the course of the optic nervethe stalk is seen at the bottom of the specimen . the sphenochoanal polyp specimen after surgery . the stalk is seen at the bottom of the specimen . figure 3endoscopic view of the dilated ostium of the sphenoid polyp caused by the sphenochoanal polyp . endoscopic view of the dilated ostium of the sphenoid polyp caused by the sphenochoanal polyp . postoperatively , saline was applied for one week and antibiotic was given to the patient . sphenochoanal polyps originate from the sphenoid sinus and are an uncommon form of choanal polyp . the most common symptoms are nasal obstruction , snoring , and unilateral nasal discharge , although the polyps can sometimes be asymptomatic . sphenochoanal and antrochoanal polyps can be misdiagnosed as hypertrophied inferior turbinate , adenoid vegetation , pansinusitis , and nasal polyps . the presentation of a sphenochoanal polyp is similar to that of the more common antrochoanal polyp . a sphenochoanal polyp can be diagnosed preoperatively using nasal endoscopy and paranasal sinus tomography . antrochoanal polyps are treated successfully with endoscopic sinus surgery , which allows complete removal of the polyp , including its site of origin , which minimizes the risk of recurrence . as choanal polyps arise from inflamed , edematous mucosa in the paranasal sinuses , at sinus surgery the origin of the polyp and diseased mucosathey originate from the sphenoid sinus wall , exiting the sinus via the sphenoid ostium , passing through the sphenoethmoidal recess , and reaching the choana . in this case , the nasal polyp was not diagnosed as a sphenochoanal polyp preoperatively as the polyp obscured the cavity and was not clear radiologically . when there is a lack of maxillary opacity with choanal polyps , one should think of the possibility of sphenochoanal polyp . sphenochoanal polyps usually pass through the sphenoethmoidal recess directly and do not reach the middle meatus unless very large . opacification in the maxillary sinus , such as in our case , might lead to a misdiagnosis . intraoperative imaging provides near real - time imaging that has the potential to improve surgical outcomes and reduce operative morbidity . ct can also help to assess the origin of nasal polyps and surrounding essential structures , such as the carotid artery and optic nerve . at surgery , the polyp stalk was not from the maxillary sinus , but from the sphenoid sinus through an enlarged sphenoid sinus . forceps are also used to excise the polyp instead of a microdebrider , as the latter might damage the optic nerve and carotid artery when used inside the sphenoid sinus . uncontrolled pulling on the nasal polyp with forceps is dangerous due to the proximity of the carotid artery and optic nerve , which can be damaged during surgery . in our case , the sphenochoanal polyp was excised en bloc and there were no complications involving the optic nerve . isolated sphenoid sinus disease is under - reported due to a lack of recognition and experience . the stalk of the polyp should not be excised in an uncontrolled manner due to the proximity of the optic nerve and carotid artery .\noutput:\n" }, { "from": "agent", "value": "isolated sphenoid pathology is uncommon . nasal polyps that originate from the anterior wall of the sphenoid sinus and reach the nasopharynx are called sphenochoanal polyps . the atypical location of sphenochoanal polyps leads to misdiagnosis , and surgery risks injuring the surrounding structures , such as the optic nerve , carotid artery , and brain . for the differential diagnosis of sphenochoanal polyps , nasal endoscopy and computed tomography are very important . we present the clinical and radiological features of a sphenochoanal polyp and review the status of the optic nerve during endoscopic surgery for a sphenochoanal polyp ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in vitro fertilization - embryo transfer ( ivf - et ) is an increasingly common treatment for infertility in sub - saharan african . however , the region remains resource - constrained and this treatment option correspondingly places a tremendous financial burden on clients , meaning that a client 's first attempt may well be the last . thus , it is imperative for caregivers in this region to take measures to enhance the likelihood of success of each attempt . cancellation before ocr may occur due to a poor response to the drugs used to stimulate the ovaries , a high risk of over - response to the fertility drugs and developing ovarian hyperstimulation syndrome , any situation or illness preventing egg collection at the time of oocyte maturation , or post - surgical adhesions and / or displacements impeding the accessibility of the ovaries . other reasons include the incorrect timing of human chorionic gonadotropin ( hcg ) injections , triggering the release of the mature eggs before recovery , and the individual choice of patients to postpone the cycle for reasons that may be personal . a poor response to ovarian stimulation is the most common reason for cycle cancellation . in order to mitigate this , a range of response predictors have been employed , including age , body mass index ( bmi ) , previous ovarian surgery , previous ovarian stimulation experiences , basal follicle - stimulating hormone levels , anti - mllerian hormone assays , the antral follicular count , and serial folliculometry with ultrasound . our local experience showed that poor ovarian response to stimulation based on ultrasound folliculometry was a common reason for cycle cancellation . we observed that a perceived poor ovarian response was occasionally due to the inadvertent non - visualization of developing follicles caused by ovarian displacement or encasement from previous surgery . thus , we instituted a protocol in which , prior to cycle cancellation for poor ovarian response , scrupulous attention was paid to proxy indicators of the response such as estradiol levels , basal follicle - stimulating hormone or anti- mllerian hormone levels , endometrial thickness , and other individual clinical characteristics before arriving at a final decision . we present our experiences over the past 24 months ( july 2013 to june 2015 ) in a case series , describing patients in whom the meticulous review of proxy indicators for ovarian response provoked a painstaking ultrasound search for the developing ovarian follicles with positive results , allowing cycle cancellation to be averted . the need for transabdominal aspiration was recognized during follicular monitoring when one or both ovaries were not clearly visualized transvaginally and were much more apparent transabdominally . at the time of ocr , the urinary bladder was emptied by patient voiding or in - and - out catheterization , and we then attempted to access the ovaries transvaginally using the usual technique , additionally applying abdominal pressure to push the ovaries into the pelvis . we then converted to transabdominal retrieval using analgesia and conscious sedation ( with pentazocine and diazepam ) as typically used \" should be added for transvaginal aspiration . the operator resumed scanning the patient 's abdomen using regular ultrasound gel and an abdominal probe ( 3.5 mhz probe , mindray digi prince dp6600 , mindray , shenzhen , china ) to identify the area in the abdominal wall that would provide the most feasible and safest access to the ovary or ovaries . the gel was wiped off and , using sterile techniques , the predetermined abdominal wall area , including the skin and subcutaneous tissues , was injected with local anesthetic ( 1 % lidocaine hydrochloride ) . the abdominal area was then cleaned with sterile water and under ultrasound guidance , using a 6.5 mhz vaginal probe with a needle guide , a standard retrieval needle was inserted through the abdominal wall to aspirate the follicles . a deliberate effort was made to aspirate the follicles via a single transabdominal needle insertion in order to minimize the quantity of skin punctures . the need for transabdominal aspiration was recognized during follicular monitoring when one or both ovaries were not clearly visualized transvaginally and were much more apparent transabdominally . at the time of ocr , the urinary bladder was emptied by patient voiding or in - and - out catheterization , and we then attempted to access the ovaries transvaginally using the usual technique , additionally applying abdominal pressure to push the ovaries into the pelvis . we then converted to transabdominal retrieval using analgesia and conscious sedation ( with pentazocine and diazepam ) as typically used \" should be added for transvaginal aspiration . the operator resumed scanning the patient 's abdomen using regular ultrasound gel and an abdominal probe ( 3.5 mhz probe , mindray digi prince dp6600 , mindray , shenzhen , china ) to identify the area in the abdominal wall that would provide the most feasible and safest access to the ovary or ovaries . the gel was wiped off and , using sterile techniques , the predetermined abdominal wall area , including the skin and subcutaneous tissues , was injected with local anesthetic ( 1 % lidocaine hydrochloride ) . the abdominal area was then cleaned with sterile water and under ultrasound guidance , using a 6.5 mhz vaginal probe with a needle guide , a standard retrieval needle was inserted through the abdominal wall to aspirate the follicles . a deliberate effort was made to aspirate the follicles via a single transabdominal needle insertion in order to minimize the quantity of skin punctures . a 36 - year - old nullipara presented for treatment in 2014 with an 8 - year history of secondary infertility and a previous myomectomy that was performed in 2006 . her bmi was 24.7 kg / m , and she was counseled and selected for ivf - et treatment following the confirmation of bilateral tubal blockage . she underwent controlled ovarian hyperstimulation following our protocol , and was commenced on five ampoules of human menopausal gonadotropin ( hmg ) ( 75 iu per ampoule ) daily . a baseline transvaginal scan ( tvs ) at the commencement of stimulation ( on day 3 of her menses ) showed antral follicles in both ovaries and no residual follicles or cysts . on stimulation day 5 , a tvs revealed tiny follicles in the left ovary , but the right was not visualized . on stimulation day 8 , a tvs revealed a poorly defined left ovary with very tiny follicles , whereas the right ovary was not visualized . her stimulation day 5 estradiol level of 413 pg / ml and endometrial thickness of 7.8 mm were suggestive of apparent follicular development ( i.e. , a good response ) . this necessitated a further search using a transabdominal scan , which showed four follicles in the right ovary and two follicles in the left ovary , with the largest measuring 15.5 mm . on stimulation day 11 , the six follicles were still visualized on a transabdominal scan , with the largest measuring 20.1 mm , and the endometrial thickness was 10.5 mm . she underwent an intramuscular injection of 10,000 iu of hcg on the same day and ocr was carried out 34 hours after the hcg injection . at the time of ocr , seven follicles were aspirated transabdominally and five oocytes were retrieved . a pregnancy test was positive 2 weeks after embryo transfer and clinical pregnancy was confirmed by ultrasound ( a single live gestation ) 4 weeks after transfer . the second case , also a 36 - year - old , presented with a 5 - year history of primary infertility . her bmi was 26.7 kg / m , and further investigations revealed bilateral tubal blockage and mild oligospermia . following clinical evaluation and discussion , the couple gave informed consent for ivf - et . she subsequently underwent controlled ovarian hyperstimulation following our protocol , commencing at five ampoules ( 375 iu ) per day of hmg . on the fifth day of stimulation , a tvs revealed multiple tiny follicles in the right ovary , but the left ovary was not visualized . her estradiol level was 456 pg / ml on the eighth day ; the ovaries were not visualized on a tvs , but the endometrial thickness was 8.1 mm . therefore , a transabdominal scan was performed , showing nine developing follicles in both ovaries , with the largest measuring 13.6 mm . a good response was demonstrated on transabdominal folliculometry , as 12 follicles were visualized on the day 11 of stimulation , with the largest measuring 20.5 mm . ten follicles were aspirated transabdominally , yielding seven oocytes ; of these , three were fertilized and three good - quality embryos were transferred on day 3 . a pregnancy test was positive 2 weeks later , and ultrasound confirmed a viable twin pregnancy 6 weeks after et . a 32 - year - old with a bmi of 28.9 kg / m presented to the clinic with a 2 - year history of primary infertility . a hysterosalpingogram showed bilateral tubal occlusion with uterine fibroids , and the semen analysis was normal . she was counseled to undergo a myomectomy prior to definitive ivf - et treatment ; she consented and underwent a successful myomectomy . six months after the myomectomy , she commenced ovarian stimulation for ivf following our protocol . she was commenced on four ampoules , and on the fifth day of stimulation , her estradiol level was 514 pg / ml , but the follicles were barely visualized on a tvs , and the hmg was increased to five ampoules . on the eighth day of stimulation , her ovaries were not visualized , but the endometrial thickness was 8.5 mm ; following a detailed search on a transabdominal scan , nine follicles were found , with the largest measuring 13.9 mm . transabdominal folliculometry was continued , and on stimulation day 12 , she had over 12 follicles , with the largest measuring 22 mm . at this point , hcg was administered , and she went on to undergo transabdominal retrieval 35 hours after hcg administration . approximately 18 follicles were aspirated , with an oocyte yield of 10 , of which six were fertilized , and three good - quality embryos were transferred on the third day after ocr . a 39 - year - old with a bmi of 23.4 kg / m presented with a 5 - year history of primary infertility . she had two previous myomectomies in 2003 and 2012 , as well as undergoing two previous failed intrauterine insemination attempts . she was counseled and selected for ivf - et treatment following our protocol , and was commenced on five ampoules of hmg ( 75 iu per ampoule ) daily . a baseline tvs at the commencement of stimulation ( on day 3 of her menses ) showed antral follicles in both ovaries and no residual follicles or cysts . on stimulation day 5 , tvs revealed tiny follicles in the right ovary , but the left ovary was not visualized . on stimulation day 8 , we experienced difficulties visualizing both ovaries . her stimulation day 5 estradiol level of 311 pg / ml and endometrial thickness of 7.2 mm were suggestive of possible follicular development , necessitating further search using a transabdominal scan , which showed two follicles on the right ovary and one on the left ovary , with the largest measuring 12.5 mm . the hmg was increased to six ampoules daily and her follicular response was monitored using the transabdominal approach . on stimulation day 11 , seven follicles were found , with the largest measuring 20.6 mm . a day 3 transfer of two good - quality embryos was carried out successfully , but a pregnancy test was negative 2 weeks later . a 36 - year - old nullipara presented for treatment in 2014 with an 8 - year history of secondary infertility and a previous myomectomy that was performed in 2006 . her bmi was 24.7 kg / m , and she was counseled and selected for ivf - et treatment following the confirmation of bilateral tubal blockage . she underwent controlled ovarian hyperstimulation following our protocol , and was commenced on five ampoules of human menopausal gonadotropin ( hmg ) ( 75 iu per ampoule ) daily . a baseline transvaginal scan ( tvs ) at the commencement of stimulation ( on day 3 of her menses ) showed antral follicles in both ovaries and no residual follicles or cysts . on stimulation day 5 , a tvs revealed tiny follicles in the left ovary , but the right was not visualized . on stimulation day 8 , a tvs revealed a poorly defined left ovary with very tiny follicles , whereas the right ovary was not visualized . her stimulation day 5 estradiol level of 413 pg / ml and endometrial thickness of 7.8 mm were suggestive of apparent follicular development ( i.e. , a good response ) . this necessitated a further search using a transabdominal scan , which showed four follicles in the right ovary and two follicles in the left ovary , with the largest measuring 15.5 mm . on stimulation day 11 , the six follicles were still visualized on a transabdominal scan , with the largest measuring 20.1 mm , and the endometrial thickness was 10.5 mm . she underwent an intramuscular injection of 10,000 iu of hcg on the same day and ocr was carried out 34 hours after the hcg injection . at the time of ocr , seven follicles were aspirated transabdominally and five oocytes were retrieved . a pregnancy test was positive 2 weeks after embryo transfer and clinical pregnancy was confirmed by ultrasound ( a single live gestation ) 4 weeks after transfer . the second case , also a 36 - year - old , presented with a 5 - year history of primary infertility . her bmi was 26.7 kg / m , and further investigations revealed bilateral tubal blockage and mild oligospermia . following clinical evaluation and discussion , the couple gave informed consent for ivf - et . she subsequently underwent controlled ovarian hyperstimulation following our protocol , commencing at five ampoules ( 375 iu ) per day of hmg . on the fifth day of stimulation , a tvs revealed multiple tiny follicles in the right ovary , but the left ovary was not visualized . her estradiol level was 456 pg / ml on the eighth day ; the ovaries were not visualized on a tvs , but the endometrial thickness was 8.1 mm . therefore , a transabdominal scan was performed , showing nine developing follicles in both ovaries , with the largest measuring 13.6 mm . a good response was demonstrated on transabdominal folliculometry , as 12 follicles were visualized on the day 11 of stimulation , with the largest measuring 20.5 mm . ten follicles were aspirated transabdominally , yielding seven oocytes ; of these , three were fertilized and three good - quality embryos were transferred on day 3 . a pregnancy test was positive 2 weeks later , and ultrasound confirmed a viable twin pregnancy 6 weeks after et . a 32 - year - old with a bmi of 28.9 kg / m presented to the clinic with a 2 - year history of primary infertility . a hysterosalpingogram showed bilateral tubal occlusion with uterine fibroids , and the semen analysis was normal . she was counseled to undergo a myomectomy prior to definitive ivf - et treatment ; she consented and underwent a successful myomectomy . six months after the myomectomy , she commenced ovarian stimulation for ivf following our protocol . she was commenced on four ampoules , and on the fifth day of stimulation , her estradiol level was 514 pg / ml , but the follicles were barely visualized on a tvs , and the hmg was increased to five ampoules . on the eighth day of stimulation , her ovaries were not visualized , but the endometrial thickness was 8.5 mm ; following a detailed search on a transabdominal scan , nine follicles were found , with the largest measuring 13.9 mm . transabdominal folliculometry was continued , and on stimulation day 12 , she had over 12 follicles , with the largest measuring 22 mm . at this point , hcg was administered , and she went on to undergo transabdominal retrieval 35 hours after hcg administration . approximately 18 follicles were aspirated , with an oocyte yield of 10 , of which six were fertilized , and three good - quality embryos were transferred on the third day after ocr . a 39 - year - old with a bmi of 23.4 kg / m presented with a 5 - year history of primary infertility . she had two previous myomectomies in 2003 and 2012 , as well as undergoing two previous failed intrauterine insemination attempts . she was counseled and selected for ivf - et treatment following our protocol , and was commenced on five ampoules of hmg ( 75 iu per ampoule ) daily . a baseline tvs at the commencement of stimulation ( on day 3 of her menses ) showed antral follicles in both ovaries and no residual follicles or cysts . on stimulation day 5 , tvs revealed tiny follicles in the right ovary , but the left ovary was not visualized . on stimulation day 8 , we experienced difficulties visualizing both ovaries . her stimulation day 5 estradiol level of 311 pg / ml and endometrial thickness of 7.2 mm were suggestive of possible follicular development , necessitating further search using a transabdominal scan , which showed two follicles on the right ovary and one on the left ovary , with the largest measuring 12.5 mm . the hmg was increased to six ampoules daily and her follicular response was monitored using the transabdominal approach . on stimulation day 11 , seven follicles were found , with the largest measuring 20.6 mm . a day 3 transfer of two good - quality embryos was carried out successfully , but a pregnancy test was negative 2 weeks later . techniques for ocr have evolved over the years ; it was first performed laparoscopically , and then ultrasound - guided retrieval ( transabdominal - transvesical and transvaginal ) was introduced . in contemporary ivf - et treatment cycles , the transvaginal route of retrieval has become the default ocr technique , although some clinical situations may prohibit this approach . this case series has demonstrated that in scenarios of transvaginal ovarian inaccessibility , ocr using transabdominal ultrasound - guided follicular aspiration can be done safely and efficiently with the consequent avoidance of cycle cancellation . a previous study noted that inaccessibility of the ovaries transvaginally is uncommon , but does occur , especially in situations involving anatomic distortions . in agreement with this observation , we noted that all four cases in this series had a prior history of abdominal surgery , which likely caused anatomical displacement of the ovaries . ovarian or pelvic surgery has also been associated through varying mechanisms with a decline in ovarian reserve and function , with consequent poor response during ivf - et treatment cycles . the pertinent finding of this study is the need for the rigorous appraisal of multiple proxy indices for ovarian response as a means of follicular monitoring in order to arrive at informed treatment decisions . in these cases , an apparent poor response was noted on transvaginal folliculometry , but the backdrop of previous abdominal surgery and values for estradiol and endometrial thickness indicating a favorable response prompted a more thorough search for developing follicles . researchers have shown that after 4 days of gonadotropin stimulation , an estradiol level of 350 pg / ml is highly predictive of successful ovarian follicular response , a higher embryo grade , and successful pregnancy outcomes , whereas a value of 75 pg / ml is predictive of a poor response and cycle cancellation . additionally , proliferation of the endometrium to a thickness of at least 7 mm has been associated with good follicular response and favorable ivf - et outcomes . thus , one can hypothesize that if favorable estrogen levels and endometrial thickness are noted , then there must be follicles somewhere in the body , meaning that the clinical imperative is to identify those follicles and prevent the devastating outcome of cycle cancellation . transabdominal retrieval is not without complications , ranging from damage to adjacent structures and contamination of the follicular aspirate to multiple punctures on the abdominal skin with increased potential for discomfort , infection , or scarring . additionally , previous studies have documented poor oocyte yield and treatment outcomes in comparison with transvaginal ocr . in this study , despite the potential for complications from pelvic adhesions , we successfully aspirated follicles transabdominally under ultrasound guidance without damaging other abdominal structures and with an appreciable oocyte yield . although we did not compare the oocyte yield with that obtained using a transvaginal approach in this series , the satisfactory oocyte yield may have been due to a back - ground positive response to stimulation , as demonstrated by the estradiol levels and endometrial thickness , as well as other factors that may influence ivf outcomes . the necessity of a meticulous approach to the procedure of transabdominal retrieval can not be over - emphasized . additionally , the patients in this case series were not obese and their ovaries were displaced closer to the skin anteriorly by post - surgical adhesions . we may posit that transabdominal retrieval can be carried out safely and efficiently in indicated cases with good outcomes . infertility remains a challenge in sub - saharan africa , placing attendant social , psychological , and economic burdens on the individuals involved . the need for judicious patient selection , the appraisal of several clinical indices , and the individualization of care should be emphasized as a means of improving treatment outcomes and enhancing the satisfaction of clients .\noutput:\n" }, { "from": "agent", "value": "controlled ovarian hyperstimulation is one of the major steps of in vitro fertilization . the inaccessibility or non - visualization of developing follicles on transvaginal sonography ( the preferred imaging method ) may be misjudged as a poor response , resulting in cycle cancellation . it is necessary to scrupulously appraise proxy indicators for ovarian response , such as estradiol levels , endometrial thickness , and other individual clinical characteristics . this can prompt meticulous transabdominal ultrasound follicular monitoring and oocyte retrieval with the goal of averting cycle cancellation and improving treatment outcomes ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: all living organisms are constantly challenged by microorganisms and a variety of particles ( from air pollution and cellular stresses ) that represent a health threat . to counteract this burden , the innate immune system needs to react promptly and adequately to eliminate them , while at the same time to preserve tissue normal function . in the last decadethere has been an enormous progress in the study of the molecular mechanisms that allow the host to fight against any antigenic stimuli and to keep internal homeostasis . in general , the innate immune host defense includes three essential sequentially events : ( 1 ) microbial recognition , ( 2 ) activation of signaling pathways , and ( 3 ) effector mechanisms . hosts are able to recognize distinct pamps present in microorganisms through a wide variety of prrs . to date , a broad range of prrs have been reported that include tlrs , nlrs , rlrs , and clrs ( for a complete description , see ) . the different subcellular localization of prrs and the broad array of pamps that can be recognized by them , allows the host to sense a large number of pathogen bacteria and develop an adequate immune response . upon recognition of pamps by prrs signal transduction pathways are activated that converge on transcription factors , such as nf - b , ap - 1 or irfs . activation of these transcription factors regulates the inflammatory and innate immune response through the expression of proinflammatory mediators and antimicrobial effectors . since some pathogenic bacteria possess pamps that can be simultaneously recognized by several prrs and this leads to the activation of common transcription factors , it is likely that a collaborative response among different signaling molecules may exert regulatory functions after recognition of pathogenic bacteria . therefore , the aim of this review is to discuss recent findings on the collaborative activity of tlrs and nlrs in the modulation of the inflammatory response induced by virulence factors of pathogenic bacteria . animals , including humans , respond to a wide range of antigenic stimuli in order to preserve their homeostatic conditions . professional ( macrophages , neutrophils , and dendritic cells ) and nonprofessional ( epithelial and endothelial cells ) phagocytes express various prrs that recognize pamps as well as other nonbiological stimuli . among the most important pampsare lipoteichoic acid ( lta ) and peptidoglycan ( pgn ) from gram - positive bacteria , lipopolysaccharide ( lps ) from gram - negative bacteria , lipoarabinomannan ( lam ) , lipopeptides , lipoglycans and lipomannans from mycobacteria , glycosylphosphatidylinositol ( gpi ) , anchored lipids from trypanosoma cruzi , zymosan isolated from yeast , profilin from toxoplasma gondii , and dna from bacteria and mycobacteria . to date , a broad range of prrs have been reported , such as tlrs , nlrs , rlrs , and clrs . tlrs constitute a family of receptors , with different specificities , 10 in humans and 12 in murines . they are able to recognize a structural diversity of pamps like glycans , lipids , proteins , lipoproteins , and nucleic acids and are widely known as key players of the inflammatory and innate immune response . tlr1 , tlr2 , tlr4 , tlr5 , tlr6 , and tlr11 are predominantly expressed on the cell surface , although it has been reported that after ligand binding , tlr2 and tlr4 are internalized to phagosomes . tlr3 , tlr7 , tlr8 , tlr9 , and tlr13 are expressed in intracellular vesicles such as the endoplasmic reticulum , endosomes , lysosomes , and endolysosomes and mainly recognize nucleic acid . tlrs are expressed in a broad variety of cells such as dendritic cells , macrophages , neutrophils , monocytes , t and b cells , epithelial cells , endothelial cells , fibroblasts , and even neural cells ( table 1 ) ; however , each type of cell contains a specific set of tlrs . monocytes , mature macrophages , and dendritic cells virtually express all tlrs , while tlr4 and tlr5 are also expressed in intestinal epithelium . moreover , it has been reported that plasmacytoid dendritic cells and mast cells express tlr7 and tlr8 , respectively . interestingly , tlr12 colocalize with tlr11 in endoplasmic reticulum of macrophages . tlr signaling has been shown to be involved in several functions in gut , such as epithelial cells proliferation , iga production , maintenance of tight junction , antimicrobial peptide expression and pathogen bacteria recognition . airway epithelial cells express tlr1 , tlr2 , tlr3 , tlr4 , tlr5 , and tlr6 , although tlr4 has a constitutive expression and intracellular localization . however , tlr7 and tlr9 are only expressed in primary airway epithelial cells . tlrs also play a major role in cutaneous host defense against microorganisms . normal keratinocytes of the epidermis constitutively express tlr1 , tlr2 , and tlr5 , while tlr3 and tlr4 are barely detectable . however , other work showed evidence that keratinocytes express tlr4 at the mrna and protein level . latter it has been shown that keratinocytes respond to double - strand rna ( dsrna ) and express a functional tlr3 . interestingly , tlr6 and tlr9 , but not tlr7 and tlr8 , are also expressed by keratinocytes . this family contains 16 members that have been categorized into five structurally different subfamilies : nlra , with an acidic transactivation domain ; nlrb , with a baculovirus inhibitor of apoptosis protein repeat ; nlrc , with a card domain ; nlrp , with a pyrin domain ; and nlrx that contains an uncharacterized domain . probably , the nlrc receptors nod1 and nod2 that recognize intracellular bacterial products , as well as nlrps that respond to multiple stimuli to form a multiprotein complex termed the nalp - inflammasome , are the best characterized so far and will be discussed below . the expression of nlrs has been described in a variety of cellular types ( table 1 ) , for example , nod1 is ubiquitously expressed in various cell types such as macrophages , human mononuclear cells , intestinal epithelial cells , and dendritic cells , while nod2 is expressed at higher levels in phagocytic cells and paneth cells of the small intestine . nod1 and nod2 have emerged as key pathogen recognition molecules of the innate immune responses . since the first report of nod1 as a receptor of invasive shigella flexneri , other works have shown that nod1 is the receptor involved in the cytosolic recognition of invasive gram - negative bacteria or pgn delivered into the epithelial cells through outer membrane vesicles ( omv ) derived from these types of bacteria or injected through type three secretion systems ( ttss ) . the participation of nod1 in gram - negative bacteria sensing might represent a selective advantage to the host because these types of bacteria are a common threat of the epithelial cells lining the intestinal mucosa . nod1 and nod2 have been shown to detect enteric bacteria such as shigella , salmonella , listeria , yersinia , pathogenic escherichia coli strains , and mycobacterium species . the expression of nod2 has also been associated with the chronic intestinal inflammation in crohn 's disease , where stimulation with muramyl dipeptide ( mdp ) seems to play an important role . in contrast to nod1 that is expressed in a wide range of cells and tissues , the expression of nod2 seems to be restricted to macrophages , neutrophils , dendritic cells , and lung epithelium . specifically in the lung , several reports have shown that nod1 is expressed in epithelial cells , endothelial cells , human airway smooth muscle cells , and leukocytes and responds to pathogens such as chlamydophila pneumoniae , legionella pneumophila , klebsiella pneumoniae , haemophilus influenzae , and pseudomonas aeruginosa . nod2 has been found mainly in macrophages , neutrophils , and bronchial cells and senses streptococcus pneumoniae , staphylococcus aureus , e. coli , c. pneumoniae , and m. tuberculosis . nlrps are a subgroup of nlrs constituted by proteins such as nlrp1 , nlrp3 , nlrp4 , nlrp6 , nlrp7 , and nlrp12 that are involved in the formation of multiprotein complexes termed inflammasomes . these complexes consist of one or two nlr proteins , the adapter molecule apoptosis associated speck - like containing a card domain ( asc ) and pro - caspase - 1 . these inflammasomes might sense several microbial products and a variety of stress and damage associated endogenous signals . probably the best characterized inflammasome is the one formed by the nlrp3 scaffold , the asc adaptor and caspase - 1 , and its expression is induced by inflammatory cytokines and tlr agonists in myeloid cells and human bronchial epithelial cells . as the other inflammasomes , the nlrp3 inflammasome mediates the caspase -1-dependent conversion of pro - il - 1 and pro - il - 18 to il - 1 and il - 18 and are involved in a form of cell death termed pyroptosis . nlrps respond to a broad variety of bacteria and it has been shown that nlrp3 is activated by the lung pathogenic microorganisms k. pneumoniae , listeria monocytogenes , s. pneumoniae , s. aureus , c. pneumoniae , m. tuberculosis , l. pneumophila , influenza virus , porphyromonas gingivalis , aspergillus fumigatus , and aeromonas veronii . nlrp3 seems to be involved in the host defense against the enteric pathogens citrobacter rodentium and clostridium difficile in mice ; however , this response is far from being fully characterized . although nlrp1 was the first nlr described as a part of an inflammasome , its mechanism of activation is not well studied . it is abundantly expressed in lymphocytes , respiratory epithelial cells , and myeloid cells . the best - characterized activator of nlrp1 is the lethal toxin ( lt ) from bacillus anthracis ; lt activates caspase - 1 and induces rapid cell death via nlrp1 . a recent work showed that nlpr1 inflammasome is activated by t. gondii in mice and rats infection models . nlrp7 is only present in human peripheral blood mononuclear cells after lps and il - 1 stimulation . despite its function in bacterial infectionsthe experimental evidence indicates that nlrp7 is activated in macrophages by bacterial lipopeptides and mycoplasma as well as s. aureus infection , leading to formation of an inflammasome . nlrps also negatively control the inflammatory response by lowering the nf - b activation and ifn production . they regulate autophagy during group a streptococcal infection by interacting with the autophagy regulator beclin - 1 . on the other hand , nlrp6 inhibits nf - b signaling downstream of tlrs in macrophages in vitro and mouse in vivo , which seems to be important to regulate the immune response against components of the gut microflora . also it has been described that ablation of nlrp6 confers resistance to l. monocytogenes and salmonella typhimurium infections . although the lack of nlrp6 gene could be beneficial to control infection caused by these pathogens , it must be studied how its deficiency might affect the gut homeostasis . it is expressed in myeloid cells and its expression is reduced by tnf and tlr stimulation . however , a recent report has demonstrated that nlrp12 does not significantly contribute to the in vivo host innate immune response to lps stimulation , k. pneumoniae infection , or m. tuberculosis . early experiments revealed that flagellin delivered into the cytosol is an important bacterial component for the activation of the nlrc4 inflammasome independently of tlr5 activation . besides nlrc4 regulates of host defense by activating caspase - 1 and il - 1 / il - 18 secretion in macrophages infected with salmonella enterica serovar typhimurium , l. pneumophila , and p. aeruginosa . s. flexneri , a pathogen bacterium lacking flagellum , also induces the activation of the nlrc4 inflammasome through prgj , a protein that forms the basal body rod of the type three secretion system . furthermore , nlrc4 protects the gut from chemically induced acute colitis as well as the mortality caused by dissemination of salmonella beyond the gut . on the other hand , the absent in melanoma - 2 ( aim2 ) protein is a member of the ifi20x / ifi16 ( pyhin ) protein family that binds dna from virus and bacterial pathogens . upon dna sensing , aim2 triggers the assembly of the inflammasome , leading to caspase - 1 activation , il - 1 maturation and pyroptotic cell death . several studies have shown that aim2 inflammasome is important in the recognition of dna from pathogen bacteria , such as francisella tularensis in macrophages , francisella novicida in dendritic cells , l. monocytogenes in macrophages , mycobacterium sp . in macrophages , s. pneumoniae in macrophages , and p. gingivalis in gingival epithelial cells . even aim2 inflammasome is a critical molecular platform for regulating il - 1 release and survival during acute central nervous system ( cns ) s. aureus infection . initially , sensing of pathogenic bacteria by host activate signaling pathways that turn on mechanisms to kill the microorganism . however , when the infection and inflammatory response have been resolved different mechanisms are launched to repair any tissue damage and return to the basal state . this means that initiation , control , and termination of the inflammatory response and infection must be highly regulated . the inflammatory response is under the control of the nf - b , ap - 1 or irfs transcription factors , which driving the expression of genes that mediate several processes such as cell proliferation and release of antimicrobial molecules and cytokines that regulate the immune response . in the following sections , the signaling mechanisms activated by tlrs , nlrs , and the collaborative action of both are discussed . tlr signaling pathways have been studied and reviewed extensively and it is known that they play a crucial role against pathogenic microbial infection through the induction of inflammatory cytokines and type i interferons ( type i ifns ) . tlr signaling is activated in a myeloid differentiation primary response gene 88 - ( myd88 - ) dependent and tir - containing adaptor - inducing ifn -- ( trif - ) dependent manner , with myd88 signaling predominantly leading to the activation of nf - b , while trif signaling leading to both interferon regulatory factor 3 ( irf3 ) and , to a lesser extent , nf - b activation ( figure 1 ) . tlrs have an extracellular leucine - rich repeat ( lrr ) domain , a transmembrane domain and a cytoplasmic toll / il - 1 receptor ( tir ) domain . the lrr domain of tlrs is involved in the recognition of proteins ( e.g. flagellin and porin from bacteria ) , carbohydrates ( e.g. zymosan from fungi ) , lipids ( lps ) , lipid a , and lipoteichoic acid ( lta from bacteria ) , nucleic acids ( cpg - containing dna from bacteria and viruses and viral rna ) , protein or peptide derivatives ( lipoprotein and lipopeptides from various pathogens ) , lipid derivatives ( lam from mycobacteria ) , profilin from t. gondii , and diacyl - lipopeptides from mycoplasma . on the other hand , the tir domain of tlrs shows homology with the cytoplasmic region of the il - 1 receptor and interacts with tir - domain - containing adaptors such as myd88 , tir - containing adaptor protein ( tirap ) , trif and trif - related adaptor molecule ( tram ) . in the myd88 signaling pathway , stimulation of tlrs triggers its association with myd88 , which in turn recruits il - 1r - associated kinase 4 ( irak4 ) , allowing the assembly of irak1 . irak4 then induces the phosphorylation of irak1 , which in turn interacts with tumor - necrosis - factor receptor - associated factor 6 ( traf6 ) . phosphorylated irak1 and traf6 then dissociate from the receptor and form a complex with transforming - growth factor -- activated kinase 1 ( tak1 ) , tak1 - binding protein 1 ( tab1 ) , and tab2 at the plasma membrane , promoting the phosphorylation of tab2 and tak1 . irak1 is degraded at the plasma membrane and the remaining complex , consisting of traf6 , tak1 , tab1 , and tab2 , associates with the ubiquitin ligases , ubiquitin - conjugating enzyme 13 ( ubc13 ) and ubiquitin - conjugating enzyme e2 variant 1 ( uev1a ) in the cytosol . ubiquitination of traf6 induces the activation and phosphorylation of mitogen - activated protein kinases ( mapks ) , jun n - terminal kinase ( jnk ) , p38 , extracellular signal - regulated kinase ( erk ) , and the inhibitor of nuclear factor - b - ( ib - ) kinase ( ikk ) complex , which consists of ikk - , ikk - , and ikk - ( also known as ikk1 , ikk2 , and nemo , resp . ) the ikk complex then phosphorylates the inhibitor of nf - b ( ib ) , which leads to its ubiquitination and subsequent degradation by the proteasome 26s , allowing the translocation of nf - b to the nucleus and expression of inflammatory cytokines , chemokines , costimulatory molecules , and other effectors necessary to build up the host cell weapons against the invading pathogen . the variety of genes induced to express by tlrs may be due to the existence of several adaptors that possess tir domains . except for tlr3all tlrs recruit myd88 and only tlr1 , tlr2 , tlr4 , and tlr6 recruit the additional adaptor tir - domain - containing adaptor protein ( tirap , also known as myd88 - adaptor - like protein , mal ) that functions as a bridge between the tir domain and myd88 . apart from the activation of nf - b and map kinases , the trif - dependent signaling pathway also induces the activation of ifn . trif contains a rip homotypic interaction motif ( rhim ) in its c - terminal region that mediates the interaction with members of the receptor - interacting protein ( rip ) family . it was observed that trif activates nf - b either by direct interaction with traf6 or through rip - 1 . both trif / rip - 1 and trif / traf6 pathways converge at the ikk complex to achieve maximum activation of nf - b - dependent gene expression . expression of the ifn gene is controlled by cooperative activation of nf - b , atf2 / c - jun , irf3 , and irf7 . activation of traf3 by trif is important to generate a link between trif and tank - binding kinase 1 ( tbk1 , also known as nf - b activating kinase , nak ) , and this in turn activates tbk1 and ikk . tbk1 and ikk then activate these two molecules that are responsible for the activation of traf family member - associated nf - b activator ( tank ) , which phosphorylates irf3 and irf7 . phosphorylated irf3 and irf7 form homodimers and move to the nucleus where it binds to ifn - stimulated response elements ( isre ) , resulting in the production of type i ifns and ifn stimulatory genes ( isgs ) . although irf7 is considered as the master regulator of ifn - response , irf5 also seems to function downstream of tlr7 or tlr9 , and perhaps tlr8 signaling , although its expression is mainly restricted to b cells , macrophages , monocytes and dendritic cells where can induce de inf - production . moreover , irf1 has been identified as a downstream signaling element of tlr7 in dendritic cell infected with candida albicans . as stated above , the nlrs nod1 and nod2 regulate proinflammatory cytokine expression induced by intracellular bacterial ligands . nod1 recognizes mainly gram - positive pgn fragments containing the n - acetylglucosamine - n - acetylmuramic acid tripeptide motif with diaminopimelic acid ( dap ) . nod2 detects muramyl dipeptide ( n - acetylmuramic acid - l - alanyl - d - isoglutamine ) , which is a motif common of pgn from both gram - negative and gram - positive bacteria . in general , nlrs possess a c - terminal lrr domain , often involved in ligand recognition , a central nod , and a variable n - terminal effector domain that is used to classify nlrs . once bacteria or their components reach the host cytosol by phagocytosis , invasion , membrane vesicles , or secretion systems , the interaction of nlrs with pgn takes place , although whether it is a direct or indirect contact is still unclear . however , it has been well documented that the inflammatory response initiated by nod1 and nod2 induces the expression of proinflammatory cytokines , chemokines , and antimicrobial peptides by activating nf - b and ap - 1 ( figure 2 ) . a direct interaction between nod2 and nf - b - inducing kinase ( nik ) that triggers the p100 / p52 - dependent induction of the noncanonical nf - b pathway was demonstrated by pan et al . . although the nlr signaling pathway is far from being fully characterized the general model shows that sensing of pgn leads to transient recruitment of rip - 2 through card - card interaction . the rip - 2 recruitment leads to ikk complex activation and the subsequent nf - b activation through phosphorylation and ubiquitination of ib , inducing proinflammatory cytokines production . moreover , recruitment of rip - 2 by nod1 also activates jnk , and nod1 / 2 seems to participate in the activation of the type i ifn pathway . cellular inhibitor of apoptosis protein 1 and 2 ( ciap1 and ciap2 ) are e3 ubiquitin ligases important for ubiquitination of rip - 2 and for signaling downstream of both nod1 and nod2 . tak1 in turn phosphorylates and activates the mapks p38 / jnk and nf - b pathways , leading to cytokine , chemokine , and antimicrobial peptide production . as it was explained earlier tlrs and nlrs regulate the cytokine and chemokine expression in response to bacterial ligands through their respective signaling pathways . it is likely that tlrs and nlrs act in a collaborative / synergistic , complementary , or compensable manner , with the aim to increase the sensitivity to detect and efficiently eliminate pathogenic bacteria . a number of reports that analyze the interaction between tlrs and nlrs have been published ( table 2 ) . in human monocytic thp - 1 cells a marked synergistic secretion of il - 8 was induced by synthetic agonists of nod1 / 2 and tlr2 / 4/9 . this enhanced il - 8 mrna expression and nf - b activationthis synergism between nod1 / 2 and tlrs was also observed in the production of antimicrobial peptides pgn recognition proteins ( pgrps ) and - defensin 2 in human oral epithelial cells via nf - b . interestingly , costimulation of nod1 / 2 and tlrs did not have any effect on il - 8 production , which suggests a cell - type specific inflammatory response . likewise , in human monocytes and dendritic cells the nod1 / 2 ligands , dap and mdp , respectively , exert a synergetic activity with lps in the expression of proinflammatory cytokines tnf - , il - 1 , il - 6 , and il - 8 . the synergistic effect of mdp and tlr2 / 3/4 ligands on il - 6 and il - 12p40 expressionwas also observed in wild type and nod2 macrophages , via nf - b , p38 and erk signaling pathways . additionally , treatment of human dendritic cell ( dc ) with mdp and the nod1 agonist fk565 along with tlr3 / 4/9 agonists synergistically induced il - 12p70 and inf - production . another nod1 ligand m - tridap markedly increased the response induced by lps for multiple cytokines such as il - 1 , il - 1 , il - 4 , il - 6 , gm - csf , il - 10 , and tnf - . in the same study carried out by van heel et al . a strong synergistic increase in il - 1 productionwas observed for tlr1 / 2 , tlr2 / 6 , tlr4 , tlr5 , and tlr7 / 8 ligands ( pam3cyslys4 ; malp2 ; lps ; flagellin from s. typhimurium and r - 848 , resp . ) combined with m - tridap . assays performed with homozygotic macrophages for the 3020insc mutation and / or tlr2 mice demonstrated that the nod2 ligand mdp has a synergistic effect on the induction of tnf - , il - 1 , and il - 10 upon costimulation with specific tlr2 agonists pam3cys and malp2 . in a more recent work , it was shown that nod1 and tlr2 cooperate to enhance human cd8 t cells proliferation and expansion , and this cooperating action caused an enhanced secretion of il - 2 , ifn - , and tnf - that was related to increased activation of nf - b , jnk , and p38 signaling pathways . simultaneous stimulation of monocytes - derived dc with nod1 and nod2 ligands combined with tlr7 / 8 or tlr4 agonists results in highly increased production of il - 1 and il - 23 and expression of the inhibitor suppressor of cytokine signaling 2 ( socs2 ) , where the nod1 / tlr agonists combination was more relevant for the synergistic activity observed . altogether , these results clarify the existence of a cooperative action of tlrs and nlrs , which become relevant in the context of infection by bacteria that can be recognized by extra - and intracytosolic receptors . they found a synergistic action between these two receptors for cytokine expression that was lost in cells from individuals homozygous for nod23020insc mutation or macrophages harvested from tlr2 mice ( table 3 ) . the same authors also found that macrophages from tlr2 and tlr4 knockout mice and nod2 mutant had a decreased production of tnf - , il - 1 , il - 6 , and il - 10 , which suggest that collaborative activity of these prrs is important to balance the amount of pro- and anti - inflammatory response in m. paratuberculosis infection . evidence on the collaborative activity between tlr2 and nod2 was obtained by measuring il - 10 secreted from macrophages challenged with s. pneumoniae cell - wall ( pncw ) fragments . interestingly , in this il - 10 production participated the protein adaptors rip - 2 and myd88 , reflecting that both canonical signaling pathways were involved . infection of mice mesothelial cells ( mc ) with l. monocytogenes caused an increased production of cxcl1 and ccl2 chemokines , which was notably decreased in mc deficient in nod1 and rick . c. pneumoniae , which is a common pathogen that causes pneumonia in humans can be recognized by tlr2 and tlr4 , as well as by nod1 / 2 . sensing of c. pneumoniae by these receptors induced a reduction in the expression of il - 6 , il - 12p40 , and ifn - in rip - 2 mice at day 3 after infection compared with wild - type mice . however , at days 5 and 14 after infection , the production of these cytokines was significantly increased in wild - type mice , indicating an initial impaired and delayed kinetics of cytokine production in c. pneumonia - infected rip - 2 mice . thus , the collaborative activity of both nlrs and tlrs is fundamental for efficient pathogen bacterial clearance . this idea has been supported by later experiments in which nlrc4 was necessary to eliminate l. pneumophila , while tlr5 was necessary to recruit neutrophils . furthermore , it has been demonstrated that activation of rip2 - , myd88 - , and naip5 / nlrc4 - dependent signaling pathways triggers a coordinated and synergistic response that protects the host against lethal infection by l. pneumophila . however , contrasting results were observed in p. aeruginosa macrophage infection , since nlrc4 and caspase - 1 activation attenuated the autophagy activated by tlr5 and reduced the type i interferon production , besides nlrc4 dampens a beneficial il -17-mediated antimicrobial host response through il - 18 secretion . on the other hand , in dcsinfected with helicobacter pylori , the cooperative interaction between tlr2 and nod2 showed to be important for il - 1 production and nlrp3 activation . this cooperative interaction in h. pylori infection was confirmed in il - 1 - and il - 1 receptor - deficient mice in which the clearance of bacteria from the stomach was impaired compared with wild - type mice . costimulation of balb / c mice with nod1 and tlr5 ligands showed to be important for efficient s. enterica clearance and improved mice survival . this effect was accompanied with an increase in il - 5 , il - 6 , il - 13 , il - 21 , il - 22 , tnf - , and - defensin 3 in small intestine . more evidence of nod2 and tlr2 cooperative action was obtained in dc stimulated with pgn from s. aureus . analysis of il - 6 and il - 1 production , revealed an additive effect of both receptors in keratinocytes from murine oral epithelium , since in tlr2 - or nod2 - deficient keratinocytes the cytokine release was decreased by approximately 50 % compared to wild - type cells . infection of mouse macrophages with vibrio vulnificus and vibrio cholerae revealed the activation of caspase - 1 via the nlrp3 inflammasome . in this work , experiments made with mice doubly deficient in myd88 and trif ( mydtrif ) , demonstrated that nlrp3 activation required nf - b - dependent tlr stimulation . altogether , these results indicate that several sensors are necessary to fight against pathogenic bacteria . moreover , the specific combination of prrs seems to be coordinated according to the bacteria or pamps involved , which subsequently affect the host response by driving collaborative / synergistic activity . most studies have focused on the characterization of the inflammatory response triggered by several virulence factors alone . however , it is important to take into account that in physiological conditions the participation of several prrs that respond to different pamps could be more effective for the host to combat infections . regarding this issue , the experimental evidence accumulated so far has pointed out that the host response against pathogenic bacteria may be the sum of several pathways induced by the recognition of different pamps by different prrs , which in turn trigger and shape the subsequent innate and adaptive immune responses . although synergistic activity among nlrs and tlrs has been demonstrated , the subjacent mechanisms are not clear . both receptors are able to activate nf - b , mapks , ap - 1 , or irfs signaling pathways ; however , the molecules that are involved in the synergistic activation of these pathways have not been identified . then , for a better understanding of the molecular mechanisms by which nlrs and tlrs collaborate , this synergistic activity will have to be further analyzed . since trls and nlrs play a fundamental role in the eradication of invading pathogen microorganisms through the induction of inflammatory and antimicrobial peptides , this collaborative activity could be exploited to modulate or improve the host response against pathogenic bacteria that causes an exacerbated inflammatory response . finally , there is a growing interest in targeting these prrs for the treatment of sepsis , but also to fight against inflammatory diseases such as cancer , rheumatoid arthritis , inflammatory bowel disease , and systemic lupus erythematosus . several approaches , like ligand mimetics to activate prrs and antibodies or molecules to inhibit them , have been used to identify therapeutics targets . however , something that should be taken into account in the development of these strategies is the collaborative activity among different prrs .\noutput:\n" }, { "from": "agent", "value": "early sensing of pathogenic bacteria by the host immune system is important to develop effective mechanisms to kill the invader . microbial recognition , activation of signaling pathways , and effector mechanisms are sequential events that must be highly controlled to successfully eliminate the pathogen . host recognizes pathogens through pattern - recognition receptors ( prrs ) that sense pathogen - associated molecular patterns ( pamps ) . some of these prrs include toll - like receptors ( tlrs ) , nucleotide - binding oligomerization domain - like receptors ( nlrs ) , retinoic acid - inducible gene - i - ( rig - i - ) like receptors ( rlrs ) , and c - type lectin receptors ( clrs ) . tlrs and nlrs are prrs that play a key role in recognition of extracellular and intracellular bacteria and control the inflammatory response . the activation of tlrs and nlrs by their respective ligands activates downstream signaling pathways that converge on activation of transcription factors , such as nuclear factor - kappab ( nf - b ) , activator protein - 1 ( ap - 1 ) or interferon regulatory factors ( irfs ) , leading to expression of inflammatory cytokines and antimicrobial molecules . the goal of this review is to discuss how the tlrs and nrls signaling pathways collaborate in a cooperative or synergistic manner to counteract the infectious agents . a deep knowledge of the biochemical events initiated by each of these receptors will undoubtedly have a high impact in the design of more effective strategies to control inflammation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: john w. dobbins in 1977 , is attributable to several factors , including environmental causes , food allergy and disruption of immune defence system in the digestive tract . the main symptoms of ee include dysphagia and a sensation of food impingement in the retrosternal area . its clinical features resemble those of gastroesophageal reflux disease ( gord ) however ; proton pump inhibitors are not effective in ee patients . the current study emphasizes the importance of considering ee in the differential diagnosis of patients with chronic dysphagia . a male patient of 35 years age presented to our general surgery clinic with complaints of difficulty in swallowing , sensation of food sticking in the back of the breast while eating , stomach ache , weight loss and weakness for nearly a year . normal values were obtained for complete blood count serum crp , sedimentation and total serum ige of the patient . standing abdominal x - ray and abdominal ultrasonography failed to reveal any evidence of pathology . mucosal fissure and erosional areas were observed in the middle distal esophagus using upper gi endoscopy and are probably associated with reflux esophagitis ; biopsies were made of the same ( fig . 1 ) . pathological examinations of the endoscopic biopsies revealed evidence of chronic esophagitis in esophagus , chronic helicobacter pylori - positive pangastritis in stomach and chronic duodenitis in the duodenum . the examination showed eosinophilic infiltration only in the esophagus ( fig . 2 ) . histological examination ( 40 x ) revealed more than 30 eosinophils per field ( fig . the patient was diagnosed with eosinophilic esophagitis and administered dexamethasone i.m as well as treatment for h. pylori eradication which resulted in relief of the symptoms . the patient was also instructed to avoid consumption of milk and dairy products , which caused the development of symptoms . the control endoscopic examination and pathological evaluation made after 3 months , failed to reveal evidence of esophageal eosinophilic infiltration , relapse did not occur during the following 2 years . e 40 esophagus mucosa . the image of linear erosional areas in middle and distal esophagus . studies conducted in the usa suggest that ee could affect all age and ethnic groups but is more common among children . in adults , it chiefly occurs during the 30s and 40s , with a male : female prevalence rate of 3:1 . the incidence and prevalence of ee are 1 / 10000 and 4 / 10000 , respectively , in children , and 26 / 10000 and 27 / 10000 respectively , in adults . existing data support a family liability in ee , underscoring the importance of genetic factors . john w. dobbins in 1997 , is also termed allergic , primer or idiopathic eosinophilic esophagitis . as with the other parts of the gastrointestinal system , eosinophil accumulation in esophagusis not observed under normal conditions and detection of any number of eosinophils in the mucosa of the esophagus is indicative of a pathological situation . previous research has implicated two chief mechanisms in the pathogenesis of ee exposure to allergens , which initiates immune response and loss of immune tolerance . ee is frequently found in conjunction with other allergic diseases and most ee patients also suffer from other atopic diseases . the identification of atopic diseases in ee patients and response obtained to elimination diet or elementary dietary applications reinforce the idea that ige - mediated allergic mechanisms are associated with the in etiopathogenesis of ee . however , ige levels are not detectable in every patient , but are chiefly observed in the pediatric age group , where food allergy has been reported as the most frequent ( 90 % ) etiology . the exact pathogenesis of ee is unclear , but increased expression of il - 4 , il - 5 and il - 13 has been detected during examination of inflamed esophageal tissue . in addition , mutation and excessive expression of the gene that encodes oetaxin - 3 , an important protein for eosinophil transition , and inflammation has been observed in nearly half of the children with the ee . vomiting , stomachache and gord are the more frequently observed symptoms in children with ee , whereas difficulty in swallowing over a prolonged duration ( 90 % ) or repeated sensation of food sticking ( 60 % ) are the most frequent indications in children of over 12 years age and in adults . the diagnosis of ee is made upon evaluation of the results of both endoscopic and histopathological tests , while the differential diagnosis of the ee is dependent on gord , as ee could be confused with achalasia , eosinophilic gastroenteritis and hypereosinophilic syndrome . an accurate diagnosis of ee could be made upon observations of eosinophilic infiltration in the squamous epithelium of the esophagus . an eosinophil count of 15 per high power field ( hpf ) upon histological examination is generally considered sufficient for a diagnosis of ee in symptomatic patients , although the exact eosinophil count per hpf for a definite diagnosis of eo has not yet been clearly established . moreover , eosinophilic infiltration in the mucosa of the esophagus in ee patients does not show homogeneous distribution , and employing more than one tissue sample from the middle and proximal region of the esophagus is recommended for diagnosis . accordingly the rate of diagnosis of ee is 55 % with a single mucosal biopsy , but 100 % when five biopsies are utilized . endoscopy examination is likely to reveal symptoms such as linear erosions , concentric circles , esophageal mucosa ( crepon mucosa ) and white exudative lesions containing microabscesses ; of these , white exudates and linear erosions are the most frequently detected indicators of ee . a prospective study showed that the frequency of ee among patients with dysphagia to solid food but without any endoscopic pathology is about 10 % . high esophageal stricture is often observed in eosinophilic esophagus and is more common among middle - aged men with white skin . the treatment of ee involves the identification and avoidance of systemic and topical steroids as well as allergens . identification of the allergy triggers , if present , is essential for their inactivation or avoidance . ee is a disease characterized by eosinophilic inflammation , which is a rare occurrence . because its symptoms are not particular to the disease , it could often be confused with reflux esophagitis . therefore , accurate and effective treatment is dependent on the diagnosis of eosinophilic esophagitis in patients with dysphagia and sensation of food sticking , followed by a confirmation of the diagnosis through multiple esophageal biopsies .\noutput:\n" }, { "from": "agent", "value": "eosinophilic esophagitis ( ee ) is attributable to environmental factors , allergens and several immunological causes . the most typical symptoms include dysphagia and sensation of food impingement in the retrosternal area . although its clinical features resemble those of gastroesophageal reflux , proton pump inhibitors are not effective for its treatment . the diagnosis of ee is dependent on the pathological detection of eosinophilic infiltration in esophageal mucosa . in this study , we evaluated a patient who applied to our clinic with complaints of long - term difficulty in swallowing , sensation of food sticking while eating and weight loss ; the patient was diagnosed with ee , following biochemical , radiological , endoscopic and pathological assessments and was treated with steroids . the results show that ee should be considered in the differential diagnosis of patients with dysphagia and food impingement in the retrosternal area , and the diagnosis should be confirmed through multiple esophageal biopsies ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: atrial fibrillation ( af ) is the most common form of cardiac arrhythmia , associated with high morbidity and mortality . based on the estimate of the heart and stroke foundation , af affects approximately 250,000 canadians . this condition is characterized by disorganized , rapid , and irregular activity of the two upper chambers of the heart ( atria ) , associated with irregular and rapid response of the two lower chambers of the heart ( ventricles ) . patients with af are at higher risk of clot formation and subsequent adverse hemodynamic events such as stroke . af increases the risk of stroke four - to five - fold across all age groups and is responsible for 10 % 15 % of all ischemic strokes . the rate of hospitalization for af in canada was approximately 583 per 100,000 people , between 1997 and 2000 , with an average of 129,000 hospitalizations per year . af may be classified on the basis of electrocardiographic findings or the frequency of episodes and the ability of an episode to convert back to sinus rhythm . recurrent af can be subclassified as paroxysmal ( self - terminating , usually 24 hours ) , persistent ( sustained 7 days ) , or permanent . there are two main strategies for af treatment : rhythm control ( cardioversion and maintenance of sinus rhythm with antiarrhythmic drugs ( aads ) ) and rate control ( atrio - ventricular ( av ) nodal blockers and anticoagulation ) . various treatment options are available for rhythm control including medication , electrical ( direct - current ) cardioversion , or surgical procedures . aad therapy is recommended as a first choice for restoration of normal sinus rhythm ( nsr ) . three class i drugs ( flecainide , quinidine , and propafenone ) and two class iii drugs ( sotalol and amiodarone ) are commonly used in canada for treatment of af . due to the limitations of these drugs in maintenance of nsr , along with side effects , nonpharmacological approaches including catheter ablation have been recently considered in treatment of af . the current standard surgical treatment is the cox - maze procedure , which requires open heart surgery . because of the invasive nature of the cox - maze procedurethe goals of catheter ablation procedures are to eliminate triggers of af and to modify the atrial substrate ( s ) responsible for the maintenance of af . given that the pulmonary veins ( pv ) represent a critical anatomic site for the treatment of af , minimally invasive procedures often involve the isolation of the source of abnormal impulses originating from these veins . in a minimally invasive catheter ablation procedure , a catheter is inserted through the femoral vein to access the heart and burn abnormal foci of electrical activity by direct contact or by isolating them from the rest of the cardiac atrium . antiarrhythmic drug therapy presents the advantage of being a noninvasive and commonly available therapeutic option but it may require chronic administration . ablation of af is associated with larger upfront costs but may be more successful in maintaining normal sinus rhythm over time . therefore , there may be a trade - off between higher costs and better outcomes with af ablation compared to antiarrhythmic medications . the objective of this paper is to assess the cost - effectiveness of treating paroxysmal af patients with catheter ablation compared to antiarrhythmic drug treatment . a canadian specific cost - effectiveness analysis was conducted using a combined decision tree and markov model for patients with af . the treatment comparators in the model are ( 1 ) af catheter ablation and ( 2 ) antiarrhythmic drug treatment ( amiodarone 200 mg per day ) . the starting population are 65 - year - old males with paroxysmal af previously unsuccessfully treated with an aad . the chads2 index predicts the annual probability of stroke for individuals based on a risk score ranging from 0 to 6 . this assumption is based on the mean chads2 score ( 2.1 ) amongst participants in the national registry of atrial fibrillation . the analysis was taken from the perspective of a publicly funded health care system . in the basecase analysis , the time horizon of the model was set to five years with a cycle length of three months . although the clinical impact of af treatment may go beyond five years , this time horizon was chosen due to the short - term nature ( i.e. , 12 months ) of the randomized clinical trials comparing af ablation with aad . the model is comprised of both a one - year decision tree and a longer - term markov model . figures 1 and 2 graphically present the structure of the short - term and long - term models , respectively . as shown in figure 1 , a proportion of patients undergoing ablation are at risk of operative complications . these include cardiac tamponade , pulmonary vein stenosis , ischemic stroke , and transient ischemic attack . patients without an operative complication or with a nonstroke complication end the short - term model either in normal sinus rhythm ( nsr ) or with atrial fibrillation ( af ) . patients in the aad treatment group follow similar pathways as af ablation patients during the one - year model . aad patients are not at risk of operative complications but are at risk of pulmonary toxicity , which can be fatal , reversible , or irreversible . the proportion of patients in nsr after one year is based on freedom of af outcomes from randomized controlled trials ( rcts ) comparing af ablation with aads . patients who are alive and not suffering a stroke after the one - year model enter the markov model in either the nsr health state or the af health state . in each three - month model cycle , patients are at risk of ischemic stroke and major bleeding events due to concomitant anticoagulants . af ablation patients are assumed to discontinue warfarin three months after their procedure , resulting in different bleeding risks between af ablation patients and aad treated patients . patients in the af ablation treatment arm who do not achieve normal sinus rhythm after 1 year or have a subsequent recurrence of af are assumed to switch to aad treatment . patients in the aad treatment arm who do not achieve normal sinus rhythm after 1 year or have a subsequent recurrence of af are assumed to remain on aad treatment . there are separate health states to distinguish between the first and subsequent years after ischemic stroke and ich . in every three - month cycle , patients in the nsr health state can revert back to the af health state . these parameters were used to estimate the expected qalys and the expected number of strokes for each treatment group . these include the probability of achieving nsr for each treatment group ; the probability of ischemic stroke ; the probability of major bleeding ; the probability of reverting to af after achieving nsr ; the probability of af ablation procedural complications ; the probability of pulmonary toxicity while being on an aad ; utility values for the various health states ; mortality associated with the various health states . data from a systematic review conducted as part of a health technology assessment on af ablation was used to estimate the probability of normal sinus rhythm 12 months after ablation or antiarrhythmic treatment . the probability of being in normal sinus rhythm at one year was derived from data presented in a systematic review conducted by assasi et al . . in this systematic review , the authors identified five rcts that evaluated the proportion of patients in normal sinus rhythm 12 months after receiving either af ablation or second - line ant - arrhythmic therapy . for the aad treatment strategy , the probability of being in nsr after one year was estimated by pooling data from the aad arms of these five rcts using random effects meta - analysis . the pooled probability of being in nsr at 12 months for the aad treatment arm was estimated to be 0.26 ( 95 % ci : 0.17 , 0.34 ) . table 1 provides the proportion of aad in nsr at one year for each of these studies . assasi et al . reported the relative risk of being in nsr at 12 months for af ablation patients compared to aad patients to be 2.93 ( 2.09 , 4.11 ) in five rcts of previous aad failures . based on this relative risk and the probability of being in nsr for the aad treatment arm , the probability of af ablation patients being in nsr at one year was estimated to be 0.756 ( 2.930.26 ) . the annual probability of ischemic stroke for patients while in the af health state was based on the chads2 classification system published by gage et al . . the probability of stroke by chads2 score was estimated using a us registry of patients with af . the chads2 stroke probabilities were applied to patients while being in the af health state of the model . a chads2 risk score of 2 , which corresponds to an annual risk of stroke 0.04 , , the model is run assuming different risk scores . a post hoc study investigating the risk factors for ischemic strokes amongst patients enrolled in the affirm trial found that patients with af had a 1.6 times greater risk of stroke than patients who were in normal sinus rhythm after treatment . therefore , patients with normal sinus rhythm were assumed to have a relative risk reduction of stroke compared to patients with af of 1/1 .6 , which is equal to 0.625 . for example , if patients with af are assumed to have a 0.04 annual risk of stroke , patients in normal sinus rhythm would be assumed to have an annual risk of stroke of 0.040.625 , which is equal to 0.025 . in sensitivity analysis , the model is run assuming that being in normal sinus rhythm has no impact on stroke risk . it is assumed that the proportion of patients taking warfarin in both treatment groups entering the model was 0.44 . this was based on the percentage of patients in the fractal registry that remained long term users of warfarin therapy after being diagnosed with atrial fibrillation . the probability of bleeding while being on warfarin and aspirin therapy was based on data presented in a systematic review and meta - analysis published by lip and edwards . first , the annual risk of major bleed while not receiving either warfarin or aspirin therapy was estimated based on details reported for the placebo arms of the studies included in the systematic review . these details included the number of patients and number of major bleeds in the placebo arm of each included study along with the mean duration of each study . based on this data , the annual rate of a major bleed in the absence of warfarin or aspirin therapylip and edwards reported the relative risk of a major bleed for placebo compared to warfarin to be 0.45 ( 95 % ci 0.25 , 0.82 ) . this relative risk was applied to the rate of major bleed without warfarin therapy to estimate the annual probability of major bleed while on being warfarin therapy . the annual probability of major bleed while being on warfarin therapy was estimated to be 0.0129 ( 0.004581 / 0.45 ) . data from the stroke prevention in atrial fibrillation ii study were used to estimate the proportion of major bleeds that are ichs . the annual rate of major haemorrhages along with the annual rate of ich for patients on aspirin and warfarin therapy was presented . based on this data , the proportion of major bleeds that are ichs was estimated to be 0.332 . the probability of recurrence of af after achieving nsr was derived from a long - term observational study of af ablation and aad treatment by pappone et al . who reported the probability of being free of af at one , two , and three years for both aad and ablation treated patients . based on the one - and three - year data , the annual probability of af recurrence for patients achieving nsr was estimated to be 0.036 for af ablation treated patients and 0.221 for aad treated . the probability of af ablation procedural complications was taken from a systematic review of rct and non - rct studies evaluating catheter - based af ablation procedures . the probabilities of ischemic stroke , transient ischemic attack , cardiac tamponade , and pulmonary veins stenosis resulting from af ablation are 0.003 , 0.002 , 0.008 , and 0.016 , respectively . the probability of pulmonary toxicity while being on aad treatment was based on data presented by vorperian et al . . the authors report that 1.9 % of amiodarone patients from their four included studies suffered from pulmonary toxicity . based on the weighted mean followup in the studies ( 27.54 moths ) , the annual probability of pulmonary toxicitythe proportion of cases of pulmonary toxicity that are irreversible was assumed to be 0.25 . the probability of death following pulmonary toxicity was assumed to be 0.091 as reported by dusman et al . . general population age and gender specific mortality rates based on canadian life tables were applied to patients in the model in the absence of events ( e.g. , ischemic stroke and major bleeds ) . several sources were used to derive mortality rates for patients who suffer an ischemic stroke during the model . reported various outcomes for 34,448 patients hospitalized for first stroke in canada . amongst the outcomes reported were 28 - day mortality rates by age group and gender according to stroke type . the 28 - day mortality rates for patients with strokes classified as cerebral infraction ( icd - 9434,436 ) were applied to patients suffering an ischemic stroke in the model . to account for the increased risk of death following the remainder of the first year after stroke , data from another canadian - based publication was used . tu and gong reported mortality for patients hospitalized for acute stroke in canada at 30 days ( 18.9 % ) and at one year ( 32.0 % ) . the ratio of one - year mortality to 30 - day mortality reported in this study can be estimated as 1.78 ( 0.32 / 0.189 ) . in the model , this factor was applied to the 28 mortality rates reported by johansen et al . in order to estimate one - year age and gender specific mortality rates for ischemic stroke . for poststroke mortalitythirty - day age and gender specific mortality after intracranial hemorrhage ( ich ) ( icd9 - 431 ) was taken from the canadian - based study by johansen et al . . to estimate one - year mortality , the 30 - day mortality rates were increased by a factor of 1.2 . this adjustment factor was based on a study on long - term mortality post - ich . reported mortality to be 0.48 and 0.59 at one month and one year , respectively . while being in the normal sinus rhythm health state , patients were assigned age and gender specific general population utility values . no existing published studies primarily reporting utilities for af were identified . however , reynolds et al . do describe various utility estimates they derived as part of their cost - effectiveness analysis of the radio frequency af ablation . reynolds et al . specifically transformed patient level sf - 12 responses for patients enrolled in the fractal registry to utility scores using the brazier algorithm . reynolds et al . reported the average change in utility in patients with no documented recurrences of af over 12 months to be 0.046 . based on this data , a disutility of 0.046 was applied to patients while being in the af health state . estimated utilities transforming sf - 36 patient level responses from patients before and after af ablation from two other patient populations . however , we felt the data from the fractal trial to best represent the change in utility moving from an af to nsr health state , as the other studies evaluated intervention specific changes in utility values . riviero - arias et al . provided estimates of poststroke utility scores according to modified rankin score ( mrs ) . in a canadian - based cohort study , goeree et al . reported the distribution of discharge modified ranking score according to the type of stroke ( ischemic , haemorrhagic , and transient ischemic attack ) . the mrs specific utility values reported by riviero - arias et al . were applied to the distribution of hospital discharge mrs reported by goeree et al . in order to derive a weighted average utility weight for ischemic and haemorrhagic stroke . based on this data , the utility weight applied to patients after ischemic and haemorrhagic stroke was 0.46 and 0.28 , respectively . a disutility of 1.0 for seven days was applied to the af ablation complications . for pulmonary toxicity , the mean length of stay for a pulmonary toxicity related hospitalization was estimated to be 13 days . this was based on hospitalizations identified from the ontario case costing initiative database with a primary diagnosis of j70 .2 ( acute - drug induced interstitial lung disorders ) , j70 .3 ( chronic drug - induced interstitial lung disorders ) , j70 .4 ( respiratory conditions due to drug - induced interstitial lung disorders , unspecified ) , or j84 .1 ( idiopathic pulmonary fibrosis ) . for irreversible pulmonary toxicity , the cost of an entire inpatient stay for an ablation procedure was estimated using data from the ontario case costing project . we specifically used the average cost of hospitalizations with a primary procedure code indicating catheter ablation using a percutaneous transluminal approach ( 1.hh.59.gp - aw ) and the most responsible diagnosis of atrial fibrillation ( i480 ) . based on these criteria , the mean cost per af ablation hospitalization was estimated to be $ 7,056 . the physician fees for an af ablation procedure were estimated using expert opinion on applicable physician fee codes and fees listed in the ontario schedule of benefits for physician services . the total physician fees for an af ablation procedure were estimated to be $ 2,534 the total cost per af ablation used in the model was $ 9,590 . the number of ablation procedures per patient was derived from a survey of electrophysiology laboratories published by cappato et al . . reported that amongst 8745 af ablation patients , 2389 ( 27 % ) required one or more ablation procedures . therefore , in the model it was assumed that each patient would require 1.27 ablation procedures and the total procedure costs applied to the af - ablation arm were $ 12,179 ( $ 9,5901.27 ) . in the first year after ablation , patients were assumed to be followed up with three cardiologist consultations and undergo a ct scan during the first year after ablation . the cumulative cost of followup in the first - year follow - up was $ 666 . the cost of procedural complications was estimated from a published canadian - based costing study by khaykin et al . . the unit costs of cardiac tamponade , pv stenosis , stroke , and transient ischemic attack specifically were $ 5,842 , $ 8,487 , $ 14,1872 , and $ 4.297 , respectively . these costs included inflation to 2010 $ cdn using the healthcare component of the consumer price index . the mean cost per hospitalization with a primary diagnosis potentially related to pulmonary toxicity was found to be $ 20,436 . these were hospitalizations with a primary diagnosis code of j70 .2 ( acute drug - induced interstitial lung disorders ) , j70 .3 ( chronic drug - induced interstitial lung disorders ) , j70 .4 ( respiratory conditions due to drug - induced interstitial lung disorders , unspecified ) , or j84 .1 ( idiopathic pulmonary fibrosis ) . for irreversible pulmonary toxicity , these costs included inflation to 2010 $ cdn using the healthcare component of the consumer price index . unit costs for medications were based on reimbursement prices from the ontario drug benefit formulary . an 8 % pharmacy markup was applied to the raw drug costs along with a $ 7.00 dispensing fee . it was assumed that a 90 - day supply of the drug would be dispensed each time . both patients with normal sinus rhythm and those in the af health state were assigned amiodarone costs each cycle . an 8 % pharmacy markup was applied to the raw drug costs along with a $ 7.00 dispensing fee . it was assumed that a 90 - day supply of the drug would be dispensed each time . in addition , an annual monitoring cost for warfarin of $ 387.54 was assumed in the model . this cost included inflation to 2010 $ cdn using the healthcare component of the consumer price index . the cost of stroke was estimated from a canadian - based costing study by goeree et al . . in this study , the total one year health care cost for patients suffering an ischemic stroke was found to be $ 53,576 . costs for the second year and after stroke were assumed to be equal to the sum of the costs for long - term care , home care , prescription medications , outpatient visits , doctor visits , and assistive devices . these costs amounted to $ 6,265 and $ 4,841 for ischemic and haemorrhagic stroke , respectively . after inflating to 2010 $ cdn , the first - year costs for ischemic and haemorrhagic were $ 61,413 and $ 58,159 , respectively . each subsequent year 's costs for ischemic and haemorrhagic stroke were $ 6,801 and $ 5,843 , respectively . the cost of a major bleed used in the model was $ 6,023 and was based on the average cost of a hospitalization with a case mix group for a gastrointestinal bleed ( cmg 281 ) . parameter uncertainty is evaluated using probabilistic sensitivity analysis ( psa ) and is presented in the form of a cost - effectiveness acceptability curve for the af ablation strategy . table 2 presents the distributions , parameters , and resultant 95 % confidence intervals for model parameters . cost - effectiveness specifically results presented are varying discount rates , model time horizon , the annual probability of af recurrence after ablation , and the disutility of being in the af health state . additionally , the model was run under the assumption that restoration of nsr does not impact the stroke risk and under the assumption that amiodarone treatment is discontinued for patients not in normal sinus rhythm . model results according to age and gender were tested along with model results by baseline chads2 stroke risk score . sensitivity analysis on age and gender was conducted under two scenarios . in the first scenario , the probability of stroke was the same for all ages given a specific chads2 score . in the second scenario , the risk of stroke is varied according to age using framingham stroke risk data . wolf et al . presented the 10 - year risk of stroke according to age and gender . using this data , the relative risk for stroke for different ages relative to 65 year olds was estimated and applied to the risk of stroke based on a chads2 risk score of 2 . as shown , the ablation treatment group was estimated to incur $ 8,539 in incremental expected costs compared to the aad treatment group . the model estimated that the ablation group had more expected qalys and fewer expected number of strokes compared to the aad treatment group . the ablation treatment arm specifically was estimated to result in 0.033 fewer expected number of strokes and 0.144 more quality adjusted life years compared to the aad treatment arm . based on the expected costs and qalys estimated by the model , the incremental cost per qaly of the ablation arm compared to the aad arm is $ 59,194 . therefore , using the basecase analysis , ablation would be considered cost - effective if societies ' willingness to pay for a qaly is $ 59,194 or higher . otherwise , aad therapy is the cost - effective treatment strategy . figure 3 presents the cost - effectiveness acceptability curve for the af ablation strategy compared to the aad strategy . af ablation has the highest probability of being cost - effective at willingness to pay values of $ 62,000 per qaly and higher . the probability of af ablation being cost - effective at willingness to pay for a qaly threshold of $ 25,000 , $ 50,000 , $ 100,000 , and $ 150,000 was estimated to be 0.03 , 0.30 , 0.89 , and 0.98 , respectively . table 4 presents cost - effectiveness results for different patient groups based on age , gender , and chads2 index score . as shown , cost - effectiveness results varied according to age and gender . the incremental cost per qaly is estimated to be $ 57,088 for a 55 - year - old female and $ 65,129 for 75 - year - old female . for males , the incremental cost per qaly was estimated to be $ 57,167 for a 55 year old and $ 65,129 for a 75 year old . when the chads2 index score for the model cohort is 0 , the incremental cost per qaly of ablation compared to aad becomes $ 68,822 . when the chads2 index score was 4 , the incremental cost per qaly became $ 44,652 . using a 10 - year time horizon , the incremental cost per qaly became $ 14,273 for af ablation compared to aad . a 20 - year time horizon results in ablation being both less costly and more effective than the aad treatment strategy . if a zero percent discount rate is used , the incremental cost per qaly of the ablation strategy became $ 49,308 per qaly . in their economic evaluation of ablation compared to aad , reynolds et al . if this same assumption is applied in the current model , the cost per qaly of the af ablation strategy became $ 86,129 . as shown , even with the assumption that restoration of nsr does not impact stroke risk , the incremental qalys from af ablation were only reduced from 0.144 in the basecase to 0.116 . this indicates that much of the difference in qalys predicated by the model was due to the disutility applied to patients while in the af health state . if the disutility of being in af compared to nsr is 0.08 instead of the basecase value of 0.043 , the cost per qaly of af ablation becomes $ 38,390 per qaly . if the disutility of being in the af health state is 0.02 or 0.00 the incremental cost per qaly becomes $ 101,083 per qaly and $ 221,839 per qaly , respectively . the annual probability of recurrence of af in patients undergoing ablation has little impact on the cost per qaly estimate . if the annual probability of af recurrence is assumed to be 0.00 , the cost per qaly becomes $ 53,831 . if the annual probability of af recurrence is assumed to be 0.05 , the cost per qaly becomes $ 61,280 . the current study found the incremental cost per qaly of catheter ablation of af to be $ 59,194 in canada compared to treatment with amiodarone in patients previously failing an antiarrhythmic medication . based on common cost - effectiveness thresholds , our findings are similar to those from economic evaluations of af ablation conducted from the perspective of other countries . mckenna et al . evaluated the cost - effectiveness of af ablation compared to treatment with amiodarone from a uk perspective . the authors assumed a lifelong time horizon in their basecase and estimated the cost - effectiveness of af ablation to be 7,910 per qaly for patients with a chads risk score of 3 . assuming a 5 - year time horizon , the cost - effectiveness of af ablation in this patient group was estimated to be 20,831 ( $ can32 ,704 ) . reynolds et al . conducted a us - based economic evaluation of catheter ablation for af compared to treatment with amiodarone in the same population as our study . using a 5 - year time horizon theoretical basecase , the authors estimated the cost per qaly of ablation compared to amiodarone to be $ 51,131 . therefore , the increase in qalys was primarily due to better quality of life after ablation . our study is unique because it is the first to look at the cost - effectiveness of catheter ablation from a canadian perspective . one limitation is that the published rct comparing the proportion of patients achieving normal sinus rhythm after ablation or antiarrhythmic drugs is limited to 1 year followup . assumptions had to be made on the effectiveness of the two strategies on maintaining rhythm control beyond the first year . additionally , no published data was found directly comparing stroke rates between patients treated with ablation compared to those treated with aad .\noutput:\n" }, { "from": "agent", "value": "objective . the objective of this study is to evaluate the cost - effectiveness of catheter ablation for rhythm control compared to antiarrhythmic drug ( aad ) therapy in patients with atrial fibrillation ( af ) who have previously failed on an aad . methods . an economic model was developed to compare ( 1 ) catheter ablation and ( 2 ) aad ( amiodarone 200 mg / day ) . at the end of the initial 12 month phase of the model , patients are classified as being in normal sinus rhythm or with af , based on data from a meta - analysis . in the 5 - year markov phase of the model , patients are at risk of ischemic stroke each 3 - month model cycle . results . the model estimated that , compared to the aad strategy , ablation had $ 8,539 higher costs , 0.033 fewer strokes , and 0.144 more qalys over the 5 - year time horizon . the incremental cost per qaly of ablation compared to aad was estimated to be $ 59,194 . the probability of ablation being cost - effective for willingness to pay thresholds of $ 50,000 and $ 100,000 was estimated to be 0.89 and 0.90 , respectively . conclusion . based on current evidence , pulmonary vein ablation for treatment of af is cost - effective if decision makers willingness to pay for a qaly is $ 59,194 or higher ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the adhesion of circulating blood platelets to the subendothelial matrix exposed upon vessel wall injury represents the initial event of the haemostatic process required to limit hemorrhage . platelets express several membrane receptors specific for all the major adhesive ligands of the vascular extracellular matrix . among these , collagen is probably the most important subendothelial matrix component involved in thrombus formation , and platelet adhesion to collagen is associated with a complex pattern of activatory signaling pathways . integrin 21 and glycoprotein vi ( gpvi ) are the two main platelet receptors for collagen and , in the rheological conditions of low shear rates , typically present in large veins and venules , are sufficient to mediate firm platelet adhesion . at high shear rates , characteristic of small arteries and stenotic vessels , platelets are unable to efficiently interact to exposed collagen fibers , and in these conditions adhesion is preceded by platelet tethering and rolling on the site of injury . this process is mediated by the membrane gpib - ix - v complex , a platelet - specific receptor for the multimeric glycoprotein von willebrand factor ( vwf ) . at high shear stress , circulating vwf rapidly interacts with exposed collagen fibers and undergoes a conformational change that allows the interaction with the gpib - xi - v complex , decelerating platelets and favoring the subsequent stable adhesion mediated by other platelet receptors . the interaction of platelet adhesion receptors with subendothelial matrix components stimulates an intricate pattern of signal transduction pathways , that trigger spreading , secretion of soluble proaggregating molecules , thromboxane a2 ( txa2 ) synthesis and release , and phosphatydilserine exposure . these events recruit and activate additional circulating platelets to initiate a process of cell aggregation , that generates a rapidly growing thrombus at the site of damaged vessel wall . the stability of platelet adhesion and of the subsequent thrombus formation is reinforced by autocrine stimulation by the released soluble agonists , in particular adp and txa2 , and by thrombin produced through the coagulation cascade . these agonists stimulate specific g - protein - coupled receptors ( gpcrs ) expressed on platelet surface and typically lead to the activation of phospholipase c ( plc ) isoforms , that release diacylglycerol ( dag ) and inositol trisphosphate ( ip3 ) . ip3 mediates ca release from intracellular stores , whereas dag stimulates several effectors containing the dag - regulated c1 domain , such as classical and novel protein kinase c isoforms . concomitantly , other signaling molecules , including phosphatidylinositol 3 kinases ( pi3ks ) , protein tyrosine and serine / threonin kinases , and ras - like small gtpases , are activated and contribute to promote full platelet activation . these events eventually promote platelet aggregation and thrombus formation , which are supported by the stimulation of integrin iib3 , that is converted into a high - affinity state for fibrinogen , whose binding mediates interaction of adjacent cells promoting thrombus growth . several signaling pathways evoked upon platelet adhesion require the intervention of one or more ras - like small gtpases , that operate as molecular switches by cycling between an inactive state bound to gdp and an active state bound to gtp through the action of specific guanine nucleotide exchange factors ( gefs ) and gtpase - activating proteins ( gaps ) . platelets express several ras - like gtpase , including ras , ral , rho , rac and , cdc42 , but are particularly rich of members of the rap subfamily of gtpases . this paper will focus on platelet rap gtpases to highlight recent insights into the mechanism of activation and recruitment upon stimulation of the major platelet adhesion receptors . it is now well established that rap gtpases are involved in several cell functions , including growth , proliferation , cell - cell contact , and adhesion . the rap family consists of five members : two rap1 proteins ( rap1a and rap1b ) that share 90 % sequence homology and three rap2 proteins ( rap2a , rap2b , and rap2c ) which are about 70 % homologous to rap1 . an important difference between the two subfamilies is that rap2 proteins typically display a lower sensitivity to gaps , promoting a prolonged rap2 signaling compared to that of rap1 . although regulated by the same set of gefs and gaps , rap1 and rap2 can be involved in distinct processes , as shown in cell types different from platelets , suggesting that they may operate through different effectors . the biochemical basis of these different effects has not been thoroughly investigated ; however it might also be related to the differences in posttranslational modifications and subcellular localization of rap1 and rap2 isoforms . rap1b is the most abundant gtpase in platelets and represents up to the 0.1 % of total proteins , but platelets also contain rap2b , which , however , is about ten times less abundant than rap1b . very low levels of rap1a and rap2a have been detected in platelets , whereas rap2c is not present . probably because of these different levels of expression , only a limited number of studies have addressed the biochemistry and function of rap2b in platelets , while the majority of the investigations have focused on rap1b . in platelets , the most abundant and functionally relevant rapgef is certainly the ca - and dag - regulated caldag - gefi , which represents the key regulator of rap gtpases activation downstream of plc activation . the expression of low levels of other rap1gefs , as pdz - gef and caldag - gefiii , has also been reported , but in some cases their presence remains controversial . the only gap specific for rap gtpases identified in platelets is rap1gap2 , whereas rap1gap1 , spa - 1 , and e6tp1 have not been found . it has been shown that rap1gap2 is able to associate with 14 - 3 - 3 and to modulate cell adhesion when overexpressed in hela cells ; however the importance of this regulator in platelet function is still unknown . the role of rap gtpases , and in particular of rap1 , in the regulation of cell adhesion is well documented by a number of observations in different cell types . rap gtpases participate to the conversion of integrins into a high - affinity state for their ligands , that in turn allows cells to interact , in a controlled fashion , with other cells and with extracellular matrix components . the ability of integrins to bind their ligands is regulated by inside - out signaling pathways that originate inside the cell and are then transmitted to the extracellular ligand - binding domain of the receptor . integrin - mediated platelet functions include adhesion , aggregation , and thrombus formation , and thus it appears reasonable for rap1b to be involved in these responses . in this context , important information has been collected upon the generation of the genetically modified mice that do not express either rap1b , or the main rap1gef present in platelets , caldag - gefi . rap1b knockout mice display a prolonged tail bleeding time and a marked protection from platelet - dependent arterial thrombosis , demonstrating an essential role of this gtpase in both haemostasis and thrombosis . the importance of rap1b activation in thrombus formation is also confirmed by analysis of caldag - gefi knockout mice . although the clotting parameters are normal , caldag - gefi knockout mice display strong defects in haemostasis assessed by bleeding tail analysis . in addition , platelets in whole blood collected from caldag - gefi knockout mice fail to form thrombi when perfused over a fibrillar collagen surface both at low and high shear rates . moreover , the lack of caldag - gefi is also associated with defective in vivo thrombosis , that is virtually abolished in arteries and strongly reduced in venules . these alterations of the haemostatic and thrombotic functions of platelets , which are driven by both cell - matrix and cell - cell adhesion , are indicative of a role for rap1b in the regulation on platelet integrin function . platelets express at least five different integrins ( iib3 , 21 , 51 , 61 , and v3 ) and in particular integrins iib3 and 21 play a predominant role in platelet adhesion and activation . however , integrins 51 and 61 are required to mediate shear - resistant adhesion , whereas the function of integrin v3 is less understood . a number of ex vivo studies on human and murine platelets have demonstrated that rap1b plays a critical role in the regulation of integrin iib3 affinity state and , therefore , controls platelet aggregation induced by soluble agonists . important information on the mechanism of inside - out integrin activation has been collected using transfected cell lines to reconstitute this signaling pathway . these studies indicate that integrin signaling involves the interaction of the head domain of the cytoskeletal protein talin with specific sites of integrin - tail and with the plasma membrane . talin can synergize with kindlin - 1 and -2 to mediate integrin iib3 conversion into the active state ; however , the overexpression of kindlin alone is not sufficient to promote integrin activation . in talin - and integrin iib3 - expressing cho cells , the coexpression of pkc at levels comparable to those present in platelets induces a strong responsiveness to pma exposure , and the overexpression of a constitutive active form of rap1a bypasses the requirement of pkc , indicating that , in this model , rap1 lies downstream of pkc . among different potential rap1 effectors , riam ( rap1 - interacting adaptor molecule ) was shown to be involved in integrin regulation , and its overexpression in cell lines bypasses the requirement of rap1 . moreover , riam knockdown suppresses rap1 - mediated integrin activation , as well as the association between talin and integrin - tail . however , the importance of riam in platelet physiology and integrin iib3 - mediated platelet aggregation still needs to be determined and will require the development of riam knockout mouse models . further support to the hypothesis that rap1b regulates integrin affinity was provided by the analysis of rap1b and caldag - gefi knockout mice . generally , the lack of rap1b or caldag - gefi is coupled to a substantial defect in integrin iib3 activation and platelet aggregation . rap1b - deficient platelets display a reduced aggregation in response to a wide range of concentrations of agonists , as adp and epinephrine , and to low doses of collagen , thrombin receptor - specific agonist aypgkf , and ca ionophore . the lack of caldag - gefi is associated with a more severe reduction of platelet aggregation caused by the same set of agonists , whereas the dag analogue pma and high doses of thrombin induce a comparable extent of platelet aggregation in wild - type and caldag - gefi - deficient platelets . the caldag - gefi - independent pathway leading to platelet aggregation requires pkc activation , subsequent granule release , and p2y12 stimulation by secreted adp . similarly to integrin iib3 , also integrin 21 is present on the platelet surface in at least two different affinity states for its ligands , and conversion into the high - affinity state facilitates collagen - mediated platelet activation . in this context , it has been recently shown that , under certain conditions , rap1b expression is required to allow a proper integrin 21 activation . indeed , platelets from rap1b knockout mice show defective integrin 21 activation upon stimulation of the collagen receptor gpvi , but not upon stimulation of thrombin or adp receptors . however , the extent of adhesion to collagen via integrin 21 is normal in platelets from rap1b knockout mice , suggesting that adhesion to collagen under static conditions does not involve rap1b - dependent stimulation of integrin 21 . interestingly , in contrast to what was observed for rap1b - deficient platelets , platelets from caldag - gefi knockout mice display a reduced ability to adhere to immobilized collagen under static conditions , when compared to wild - type cells . moreover , alsothe ex vivo analysis of thrombus formation on immobilized collagen under flow has revealed a reduced area coverage and thrombus growth in caldag - gefi knockout platelets . interestingly , the addition of adp and txa2 increases the adhesion of caldag - gefi knockout platelets to a collagen surface at low shear rates , without restoring thrombus growth . in addition to the key role played in platelet adhesion to collagen , the expression of caldag - gefi is also required for an efficient platelet interaction with other 1 integrin ligands as laminin and fibronectin . the observed differences between rap1b and caldag - gefi knockout mice , which are particularly evident in terms of phenotype severity , may be related to possible additional functions of caldag - gefi , independent of rap1b activation , that can be required for efficient integrin - mediated adhesion . moreover , in rap1b knockout platelets rap1a or rap2b could partially compensate the lack of rap1b . indeed , although expressed at lower level rap1a can be activated by platelet stimulation in rap1b knockout platelets . by contrast , since caldag - gefi also stimulates rap2b activity in platelets , this isoform can not compensate the lack of rap1b , and this may explain the more severe phenotype of caldag - gefi knockout mice . however , it should also be considered that some discrepancy in the results obtained from caldag - gefi and rap1b knockout mice simply reflects the different experimental conditions adopted . an increasing number of observations indicate that rap gtpases and adhesive receptors are connected in a bidirectional fashion . as described above , a major role for rap gtpases is the regulation of integrin affinity for the specific ligands . in this context rap1b activationis triggered by stimulation of many gpcrs in platelets and participates to the organization of the signaling pathway for integrin inside - out activation . however , in the last years , an increasing number of studies have proved the involvement of rap1b also in integrin outside - in signaling and have documented its activation downstream of many platelet adhesive receptors . integrin 21 is a collagen receptor important for a proper hemostasis in humans , as documented by the observation that mutations of this receptor are associated with bleeding disorders and reduced platelet responses to collagen . integrin 21 is a critical platelet adhesion receptor , that interacts with collagen , by recognizing hexapeptidic sequences , such as gfoger , gloger , gasger , groger , and glogen , but it also binds tenascin , and mediates platelet adhesion to the small proteoglycan decorin . platelet adhesion via integrin 21 directly stimulates rap1b activation , without the need for further autocrine stimulation by secreted adp or released thromboxane a2 . experiments performed with platelets from genetically modified mice have shown that caldag - gefi is the only gef required for rap1b stimulation downstream of integrin 21 . the dissection of the signaling pathway involved indicates that plc2 expression and activation are mandatory for integrin 21 - triggered rap1b activation . interestingly , recruitment of platelet integrin 21 mediates the activation of plc2 by two redundant mechanisms : a classical src - mediated phosphorylation of plc2 itself and a phosphorylation - independent mechanism involving the rac gtpase . these observations indicate the existence of important crosstalk between rac1 and rap1b gtpases in the control of platelet adhesion and activation , with rac1 being potentially upstream of rap1b . as it will be discussed later , the existence of a crosstalk between rap and rac has been recently confirmed also downstream of gpvi . further analysis of caldag - gefi and plc2 knockout mice demonstrated that the lack of rap1b activation is accompanied by a significant inhibition of integrin iib3 conversion into the high - affinity binding state for fibrinogen , demonstrating that rap1b activation plays a key role in the crosstalk between integrins and regulates integrin 21 - mediated platelet aggregation . more recently , it has been demonstrated that maximal rap1b activation induced by integrin 21 downstream of plc2 requires the contribution of an additional ca - dependent signaling pathway involving the focal adhesion kinase pyk2 and the subsequent stimulation of pi3k . in fact , the lack or the impaired activation of pyk2 and pi3k causes a defective rap1b activation triggered by integrin 21 engagement . these findings outline that , as previously observed in platelets stimulated with adp or other soluble agonists , also in integrin 21 outside - in signaling rap1b activity is regulated by pi3k . since virtually no residual rap1b activity is detected in caldag - gefi - deficient platelets , this observation points to a contribution of pi3k activity in the regulation of caldag - gefi , but the molecular mechanism for this process is still to be defined . gpvi is membrane glycoprotein specifically expressed in platelets , functionally associated with the itam - containing transmembrane adapter protein fcr - chain . it is well documented that platelet gpvi is responsible for the first set of signals induced by platelet interaction with collagen and that it strongly cooperates with integrin 21 to mediate full collagen - induced response . the gpvi - fcr - chain complex initiates a tyrosine - kinase - based signaling cascade which involves src and syk kinases , the adaptor proteins lat and slp76 , and leads to phosphorylation and stimulation of plc2 . mouse or human platelets lacking gpvifcr - chain display severe defects in collagen - induced activation , integrin iib3 regulation and platelet aggregation . as part of the signaling pathways for collagen - induced platelet activation , gpvi stimulation triggers rap1b activation . this process , however , is at least partially dependent on adp secretion and the subsequent stimulation of p2y12 receptor , both in human and murine platelets . nevertheless , the existence of a direct , p2y12 - independent pathway of gpvi - mediated rap1b activation has been confirmed by the analysis of aggregation of platelets collected from wild - type and rap1b knockout mice , performed in the presence of adp receptors antagonists . these experiments show that the lack of rap1b is associated with a reduced adp - independent , gpvi - mediated platelet aggregation , demonstrating that this gtpase is required for an efficient gpvi signaling . interestingly , direct rap1b - activation - mediated downstream of gpvi depends on the activity of pi3k , and it has been demonstrated that the contribution of both the and isoforms of pi3k is required . as for the other platelet collagen receptor , integrin 21 , caldag - gefi is a specific regulator of rap1b activation also downstream of gpvi . in addition , a number of gpvi - dependent responses have been found to be impaired in caldag - gefi - deficient platelets . some of these , such as integrin iib3 activation , and platelet aggregation are consistent with the well - documented role for rap1b , and other defects , such as the reduction of erk signaling leading to a decreased txa2 synthesis , or the impaired granule secretion , point to possible novel implication for this gtpase in platelet function . the gpvi - mediated signaling pathway leading to rap1b activation involves the small gtpase rac1 . the observation that rac1 is involved in plc2 - dependent stimulation of rap1b downstream of integrin 21 has been extended in a recent work by stefanini and coauthors showing that the two gtpases exert a mutual influence also downstream of gpvi . indeed , rap1b signaling sustains rac1 activation , and , in turn , rac1 provides a feedback regulation of rap1 through caldag - gefi and p2y12 . interestingly , the ability of gpvi - fcr - chain complex to stimulate rap1b has been directly compared to the stimulation of the closely related rap2b . it has been reported that gpvi ligation results in a time - dependent rap2b activation , that is not influenced by platelet aggregation ( i.e. , integrin iib3 - mediated fibrinogen binding ) and actin cytoskeleton remodelling . differently to what was observed for rap1b , secreted adp plays only a negligible role in rap2b activation triggered by gpvi , whereas ca mobilization and pkc activation are both required . another remarkable difference between activation of rap1b and rap2b downstream of gpvi is that rap2b stimulation is largely independent from pi3k activity . however , it is important to note that pi3k inhibitors suppress thrombin - induced rap2b activation . rap1 and rap2 are therefore differently regulated by pi3k , depending on the nature of the stimulus . recently , it has been shown that rap2b activation depends on caldag - gefi and p2y12 signaling , similarly to what was already demonstrated for rap1b . according to the lower sensitivity to gaps , rap2b displays a higher baseline activation that is also a more sustained in time , compared to that of rap1b . therefore , our current information on the contribution of rap2b to platelet adhesion is still really limited . integrin iib3 ( also known as gpiib / iiia ) is the most abundant platelet membrane receptor and is responsible of the binding of platelets to soluble fibrinogen , a process that mediates platelet aggregation . as introduced before , integrin iib3 undergoes a conformational change upon platelet activation , that increases the receptor affinity for fibrinogen . this inside - out activation of the integrin function involves rap1b stimulation and its association with riam , talin and other signaling and cytoskeletal proteins , such as vinculin and kindlin . however , in addition to the key role in platelet aggregation , integrin iib3 is also able to mediate platelet adhesion to immobilized fibrinogen and to other rgd - containing ligands , including vwf , vitronectin , fibronectin , and thrombospondin . integrin iib3 interaction with its ligands initiates an outside - in signaling pathway , that contributes to the regulation of the later phases of platelet activation and is required for firm platelet adhesion and spreading on extracellular matrices , fibrin clot retraction , platelet procoagulant activity , and microparticle release . the first evidence for the involvement of rap1b in integrin iib3 outside - in signaling was obtained from studies with thrombin - stimulated platelets in the presence of integrin antagonists , including the peptide grgds , that prevent fibrinogen binding and platelet aggregation . in this contextit was initially shown that sustained rap1b activation mediated by thrombin requires the interaction between integrin iib3 and fibrinogen , as it was inhibited by the rgds peptide . the activation of rap1b by integrin iib3 has been confirmed by the direct observation that platelet adhesion to immobilized fibrinogen stimulates the accumulation of gtp - bound rap1b . integrin iib3 - mediated rap1b activation is regulated by multiple intracellular effectors , including src kinases , pkc , and cytosolic ca . moreover , rap1b - deficient platelets display a reduced spreading on fibrinogen compared with wild - type controls , whereas clot retraction is abolished , indicating that stimulation of rap1b is important for integrin iib3 - mediated platelet responses . the gpib - ix - v receptor complex , which contains four transmembrane proteins , gpib , gpib , gpix , and gpv , mediates platelet binding to vwf in a shear - dependent fashion . the vwf - gpib - ix - v interaction is required to slow down circulating platelets on the site of injury and is strongly involved in the regulation of integrin iib3 and in the formation of arterial thrombi . the adhesive function of gpib - ix - v is coupled to the generation of intracellular signals that support platelet activation mainly through the phosphorylation of the itam - bearing fciia receptor , which is physically associated with it . moreover , fciia receptor - independent signal transduction pathways occurring downstream of gpib - ix - v and leading to protein phosphorylation , calcium oscillation , and integrin iib3 activation have been identified . gpib - ix - v ligation triggers the subsequent activation of integrin iib3 that mediates firm platelet adhesion and initiates thrombus formation . despite the relevance of the initial platelet adhesion through gpib - ix - v at the site of arterial injury for the whole process of thrombus formation , the information about the ability of this adhesion receptor to trigger rap gtpases activation is extremely limited . it has been shown that platelet stimulation with vwf triggers the activation of both rap1b and rap2b and promotes their association with the cell cytoskeleton through a process involving the fciia receptor . vwf - induced rap2b translocation to the cytoskeleton , in particular , is dependent on integrin iib3 as it is prevented in the presence of anti - integrin iib3 - specific antibodies , as well as in patients affected by glanzmann 's thrombasthenia , a genetic disorder associated with the lack of expression of integrin iib3 . antibody - mediated clustering of fciia receptor , that induces its tyrosine phosphorylation and mimic the signaling pathway triggered by vwf - mediated gpib - ix - v stimulation , is coupled to rap1b activation in a fashion completely dependent on secreted adp . unfortunately , studies that used transgenic mouse models to elucidate the role of rap1b in gpib - ix - v - mediated platelet responses have not been reported . the great effort devoted to understand the roles of rap gtpases in the regulation of platelet function produced a huge amount of evidence demonstrating their critical role in haemostasis and thrombosis . as schematically summarized in figure 1 , the involvement of rap gtpases in adhesion dynamics is complex and bidirectional , as they are both activated by adhesive receptors and essential for the regulation of the adhesive properties of integrins . the crucial implication of rap gtpases in the control of cell adhesion suggests that the identification of their effectors may help to define novel possible targets for effective antiplatelet therapies for the treatment of cardiovascular diseases .\noutput:\n" }, { "from": "agent", "value": "integrins and other families of cell adhesion receptors are responsible for platelet adhesion and aggregation , which are essential steps for physiological haemostasis , as well as for the development of thrombosis . the modulation of platelet adhesive properties is the result of a complex pattern of inside - out and outside - in signaling pathways , in which the members of the rap family of small gtpases are bidirectionally involved . this paper focuses on the regulation of the main rap gtpase expressed in circulating platelets , rap1b , downstream of adhesion receptors , and summarizes the most recent achievements in the investigation of the function of this protein as regulator of platelet adhesion and thrombus formation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: clinical trials form the main source of evidence - based medicine ( ebm ) and thereby forming the backbone of clinical practice . evidence - based practice ( ebp ) has become the treatment of choice and is a combination of research , clinical experience and patient preferences . david sackett ebp is the conscientious , explicit and judicious use of current best evidence in making decisions about the care of the individual patient . it means integrating individual clinical expertise with the best available external clinical evidence from systematic research . traditional , theoretical , anecdotal reasoning has to be replaced by high quality evidence which becomes possible only by publication of high quality research data . the strength of recommendation depends on the type of evidence generated and generally it forms a pyramid . usually , the least in the cadre is the expert 's opinion followed by observational study , randomized controlled trial and finally at the top of the pyramid , meta - analysis . a recent study conducted on clinical trials in the field of dentistry reported poor publication details of the research being conducted . [ unpublished manuscript ] ebp in the ancient era used anecdotes which were transmitted by means of stories . some of knowledge regarding traditional medicines was codified and available in form of books like - ayurveda , siddha , unani , tibetan medicine , chinese traditional medicine acupuncture and korean traditional medicine which was based on evidence that was not robust in scientific methodology . ebp in ayurveda is not being considered because of the lack of good quality clinical trials and enough publications . bridging ebp and ayurveda is a task because this empowers researchers and clinicians ' decision making . considering this the present studywas conducted to identify the scope of ebp in ayurveda and obtain a holistic view on the methodological characteristics of the studies carried out in this field of medicine . the study was conducted on trials that were registered and available as public domain in clinical trial registry of india [ ctri ( www.ctri.nic.in ) ] and so was waived from obtaining ethics committee approval . all filters with regard to phase , type , recruitment status and place of trial were eliminated . ayurveda and the following information was collected for each of the obtained clinical trials : number of centres ( single / multicentre ) , type of institution ( government / private / combined ) , study design ( randomized / single / double - blinded ) , type of study ( observational / interventional ) , type of participants ( healthy / patients ) , type of health condition , phase of clinical trial ( phase 1 / 2 / 3/4 ) , publication details ( published / not published ) , postgraduate thesis or not , nature of sponsors ( academic / commercial ) , prospective or retrospective registration of clinical trials and methodological quality [ details about randomization ( method , concealment of allocation ) ] . chi - square for trend analysis was employed to assess the trend difference between types of sponsors ( academic / commercial ) . the search yielded a total of 208 trials registered in ayurveda over the specified time period ( 3 - 2010 ; 35 - 2011 ; 52 - 2012 ; 71 - 2013 , 35 - 2014 ; 12 - 2015 ) . of this 167/208 ( 80.2 % ) were single centered and only 41/208 ( 19.7 % ) were multi - centered . a total of 13/208 ( 6.25 % ) of the registered studies were sponsored by the pharmaceutical companies and no significant trend ( p = 0.6 ) was observed in this category over the years . nearly two - thirds ( 130/208 , 62.5 % ) of the studies were randomized controlled designs while 2/208 ( 0.96 % ) were non - randomized interventional trials . only 9/208 ( 4.3 % ) were observational and reported in the year 2010 and 2011 . considering the study design , only 21/130 ( 16.2 % ) were double blinded , 18/130 ( 13.8 % ) were single blinded and 8/130 ( 6.2 % ) were triple blinded . despite this 70/208 ( 33.6 % ) of the randomized interventional trialsdid not describe blinding technique and 43.75 % ( 91/208 ) of the studies were open labeled . majority of clinical trials were conducted on patients 196/208 ( 94.2 % ) and the rest were on healthy volunteers . diabetes [ 17/208 ( 8.1 % ) ] , bronchial asthma [ 12/208 ( 5.7 % ) ] , anemia [ 8/208 ( 3.8 % ) ] and hypertension [ 7/208 ( 3.3 % ) ] were the most common conditions over which trials were conducted . most of the trials were done in an academic set up [ 195/208 ( 93.7 % ) ] while the rest in private set up . the phase of the trial was unclear in [ 37/208 ( 17.7 % ) ] of the trials . of the remaining , 3/208 ( 1.4 % ) belonged to phase i , 87/208 ( 41.8 % ) in phase ii , 13/208 ( 6.25 % ) in phase iii , 11/208 ( 5.2 % ) in phase iv .21 / 208 ( 10.1 % ) trials were unclear whether it belonged to phase i or ii , 31/208 ( 14.9 % ) in phase ii or iii , and 2/208 ( 0.96 % ) in phase iii or iv . a total of 130/208 ( 62.5 % ) studies were conducted using the randomization design . regarding the method of randomization sequence generation , 43/130 ( 33.1 % ) followed coin toss , lottery and throw of dice , 60/130 ( 46.1 % ) used computer generated list , 12/130 ( 9.2 % ) used random number table and 1/130 ( 0.7 % ) used stratified block randomization and 2/130 ( 1.5 % ) followed adaptive randomization . a total of 4/130 ( 3.1 % ) mentioned that randomization was not applicable when it was actually applicable . the various methods of concealment of allocation used were alternation [ 1/208 ( 0.4 % ) ] , case record number [ 6/208 ( 2.9 % ) ] , centralized [ 3/208 ( 1.4 % ) ] , on - site computer system [ 3/208 ( 1.4 % ) ] , pharmacy controlled [ 3/208 ( 1.4 % ) ] and pre - numbered or coded [ 9/208 ( 4.2 % ) ] . a total of 94/208 ( 45.1 % ) of the studies did not use any form of allocation concealment . out of the 52/208 ( 25 % ) of the completed trials only 1 was published which needs to be highlighted . a total of 195/208 ( 93.7 % ) were done for academic purposes and 161/208 ( 77.4 % ) were post - graduate thesis studies of which only one had been reportedly published . this study aimed at identifying the status of clinical trials being conducted in the field of ayurveda . this study also emphasizes the significance of documenting these trials in the form of publications which would end up in improving the quality of treatment provided in the form of ebp . although majority of the trials were randomized , double blinded and single centered , still not all of these have mentioned the nature of randomization and allocation concealment . considerable numbers of trials were conducted on patients with unclear phase and rarely were they published . ayurveda has its roots in srilanka and india 3500 years ago and is one of the commonly practiced complementary and alternate systems of medicine ( cam ) . the use of ayurvedic medicine has increased tremendously worldwide due to cost and consumer preference . despite asian origin , a recent study in the united states of america has shown nearly 59 % of the study population used ayurveda and almost all were aware of ayurveda . patients with chronic pain , cancer and infection by human immunodeficiency virus were estimated to use ayurveda more commonly . as defined , ebm is all about analyzing and publishing the data which would help in final decision making . despite a widespread acceptance of ebp , there is a potential for the emergence of various types of biases that mainly includes limited patient involvement in the trials . the practice of evidence - based medicine requires integrating individual clinical experience with the best available external clinical evidence . the four main aspects of deciding treatment in ayurveda include tradition ( inherited from ancestors ) , conventional ( from other examples ) , belief ( with the formula of dravya , guna , virya and karma ) and ebm , a combination of all these parameters to personalize the treatment . the complexities involved in carrying out trials in ayurveda are well - known such as treatment plan based on prakriti ; difficulty in using blinding technique due to the odor and taste of ayurveda medicine ; holistic approach such as modification of behavior and dietary regimes associated with ayurveda treatment and the differential assessment of outcomes based on doshas ; lack of standardization of ayurveda medicines and variation in the method and mode of drug administration . furthermore , there is limited support from various organizations in terms of granting funds to conduct trials in ayurveda . despite these limitations , initiatives such as consolidated standards of reporting trials in herbal interventions can be utilized by the investigators / researchers while drafting protocol and registering studies that will aid them to perform these tasks credibly . more than 400,000 registered ayurvedic physicians at more than 250 government - accredited universities or colleges form a major resource for carrying out clinical trials related to the field . but , a recent review of 225 original studies published in indian ayurveda journals concluded a non - satisfactory diagnoses and inconclusive outcomes being used in nearly 90 % of the published studies . experts suggest that ayurvedic medicine needs more rigorous scientific research for evaluating safety , quality and efficacy to be acceptable to the scientific communities , . few other researchers in the field of ayurveda even suggest that instead of hierarchical approach , a circular approach to keep a balance between internal and external validity is better especially for trials evaluating cam . a similar analysis in the world health organization international clinical trial registry platform lead to similar results in ayurveda . not only in ayurveda , similar findings in the study methodology and characteristics have been reported in dentistry as well . ctri is an open registry of all the studies related to the field of biomedical research conducted in india . interventional studies related to various medical and para - medical fields such as allopathy , dentistry , complementary and alternative systems of medicine and pharmacy carried out in india have to be registered in ctri . hence , for novice researchers , an update on the various aspects of ayurvedic clinical studies such as study design , nature of intervention , details of funding and the institutions / investigators carrying out research will be available to fill their knowledge gap , avoid duplication of research that is being carried out in other centers and improving the research transparency . we found that only few clinical trials are being carried out in the field of ayurveda in india and more focus has to be on the quality of studies to generate high quality evidence based on which firm recommendations shall be made .\noutput:\n" }, { "from": "agent", "value": "ayurveda is one of the complementary and alternative systems of medicine requiring generation of high quality evidence for rational practice . evidence can be generated from study designs and the present study is an attempt to critically assess the registered studies in the field of ayurveda from clinical trial registry of india . we found low number of trials conducted with more focus required on the quality of these studies to contribute to high quality evidence ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: increasing the knowledge in a particular field is one of the methods that ensure full compliance with the principles . moreover , obtaining information on individuals level of knowledge on a specific subject can be an essential first step in developing a training program . attitudes are probably the most distinctive and the most essential concepts of contemporary social psychology . abortion is the spontaneous or induced termination of pregnancy before the fetus is viable . induced abortion refers to the termination of pregnancy using medical or surgical procedures before the fetus becomes viable . therapeutic abortion refers to the termination of pregnancy before the fetus becomes viable , due to maintenance of the mother 's health or fetal diseases . voluntary or optional abortion refers to the termination of pregnancy before the fetus is viable , on mother 's request , but not done for medical reasons . in irancriminal abortion is the voluntary termination of pregnancy and abortion of a fetus which does not have the ability to live outside the uterus , without obtaining legal permission from the competent authorities . based on the criminal justice system of the islamic republic of iran , this is a criminal act and has criminal penalties . from the perspective of the laws and regulations of the islamic republic of iran , the only permitted abortion is therapeutic abortion . around the world , 38 million induced abortions are performed annually , 56 % of which are unsafe . unofficial experiences of midwifery practitioners show that illegal abortion exists in iran and is mostly performed secretly and by non - experts . besides the mothers personal acts regarding abortion , these centers cause complications and mortality in women . a method that can be effective on issues related to induce abortion is focusing on the medical team involved including the midwives . there has been growing attention toward the field of midwifery in the past 10 - 20 years due to the who 's recognition of midwives as the most suitable medical team to take care of women during pregnancy , childbirth , and post - partum . midwives are frequently faced with people who are seeking abortions . in the islamic civilization , it is a common belief that islam , with its own comprehensiveness , provides the latest and the best ways to solve social problems and other problems that humanity is faced with . therefore , all those faithful to islam believe that personal and social disccommandments , including the scourge of abortion , can be treated by relying on the teachings of islam . one of the duties of midwives is providing training for women on different issues such as legal and ethical issues related to abortion . thus , attention to knowledge and attitude of midwives regarding the legal and religious commandments related to midwifery is important . appropriate knowledge of healthcare providers , especially midwives , regarding authorized cases of therapeutic abortion can reduce a great amount of illegal abortions . as a result , it can decrease the inconveniences caused for pregnant women and their families , as well as medical personnel . due to the impact of knowledge and attitude on individuals performances , this study aimed to assess the knowledge and attitudes of midwives regarding legal and religious commandments on induced abortion and their excitability and effectiveness , and its relation to demographic characteristics . this descriptive , analytical , cross - sectional , single - stage study was conducted in august and september 2014 in isfahan , iran . the total number of ms and bs midwives in isfahan was about 550 people ; of these , 189 working midwives participated in this study . inclusion criteria included having an ms or bs degree ; working in health centers , private gynecology clinics , hospitals , or isfahan university of medical sciences ; and lack of education of the midwife or her immediate family in the field of islamic studies or law . the data collection tool was a researcher - made questionnaire . by referring to the centers , the first part consisted of four questions about demographic characteristics ( age , work experience , education , and work place ) . the second part consisted of 13 questions regarding knowledge about religious and legal commandments on induced abortion , and awareness of legal and religious rules on induced abortion was examined based on the obtained scores . the third part consisted of eight questions about their attitude toward the implementation and effectiveness of legal and religious commandments on induced abortion . these questions were designed based on a likert scale ( 1 - 5 ) of completely agree , agree , neutral , disagree , or strongly disagree . scores were calculated for a total of 100 and they were classified into groups of 20 : 0 - 20 ( extremely weak ) , 20 - 40 ( weak ) , 40 - 60 ( medium ) , 60 - 80 ( good ) , and 80 - 100 ( very good ) . data were analyzed using spss software ( version 19 ; spss inc . , chicago , il , usa ) and descriptive - inferential statistics ( frequency , mean , standard deviation , and pearson correlation coefficient ) . content validity was used in this study to determine the validity of the data gathering tool . the questionnaire was then examined regarding the quality of the content by a number of legal and religious experts . after collecting their opinions , reliability assessment of the data gathering tool was conducted as test - retest on the basis of a pilot study conducted on 20 individuals similar to the study population . the internal validity of the questionnaire was confirmed using cronbach 's alpha ( = 0.75 ) . after receiving permission from the ethics committee of the university , an introduction letter and explanation about the purpose of the study were provided for the midwives working at the centers . then , the questionnaires were distributed among the study participants and were completed by them . the number of subjects in this study was 189 and most of them were aged 30 - 34 years [ table 1 ] . in addition , 48.7 % of the participants had less than 5 years of work experience and their mean work experience was 8.5 years . absolute and relative frequency distribution of the subjects regarding education and the place of work are shown in table 2 . absolute and relative frequency distribution of the subjects regarding their knowledge and attitudes are presented in table 3 . only 0.5 % of the subjects had very good knowledge of legal and religious commandments on induced abortions . knowledge of 33.8 % of the subjects was weak regarding religious commandments , and knowledge of 38.6 % was weak regarding legal commandments . most of the subjects ( 52.9 % ) had an attitude score of 40 - 60 . there was no significant positive relationship between the level of knowledge , and age and work experience ( r = 0.045 , r = 0.037 ) . there was also no significant relationship between attitude , and age and work experience ( r = 0.039 , r = 0.016 ) . there was a significant positive correlation between knowledge about legal commandments on induced abortion and workplace . however , there was no significant correlation between the level of knowledge and attitude , and education level . distribution of age frequency and mean in units distribution of education and workplace in units absolute and relative frequency distribution of knowledge and attitudemean age of the participants was 33.39 ( 7.40 ) years and their mean work experience was 8.63 year . the highest frequency was related to the age group of 30 - 34 years and work experience of less than 5 years . in the study conducted in 2011 by ghadi pasha et al . on the awareness of gynecologists and midwives regarding therapeutic and criminal abortion laws , this was consistent with the present study results . in the study by banaiian and sereshti on the knowledge of midwives regarding legal and religious commandments of midwifery ,66.2 % of the participants were technicians , 25.2 % were undergraduates , and the rest were postgraduates . however , in the present study , due to the lack of specialized midwifery activities for lower than undergraduate levels of midwifery , this group was not included in the study . therefore , the present results can not be compared with those of the mentioned study . nevertheless , regarding the workplace , in both studies , most of the participants were hospital employees . in fact , the study populations of the two studies have little differences . regarding the second part of the study , the results showed that the majority of the subjects had very weak to moderate levels of knowledge about the legal and religious commandments on induced abortion . haji foghaha and keshavarz , in their study , compared the knowledge of working midwives in midwifery offices , health centers , and hospitals regarding the islamic penalty laws related to medical care in shiraz , iran , in 2007 . they found that 2 % of the midwives had very little knowledge about the professional rules , 61 % had little knowledge , 21 % had moderate knowledge , and only 2 % had a good level of knowledge . in the present study , knowledge was at a higher level compared to that in the study by haji foghaha and keshavarz . this increase in the present study can be due to the fact that university staffs were also included in the present study . in addition , the present study only measured the awareness of subjects on the religious and legal commandments on induced abortion . the midwives frequently deal with this matter ; therefore , they require more education and further studying in this field . this could explain the differences between this study and the study by haji foghaha and keshavarz regarding the level of awareness and knowledge . in this study , meanattitude toward the effective implementation of legal and religious commandments on induced abortion was 55.48 ( 10.99 ) out of 100 . a study conducted in jamaica on the attitude and knowledge of midwives toward induced abortion showed that more than 70 % of the participants were unanimous in that access to induced abortion should be expanded . moreover , more than 75 % of the participants believed that more accessibility to abortion reduces maternal mortality . in contrast with the present study , this study did not specifically examine the attitudes of the subjects toward abortion laws . however , their general attitude was determined , and as mentioned , most people believed that to reduce complications , more people should be subjected to the licensing of induced abortion . in the present study , more than half of the participants believed that the legal and religious commandments on induced abortions can be implemented in iran . perhaps the rest of them , like the midwives in the study mentioned above , believed in increasing the number of people subjected to licensing of induced abortion . in this study , no statistically significant relationship was observed between age and overall awareness , awareness of religious commandments , and awareness of legal commandments . in the study by ghadi pasha et al . , there was no significant correlation between the level of knowledge and age of participants . this result can be explained that increase in age may not be an affective factor in feeling the need to improve awareness regarding this issue . therefore , planning for increased awareness , both by the authorities and midwives , for all the subjects at any age is necessary . there was no significant correlation between work experience , and overall knowledge , awareness about religious commandments and legal commandments in this study . in the study by ghadi pasha et al . , there was no significant relationship between the level of knowledge and work experience of the participants . failure to provide more information for midwives in the form of classes and workshops on the studied subject is probably the reason for this finding . midwives unwillingness to obtain more information , their high involvement in the workplace , and their activities becoming a routine can be the other reasons for this finding . it seems that , encouraging midwives to obtain more information firstly , and then , attempting to hold educational courses can be effective in increasing the awareness of midwives in this regard . amir esmaili et al . performed a study on the knowledge , attitude , and practice of nurses at hospitals in relation to the overall principle of precaution . their findings showed that there was no significant relationship between work experience , level of awareness , and attitude . as mentioned earlier , it seems that education in the field of legal induced abortion was weak for most midwives . it is also necessary to encourage midwives to enhance their knowledge by studying more about religious laws . in this study , no statistically significant differences were observed in the mean scores for general knowledge , knowledge about religious commandments , and awareness of legal laws among undergraduate and postgraduate midwives ( p 0.05 ) . in the study by banaiian and sereshti on midwives knowledge of the legal and religious commandments of midwifery and some factors related to it , there was no significant relationship between awareness and the level of education . in the present study , there was a statistically significant difference between the mean scores of overall awareness and legal awareness with regard to the workplace of midwives in isfahan ( p 0.05 ) [ table 4 ] . in the study by haji foghaha and keshavarz , data showed that the mean score of knowledge of midwives working in midwifery offices was lower than that of those working at hospitals and clinics . however , in the present study , the awareness of university midwives was also assessed and only the topic of induced abortion was examined . there was no statistically significant difference between attitude , age , working experience , education level , and workplace in the present study . aiyer et al . studied the impact of physicians attitudes toward the tendency to perform abortions . they found a significant relationship between abortion and attitude toward abortion , but no significant relationship between abortion , age , and gender . the characteristics studied in the present study were only similar to the mentioned study regarding age in that there was no relationship between age and attitude . with the increase of age , attitude does not change . therefore , it can be concluded that attitudes form at a young age , and thus , attempts should be made to correct the orientation of attitudes at a young age . comparison between participants knowledge and attitudes with the place of work in the study by rosenblatt et al . on the attitudes of physicians and their activities , there was no significant relationship between attitude and work experiences . the findings of the study by amir esmaili et al . showed that there was no significant relationship between work experience and attitude . in fact , increase in work experience has not caused any changes in the individuals attitudes and , hence , can not be expected to cause improvement in attitudes through its increase . in fact , it is necessary to look for other variables by which to improve the midwives attitudes regarding the implementation and effectiveness of laws . although induced abortion is an important issue in the field of midwifery , knowledge and attitude of midwives regarding their legal and religious commandments were not desirable in this study . therefore , the improvement of midwives awareness and changing their attitudes toward implementation and effectiveness of legal and religious commandments on induced abortion through measures such as conducting classes and workshops are recommended . furthermore , given that there was no relationship between awareness and education , improving the quality of education in universities at all educational levels is recommended .\noutput:\n" }, { "from": "agent", "value": "background : induced abortion is an important medical issue . knowledge and attitude of midwives regarding legal and religious commandments on induced abortion can be useful in confronting this issue . the aim of this study was to assess the knowledge and attitudes of midwives of isfahan regarding these rules and to find their relationship with demographic characteristics.materials and methods : this was a cross - sectional , descriptive , and analytical study . the study participants consisted of 189 midwives working in hospitals , health centers , private gynecology clinics , and university . random quota sampling method was used . data were collected using a researcher - made questionnaire . data were analyzed using mean , frequency distribution tables , pearson correlation , and spearman 's coefficient . for all tests , an error of less than 0.05 was considered.results : the majority of the participants had extremely low to moderate ( 73 % ) knowledge about the subject of the study . their attitudes toward effective implementation of these rules were mostly extremely weak to moderate ( 68.72 % ) . no correlation was observed between knowledge , age , work experience , and education . however , there was a relationship between the level of knowledge about these rules and the location of service . there was no significant correlation between attitude and demographic characteristics.conclusion : due to less knowledge of the midwives and their low attitude score in this regard , training them , improving their attitude toward these issues , and effective implementation of these laws are necessary . therefore , by identifying the factors affecting the formation of attitudes and the level of knowledge , more constructive proceedings can be taken to promote them ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: one in six individuals with type 2 diabetes mellitus ( dm ) will develop a foot ulcer in his / her lifetime ; 7 % have foot ulcers at any given time , and 15 % of foot ulcers end in amputation .1 - 3 foot ulcers are the most expensive complication of type 2 dm , accounting for about 20 % of the costs and 30 % of hospital admissions associated with treating persons with type 2 dm .1,4,5 compliance with proper foot care reduces the incidence of foot ulcers , particularly among persons with reduced severity of neuropathy .6 a study by apelqvist and agardh7 found that 25 % of clients who had foot ulcers underwent amputation , and 13 % died .7 moreover , as many as 85 % of lower extremity amputations can be avoided by prompt and appropriate treatment of diabetic foot wounds and ulcers by healthcare providers , as well as optimum foot self - care practices by individuals affected by the condition .8 - 11 unfortunately , many persons with type 2 dm do not receive adequate foot care instruction from their healthcare providers and , as such , do not perform routine foot examinations .12 optimum foot self - care practices include daily inspection of feet and inside of shoes ; daily washing of feet and careful drying afterwards ( especially the areas inbetween the toes ) ; not walking barefoot ; wearing proper footwear ( use of therapeutic shoes with pressure - relieving insoles and not sandals or poorly fitting shoes ) ; cutting toenails straight across ; not removing ingrown toenails , calluses , corns , or warts oneself ; avoiding the use of antiseptic lotions and adhesive tape on the feet ; obtaining prompt professional healthcare treatment if new lesions , cuts , bruises , and wounds are noted ; and screening of feet regularly , or at least once annually , by a healthcare provider to identify feet at risk for diabetic foot complications .13 - 17 many persons with type 2 dm , however , neglect their foot care18 and regular foot examinations because of painless neuropathic feet , which cause them to ignore even the more serious of foot injuries .1 such persons may also cause additional foot damage by subjecting their feet to further trauma ; while persons without peripheral neuropathy tend not to place weight upon an injured foot , those with peripheral neuropathy continue to do so .19 one population greatly affected by diabetic foot care is the filipino american ( fa ) community in the united states , which is a group at high risk for developing type 2 dm and its complications .20 - 23 however , in spite of the large number of filipino immigrants in the united states , many of whom are older females , little scholarly research has been conducted on them and their health . currently , no articles dealing with the foot self - care practices of fas , specifically older fa women with type 2 dm , appear to exist , even though this ethnic group s mortality rate from dm is three times higher than that of the white population .24 this research study was conducted to examine the foot self - care practices performed by fa women with type 2 dm in order to contribute knowledge that will help to optimize their health , and improve their overall quality of life . this research study involved 118 fa women residing in los angeles and orange counties , california , usa . the sociodemographic data were gathered using the baseline instrument for filipino americans with type 2 diabetes mellitus ( bifad ) instrument .25 the fa women included in the study were : ( 1 ) medically diagnosed with type 2 dm , ( 2 ) older than 30 years , ( 3 ) capable of reading and / or speaking in english , ( 4 ) southern california residents , ( 5 ) lacking disabilities ( eg , physical , mental ) that would prevent them from participating and completing the study procedures , and ( 6 ) were first - generation immigrants to the united states from the philippines . all participation was voluntary and all responses ( and participation ) were confidential , as per the study approval by the university of california los angeles institutional review board . if participants met the inclusion criteria , no additional selection criteria were used to determine either eligibility or inclusion of their responses in the database . the foot self - care data were collected using the summary of diabetes self care activities - revised and expanded ( sdsca - r & e ) measure developed by toobert et al. 26 diagnoses of type 2 dm and foot self - care practices were obtained from self - reports . the sdsca - r & e measure has four questions addressing recommended foot self - care among persons with type 2 dm . they are : ( 1 ) on how many of the last 7 days did you wash your feet ? ( 2 ) on how many of the last 7 days did you dry between your toes after washing ? ( 3 ) on how many of the last 7 days did you check your feet ? and ( 4 ) on how many of the last 7 days did you inspect the insides of your shoes ? the data were collected by the principal investigator , who was able to answer any questions the participants had about the study . statistical analyses were performed using spss software , v. 15 ( spss , chicago , il , usa ) .27 descriptive statistics ( mean , standard deviation ) , using students t tests , were calculated on the fa womens age groupings , age , education , age at immigration to the united states , and age when diagnosed with type 2 dm ( 65 years of age and 65 years of age ) . likewise , descriptive statistics ( frequency , percentage ) using one - way analysis of variance were computed for performance of foot self - care practices . the days per week were clustered in duration as 0 days ( foot self - care was never performed during the past week ) , 1 to 3 days ( representing foot self - care performed on fewer than 50 % of days in the past week ) , 4 to 6 days ( indicating foot self - care performed more than 50 % of days in the past week ) , and 7 days ( foot self - care done every day during the past week ) . further , the foot self - care data were then analyzed using spearman s rank correlation to test the direction and strength of the relationships between the dependent variables of foot self - care practices and the independent variables of age , education , age at immigration to the united states , and age when diagnosed with type 2 dm . descriptive statistics on younger ( 65 years of age ) and older ( 65 years of age ) fa women with type 2 dm are presented in table 1 . they immigrated to the united states at a mean age of 49 years and were diagnosed with type 2 dm at a mean age of 57 years . the frequencies and percentages that the women performed foot self - care practices are provided in table 2 . table 1descriptive statistics of younger ( 65 years of age ) and older ( 65 years of age ) filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ; significance determined using students t test.variableyounger participants ( n = 39 ) older participants ( n = 79 ) overall ( n = 118 ) age , years568 .2744.768.310.5 education , * years132 .4113.311.83.1 age at immigration to united states years3511 .3559.648.713.9 age when diagnosed with type 2 dm years468 .26211.056.712.6 all data meanstandard deviation ( sd ) . * p 0.01 . p 0.001 . table 2frequencies and percentages of performance of foot self - care practices among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) frequency ( days per week ) foot self - care practice01 - 34 - 67washing of feet , n ( % ) 1 ( 0.9 ) 31 ( 26.3 ) 24 ( 20.3 ) 62 ( 52.5 ) drying inbetween toes , n ( % ) 12 ( 10.2 ) 26 ( 22.0 ) 23 ( 19.5 ) 57 ( 48.3 ) checking of feet , n ( % ) 15 ( 12.7 ) 23 ( 19.5 ) 16 ( 13.6 ) 64 ( 54.2 ) inspecting inside of shoes , n ( % ) 38 ( 32.2 ) 27 ( 22.9 ) 19 ( 16.1 ) 34 ( 28.8 ) descriptive statistics of younger ( 65 years of age ) and older ( 65 years of age ) filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ; significance determined using students t test . frequencies and percentages of performance of foot self - care practices among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) most fa women reported that they washed their feet , dried their feet ( inbetween the toes ) , and checked their feet every day during the previous week . however , less than one - third of the women inspected the insides of their shoes every day during the past week ; most of them had not inspected the insides of their shoes during the previous week . the foot self - care practices and predictors of age , education , age at immigration , and age when diagnosed with type 2 dm are presented in table 3 . younger fa women with type 2 dm were more likely to report that they washed their feet every day during the past week , while older participants reported that they washed their feet less often . likewise , fa women with higher educational attainment reported that they washed their feet more frequently than those participants with lower educational attainment . moreover , fa women who immigrated at a younger age were more likely to report that they washed their feet 7 days during the past week , while those who immigrated when they were older did not perform the foot self - care practice regularly . furthermore , fa women who were diagnosed with type 2 dm at a younger age were more likely to report that they washed their feet every day during the prior week and , therefore , did so more often than those participants who were diagnosed with type 2 dm at an older age ( table 3 ) . table 3relationships of foot self - care practices and predictors among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ( examined using spearman s rank correlation coefficient ) predictorfoot self - care practiceageeducation , yearsage at immigration to united states , yearsage when diagnosed with type 2 dm , yearswashing of feet0 .247 , p = 0.0070.224 , p = 0.0150.289 , p = 0.0020.405 , p = 0.000 drying inbetween toes0 .051 , p = 0.5820.118 , p = 0.2030.047 , p = 0.6110.038 , p = 0.681 checking of feet0 .168 , p = 0.0690.035 , p = 0.7090.165 , p = 0.0740.372 , p = 0.000 inspecting inside of shoes0 .052 , p = 0.5790.051 , p = 0.5820.003 , p = 0.9750.006 , p = 0.947 correlation coefficients ( two - tailed ) and probabilities are shown . relationships of foot self - care practices and predictors among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ( examined using spearman s rank correlation coefficient ) correlation coefficients ( two - tailed ) and probabilities are shown . fa women who immigrated to the united states at a younger age were more likely to report that they dried their feet inbetween the toes every day after washing during the past week than participants who immigrated to the united states at an older age . likewise , fa women who were diagnosed with type 2 dm at a younger age were more likely to report that they dried their feet 7 days during the last week , while those participants who were diagnosed with type 2 dm when they were older dried their feet less often ( table 3 ) . fa women who were younger when they were diagnosed with type 2 dm were more likely to report that they checked their feet every day during the previous week , while those participants who were older when diagnosed with the condition did not check their feet , or checked their feet less regularly ( table 3 ) . in all , 32 % of the participants reported that they did not inspect the insides of their shoes during the past week . about 23 % reported that they performed the foot self - care practice approximately 1 to 3 days during the last week , while slightly over 16 % reported that they performed the foot self - care practice on about 4 to 6 days during the past week . almost 29 % of the participants reported that they inspected the insides of their shoes every day during the previous week ( table 2 ) . there was no relationship between the foot self - care practice of inspecting the inside of shoes and the predictors of age , education , age at immigration to united states , and age when diagnosed with type 2 dm ( table 3 ) . younger fa women with type 2 dm were more likely to report that they washed their feet every day during the past week , while older participants reported that they washed their feet less often . likewise , fa women with higher educational attainment reported that they washed their feet more frequently than those participants with lower educational attainment . moreover , fa women who immigrated at a younger age were more likely to report that they washed their feet 7 days during the past week , while those who immigrated when they were older did not perform the foot self - care practice regularly . furthermore , fa women who were diagnosed with type 2 dm at a younger age were more likely to report that they washed their feet every day during the prior week and , therefore , did so more often than those participants who were diagnosed with type 2 dm at an older age ( table 3 ) . table 3relationships of foot self - care practices and predictors among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ( examined using spearman s rank correlation coefficient ) predictorfoot self - care practiceageeducation , yearsage at immigration to united states , yearsage when diagnosed with type 2 dm , yearswashing of feet0 .247 , p = 0.0070.224 , p = 0.0150.289 , p = 0.0020.405 , p = 0.000 drying inbetween toes0 .051 , p = 0.5820.118 , p = 0.2030.047 , p = 0.6110.038 , p = 0.681 checking of feet0 .168 , p = 0.0690.035 , p = 0.7090.165 , p = 0.0740.372 , p = 0.000 inspecting inside of shoes0 .052 , p = 0.5790.051 , p = 0.5820.003 , p = 0.9750.006 , p = 0.947 correlation coefficients ( two - tailed ) and probabilities are shown . relationships of foot self - care practices and predictors among filipino american women with type 2 diabetes mellitus ( dm ) ( n = 118 ) ( examined using spearman s rank correlation coefficient ) correlation coefficients ( two - tailed ) and probabilities are shown . fa women who immigrated to the united states at a younger age were more likely to report that they dried their feet inbetween the toes every day after washing during the past week than participants who immigrated to the united states at an older age . likewise , fa women who were diagnosed with type 2 dm at a younger age were more likely to report that they dried their feet 7 days during the last week , while those participants who were diagnosed with type 2 dm when they were older dried their feet less often ( table 3 ) . fa women who were younger when they were diagnosed with type 2 dm were more likely to report that they checked their feet every day during the previous week , while those participants who were older when diagnosed with the condition did not check their feet , or checked their feet less regularly ( table 3 ) . in all , 32 % of the participants reported that they did not inspect the insides of their shoes during the past week . about 23 % reported that they performed the foot self - care practice approximately 1 to 3 days during the last week , while slightly over 16 % reported that they performed the foot self - care practice on about 4 to 6 days during the past week . almost 29 % of the participants reported that they inspected the insides of their shoes every day during the previous week ( table 2 ) . there was no relationship between the foot self - care practice of inspecting the inside of shoes and the predictors of age , education , age at immigration to united states , and age when diagnosed with type 2 dm ( table 3 ) . firstly , younger fa women , participants with higher educational attainment , those who were younger when they immigrated to the united states , and participants who were diagnosed with type 2 dm at a younger age were more likely to report that they washed their feet every day during the past week . secondly , fa women who immigrated to the united states at a younger age and those who were diagnosed with the disease at a younger age were more likely to report that they dried their feet ( inbetween the toes ) daily during the last week . thirdly , participants who were younger when they were diagnosed with type 2 dm were more likely to report that they checked their feet 7 days during the past week . finally , while almost one - third ( 29 % ) of the participants reported that they inspected the insides of their shoes every day during the previous week , there was no relationship between inspecting the inside of shoes and the predictors of age , education , age at immigration to united states , and age when diagnosed with type 2 dm . poor diabetes foot care knowledge and , consequently , lack of foot self - care ( eg , infrequent washing of feet , drying of feet inbetween toes , checking of feet , and inspecting the inside of shoes ) have been associated with an inability to sense minor injuries to the foot and a tendency toward ulceration . when individuals with type 2 dm fail to practice proper foot self - care , the likelihood of ulcers increases along with a higher risk for subsequent amputation and / or mortality .6,14,28 - 30 since individuals with type 2 dm may not be able to sense foot injuries ( eg , from foreign objects lodged within their shoes ) during or after its occurrence , frequent checking of the feet becomes crucial . for those persons who are at higher risk for foot injury , such as the older fa female participants in this study , education and treatment interventions by healthcare providers become even more critical ; failure to do so may lead to situations where the foot problems are not only costly to treat , but may also be impossible to heal ( leading to amputations ) . minor trauma can also develop from repetitive , moderate pressure ,15 such as from wearing improperly fitting shoes or sandals . because individuals with type 2 dm also suffer from peripheral neuropathy , frequent checking of the inside of shoes and use of diabetic footwear is highly recommended . adequate , acceptable , and reasonably priced footwear should be combined with good foot self - care practices .31 this research study found that participants with lower educational attainment inspected the insides of their shoes more often ( 7 days during the past week ) than participants with higher educational attainment . some explanations for nonperformance or infrequent performance of proper foot self - care practices are major depression and obesity ; 32 eye problems , decreased mobility , and loss of flexibility ; 9 lack of insurance and other financial barriers to healthcare services ; 33 and a lack of knowledge on foot care .34 however , this research study did not investigate the reasons for nonperformance or infrequent performance of proper foot self - care practices in fa women ; hence , further inquiry is recommended . since this research study only dealt with foot self - care practices , information on access to healthcare services and personal experiences pertaining to healthcare were not obtained . it would be interesting to know whether older fa women had the same access to healthcare services as younger fa women . chronic social stressors , such as discrimination , can lead to occurrence of chronic health problems . treating chronic health problems , therefore , should entail not only treating the health condition , but also dealing with the perception of discrimination and / or stressors in the client s environment .35 these issues are very important , and will need to be investigated further . since this research study only dealt with foot self - care practices , information on access to healthcare services and personal experiences pertaining to healthcare were not obtained . it would be interesting to know whether older fa women had the same access to healthcare services as younger fa women . chronic social stressors , such as discrimination , can lead to occurrence of chronic health problems . treating chronic health problems , therefore , should entail not only treating the health condition , but also dealing with the perception of discrimination and / or stressors in the client s environment .35 these issues are very important , and will need to be investigated further . proper foot self - care practices were less likely to be performed by older fa women with type 2 dm , making them more prone to the development of foot problems , such as ulcers , infections , and disfigurations . it is not known why this phenomenon was observed in this segment of the population . hence , more research is needed to determine the reasons for this observation and to develop the best ways to increase optimum foot self - care behaviors in this vulnerable population . preventive practices must be emphasized in older fa women with type 2 dm to prevent foot ulcers , foot infections , and subsequent amputations .\noutput:\n" }, { "from": "agent", "value": "introductionto determine the foot self - care practices performed by filipino american ( fa ) women with type 2 diabetes mellitus ( dm ) . methodthe summary of diabetes self care activities - revised and expanded measure was administered to 118 fa adult female immigrants with type 2 dm.resultsyounger fa women ( < 65 years ) , participants with higher education , those who immigrated to the united states ( us ) at younger ages , and participants diagnosed with type 2 dm at younger ages reported they washed their feet every day during the past week . moreover , fa women who immigrated to the us at younger ages and participants who were diagnosed with the disease at younger ages reported that they dried their feet ( in between toes ) daily during the previous week . further , fa women who were diagnosed with type 2 dm at younger ages were more likely to report that they checked their feet every day during the past week , when compared with participants who were diagnosed with the disease at older ages . finally , most fa women did not inspect the inside of their shoes.conclusionfoot self - care practices were less frequently performed by older fa women with type 2 dm ( 65 years ) , making them more prone to the development of foot problems such as ulcers , infections , and disfigurations . optimum foot self - care practices must be encouraged in older fa women to prevent such foot problems , and subsequent amputations ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: esophageal cancer is the sixth cause of death in the world , which kills about 386000 people each year . regarding diagnosis andthe survival rate for these patients is very low and only 12 % and 4 % for female and male patients , respectively in caspian region . the highest number of outbreaks was reported in north parts of china ( average of 100 to 180 per 100,000 people ) . while in the usadiari et al . in 1975 in tehran university reported that the northern region of iran - including ardebil , gilan , mazandaran , golestan and north khorasan provinces is highest incidence region in iran , in this regions gilan province has the lowest incidence and north khorasan has the highest incidence . estimation of survival rate in patients with esophageal cancer can help improve the preventive and curative services and assess the effectiveness of new treatments . victim s quality of life is very important and we should pay more attention to this matter . many studies have been conducted in the past two decades in relation to survival rate of esophageal cancer in iran . this systematic review assesses all accessing electronic databases to determine valid estimation of survival rate among patients with esophageal cancer in different regions of iran . sources for the data the systematic review carried out about survival rate of esophageal cancer that required search all available sources and electronic databases related articles and dissertations as well as the meta - analysis . these databases include the reliable domestic databases such as iranmedex , medlib , magiran and sid as well as the foreign websites such as pubmed / medline , isi web of knowledge and scopus . we queried the articles and dissertations using sensitive keywords including cancer , esophagus , survival neoplasms and longevity and a combination of them . in order to prevent any bias , which evaluated the survival time and longevity of the esophageal cancer and published up to 2011 entered into the first step of study without any kind of limitations . after preliminary review , review articles about esophageal cancer without any evaluations on the survival time and papers with insufficient data were omitted from the study . in second stepwe evaluated 340 articles on esophageal cancer among them 40 ones were repetition , 145 ones irrelevant that omitted from study . finally 18 articles with proper quality were entered into the process of meta - analysis ( chart 1 at the bottom of the text ) . this form included sample size , study region , gender , 1 year to 5 year survival rate , histology type , as well as affected area of esophagus . in every articlethe one to five year survival rate was considered as the probability of a two - term distribution and its variance was calculated using two - term distribution . incongruity of the studies was determined using the q - test and i2 measure . due to the incongruity of the studies we used the random effect model for combining the results of them . the analysis in the sub - groups was carried out regarding the under - study region ( north , center , east and tehran ) . overall , 18 articles included according to inclusion criteria in the meta - analysis . looking for sample sizes , 2932 patients enrolled study .11 articles ( 61 % ) were performed in the northern parts of iran , 3 ones ( 16.6 % ) were carried out in central parts ; one ( 5.5 % ) was conducted in the eastern parts and 3 ones ( 16.6 % ) were accomplished in tehran province . studies were published between 1 january 1989 and 31 august 2010 ( table 1 ) . according to results from meta - analysis , the one - five year survival rate for esophageal cancer in this study were 47 % ( ci 95 % : 34 - 61 ) , 31 % ( ci 95 % : 18 - 44 ) , 22 % ( ci 95 % : 13 - 31 ) , 21 % ( ci 95 % : 4 - 38 ) and 12 % ( ci 95 % : 8 - 16 ) , respectively ( table 2 ) . geographical variation results on survival rate in our study indicated the one year survival rate in northern region , with eight articles enrolled in meta - analysis was45 % ( ci 95 % : 28 - 62 ) , in the northwest region , with one study was 68 % ( ci 95 % : 61 - 75 ) , in the central region , with one study was 55 % ( ci 95 % : 50 - 68 ) and in tehran was 33 % ( ci 95 % : 25 - 41 ) . the pooled rate one year survival rate according to result of meta - analysis was 47 % ( ci 95 % : 34 - 61 ) ( graph 1 ) . graph 2 shows the overall rate of five year survival according to meta - analysis was 12 % ( ci 95 % : 8 - 16 ) . in recent decades some success has been obtained in the management and cure of esophageal carcinoma . esophageal tumors are considered an endemic disease in iran particularly in the brinks of the caspian sea . in our studythe five year survival rate is equal to 12 % . in a study carried out in 2008 by agrawal et al , the survival rate in patients during the first five years after diagnosisis reported 13 % that conforms to results of our study . in a study by bashash2011 , which tries to compare the survival rate for stomach and esophageal cancers in ardebil in iran and british colombia in canada , the one year survival rate was estimated 17 % in ardebil and 33 % in british colombia . this significant difference shows a geographic variation in survival rate of esophageal cancer in different parts of the world perhaps due to differences in health and wellness of people in different areas . also in this study the mortality of esophageal cancer was more than the fatality of stomach cancer . in netherlandsthe five year survival rate for men and women was 12.8 % and 9.8 % , respectively . this study conforms to results of our study which shows the five year survival rate was 12 % . in japan 2012 , by tamura et al the five year survival rate of esophageal cancer was estimated 42.9 % and in similar article in usa 2012 blackmon et al . thus our result is considerably lower than developed countries such as japan and the usa . second some articles did not give the survival rate by year and just report the five - year survival rate . of the 18 final articles , 11 were performed in the northern reigns of the country including golestan , mazandaran , as well as gilan and ardebil provinces . the reason for this can be attributed to highest rate of esophageal cancer in northern regions in iran . in other regionsso the survival rate in other regions of iran is not clear due to the lack of sufficient data and due to the scarcity of studies , the reported estimations do n't have sufficient accuracy . according to results of thisstudy the one year survival rate ( 47 % ) of esophageal cancer in iran is almost five times more than the five year survival rate ( 12 % ) . hence , the early diagnosis of the disease is very important in order to prolong the survival of the patients . according to results of this study the one year survival rate ( 47 % ) of esophageal cancer in iran is almost five times more than the five year survival rate ( 12 % ) . hence , the early diagnosis of the disease is very important in order to prolong the survival of the patients .\noutput:\n" }, { "from": "agent", "value": "backgroundesophageal cancer is often diagnosed in the last stages where the chance of patient s survival is very low . the aim of this systematic review was presentation of valid estimation of survival in patients with esophageal cancer in different regions of iran.methodsa systematic review was carried out based on the reliable domestic medical databases including : sid , magiran , irandoc and iranmedex as well as reliable foreign databases like pubmed and scopus using cancer , esophagus , survival neoplasms and longevity as keywords . then all the reviewed articles and dissertations which met the entry criteria were analyzed . the data were analyzed by using meta - analysis method ( random model ) and by means of stata software application version 11.1 . resultsin 18 studies the total numbers of 2932 people were analyzed . the one year survival rate in iran is estimated at 47 percent ( 95 % ci : 34 - 61 ) and the five year survival rate is estimated at 12 % ( 95 % ci : 8 - 16 ) . the two , three and four year survival rates were 31 % ( 95 % ci : 18 - 44 ) , 22 % ( 95 % ci : 13 - 31 ) and 21 % ( 95 % ci : 4 - 38 ) , respectively.conclusionaccording to the findings one year survival rate for esophageal cancer in iran is almost four times higher than its five year survival rate . moreover the five year survival rate in iran is less than many other countries ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: diamond - blackfan anemia ( dba ) is a rare genetic disease mostly diagnosed in the first year of life . different mutations on genes codifying for large and small subunits of ribosomal proteins ( rpl and rps ) have been described as disease causative . additionally , genotype phenotype correlations have been established . we report an atypical case of a previously healthy 35 - year - old patient presenting with severe aregenerative anemia which was ultimately found to be genetic in origin . fanconi anemia was discarded and a nonclassical dba caused by a de novo and previously nondescribed mutation located in the exon 5 of the rpl11 gen was diagnosed . this case report pointed out that a late onset anemia presenting in an adult patient is not incompatible with a genetic - in - origin disease with an atypical presentation . diamond - blackfan anemia ( dba ) is a rare disease characterized primarily by normochromic macrocytic anemia and reticulocytopenia . classical dba affects about seven out of every million live births and presents during the first year of life . about 40 % of patients display physical malformations , mostly craniofacial ( ophthalmological disorders including ) , and at the extremities . recent advances in identifying the genotype that underlies dba have shown involvement of genes encoding both large ( rpl ) and small ( rps ) ribosomal subunit proteins . however , as mutated genes have been discovered in dba , nonclassical cases with less distinct phenotypes are being described in adults as well as in children . here , we are reporting a 35 - year - old patient with congenital thumb hypoplasia who presented to us with severe aregenerative anemia finally being diagnosed with a nonclassical dba caused by a de novo and previously nondescribed mutation located in the exon 5 of the rpl11 gen . a spanish 35 - year - old male patient , with a surgical history of interventions in both hands because of congenital hypoplasia of the thumb of the right hand and syndactyly between first and second fingers of the left hand , attended the emergency department complaining of progressive fatigue and headache for the past 15 days . severe normocytic normochromic reticulocytopenic anemia was disclosed ( hb 7.2 gr / dl ( 1318 gr / dl ) , mcv 92.9 fl ( 8090 fl ) , reticulocyte 1310 / l , wbc 4.310 / l ( 41110 / l ) with normal differential and platelets 34210 / l ( 15040010 ) . anemia studies were as follows : iron 227 g / dl ( 65175 g / dl ) , ferritin 664 ng / ml ( 22322 ng / ml ) , transferrin saturation 100 % ( 2050 % ) , b12 vitamin 486 pg / ml ( 211911 pg / ml ) , and folic acid 2.8 ng / ml ( 5.417 ng / ml ) . autoimmunity screening ( ana , ena , anti - dna , c3c4 , ancap , ancac ) was normal . serologies for hiv , hbv , hcv , syphilis , and ebv were all negative . bone marrow ( bm ) aspiration showed moderate hypoplasia of the erythroid lineage with myeloid and megakaryocytic cells of a normal aspect and without any signs of dysplasia ( see figure 1 ) . a ct - scan of the thorax , abdomen , and pelvis and an abdominal ultrasound were both normal . skeleton plain radiographs showed fusion of the phalanges of the finger with the thumb metacarpal in the left hand and absence of the first finger in the right hand ( see figure 2 ) . malformations in both hands . left hand , fusion of the phalanges of the finger with the thumb metacarpal . the patient underwent a complete ophthalmologic evaluation including best corrected visual acuity , slit - lamp biomicroscopy , and dilated ophthalmoscopic examination after instillation of phenylephrine 2.5 % and tropicamide 1 % . no refractive defects , no epicanthus palpebralis , no strabismus , no microcornea , no microphthalmia , no posterior embryotoxon , no cataracts , and no signs of congenital glaucoma were found 8 . fanconi anemia was excluded by means of chromosomal fragility studies performed on the peripheral blood with c mitomycin and diepoxybutane and complementation studies for fanconi genes in cultured skin fibroblasts that were all negative . a molecular study for dba genes was performed and c489_490delgcinst heterozygous mutation in exon 5 of the rpl11 gene was detected . this mutation produces a variation in the composition of the last 16 amino acidic residues of the normal protein . molecular studies of the rpl11 gene were done in both parents and her sister and disclosed normal results . according to the description of the majority of dba patients , our patient had aour patient also exhibited other variations of the rps19 ( ivs4 + 14g a ) and rps26 ( 5utr - 22c g ) genes , that were considered as polymorphism and not pathological variations . according to the diagnostic criteria previously established at an international consensus conference 1 , our patient should be classified as sporadic nonclassical form of dba ( insufficient diagnosis criteria and gene mutation described inthe patient was initially treated 3 with prednisone ( 1 mg / kg / 24 h ) , folic acid , and vitamin b12 . a short course of high doses of intravenous methylprednisolone ( 500 mg per day for 5 consecutive days ) was administered and later on steroids were tapered until complete discontinuation , because of its inefficacy and adverse effects . we decided to ask for an off - label use of cyclosporine to reduce the number of transfusions . cyclosporine was approved by ethic committee of university hospital principe de asturias and the patient 's written informed consent was requested . six months after initial presentation , cyclosporine at a dose of 5 mg / kg / day , twice a day was started and subsequently eight months after presentation danazol at a dose of 400 mg per day was added . with this combination , we observed a progressive erythroid response and transfusions were avoided ( last transfusion on 31st july 2012 ) . since january 2013 a slow reduction in cyclosporine dose was initiated until its complete discontinuation on november 2013 . he was treated with acyclovir , sulfametoxazol and trimetroprim because he has been treated with cyclosporine for eighteen months . two years after diagnosis the ophthalmologic evaluation did not reveal any change despite corticosteroids treatment . a familiar hla typing was performed and his only sister was found to be hla genetically identical . a molecular study of the rpl11 gene was performed on both parents and his only sister and were all normal . until nowwe described a real clinical case of diamond - blackfan anemia in adulthood 4 ( debut at 35 years old ) . classical dba affects about seven per million live births and presents during the first year of life . our case illustrates that late onset is not incompatible with the diagnosis of dba . in the last 20 years , different mutations and deletions in nine ribosomal protein genes ( rpl and prs ) have been discovered and being associated with a haploinsufficiency development of dba . defects in the rps195 ,7 gene , encoding the ribosomal protein s19 , are the main known cause of diamond - blackfan anemia and account for more than 25 % of cases . two new genes 2 ( rpl5 , rpl11 ) , encoding for ribosomal proteins of the large subunit , . found mutations in rpl11 in about 5 % and 7 % , respectively , of dba patients . our patient has a previously undescribed mutation in exon 5 of rpl11 , according to the description of the majority of dba patients . reported that rpl5 and rpl11 mutations are more frequently associated with physical malformations than are rps19 mutations . mutations in rpl11 were predominantly associated with thumb abnormalities ( like our patient ) and craniofacial malformation . it was a de novo mutation as it was not found either in his parents or in his sister . the rpl11 gene mutations have previously been associated with congenital bone malformations as those presented at the birth in our patient . although we may assume that our patient was born with this rpl - 11 mutation , he did not develop anemia until the age of 35 years . we decided to start on cyclosporine to avoid the secondary effects of steroids but it was the addition of danazol what produced a real improvement of the hemoglobin levels . a continued and stable erythroid response has been observed under danazol therapy after cyclosporine withdrawal . since june 2012 , our patient has not received any red - blood - cell transfusion and has maintained the haemoglobin up to 10 gr / dl . the last control was in july 2014 and he has haemoglobin 13.4 gr / dl . in conclusion , diamond - blackfan anemia is a rare genetic disease mostly diagnosed in the first year of life , nevertheless late onset is not incompatible with the diagnosis of dba . different mutations on genes codifying for large and small subunits of ribosomal proteins have been described , as disease causative and also genotype phenotype correlations have been established . the identification of the affected gene in a congenital disorder , such as dba , is often the key that suddenly enables understanding of the molecular pathogenesis and development of novel therapies . recently , several aspects of dba pathophysiology have been uncovered , including : genome - wide studies to find structural aberrations , and mutation analysis of all ribosomal proteins and ribogenesis factors , ribogenesis factors . more studies are required that will hopefully result in better diagnosis and treatment of this disease that profoundly impairs the quality of life of young patients and their families .\noutput:\n" }, { "from": "agent", "value": "key clinical messagediamond - blackfan anemia ( dba ) is a congenital erythroid aplasia usually diagnosed in the early infancy and associated with mutations or large deletions in 11 ribosomal protein ( rp ) genes . adult patients with severe , transfusion dependence , aregenerative anemia might have a genetic - in - origin disease with an atypical presentation . late onset nonclassical dba should be ruled out and mutations of rp genes studied ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: rheumatoid arthritis ( ra ) is a chronic inflammatory disease of polyarticular arthritis affecting approximately 1 % of adults worldwide . it typically leads to deformity and destruction of the joints and systemic disorders throughout the body as well . although the etiology and pathogenesis of ra remain unknown , immunological hyperreactivity caused by large numbers of t cells , mostly cd4 , and plasma cells is generally considered to be important to contribute its development . the clinical diagnosis of ra is based on several criteria , including physical symptoms , joint radiographs , and serological tests . in the acr / eular 2010 classification criteria , definite ra is defined based on the confirmed presence of synovitis in at least 1 joint , absence of an alternative diagnosis that better explains the synovitis , and achievement of a total score of 6 or greater ( of a possible 10 ) from the individual scores in 4 domains : number and site of involved joints ( score range 05 ) , serologic abnormality ( score range 03 ) , elevated acute - phase response ( score range 0 - 1 ) , and symptom duration ( 2 levels ; range 0 - 1 ) . multiple studies have revealed ra - related autoantibodies and numerous biomarkers including cytokines / chemokines as well as erythrocyte sedimentation rate ( esr ) and c - reactive protein ( crp ) orchestrate pathological processes in ra . during the course of the disease , ra patients need to be diagnosed very early , possibly before diagnostic criteria are fulfilled or maybe even before clinical symptoms are apparent . early identification of patients with ra will help improve clinical outcomes with early treatments . finally , screen tests for prediction of response to therapy and progression of the diseases are also necessary . a biomarker , also known as biological marker , generally refers to a measured characteristic which may be used as an indicator of some biological state or condition . this term occasionally refers to a substance whose presence indicates the existence of living organisms . biomarkers play pivotal roles in disease diagnosis and interventions at early stage and are also helpful in knowing the state of treatment and how body is acting or responding to the medication . therefore , exploring and measuring biologic markers in blood or in joint fluids may serve as not only indicators of diagnosis but also indicators of prognosis and the subsequent response to therapy . a good biomarker can be used to measure the disease progress and the treatment effectiveness . , we discuss the biomarkers and pathogenic - related cytokines involved in clinic , pathogenesis , and prospection in ra . the biomarkers currently used for the diagnosis of ra are mostly clinical . now there are several useful clinical biomarkers , including various autoantibodies , such as rheumatoid factors ( rf ) , anti - perinuclear factor ( apf ) , anti - keratin antibodies ( aka ) , anti - filaggrin antibodies ( afa ) , and anti - cyclic citrullinated peptide antibodies ( anti - ccp ) . erythrocyte sedimentation rate ( esr ) and c - reactive protein ( crp ) also have associations with ra . rheumatoid factor ( rf ) , an antibody to the igg fc region , is a classic feature of the disease with sensitivity of 6080 % , but its specificity is not very high since it can also be detected in other autoimmune diseases , such as systemic lupus erythematosus ( sle ) and sjogren 's syndrome ( ss ) . the key pathogenic markers are igm and iga rheumatoid factors in ra . showing perinuclear fluorescence , apf is probably an antibody of the 7s gammaglobulin type against keratohyalin granules in buccal mucosa cells and is high in ra patients compared to the healthy people . aka , a naturally occurring antibody that reacts with the keratinized tissue , is found in the serum of around 60 % ra patients but not in healthy people . autoantibodies induced by citrullination , conversion of peptidyl - arginine to peptidyl - citrulline , can be measured efficiently by using cyclic citrullinated peptides ( ccp ) as antigens . the detection of anti - ccp antibodies , as well as rfs , particularly iga - rf , has a strong predictive value for diagnosis in early ra . not only esr but also anti - ccp is an important predictor of early bone mineral density loss . similar to rf , antibodies against citrullinated proteins ( acpa ) have correlation with bone destruction , but the latter is associated with larger bone erosions by directly initiating the differentiation of bone - resorbing osteoclasts . moreover , the bone loss caused by acpa occurs before disease onset in acpa - positive patients . the knowledge on acpa made great advancement in the field of ra in the past decade and this biomarker has already been included into the acr / eular 2010 diagnostic criteria . using both rf and acpa may be helpful in diagnosis and classification of ra . furthermore , anti - mutated citrullinated vimentin ( mcv ) antibodies have been reported as a fairly sensitive serological marker of ra and were significantly higher in early ra patients . in clinical management of ra , crp and esrare commonly ordered tests to guide diagnosis of ra besides the measurements of the mentioned autoantibodies . increased crp was detected before the onset of ra and also indicated the activity of the disease during the course of the disease . erythrocyte sedimentation rate ( esr ) is a nonspecific measure of inflammation and can be useful not only in diagnosing autoimmune diseases , such as rheumatoid arthritis , but also in monitoring the disease process . the combination of esr and crp may improve sensitivity and specificity of the diagnosis of ra . what is more , levels of serum calreticulin ( crt ) are now detected to be increased in patients with ra compared with those controls and have a significant correlation with disease activity in ra . likewise , there is an autoantibody system that discriminates between citrulline - and homocitrulline - containing antigens in the sera of ra patients . anti - carbamylated protein ( anti - carp ) antibodies igg and iga were observed in ra sera . interestingly , these anti - carp antibodies are also present in around 20 % of the acpa - negative ra patients and have association with more severe joint damage , indicating they could serve as a unique and relevant serological marker for acpa - negative ra . important associations between the above clinical markers and severity of ra have been noted and used in aiding diagnosis of ra , monitoring disease progress , and assessing prognostic in patients with established disease . besides the clinically used biomarkers , scientists have been engaging in investigating potential biologic markers for many years . cytokines serve as molecular messengers between cells and there are multiple studies revealing that numbers of cytokines have been involved in the pathogenesis of ra by triggering or regulating the inflammatory responses ( figure 1 ) . overexpressions of certain cytokines , such as il - 1 , il - 6 , il - 8 , il - 17 , il - 21 , tumor necrosis factor ( tnf ) - and granulocyte - macrophage colony - stimulating factor ( gm - csf ) , were observed in ra patients . these cytokines could promote synovial membrane inflammation and osteocartilaginous resorption via stimulation of osteoclastic mediators . autoreactive t cells , such as th1 and th17 cells , are thought to play important roles in autoimmune pathology of ra . the percentage of interferon ( ifn ) - expressing cells was slightly increased in peripheral blood mononuclear cells ( pbmc ) but highly increased in synovial fluid mononuclear cell ( sfmc ) of ra patients . il - 12 , a th1 cytokine , was increased in serum and synovial fluid in ra and its level correlated with disease activity score . th17 profile therefore has shown pathogenic role in ra . increased il - 17 was reported in the sera and synovial fluid of ra patients . neutralizing il - 17 treatment reduced the severity and slowed the progression of collagen - induced arthritis ( cia ) , a mouse model of human rheumatoid arthritis . secreted by th17 , il - 21 and il - 22 were also observed at a high level in ra patients compared to the healthy controls or osteoarthritis ( oa ) patients . in addition , il - 21 autoregulated its own production in human cd4 + t cells and enhanced th17 proliferation , leading to the expression of rorc production , and was strongly associated with the levels of auto - antibodies and disease severity as well . il - 23 is known to promote il - 17 production and was detected in ra synovial fibroblasts , but , like a loop , it can be upregulated by il - 17 in ra synovial fibroblasts via pi3 - kinase / akt - , nf - b - , and p38 - mapk - mediated pathways . il - 23 directly induced osteoclast differentiation by upregulation of receptor activator of nf - b ( rank ) in mouse myeloid precursor cells and rank ligand ( rankl ) in human fibroblast - like synoviocytes . rank / rnakl signaling regulates the formation of multinucleated osteoclasts from their precursors as well as their activation and survival in normal bone remodeling and in a variety of pathologic conditions . in rasynovial tissue , p19 subunit and rankl have positive correlation and might contribute to bone destruction in ra . il - 1 is produced by a variety of cells that are part of the innate system and mediates bone resorption and cartilage destruction . the il -1-nf-b axis is central in the production of proinflammatory mediators in the inflamed synovium . nf - b activation by il - 1 induced the gene expressions of matrix metalloproteinases ( mmps ) that are major products of cytokine stimulated fibroblast - like synovial cells ( fls ) and efficiently degrade the collagenous components of cartilage and bone , leading to the joint deformity and pain in the patient with ra . additionally , proinflammatory cytokine , il - 6 , has important effects on the differentiation and activation of b and t cells , macrophages , osteoclasts , chondrocytes , and endothelial cells and broad effects on hematopoiesis in the bone marrow . together with tgf - , il - 6 is the key inducer of th17 via signal transducer and activation of transcription - 3 ( stat - 3 ) and its level was significantly associated with clinical symptoms and levels of clinical biomarkers . additionally , tnf - has shown its contribution to the pathogenesis of ra at early stage . it is produced locally in the joint by synovial macrophages and lymphocytes infiltrating the joint synovium . tnf has been recognized as a key pathogenic cytokine that drives a pathogenic cytokine milieu leading to tissue damage . other cytokines / chemokines , such as il - 8 , il - 9 , il - 15 , leukemia inhibitory factor ( lif ) , granulocyte colony - stimulating factor ( g - csf ) , chemoattractant protein - 1 ( mcp - 1 ) , growth - related oncogenes gro - and gro - , ccl19 , cxcl12 , and cxcl13 , were upregulated in preclinical or clinical period of ra development by induction of il - 17 or tnf - and il - 1 synergically . therapeutic strategies that specifically block these investigational inflammatory cytokines are expected to be highly effective in treating ra patients . the biological therapeutics include tnf inhibitors , il - 1 inhibitors , il - 6 inhibitors , and il - 17 inhibitors , as well as b cell depletion , costimulatory blockers , and jak inhibitors . on one hand these approaches neutralize the inflammatory mediators and show effectiveness in clinical trial ; on the other hand , their effect can be evaluated by measuring the concentration of the inflammatory cytokines combined with clinical biomarkers , such as rf , acpa , esr , and crp . recently , several interleukins involved in inflammatory joint diseases have been identified and characterized ( figure 1 ) . il - 7 , which is an il - 2 cytokine family member , involves t cell - driven autoimmunity , inflammation , and tissue destruction . in addition , il - 7 and il - 7r were coexpressed on ra synovial tissue lining and sublining macrophages and endothelial cells . this cytokine can stimulate tnf - and ifn - production and its level correlates with disease activity , suggesting it has value as a diagnostic biomarker predicting the progression to ra . the overproduction of il - 33 , a newly identified inflammatory cytokine , was found in synovial fluids of ra patients . it could be upregulated by hypoxia - inducible factor - 1 ( hif - 1 ) which was also increased in ra synovium through the activation of p38 and erk pathways . andthese two participants exacerbate the disease severity and may serve as new therapeutic targets in biologic treatment . il - 34 , expressed by giant cell tumours of bone , plays a critical role in macrophage differentiation and osteoclastogenesis . in ra patients , the secretion of il - 34 was upregulated in fls by tnf - or il - 1 induction and was mediated by the transcription factor nuclear factor b ( nf - b ) and activation of c - jun n - terminal kinase ( jnk ) , indicating its osteoclastogenic role in ra . increased il - 36 ( one form of il - 36 ) expression was found in ra synovium and could lead to il - 6 and il - 8 production by synovial fibroblasts through p38 / nfb activation in vitro . il - 36 , known as il - 1f8 , was found to be expressed in synovial membrane in cia and synovial membrane biopsies from ra patients . another member of il - 1 family which was detected in various inflammatory diseases including ra is il - 37 which interacted intracellularly with smad3 . in contrast to the inflammatory cytokines , il - 35 is an inhibitory cytokine that contributes to regulatory t ( treg ) cells function and suppresses the pathogenic cells , such as th1 and th17 cells . il - 35 belongs to il - 12 family and is mainly produced by cd4 + foxp3 + treg cells . il - 27 is a novel member of il - 12 family and has two sides ' properties , pro- or anti - inflammatory in ra . significantly higher concentration of il - 27 was found in plasma and synovial fluid of ra patients than in oa patients . expressions of icam - 1 , vascular cell adhesion molecule , inflammatory chemokines , such as il - 6 , ccl2 , cxcl9 , cxcl10 , and mmp - 1 , in ra fls were induced under il - 27 stimulation . although il - 27 shows its pathogenic role , it was also found to have suppressive function in macrophage responses to tnf - and il - 1 . furthermore , il - 27 also promotes cd4 + foxp3 - t regulatory cell to produce il - 10 and downregulate il - 6 and il - 1 in early cia , which resulted in suppression of th17 and monocyte migration and vascularization . although numerous studies revealed the new candidates participating in development of ra , their exact mechanisms by which these molecules modulate the proinflammatory or anti - inflammatory response still require elucidation . these emerging players not only give us new evidences in complicated pathogenesis of ra but also suggest new strategies of therapeutic intervention in ra since current biotherapies are not effective for all ra patients . ra is a chronic and systemic autoimmune disease that affects many tissues and organs , especially flexible joints . biomarkers , not only already clinically used but also under investigation , play important roles in the development of chronic human diseases which include ra . they may serve as indicators for clinical observation on the disease progression and the therapeutic effect . furthermore , some of the biomarkers can also be or has already been a therapeutic target for the treatment . we expect that targeting specific biomarkers with the least side effects will bring hope to ra patients .\noutput:\n" }, { "from": "agent", "value": "rheumatoid arthritis ( ra ) is a common autoimmune disease with unknown etiology and pathogenesis . although major therapeutic advances have been made in recent years , there is no cure for the disease . current medications mainly reduce inflammation in order to relieve pain and slow joint damage , but many have potentially serious side effects . therefore , to find specific biomarkers will benefit both ra patients to find relief from the disease and physicians to monitor the disease development . a number of biomarkers have been discovered and used clinically , and others are still under investigation . the autoantibodies , which are widely used in diagnosis and prognosis , novel biomarkers , which reflect clinical disease activity , and newly found biomarkers and pathogenic - related cytokines are discussed in this review ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: lack of physical activity is a trend that is expanding across age brackets in the united states . in older adults , obesity and lack of physical activityhowever , the trends in physical activity among younger adults remain under - represented in the literature . this is particularly relevant , given that studies have shown that college students , on an average , do not accumulate the recommended amount of physical activity for an adult and 60 % of college students are unaware that adults should exercise five days a week for 30 minutes at moderate intensities . in general , there is a lack of physical activity among us college students . these students are also engaged in sedentary activities , which reduce the available time for health promoting behaviors and academic pursuits . sedentary activity for students comes in many forms , but a good amount of these activities fall into the square tube category , such as , watching tv , surfing the internet , and playing video games . the amount of time that college students spend on the internet has been shown to relate to reduced academic performance . it has also been demonstrated that the time spent by college students in communicating through electronic media is related to the higher levels of distractibility for academic tasks . evidence also exists that among high school aged students , time spent playing videogames is negatively correlated with academic performance . however , a study that examined a community college population did not report a relationship between videogames and academic markers . it would appear that sedentary activity can impact academic performance ; however , the link between academic performance and video game use requires further study in the collegiate population . a recent study has demonstrated acute and chronic effects of aerobic exercise on cognitive performance . best reported in a recent review of the research on aerobic exercise and children 's executive function , that cognitively engaging aerobic exercise seemed to be linked to higher levels of executive function . tomporowski et al . also reported a similar relationship between cognition and exercise among children . however , until recently there was a lack of plausible mechanistic understanding of these reported relationships . one initial hypothesis suggested that increased cerebral oxygenation due to aerobic exercise was the reason for the increase reported in cognitive function . a recent study by ando et al . testedthe hypothesis that increased cerebral oxygenation may account for the differences seen in cognition , post exercise : however , the results demonstrated improvements in cognitive function that were judged to be independent of cerebral oxygenation . a second possible mechanism behind the changes associated with aerobic exercise was centered on exercise - induced increases in the brain derived neurotrophic factor ( bdnf ) . examined the effects of acute and chronic cycling exercise and found that the exercise - induced changes in bdnf and in the hippocampal function improved the performance in memory recall . , mirrors findings based on animal models that reported a similar relationship between exercise , increased bdnf , and increased hippocampal plasticity . importantly , griffin et al . also reported a chronic effect of exercise , after five weeks , where cognitive function and bdnf responses to exercise were increased . this last finding lends credence to the cross - sectional reports that increased levels of aerobic activity or physical activity are related to better cognitive function or academic performance . there are numerous studies that have examined this trend in a cross - sectional manner with high school aged students and younger ones too . however , there is only one study to date that has examined this in a group of college students . this study has been done in a small group ( n = 224 ) of nursing students in kuwait and it has not reported a significant relationship . however , given the many variables that contribute to cognitive function it is likely that in a small cohort study , the statistical power would not be sufficient to reveal any relationships . the present investigations ought to determine if the aerobic activity level of college students was associated with higher grade point averages among the nursing and kinesiology undergraduate students , who would likely be heavily involved in health promotion and education in future careers . the research questions to be addressed included : determining the differences in students grade point average by both aerobic and weightlifting activities , and finally , based on the strength of the relationship , making recommendations for aerobic exercise habits for college students . the present investigation was reviewed and approved by the institutional review board at the university of louisiana at lafayette . the participants gave written informed consent prior to completing the leisure and physical activity questionnaire ( lpa ) , and were free to withdraw at any time after commencing the study . data was collected during the spring semester , ensuring that the freshmen surveyed had achieved a grade point average ( had been enrolled long enough to have earned quality points during a previous semester ) . students who enrolled in spring , who could not report a grade point average , were excluded from the data analysis . leisure and physical activity ( lpa ) is a short self - report instrument designed to assess a college student 's sedentary / non - sedentary activity , class rank , gender , and grade point average . the demographic variables are recorded as follows : class rank as freshman , sophomore , junior or senior , gender as female or male , and grade point average between 0.0 and 4.0 . sedentary activity types assessed are time spent in typing / schoolwork , web surfing / entertainment , video gaming . each sedentary / non - sedentary activity type classification has further descriptors for clarification : web surfing / entertainment included ( television , facebook , myspace , etc . ) andthese activities have been assessed for frequency ( 0 - 2 days , 3 - 5 days , 6 - 7 days ) per week as well as duration per about 0 - 15 minutes , 16 - 30 minutes , greater than 30 minutes . each frequency and duration has been assigned a score of one to three points for each of the possible responses . grade point average has been assessed via predetermined ranges of answers ( 0 - 0.99 , 1 - 1.99 , 2 - 2.99 , 3 - 3.99 , 4.0 or above ) . aerobic exercise ( running , walking , biking , aerobics classes , etc . ) and weightlifting ( machine , freeweight , etc . ) have been assessed in a similar fashion for frequency and duration . the total scores for each item assessed were computed as the sum of the frequency and duration scores . this instrument demonstrated a low item to total correlations ( r 0.20 ) , suggesting that the items were measuring different constructs as was the intention when the survey was designed . in pilot testing , the weightlifting total score demonstrated a significant correlation ( r 0.80 , p 0.05 , n = 58 ) to the criterion measure hand - grip strength , assessed via a hand grip dynamometer ( jamar hand dynamometer , sammons prestons bolingbrook , il ) . similar results were found in another pilot study for the aerobic total score and vo2 max ( r 0.60 , p 0.05 , n = 12 ) assessed via a graded exercise test , utilizing a modern metabolic cart ( parvomedics trueone 2400 , parvomedics , sandy , ut ) . both the weightlifting and aerobic total scores were not significantly different pre - to post - test in a large sample testretest reliability study ( n = 389 , p 0.05 ) that examined the stability of the survey after a one - month time period . histograms of the distribution of data collected for variables of interest via the lpa survey can be seen in figures 13 . scores range from 0 for no activity to 6 the highest possible response for weightlifting activity histogram of total aerobic activity . scores range from 0 for no activity to 6 the highest possible response for aerobic activity histogram of reported grade point average . possible responses were 00.99 ( 1 ) , 11.99 ( 2 ) , 22.99 ( 3 ) , 33.99 ( 4 ) , 4.0 and above ( 5 ) data were analyzed for the relationship between the non - parametric correlation analysis and pearson 's chi - square test due to the ordinal and interval nature of the survey data . all analyses were conducted with a modern statistical software package ( ibm corp , spss version 20.0 , armonk , ny ) . the present investigation was reviewed and approved by the institutional review board at the university of louisiana at lafayette . the participants gave written informed consent prior to completing the leisure and physical activity questionnaire ( lpa ) , and were free to withdraw at any time after commencing the study . data was collected during the spring semester , ensuring that the freshmen surveyed had achieved a grade point average ( had been enrolled long enough to have earned quality points during a previous semester ) . students who enrolled in spring , who could not report a grade point average , were excluded from the data analysis . leisure and physical activity ( lpa ) is a short self - report instrument designed to assess a college student 's sedentary / non - sedentary activity , class rank , gender , and grade point average . the demographic variables are recorded as follows : class rank as freshman , sophomore , junior or senior , gender as female or male , and grade point average between 0.0 and 4.0 . sedentary activity types assessed are time spent in typing / schoolwork , web surfing / entertainment , video gaming . each sedentary / non - sedentary activity type classification has further descriptors for clarification : web surfing / entertainment included ( television , facebook , myspace , etc . ) andthese activities have been assessed for frequency ( 0 - 2 days , 3 - 5 days , 6 - 7 days ) per week as well as duration per about 0 - 15 minutes , 16 - 30 minutes , greater than 30 minutes . each frequency and duration has been assigned a score of one to three points for each of the possible responses . grade point average has been assessed via predetermined ranges of answers ( 0 - 0.99 , 1 - 1.99 , 2 - 2.99 , 3 - 3.99 , 4.0 or above ) . aerobic exercise ( running , walking , biking , aerobics classes , etc . ) and weightlifting ( machine , freeweight , etc . ) have been assessed in a similar fashion for frequency and duration . the total scores for each item assessed were computed as the sum of the frequency and duration scores . this instrument demonstrated a low item to total correlations ( r 0.20 ) , suggesting that the items were measuring different constructs as was the intention when the survey was designed . in pilot testing , the weightlifting total score demonstrated a significant correlation ( r 0.80 , p 0.05 , n = 58 ) to the criterion measure hand - grip strength , assessed via a hand grip dynamometer ( jamar hand dynamometer , sammons prestons bolingbrook , il ) . similar results were found in another pilot study for the aerobic total score and vo2 max ( r 0.60 , p 0.05 , n = 12 ) assessed via a graded exercise test , utilizing a modern metabolic cart ( parvomedics trueone 2400 , parvomedics , sandy , ut ) . both the weightlifting and aerobic total scores were not significantly different pre - to post - test in a large sample testretest reliability study ( n = 389 , p 0.05 ) that examined the stability of the survey after a one - month time period . histograms of the distribution of data collected for variables of interest via the lpa survey can be seen in figures 13 . scores range from 0 for no activity to 6 the highest possible response for weightlifting activity histogram of total aerobic activity . scores range from 0 for no activity to 6 the highest possible response for aerobic activity histogram of reported grade point average . possible responses were 00.99 ( 1 ) , 11.99 ( 2 ) , 22.99 ( 3 ) , 33.99 ( 4 ) , 4.0 and above ( 5 ) data were analyzed for the relationship between the non - parametric correlation analysis and pearson 's chi - square test due to the ordinal and interval nature of the survey data . all analyses were conducted with a modern statistical software package ( ibm corp , spss version 20.0 , armonk , ny ) . participants in the present investigation ( age : 21.24.7 years , female n = 317 , male n = 423 , freshman 16.5 % , sophomore 24.4 % , junior 26.0 % , senior 28.3 % , and post - baccalaureate 3.1 % ) were 740 students enrolled in undergraduate course studies in either nursing or kinesiology ( health promotion , exercise science , sport management ) at the southern and midwestern universities ( southern 34.2 % , midwestern 65.8 % ) . the data demonstrated expected trends for distribution , as the mean response to grade point average demonstrated that a majority of student 's reported grade point averages in the range of 3 - 3.99 , with the second highest response being 2 - 2.99 . the aerobic activity total score demonstrated a normal distribution , with only a slight skew toward the higher scale scores , whereas , the weightlifting activity demonstrated a bimodal distribution . gender demonstrated a significant non - parametric correlation to the total weightlifting activity ( p .05 ) . pearson 's analysis revealed differences in grade point average with aerobic activity ( = 44.29 , p 0.001 ) , with higher levels of aerobic activity being associated with higher grade point averages [ figure 4 ] . a non - significant trend was observed toward differences in grade point average with weightlifting activity ( = 22.69 , p = 0.61 ) , with higher weightlifting activity being associated with lower grade point averages [ figure 5 ] . possible responses for grade point average were 00.99 ( 1 ) , 11.99 ( 2 ) , 22.99 ( 3 ) , 33.99 ( 4 ) , 4.0 and above ( 5 ) . error bars represent 95 % confidence intervals mean response to grade point average by weightlifting activity . possible responses for grade point average were 00.99 ( 1 ) , 11.99 ( 2 ) , 22.99 ( 3 ) , 33.99 ( 4 ) , 4.0 and above ( 5 ) . error bars represent 95 % confidence intervals differences in reported grade point average were also noted by reported time spent typing and completing schoolwork ( = 62.40 , p 0.001 ) , with higher reported amounts of studying being associated with higher gpas . in addition , differences in gpa were found for reported time spent video gaming , with higher amounts of video gaming being associated with lower gpas ( = 57.09 , p 0.001 ) . the present investigation fills a gap in the literature by expanding findings among elementary , middle , and high school students in regard to the association of physical activity and academic performance . fox et al . reported that among a large cohort of middle and high school students , participation in team sports was associated with higher gpas . stevens et al . reported that physical activity was associated with higher achievement scores in both mathematics and reading . although in these investigations physical activity was only one of the many correlates to academic performance , nonetheless increased levels of physical activity garnered through team sport or increased activity outside of the physical education courses was related to academic performance . , in a recent review of the findings in children , suggested that exercise might enhance children 's mental functioning . the present investigation builds upon the evidence of a relationship between physical activity and exercise to academic performance by demonstrating similar findings among midwestern and southern university students . it should be noted that a previous study conducted in kuwait reported no relationship between results of a health promoting lifestyle , which included assessment of reported physical activity and academic performance . however , the kuwait study examined a smaller sample of students ( n = 224 ) and the students were all nursing majors . the limited sample size and relative similarity of population may , in part , be responsible for this finding . the present investigation included a larger sample ( n = 740 ) from two different geographic regions within the united states . although the results of the present investigation leave much of the variance in gpa unexplained , it has been demonstrated that there are many other factors that are related to academic performance such as the socioeconomic status . physical activity in college students has also been shown to relate to a number of other factors such as happiness , consumption of fruit and to be largely dependent on self - efficacy for exercise of the student . as physical activity is only one variable of many that can explain some variance in academic performance , it is understandable why the demonstrated effect sizes are smaller in magnitude and why a small sample size , such as in al - kandari and vidal , would likely result in a non - finding . although the relationships are small , college students academic achievement is critical , therefore , any demonstrated relationship to academic performance is an important finding . the secondary trend that weightlifting was negatively related to academic performance was not a surprising one . the recent physiological findings regarding bdnf suggest a plausible mechanism by which aerobic exercise may enhance the cognitive function . given the lack of evidence in younger populations , a plausible explanation for the negative impact of resistance exercise and academic performance may be that the two are unrelated and time spent engaged in resistance training reduces the available time for academic pursuits . this may be similar to the reported negative relationship with video gaming , as time spent engaged in video gaming would reduce time spent in studying . this relationship warrants further investigation in order to understand and more fully characterize the relationship . on the basis of the results of the present investigation , it can be suggested that colleges and universities focus on the facilitation of aerobic exercise for students , through either outdoor or indoor opportunities . given the number of universities across the country that currently have or are in the process of building large student centers for exercise , it can be suggested that these centers be constructed and staffed in such a manner that aerobic exercise is encouraged . in addition , colleges and universities can further encourage aerobic activity through offering physical education or activity courses to students who are focused on learning and practicing exercise types that promote aerobic fitness . these courses can be offered for a variety of different exercise modes , such as fitness walking , jogging , and swimming . the provision of aerobic exercise can also be met through an active recreation and intramural sports program . if activities or sports are offered that promote aerobic activity , this will increase the availability of fitness - related activities to the students . a university or college with well - designed facilities , physical education and activity courses , and recreation departments , which all promote aerobic exercise , will offer students an ideal setting to engage in aerobic exercise . although resistance training showed a negative trend toward academic performance in the present investigation , centers should still incorporate strength training equipment , as resistance training is an important component for the development of overall health - related lifetime fitness .\noutput:\n" }, { "from": "agent", "value": "context : lack of physical activity is a contributor to the obesity epidemic and is speculated to relate to reduced academic performance ; however , this link has yet to be examined within the college population.aims : the purpose of this study in a group of undergraduate students , was to determine if aerobic exercise activity was related to academic performance.materials and methods : the participants for this study included 740 students at multiple universities enrolled in nursing and kinesiology studies . the participants completed the leisure and physical activity questionnaire.results : pearson 's 2 analysis revealed differences in grade point average with aerobic activity ( 2 = 44.29 , p 0.001 ) as well as a trend toward differences in grade point average with weightlifting activity ( 2 = 22.69 , p = 0.61 ) . conclusions : based on these findings it can be suggested that college students engage in greater aerobic exercise ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: birth defects are an important contributor to infant mortality among all racial / ethnic groups . major congenital anomalies are defined as those that threaten life , require major surgery , or lead to a significant disability . between 2 % and 3 % of all infantshave a major congenital anomaly identified at birth and approximately 6 % to 10 % of such infants die within the first year of life ( 1 ) . in more than 60 % of such cases , the etiology of the congenital birth defect is unknown and primary prevention is impossible . in approximately 20 % of congenital cases , the causes are monogeneous defects , 50 % are caused by chromosome aberrations and 20 % by virus infections , such as rubella , cytomegalovirus , and herpes virus ( 2 , 3 ) . many environmental factors have been suspected to play an etiologic role in the formation of congenital anomalies . chemical pollutants , dietary imbalances , ionizing radiation , pharmaceutical substances , and infections provide examples of known or suspected agents ( 4 ) . unlike animal studies , molecular and biochemical studies in pregnant women are impossible . therefore , epidemiological data about congenital malformations is of vital importance to scientific research on pathomorphogenesis , aimed at prevention and public health education ( 3 ) . only a small number of reports on birth defect monitoring are available from general hospitals ( 5 - 7 ) . thus , our aim is to establish a multi - center birth defects monitoring system for the evaluation of the prevalence and serial occurrence of birth defects in korea . the study materials were all recorded deliveries at 10 medical centers in korea , between may 1999 and october 2002 . the ten medical center were : the samsung cheil hospital , samsung medical center , asan medical center , cheil women 's clinic , ilsan cheil hospital , bombit women 's hospital , ewha women 's university mokdong hospital , kangnam st . records were obtained monthly , from delivery units and pediatric clinics by a visiting nurse . trainedstaff from each center provided the medical records that included delivery files , stillborn files and newborn files . the entire medical record of each case was reviewed for followings : hospital stay , prenatal diagnostic test results , birth certificate work sheet , labor and delivery records , progress notes , pathology / autopsy findings , physical examination findings , and a discharge summary . all live births , stillbirths , and spontaneous abortions after the 16th week of gestation were included . all neonates born at one of the 10 centers were examined by a pediatrician within the first week of life . in addition to the clinical examination , information from the prenatal and postnatal ultrasound examinations of the heart , brain and other organs were recorded . chromosome analysis was available for a number of birth defects that were coded according to the eurocat ( european registration of congenital anomalies and twins , an european union registry ) ( 4 ) and the international clearing - house for birth defects monitoring system ( icbdms ) ( 8 ) . the nineteen groups of malformations as described by the icbdms ( 8 ) were 1 ) anencephaly , 2 ) spina bifida , 3 ) encephalocele , 4 ) hydrocephaly , 5 ) microtia , 6 ) cleft palate , 7 ) total cleft lip , 8 ) esophageal atresia or stenosis , 9 ) anorectal atresia or stenosis , 10 ) hypospadias , 11 ) renal agenesis / dysgenesis , 12 ) limb reduction defects , 13 ) omphalocele , 14 ) gastroschisis , 15 ) abdominal wall defects , 16 ) diaphragmatic hernia , 17 ) transposition of the great vessels , 18 ) hypoplastic left heart syndrome , and 19 ) down syndrome . the study materials were all recorded deliveries at 10 medical centers in korea , between may 1999 and october 2002 . the ten medical center were : the samsung cheil hospital , samsung medical center , asan medical center , cheil women 's clinic , ilsan cheil hospital , bombit women 's hospital , ewha women 's university mokdong hospital , kangnam st . records were obtained monthly , from delivery units and pediatric clinics by a visiting nurse . trainedstaff from each center provided the medical records that included delivery files , stillborn files and newborn files . the entire medical record of each case was reviewed for followings : hospital stay , prenatal diagnostic test results , birth certificate work sheet , labor and delivery records , progress notes , pathology / autopsy findings , physical examination findings , and a discharge summary . all live births , stillbirths , and spontaneous abortions after the 16th week of gestation were included . all neonates born at one of the 10 centers were examined by a pediatrician within the first week of life . in addition to the clinical examination , information from the prenatal and postnatal ultrasound examinations of the heart , brain and other organs were recorded . chromosome analysis was available for a number of birth defects that were coded according to the eurocat ( european registration of congenital anomalies and twins , an european union registry ) ( 4 ) and the international clearing - house for birth defects monitoring system ( icbdms ) ( 8 ) . the nineteen groups of malformations as described by the icbdms ( 8 ) were 1 ) anencephaly , 2 ) spina bifida , 3 ) encephalocele , 4 ) hydrocephaly , 5 ) microtia , 6 ) cleft palate , 7 ) total cleft lip , 8 ) esophageal atresia or stenosis , 9 ) anorectal atresia or stenosis , 10 ) hypospadias , 11 ) renal agenesis / dysgenesis , 12 ) limb reduction defects , 13 ) omphalocele , 14 ) gastroschisis , 15 ) abdominal wall defects , 16 ) diaphragmatic hernia , 17 ) transposition of the great vessels , 18 ) hypoplastic left heart syndrome , and 19 ) down syndrome . during the 4 - yr period ( may 1999 - october 2002 ) , we observed 1,537 cases of birth defects among 86,622 births , including live births and stillbirths , the prevalence rate being 1.8 % . the mean maternal age was 29.9 ( 4.1 , 95 % ci ) yr , with a range 19 - 45 yr . nineteen percent ( 291 cases ) of the birth defects were associated with an elderly mother ( 35 yr ) . the mean gestational age at delivery was 32.58.6 weeks , ranging from 11 weeks to 43 weeks . the mean birth weight was 2,1981,319.5 g , with a range from 5 g to 5,060 g. non - living births ( termination or intra - uterine fetal death ) accounted for 31.5 % of deliveries , and 438 babies ( 28.5 % ) were born via cesarean section . five cases had ( 0.3 % ) ambiguous genitalia , and in 45 cases ( 2.9 % ) , the gender of the fetus could not be determined . table 3 shows the comparison of incidences of 19 congenital anomalies in korea as defined by icbdms ( 5 ) with those in japan and china and with atlanta , u.s.a . as determined by the metropolitan atlanta congenital defects program ( macdp ) ( 9 ) . among 1,537 birth defect cases , 260 cases ( 16.9 % ) down syndrome was most common ( 137 cases ) , followed by edwards syndrome ( 57 cases ) . table 5 shows the birth defects according to the involved organs . the highest proportion of birth defects ( 17.5 % ) involved the cardiovascular system , followed by the genitourinary system ( 15.6 % ) . thirty - four cases had polydactyly of the hand ( 4.0 per 10,000 fetuses ) and 20 cases had polydactyly of the foot ( 2.4 per 10,000 fetuses ) . syndactyly of the hand and foot occurred in 9 cases ( 1.2 per 10,000 fetuses ) and 7 cases ( 0.8 per 10,000 fetuses ) , respectively . the concept of congenital malformation is not strictly defined , and includes functional and metabolic disorders that , although present , may not necessarily be recognizable at birth ( 10 , 11 ) . the two most commonly used classification systems are : ( 1 ) the international classification of diseases system ( 12 , 13 ) , and ( 2 ) the international clearinghouse for birth defects monitoring system ( icbdms ) ( 14 ) . in our study , the classification of birth defects was performed according to the european registration of congenital anomalies and twins ( eurocat ) and the icbdms ( 1994 ) system . the eurocat program was initiated in 1979 . this surveillance system details 900,000 births per annum in 17 countries . the international clearing - house for birth defects monitoring system ( icbdms ) is a who - related non - governmental organization , and more than 25 countries including the united states , england , france , australia , japan , and china participate in the program . this system is a nationwide hospital - based monitoring system that covers about 10 % of all births in japan . in our study , the 10 medical centers ( six tertiary centers , one secondary center , and three large local obstetric clinics ) covered only about 3 % of births in korea . during the 4 - yr study period , the overall incidence of birth defects from the 10 medical centers in korea was 1.8 % . this is lower than the incidence of 2.4 % provided by the eurocat registration system , which tends to produce lower figures than other passive registries ( 15 ) . moreover , it has been reported that active monitoring systems detect 50 % more congenital malformations than passive monitoring systems ( 16 ) . therefore , the prevalence of birth defects in this study would be lower than the actual incidence . the incidence of total chromosomal abnormalities was 0.3 % and the incidence of the trisomy 21 was 9.2 per 10,000 births , which is slightly lower than the incidence in glasgow ( 12.4 per 10,000 births ) ( 17 ) , in atlanta , u.s.a . ( 11.3 per 10,000 births ) , and in japan ( 10.4 per 10,000 births ) ( 15 ) . in the present study , the most frequent abnormality was a cleft lip with or without a cleft palate with a prevalence of 10.3 per 10,000 births , which is higher than in the atlanta ( u.s.a . ) study ( 9.9 per 10,000 births ) , but lower than in japan ( 15.9 per 10,000 births ) or china ( 13.6 per 10,000 births ) ( 15 ) . the incidence of cleft palate without cleft lip in korea was found to be 1.4 per 10,000 births , which is lower than in other countries ; japan : 4.8 per 10,000 births , china : 2.4 per 10,000 births , and u.s.a . and the incidence of renal agenesis / dysgenesis in korea was 7.6 per 10,000 births , which is higher than in japan ( 4.3 per 10,000 births ) and in the u.s.a . the incidence of anencephaly and microtia in korea ( 3.3 per 10,000 births and 2.7 per 10,000 births ) were also higher than in japan ( 1.9 per 10,000 births and 1.6 per 10,000 births ) and in the u.s.a . ( 1.8 per 10,000 births and 0.9 per 10,000 births ) . the incidence of hypospadia ( 1.2 per 10,000 births ) and spina bifida ( 0.2 per 10,000 ) in korea were lower than in japan ( 3.5 / 3.2 per 10,000 births ) and in the u.s.a . the incidences of hydrocephalus ( 3.6 per 10,000 births ) and limb reduction defect ( 1.3 per 10,000 births ) in korea were lower than in japan ( 7.5 / 3.8 per 10,000 births ) and in the u.s.a . the incidence of gastroschisis ( 1.6 per 10,000 births ) and abdominal wall defect ( 1.4 per 10,000 births ) were lower than in japan ( 2.3 / 7.1 per 10,000 births ) and in the u.s.a . the incidence of omphalocele ( 3.0 per 10,000 births ) was lower than in japan ( 4.6 per 10,000 births ) but higher than in the u.s.a . the frequency of birth defects varies markedly between countries and depends on the observation time after birth , the types of malformations included , and on differences in the reporting and statistical procedures used ( 18 ) . on the other hand , this difference in the frequency of birth defects within countries would be affected by ethnicity , eating habits , and environmental factors , or combined . the highest proportion of birth defects involved the cardiovascular system ( 17.5 % ) followed by the genitourinary system ( 15.6 % ) . recently , it was proposed that poor semen quality , cryptorchidism , hypospadias and testicular cancer are symptoms of one underlying entity , testicular dysgenesis syndrome ( tds ) ( 19 ) . tds may be caused by genetic or environmental factors , or both . even though the clinical symptoms appear postnatallyin addition , there are many recent reports that environmental factors , especially endocrine disrupting chemicals ( edcs ) , can be the cause of congenital malformation ( 20 ) . these edcs may cause a variety of defects in the endocrine and reproductive systems ( 21 , 22 ) . however , little is known about the underlying biochemical and molecular mechanisms , or the determinants of teratologic susceptibility , particularly in humans ( 20 ) . possible explanations for the lower incidence of birth defects in the present study than in the eurocat program are : ( 1 ) we included neonates only within the first week of life , so that the defects recognizable thereafter might have been lost ; ( 2 ) in stillbirth cases , autopsy is carried out less frequently than in the eurocat program . the lower frequency of autopsy in our study might have resulted in a lower derection rate of defects in the internal organs . our aim is to establish a multi - center birth defects monitoring system to evaluate the prevalence and serial occurrence of birth defects in korea . birth defect registries that acquire data through active rather than passive reporting can provide additional important data on birth defects ( 21 ) . such a multicenter birth defects monitoring system can provide high - quality information on birth defects in korea . to check the serial occurrence of birth defects , it is necessary to increase the number of participating hospitals and to launch a nation - wide multi - center study .\noutput:\n" }, { "from": "agent", "value": "the aim of this study was to establish a multi - center birth defects monitoring system to evaluate the prevalence and the serial occurrence of birth defects in korea . ten medical centers participated in this program . a trained nurse collected relevant records from delivery units and pediatric clinics in participating hospitals on a monthly basis . we observed 1,537 cases of birth defects among 86,622 deliveries , which included live births and stillbirths . the prevalence of birth defects was 1.8 % , and the sex distribution of the birth defect cases was 55.2 % male and 41.6 % female . the highest proportion of birth defects was in the cardiovascular system ( 17.5 % ) , followed by birth defects involving in the genitourinary system ( 15.6 % ) . chromosomal anomalies were detected 30.0 per 10,000 births . of these chromosomal anomalies , down syndrome was most frequently observed . this study led to an establishment of a multi - center active monitoring system for birth defects . to better understand the serial occurrence of birth defects in korea , it is necessary to increase the number of participating hospitals and to launch on a nation - wide multi - center study ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: mechanical ventilation ( mv ) is the second most frequent therapeutic intervention performed in icus ( after treatment of cardiac arrhythmias ) , and is the most important intervention in patients with respiratory failure . however , it is associated with several complications , including increased risk of pneumonia , impaired cardiac function , and development of lung injury . there is now unequivocal evidence from both experimental and clinical studies that mv can cause or aggravate acute lung injury ( ali ) - a concept termed ventilator - induced lung injury ( vili ) . many of the pathophysiological consequences of vili mimic those of acute respiratory distress syndrome ( ards ) . is this relationship a coincidence or could there be a more sinister explanation - we address this issue later in this commentary . in the 1960s , pathologists recognized a new , severe pulmonary lesion that they called ' respirator lung ' ; in the 1970s webb and tierney developed a model of vili , and in the late 1980s dreyfuss and colleagues determined that lung stretch was a critical factor leading to vili . in 1998tremblay and slutsky coined the term ' biotrauma ' to describe the pulmonary and systemic inflammatory response triggered by lung cell distension , disruption , and / or necrosis after the application of mv . although a consensus conference in 1994 recommended that plateau pressure should generally be limited to 35 cmh2o , little change in ventilator practice occurred until publication of the ards network study , which demonstrated that a lung protective strategy using a tidal volume ( vt ) of 6 ml / kg predicted body weight decreased mortality in patients with ali . this study confirmed that vili was not just an interesting experimental entity , but was also an important clinical problem . this study led to the widespread , albeit not universal , use of lung protective strategies in patients with ali . however , the ards network trial did not address the issue of how to ventilate patients who do not have ali . on the one hand , one could argue that such a strict lung protective strategy using small tidal volumes is not necessary as these patients do not have widespread pulmonary changes observed in patients with ali and are therefore not at great risk of vili . furthermore , the use of low vt might lead to de - recruitment of lung units , increased hypoxemia and hypercapnia . on the other hand , the upper limit of plateau pressure that ensureslung protection may be substantially lower than 30 cmh2o , and small vt may be beneficial . evidence that lower vt may be advantageous in patients without ali has been provided by observational studies demonstrating that ventilation with higher vts early in the icu course is associated with subsequent development of ali . however , observational studies are prone to bias , particularly because it is not clear why the attending physician chose a large versus small vt for any given patient . as such , a randomized trial addressing the hypothesis that a small vt could prevent or attenuate vili in critically ill patients without ali / ards is important and timely . in this issue of critical care , determann and colleaguesreport the results of a randomized controlled trial comparing two vts ( 6 versus 10 ml / kg predicted body weight ) in ventilated patients without ali . bronchoalveolar lavage fluid and plasma cytokine levels were used as surrogate endpoints for early identification of the pulmonary inflammation associated with ali . the study was stopped prematurely after the second interim analysis ( n = 150 patients ) because investigators from one of the two participating centres were uncomfortable continuing the study since the development of ali was significantly greater in the control arm . methodologically , this is somewhat unusual in that current practice is that interim analyses are carried out by a committee who are not investigators in the study ; indeed , it is uncommon for investigators to even be aware of interim outcome data by study group . we think that stopping the trial early was unnecessary and unfortunate ; there was no strong safety signal , with virtually identical trends in terms of duration of mv and mortality rate in both groups . early stopping tends to overestimate treatment effects ; this is particularly true for studies with low event rates , as was the case in this study , in which only 12 patients in total developed ali . first , there are insufficient data to conclude that all icu patients must be ventilated with a vt of 6 ml / kg . we agree with the authors who recommend that a large randomized controlled trial is needed before being able to draw this conclusion . nonetheless , using small vts in patients without ali may be a reasonable strategy , and there appears to be little evidence of harm if clinicians address issues related to maintenance of sufficient positive end - expiratory pressure ( peep ) , and possibly the respiratory acidosis that may arise . second , as hinted at above , it is interesting to speculate on the relationship between mv and ali . if determann and colleagues ' data are correct , should we begin to consider that ali / ards is a consequence of our efforts to ventilate patients , rather than progression of the underlying disease ? injurious ventilatory strategies have been shown to increase alveolar - capillary leak , worsen oxygenation , cause pulmonary infiltrates , decrease lung compliance and cause an increase in lavage and systemic cytokines - all hallmarks of ali / ards . in the context of increased alveolar - capillary leak , use of excessive intravenous fluids - often used to treat shock in patients at risk for ali - can cause increased lung water , and again worsen mechanics and gas exchange , and indeed worsen clinical outcomes . it may not be a coincidence that ards was first described in the late 1960s , at the time of the vietnam war - it is also called ' da nang lung ' or ' shock lung ' - when patients were resuscitated aggressively on the battle - field . finally , endotracheal intubation affects host defence and can lead to development of colonization / pneumonia , a predisposing factor for ali . as such , is ali / ards largely a ' man - made ' syndrome , and is it a consequence of the aggressive regimens we have adopted to treat acutely ill patients ? if so , and if the results of determann and colleagues vis - - vis the marked decrease in development of ali in patients treated with low vt turns out to be correct , it would mark an inflection point in which ali / ards is no longer a syndrome that must be treated , but is a syndrome that should be prevented . ali : acute lung injury ; ards : acute respiratory distress syndrome ; mv : mechanical ventilation ; vili : ventilator - induced lung injury ; vt : tidal volume . jv and as equally participated in the writing of the drafts and the final manuscript . jv is supported by grants from fondo de investigacin sanitaria of spain ( # 07/0113 ) , and as from the canadian institutes of health research .\noutput:\n" }, { "from": "agent", "value": "in this month 's issue of critical care , determann and colleagues report the results of a randomized controlled trial comparing the effects of mechanical ventilation ( mv ) with two tidal volumes ( 6 versus 10 ml / kg predicted body weight ) on cytokine levels in lung lavage fluid and plasma as a surrogate for early identification of acute lung injury ( ali ) and / or acute respiratory distress syndrome ( ards ) . the study was stopped early after an interim analysis - when 150 patients were enrolled - showing that the incidence of ali / ards according to the current definition was 10.9 % higher in the 10 ml / kg group , although duration of mv and mortality was similar in both groups . we examine these interesting results after providing a brief historical perspective and discuss the limitations and implications of the study ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a cutaneous sinus of dental origin is a relatively uncommon occurrence and may be easily misdiagnosed . they do not always arise close to the underlying infection and dental symptoms may be absent ( 1 ) . often patients seek care from general physicians and surgeons with other diagnoses being made such as furuncles , basal cell and squamous cell carcinomas . it has been estimated that half of all patients undergo surgical excisions , multiple biopsies , antibiotic courses and even radiotherapy before definitive diagnosis ( 1,2,3 ) . misdiagnosis worsens the chronicity of the lesion and has pronounced effects on facial aesthetics due to unnecessary treatments resulting in further skin scarring . once the correct diagnosis is made , definitive treatment , through either tooth extraction or root canal therapy to eliminate the source of infection , is simple and effective . a 40 - year - old male presented to the oral and maxillofacial surgery department with a 3 - year history of a cutaneous sinus affecting the left cheek . he complained of intermittent swelling affecting the left face with a discharge of pus onto the left cheek . he had suffered an alleged assault 3 years prior and was struck with fists and glass bottles to the left face . he suffered no other medical conditions , did not take any medications and had no allergies . he had only recently registered with a dentist . in the 12 months prior to his presentation the patient had been referred to a local plastic surgery department via his general medical practitioner and had received treatment with no resolution of symptoms . the lesion was refractory to oral antibiotics and he had undergone excision biopsy of the cutaneous sinus followed by a z - plasty scar revision . on examination there was scarring to the left mental region with evidence of previous revision surgery and a draining cutaneous sinus ( fig . 1 & 2 ) . showing scarring to the left mental region with evidence of previous revision surgery and a draining cutaneous sinus intra - orally there was a crowned lower left first premolar which was not tender to percussion . image showing scarring to the left mental region with evidence of previous revision surgery and a draining cutaneous sinus plain radiographs revealed a periapical radiolucency of the lower left first premolar . cone beam computed tomography ( cbct ) showed the gp point to be in communication with the periapical area ( fig . ct showing gutta percha point communicating with the periapical area he was diagnosed with an oral cutaneous sinus associated with a non - vital lower left first premolar . a cutaneous dental sinus is a channel that leads from a dental focus of infection to drain onto the face or neck ( 2 ) . they are typically formed by periapical abscesses , which result from inflammatory degeneration of the pulp and periodontal membrane ( 4 ) . the inflammatory and immunological processes then induce bone resorption , resulting in the formation of an intraoral or cutaneous sinus . the point of drainage usually depends on the location of the apex of the affected tooth in relation to the muscular attachments of the bone and will follow the path of least resistance through the fascial planes of the face ( 5 ) . approximately 80 % of cutaneous sinuses that occur arise from mandibular teeth and thus appear on the chin or submental region ( 6 ) . rarely , a dental cyst or un - erupted tooth can be the source of the infectionlesions may resemble a pyogenic granuloma , actinomycosis , a thyroglossal duct cyst , a branchial cleft cyst , a furuncle , a squamous cell carcinoma and an epidermal cyst ( 1 ) . careful questioning of the patient about past symptoms may help identify a dental cause but symptoms may not be present in all cases . sinus tracts are most commonly found on the chin , submental region or in the submandibular area ( 7 ) . there is periodic drainage and crusting in some cases and the lesion is depressed below the normal skin surface . in particular , the examiner should look for dental caries or restorations and periodontal disease . a gp point can be used to trace the sinus tract to its origin , which is usually a nonvital tooth . biopsy , if performed , will show nonspecific findings such as hyperplasia and chronic inflammation ( 8 ) . once the correct diagnosis is made , root canal therapy or surgical extraction is the treatment of choice and antibiotics may be used as an adjunct to surgical therapy . . surgical revision of the scar can be undertaken to provide better a cosmetic result . failure of a cutaneous sinus tract to heal after adequate root canal treatment or extraction requires further evaluation and biopsy . as in this case , clinicians should be aware of the fact that any cutaneous lesion of the face and neck can be of dental origin and should seek communication and evaluation from appropriate specialists and general dental practitioners .\noutput:\n" }, { "from": "agent", "value": "we report a case of a cutaneous sinus related to a non - vital lower premolar . the case was misdiagnosed by non - dentally trained medical staff and subsequent treatment proved ineffective . following referral to an oral and maxillofacial clinic the correct cause was established . correct treatment was followed by rapid resolution of signs and symptoms.this case highlights the need for healthcare professionals dealing with such patients to be aware of the dentition as a cause for cutaneous sinuses in the head and neck region . those professionals not dentally qualified should enquire about dental pain and consider referral to the dental practitioner or a specialist department for further evaluation . even those with a dental background can be fooled and a through history and examination is paramount , supplemented by special investigations were appropriate ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: metformin hydrochloride ( met ) is an oral biguanide and chemically it is n , n - dimethylimidodicarbonimidic diamide ( figure 1 ( a ) ) , which reduces the elevated blood glucose concentration in patients with diabetes but does not increase insulin secretion . it does not lower the glucose levels in nondiabetic subjects . chemically glimepiride ( glm ) is ( figure 1 ( b ) ) 3 - ethyl -4-methyl - n - [ 2 - [ 4 - [ ( 4 - methylcyclohexyl ) carbamoylsulfamoyl ] phenyl ] ethyl ] -5-oxo-2h - pyrrole -1-carboxamide . glm is an oral hypoglycemic agent that acts by stimulating the release of insulin from functioning pancreatic beta cells and increasing sensitivity of peripheral tissues to insulin . chemically , atorvastatin calcium ( atr ) ( figure 1 ( c ) ) is ( r , 8r ) - 2 ( 4 - flurophenyl ) - , - dihydroxy - 5 - ( 1 - methylethyl ) -3-phenyl-4 - [ ( phenylamino ) carbonyl ] - 1h - pyrrole -1-heptonoic acid trihydrate . atorvastatin calcium ( atr ) is a competitive inhibitor of hmg - coa reductase used in the treatment of hyperlipidemia . fixed dose combination drugs are used to maintain steady state of glucose and lipid levels in blood plasma . tablet dosage form ( tripill ) contains an oral lipid lowering agent , atorvastatin , and two oral antihyperglycemic drugs , glimepiride and metformin hydrochloride . the combination of these three drugs complements each other and provides a reduction in plasma cholesterol along with glycemic control , thereby providing comprehensive control of diabetes associated with dyslipidemia . the objective of the present investigation is to develop a simple and novel method for the simultaneous estimation met , glm , and atr by employing hplc . the literature search reveals that , few methods were reported for this combination in dosage form and in plasma , there are some other methods that are reported for individuals as well as individual drugs with other drug combinations . the analytical method employed for the quantitative determination of drug in formulation plays a significant role in the evaluation and interpretation of drug release from the formulation . therefore , a complete validation of analytical methods was performed according to ich guidelines to yield reliable results that could be satisfactorily interpreted . so , the proposed method can be employed for the determination of three dugs in bulk and combination formulations ( tripill ) as well as in future studies of these drugs . the instruments employed in this study are hplc - perkin elmer , uv - 200 series with the total chrome software , waltham , usa ; sonicator - sharp analytical , hyderabad , india ; analytical balance - sartorius , german ; millipore direct - q 3 u.v . atr , met , and glm were gift samples obtained from aurobindo pharma ( hyderabad , india ) . acetonitrile of hplc grade , o - phosphoric acid , and sodium dihydrogen phosphate were of a.r . tripll 2 tablet dosage form with concentrations of atr - 10 mg , met - 500 mg , and glm - 2 mg was purchased from the market . preparation of standard stock solution . accurately weighed 10 mg of each drug , that is , met , glm , atr and transferred into a 10 ml volumetric flask dissolved with small amount of solvent ( acetonitrile : water 50 : 50 ) and made up of the volume with 50 : 50 v / v water and acetonitrile . daily working standard solutions of mixture were prepared by suitable dilution of the stock solution with the mobile phase . preparation of a buffer . accurately weighed 2.72 g of potassium dihydrogen orthophosphate dissolved in 1000 ml of hplc grade water and ph was adjusted to 3.0 by using orthophosphoric acid . the chromatographic separation was done by using grace smart altima c - 8 column ( 2504.6 mm , 5 ) with mobile phase acetonitrile : phosphate buffer ph 3.0 ( 60 : 40 % v / v ) at a flow rate of 1 ml / min and detection wavelength was 235 nm with 25 l of injection volume . the chromatographic method was optimized by changing various parameters , such as ph of the mobile phase , organic solvent and buffer used in the mobile phase , and composition of the mobile phase on trial error basis by varying one parameter and keeping all other conditions constant . the validation parameters like linearity , sensitivity , accuracy , precision , recovery , and stability of drugs were studied according to the ich guidelines . selectivity was studied by comparing the chromatograms obtained from the blank sample with the chromatogram obtained from a standard drug mixture . the linearity of this method was evaluated by linear regression analysis , using least square method , and the linearity of drugs was found in the concentration range of 20200 g / ml for met , 10150 g / ml for atr and glm . calibration standards are prepared by spiking the required volume of working standard ( 200 g / ml ) solution into different 10 ml volumetric flasks and volume made up with mobile phase to yield concentrations of 10 , 20 , 30 , 40 , 50 , 100 , 150 , and 200 g / ml of met , glm , and atr . the lod and loq of this method were verified based on the standard deviation of response , slope . intra - and interday accuracy and precision of this method were determined at three different concentration levels in 3 different days . on each day , three replicates were analyzed with independently prepared calibration curves . the accuracy and precision were expressed as percentage accuracy and relative standard deviation ( rsd ) , respectively . g / ml ) , 100 % ( 50 g / ml ) , and 120 % ( 60 g / ml ) of standard drug was added to the extracted solution of formulation , diluted the solution and injected into hplc , then calculated the recovery . robustness of the method was done by changing slight variation in the parameters like mobile phase composition , flow rate , and wavelength . present method did not show any significant change when the critical parameters were modified ( i.e. , mobile phase composition , flow rate , and ph of buffer ) . the stability of the drug solution was determined for the short - term stability and autosampler stability . short - term stability was carried out by keeping at room temperature ( 25c ) for 24 h. autosampler stability was determined by storing the samples for 24 h in the autosampler . each sample injected three times into hplc and concentrations obtained were compared with the nominal values of the quality control ( qc ) samples . the stress studies were carried out by taking 100 mg of each drug into 100 ml volumetric flask and added 5 ml of 1 m hydrochloric acid for acid degradation , 5 ml of 1 m sodium hydroxide for alkali degradation , and 10 ml of water for hydrolytic degradation ; then samples were kept in a water bath at 60c for 1 h. after heating , the solutions in volumetric flasks were neutralized , that is , 1 m hcl with 1 m naoh , 1 m naoh with 1 m hcl and volume made up with the mobile phase separately . photodegradation was carried out by the drug was kept under uv light 254 nm for 24 h. then diluted the drug solution with mobile phase to get suitable concentration within the linearity range and injected the samples into the hplc .20 tablets were weighed and finely powdered , and an accurately weighed sample of powdered tablets equivalent to 10 mg of atr , 500 mg of met , and 2 mg of glm ( equivalent to one tablet ) was extracted with different extraction solvents like acetonitrile , methanol , water , and mobile phase . the recovery of drugs ( atr and glm ) was found to be less than 50 % when extracting by using 100 % water and the recovery of met was found to be less than 90 % when extraction carried out by using acetonitrile . the 100 % recoveries of all three drugs were found when extraction carried out by using the combination of water and acetonitrile ( 50 : 50 ) as extraction solvent . hence , the composition of 50 : 50 v / v of acetonitrile : water was used as extraction solution . the powder equivalent to one tablet was transferred and extracted with 50 : 50 of acetonitrile : water in a 100 ml volumetric flask and sonicated for 15 min . the solution obtained was diluted with the mobile phase so as to obtain a concentration in the range of linearity previously determined , and then filtered through 0.22 syringe filter . during the method development , top priority was given for the complete separation of drugs . the chromatographic method was optimized by changing various parameters , such as ph of the mobile phase , organic solvent and buffer used in the mobile phase , and composition of the mobile phase on trial error basis . phosphate buffer in various strengths are tried along with methanol and acetonitrile as organic solvent . a mixture of acetonitrile and phosphate buffer with different ph values was tried . at ph 3.0 the separation was good enough ; then the proportions of acetonitrile and phosphate buffer ph 3.0 were tested as a mobile phase with grace smart c - 8 columns . the mobile phase composition of 40 : 60 v / v phosphate buffer : acetonitrile was shown to have good resolution and retention time with minimal tailing factor in acceptable range . the method was optimized with the mobile phase composition of acetonitrile and phosphate buffer 60 : 40 ( v / v ) . there were no significant changes in the chromatographic response and peak shape with change in buffer molarity . after several trials , the method was optimized as a mixture of 20 mm potassium dihydrogen phosphate buffer ( ph 3.0 ) and acetonitrile ( 40 : 60 v / v ) at a flow rate of 1 ml / min and at 235 nm by using grace smart , altima c - 8 column . these chromatographic conditions achieved satisfactory resolution , retention time , and tailing for three drugs of met , glm , and atr . figure 2 shows that chromatogram of standard drug mixture and these are well separated from each other . the standard mixture solution was used as a system suitability solution it was injected into hplc . the retention time , tailing factor , resolution , and theoretical plates for each drug were observed . the percentage relative standard deviation ( % rsd ) of five consecutive injections for each parameter was calculated . the system suitability parameters of the present method were found to be within acceptable limits . the acceptable limits of the resolution between two adjacent peaks should be 2 and tailing factor should be 2 and the % rsd of these values should be 2 . system suitability tests confirmed that the chromatographic system was adequate for the analysis planned to be done . the linearity was performed and calibration curve is plotted between peak areas of drug against concentration of the drug . the curve was linear over the range of 20200 g / ml for met and 10150 g / ml for atr and glm . the % rsd was found to be less than 2 for all the drugs which indicates that the method is precise . the tailing factor for the drugs was always less than 2.0 and the components were well separated under all the changes carried out ( i.e. , mobile phase composition , flow rate , and ph of buffer ) . considering the modifications in the system suitability parameters and the specificity of the method , as well as carrying the experiment at room temperature , may indicate that the proposed method was robust . the stability of the drug was studied for short - term and autosampler stability using the qc samples . the samples were analyzed and compared with freshly analyzed qc samples ; no differences were found in accuracy and precision . the stability data presented in tables 4 and 5 indicate that there were no major changes observed in this study . forced degradation studies were carried out in acid , base , and neutral conditions ; atr was degraded more ( 30.19 % ) in acidic conditions than basic and neutral conditions . in basic conditionsmet was degraded more ( 30.5 % ) compared to the other two drugs ; no degradation was found in hydrolytic conditions . the amount of glm in acid and hydrolytic conditions was reduced , but there was no reduction in the amount of glm in basic conditions . two degradation peaks were appearing at retention time of 5.2 min and 9.62 min in the chromatogram under applied stress studies . hence this method could be employed for the determination of these three drugs , that is , met , glm , and atr in the presence of their degradation product . under photodegradation study atr degraded 4 % andthe chromatograms of stress conditions are shown in figure 3 and the percentage degradation of each in stress studies of met , glm , and atr were represented in ( table 6 ) . the results of assay of dosage form percentage recovery was found to be more than 98 % for all the drugs ( atr , met , and glm ) ; the data was represented in table 7 ; the chromatogram from formulation was shown in ( figure 4 ) . the developed method possesses good selectivity and specificity ; there is no interference found in the blanks at retention times of atr , met , and glm and good correlation between the peak area and concentration of the drug under optimized conditions . the observation of % rsd less than 2 for both intra - and interday measurements indicates a high degree of precision . in the present method , a grace smart , altima c - 8 column has been used at a flow rate of 1 ml / min . the stability of atr , met , and glm were found to be within the limits indicating that there is no degradation of drugs during the daily analysis . this method was applied for the simultaneous determination of atr , met , and glm in tablet dosage form .\noutput:\n" }, { "from": "agent", "value": "a simple , rapid , and precise rp - hplc method for simultaneous analysis of atorvastatin calcium , metformin hydrochloride , and glimepiride in bulk and its pharmaceutical formulations has been developed and validated . these drugs were separated by using grace smart altima c - 8 column ( 250 4.6 mm , 5 - m ) with a mobile phase consisting of acetonitrile : phosphate buffer ( 60 : 40 ( v / v ) , ph 3.0 ) at a flow rate of 1 ml / min , injection volume 25 l , and detection at 235 nm . metformin , atorvastatin , and glimepiride were eluted with retention times of 2.57 min , 7.06 min , and 9.39 min , respectively . the method was validated for accuracy , precision , linearity , specificity , and sensitivity in accordance with ich ( q2b ) guidelines . the results of all the validation parameters were found to be within the acceptable limits . the calibration plots were linear over the concentration ranges from 10 to 150 g / ml , 20 to 200 g / ml , and 10 to 150 g / ml for atorvastatin , metformin , and glimepiride , respectively . the accuracy and precision were found to be between 98.2 % 105 % and 2 % for three drugs . developed method was successfully applied for the determination of the drugs in tablet dosage form and recovery was found to be > 98 % for three drugs . the degradation products produced as a result of stress studies did not interfere with drug peaks ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: it is a real ileal diverticulum usually located on the anti - mesenteric edge in the last meter of the small bowel . the location on the ileal mesenteric edge has been rarely reported and remains controversial . indeed , it raises the question about the differential diagnosis with bowel duplication which is still not elucidated . we report a case of perforated meckel 's diverticulum that was located on the mesenteric edge of the ileum . a 45 - year - old patient admitted to the emergency unit was complaining of abdominal pain lasting for 3 days . initially , the pain was located in the epigastric region , then secondarily generalized to the whole abdomen . physical examination revealed a good general condition , a temperature of 38.8 c , a pulse rate of 120 heart beats / min , a blood pressure of 100/90 mmhg and a respiratory frequency of 28 cycles / min . plain abdominal radiography showed air - fluid levels and was suggestive of abdominal effusion ( fig . 1 ) . on biology , blood cell count was 12400 cells / mm ( normal range : 400010000 ) and creatinine was 16.8 mg / l ( normal range : 612 ) . a generalized peritonitis was then suspected , and a laparotomy was performed . on exploration , we found 400 ml of seropurulent peritoneal fluid and a perforated meckel 's diverticulum of 3.5 cm in size , which was located 60 cm from the ileocecal junction on the mesenteric edge of the ileum ( fig . 2 ) . the patient underwent a removal of the diverticulum by a segmental resection of the ileum with an end - to - end anastomosis . the postoperative course was marked by persistent peritonitis , which motivated a revision surgery that involved a peritoneal lavage and drainage . it results from the incomplete regression of the omphalomesenteric duct that connects the primitive intestine to the yolk sac during the embryonic period . the location of this diverticulum on the anti - mesenteric ileal edge has been for a long recognized as diagnostic criterion . however , some cases of location on the mesenteric ileal edge have been reported since 1941 and so were suggestive of possible ileal duplication . meckel 's diverticulum with mesenteric location can be subserosal or intra - mesenteric . in our patient , it was a subserous diverticulum . while in intra - mesenteric variety , transillumination of the mesenterythe persistence of a short vitelline artery is thought to be implicated in the pathophysiology of mesenteric diverticula . indeed , this artery yolk could in part explain the diverticular meso , which , in case of rapid growth , causes a pull on the diverticulum and then a migration of its base to the mesenteric edge . the main differential diagnosis in these cases is the ileal duplication where vascularization is dependent on the ileal vascularization , while the mesenteric diverticulum 's vascularization is most often provided by a vitelline artery . however , most authors do not consider vascularization as a differential diagnosis tool because the vitelline artery presents in only 10 % of cases . this hypothesis is supported by kurzbart et al . , who reported a case of omphalomesenteric duct persistence detected in the neonatal period that fell to the age of 3 months and became a meckel 's diverticulum without mesenteric diverticular meso . in our patient , as well as in buke 's one , pathological examination of the surgical specimen did not show meso or diverticular sac artery . , meanwhile , found a vitelline artery on ct scan . according to buke et al . , a complete regression of the vitelline artery or a clot in utero between the mesentery and the omphalomesenteric duct might also explain this anatomical variant . perforation of meckel 's diverticulum is a main cause of right lower quadrant pain as well as appendicitis . if the systematic resection of incidental meckel diverticula is not unanimous , resection of complicated diverticula is widely agreed . according to park et al . , a diverticulectomy can be achieved if there is no mass suggestive of heterotopic tissue . however , given that the risk of degeneration of these tissues that may go unnoticed , segmental ileal resection seems to be the best option to adopt . it may be followed by an ileal anastomosis when local conditions allow it . in our patient , it was realized a segmental ileal resection followed by an end - to - end anastomosis . the postoperative course was marked by a persistent peritonitis probably due to a peritoneal toilet failure . in case of massive contamination of the peritoneal cavity , segmental ileal resection seems to be the ideal therapeutic attitude given the possible presence of heterotopic tissues . in case of perforation , resection and ileostomy\noutput:\n" }, { "from": "agent", "value": "a meckel 's diverticulum is the most common congenital anomaly of the gastrointestinal tract . it is a real diverticulum that is usually located on the anti - mesenteric edge in the last meter of the ileum . its location on the mesenteric edge has been rarely reported . it may lead to several complications including perforation that may be life - threatening for the patient . we report herein a case of perforated mesenteric meckel 's diverticulum in an adult patient . upon surgical exploration by laparotomy , we found a perforated meckel 's diverticulum located on the mesenteric edge of the ileum 60 cm from the ileocoecal junction and 400 ml of seropurulent peritoneal fluid . the patient underwent a segmental ileal resection and an end - to - end anastomosis . the postoperative outcomes were marked by a persistent peritonitis that required successful revision surgery ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: immunoglobulin g4 ( igg4 ) - related sclerosing disease is a rare disease entity that is known to involve various organs including the pancreas , biliary tree , salivary gland , retroperitoneum , kidneys , and so on ( 1 ) . its etiology is still unclear and it is composed of many disorders that have specific clinical , pathological , and serologic features ( 2 ) . so far , there has been only one report of igg4 - related sclerosing diseases arising in the small bowel , and it is mainly described in the histopathologic findings ( 3 ) . in this paper , we report a case of histologically proven igg4 - related sclerosing disease involving the ileum with imaging findings on ct and small bowel series . this report is , to our knowledge , the first to describe the radiologic findings of igg4 - related sclerosing diseases of the small bowel . a 43 - year - old man was admitted to our hospital with a one - year history of intermittent abdominal pains . he had a past medical history of acute myocardial infarction 10 years ago and a six - month history of benign prostatic hyperplasia . the laboratory tests at presentation showed mild leukocytosis ( 10470 / ul ) with an elevated neutrophil percentage ( 79.6 % ) and an elevated c - reactive protein value ( 50.6 mg / l ) . contrast - enhanced abdominal ct with a 64 - row mdct ( sensation 64 , siemens medical solutions , malvern , pa , usa ) showed irregular wall thickening , losses of mural stratification and aneurysmal dilatation of the distal ileum ( fig . there were multiple enlarged lymph nodes ( maximal diameter : 1.5 cm ) around the distal ileum ( fig . adhesion of the bowel loops with traction and abrupt angulation were also revealed ( fig . there were no significant abnormal findings in the other gi tracts . clinically and radiologically , there were no significant abnormal findings in other organs . the clinical and radiologic findings were somewhat confusing and non - specific because their sum can suggest both malignancy and benign inflammatory diseases , and are not specified to one category . the patient underwent exploratory laparoscopy . at surgery , the distal ileum showed segmental wall thickening and edematous wall with interloop adhesions . pathological study confirmed the diagnosis of igg4 - related sclerosing disease , which showed intramural chronic inflammation with prominent igg4 rich - lymphoplasmacytic infiltrates [ igg4 positive cells 50 / high power field ( hpf ) ] , fibrosis , and obliterative phlebitis ( fig . the patient was discharged on day 9 in good condition with regular follow - ups in the surgical outpatient clinic . extra - pancreatic manifestations have been reported and the disease has been recognized as a systemic disease ( 5 ) . the disease is now commonly referred to as igg4 - related sclerosing disease , with similar histopathologic features in various organs characterized by sclerosing inflammation involving numerous igg4 - positive plasma cells ( 6 ) . clinically , patients with autoimmune pancreatitis are usually presented with jaundice or mild abdominal discomforts . patients with igg4 - related sclerosing disease without pancreatic involvements can manifest various symptoms and signs according to the involved organs . laboratory findings including elevated igg and igg4 serum levels and autoantibodies such as ana and the rheumatoid factor are helpful in the diagnosis of igg4 - related sclerosing disease . the histolopathological hallmark of the disease is the large number of igg4 - positive plasma cells in the tissue . cheuk and chan ( 7 ) recently proposed a diagnostic criteria of 50 igg4 + plasma cells per hpf and an igg4 + / igg + ratio 40 % , which our patient fulfilled . other important histopathologic findings include lymphoplasmacytic infiltration , sclerosis without cellular myofibroblastic proliferation , and phlebitis ( 8 , 9 ) . various organs can involve igg4 - related sclerosing diseases : the pancreas , salivary glands , hepatobiliary tract , orbit , lymph nodes , aorta , skin , central nervous system , breast , kidney , prostate , lung , thyroid , and urethra ( 3 , 12 , 13 ) . inflammatory bowel disease is occasionally associated with igg4 - related sclerosing disease ( 14 , 15 ) , but there are few reports of igg4 - related sclerosing disease primarily involving the gastrointestinal tract ( 3 ) . to our knowledge , this report is the first to describe the radiologic findings of igg4 - related sclerosing disease of the small bowel . in our case , the radiologic findings can suggest both malignant features and benign inflammatory disease features . the imaging findings that are suggestive of malignant tumors showed irregular wall thickening , loss of mural stratification , and aneurysmal dilatation of the distal ileum without small bowel obstruction . with these findings , we can suggest malignant neoplastic diseases such as lymphoma , adenocarcinoma , and metastasis . these mass - like imaging features may be related to the mass - forming characteristics of igg4 - related diseases , which can manifest inflammatory pseudotumor in many organs ( 16 ) . other imaging findings that are suggestive of benign inflammations were multifocal narrowing , traction , aggregation , and abrupt angulation of the distal ileum . these findings can suggest benign inflammatory diseases with fibrotic and stenotic features , such as crohn 's disease and tuberculosis . these fibrotic and stenotic imaging features are considered relevant to the sclerosing feature of the recently reported histopathologic findings on igg4 - related sclerosing disease of the small bowel ( 3 ) . heterogeneous mural enhancement and multiple enlarged lymph nodes were relatively non - specific findings and can be found in both malignant and benign diseases . we consider that these radiologic findings of combined malignant - looking and inflammatory fibrostenotic features might be clues to the diagnosis of igg4 - related sclerosing diseases of the small bowel . in summary , igg4 - related sclerosing disease is a rare systemic disease that involves various organs . there are few studies , however , about the igg4 - related sclerosing disease of the gastrointestinal tract . in this report , we present the first case , to our knowledge , of radiologic findings of igg4 - related sclerosing diseases arising in the small bowel . although a definite diagnosis relies on histopathological confirmation , the radiologic findings may provide a clue to the diagnosis of igg4 - related sclerosing diseases of the small bowel .\noutput:\n" }, { "from": "agent", "value": "immunoglobulin g4 ( igg4 ) - related sclerosing disease is rare and is known to involve various organs . we present a case of histologically proven igg4 - related sclerosing disease of the small bowel with imaging findings on computed tomography ( ct ) and small bowel series . ct showed irregular wall thickening , loss of mural stratification and aneurysmal dilatation of the distal ileum . small bowel series showed aneurysmal dilatations , interloop adhesion with traction and abrupt angulation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the idea that nuclear actin plays a role in gene transcription is gaining strong support . two milestone studies published in the 1980s presented circumstantial evidence that actin is implicated in the transcription of protein - coding genes ( egly et al . . however , biochemical observations that supported the idea encountered criticism , and the findings were immediately dismissed as resulting from contamination or being artifacts , primarily because of the notorious abundance of actin . moreover , filamentous actin structures that are commonly observed in the cytoplasm , made visible by certain drugs , such as phalloidin , were not revealed in the cell nucleus even by advanced light microscopy methods . skepticism in the field remained , and the question of whether actin is present in the nucleus was left to drift as an untouchable topic ( for review see pederson and aebi , 2002 ) .20 yr later , we now agree that - actin plays a role in gene transcription associated with three different entities : components of atp - dependent chromatin remodeling complexes ( for reviews see olave et al . , 2002 ; bettinger et al . , 2004 ) , rnp particles ( percipalle et al , 2001 , 2002 ) , and the three rna polymerases in the eukaryotic cell nucleus ( fomproix and percipalle , 2004 ; hofmann et al . , 2004 ; hu et al . , 2004 ; philimonenko et al . , 2004 ; kukalev et al . , mass spectrometry ( jonsson et al . , 2001 ) and immunoreactivity criteria ( hofmann et al . , 2004 ) however , the studies that have investigated the function of actin in gene transcription ( see the following paragraphs ) have not revealed whether the actin molecules involved are in monomeric or polymeric form ( for review see pederson and aebi , 2005 ) . f - actin was detected in the nuclei of neuronal cells by heavy meromyosin labeling ( amankwah and de boni , 1994 ) . nuclear actin filaments have also been observed attached to the nuclear pore complexes in amphibian oocytes ( kiseleva et al . , 2004 ) . recent immunochemical studies have detected several types of actin structures in the nucleus ( schoenenberger et al . , 2005 ) . furthermore , a pool of nuclear polymeric actin has been detected by frap in cell lines that express gfp - tagged actin and in cells microinjected with fluorescent actin binding proteins ( mcdonald et al . , 2006 ) . however , we do not know whether the actin that is engaged in transcription is monomeric , oligomeric , or filamentous . much work is currently being performed to reveal the molecular mechanisms that underlie the role of nuclear actin in transcription . we summarize and discuss these recent studies and describe a general model for the function of nuclear actin in transcription . nm1 was found in the cell nucleus ( pestic - dragovich et al . , 2000 ) , which suggested that nuclear actin and myosin may function in a concerted manner . in fact , both proteins have been found in mammalian nucleoli ( andersen et al . , 2002 ; fomproix and percipalle , 2004 ; andersen et al . , 2005 ) . chromatin immunoprecipitation has been used to study the association of actin and nm1 with rdna promoters . in spite of technical limitations due to epitope accessibility , the chromatin immunoprecipitation data strongly supports the view that both actin and nm1 are present on actively transcribing ribosomal genes ( philimonenko et al . , 2004 ) . actin is associated with both active and inactive pol - i , whereas nm1 binds to the transcription machinery through the pol - i specific transcription initiation factor ia ( philimonenko et al . , 2004 ) . based on these data , one could speculate that recruitment of the actin pol - i complex to the rdna promoter brings actin and nm1 close to each other . actin and nm1 would then be able to interact and presumably activate rdna transcription ( philimonenko et al . , 2004 ) . indeed , posttranscriptional nm1 gene silencing down - regulates preribosomal rna synthesis , and both actin and nm1 are necessary for in vitro rdna transcription ( philimonenko et al . , 2004 ) . nm1 complex plays a role in the assembly of a transcription - competent pol - i . an intriguing question is whether nm1 plays a role also in transcription by pol - ii . pol - ii transcription is inhibited by a peptide - specific anti - nm1 antibody ( pestic - dragovich et al . , 2000 ) , but there is no evidence that nm1 sits on the promoter of protein - coding genes . recent immunoelectron microscopy studies have shown that nm1 is located at nucleoplasmic transcription sites ( kysela et al . , 2005 ) , but there is evidence that nm1 is physically connected to transcribed loci via rna , not via tfii factors , as rnase treatment of living hela cells specifically depletes cellular nm1 ( fomproix and percipalle , 2004 ) . it has been suggested that actin and nm1 act as a motor that facilitates the movement of the transcription machinery relative to the dna template during transcription elongation ( for review see de lanerolle et al . , 2005 ) . this suggestion is based on several observations : the atpase activity of myosin depends on actin , actomyosin motors function in the cytoplasm , and both actin and myosin are present in the cell nucleus ( pestic - dragovich et al . , 2000 ) . it is an attractive idea that actin functions by the same mechanism in both the nucleus and cytoplasm . the motor hypothesis , however , has not been experimentally validated , and several considerations argue against this hypothesis . rna polymerase by itself is a molecular motor ( for review see gelles and landick , 1998 ) , and therefore the requirement for an additional motor coupled to the transcriptional machinery seems redundant . actin associates with chromatin remodeling factors and histone - modifying enzymes ( see the following paragraph ) without requiring myosin . current knowledge does not allow us to formally exclude any molecular mechanism , but these observations suggest that the role , or at least one of the roles , of actin in transcription does not require nm1 and does not depend on motor activity . important clues concerning the role of nuclear actin came when nuclear proteins associated with actin were identified . studies of chromatin regulation induced by antigen - receptor signaling in lymphocytes led to the identification of - actin and baf53 , an actin - related protein ( arp ) , as components of the baf ( brg - associated factor ) chromatin remodeling complex ( zhao et al . , 1998 ) . after this initial observation , many other swi / snf - like complexes and histone - modifying factors in different organisms have been found to be associated with actin and / or arps , and numerous investigations have reinforced the idea that there is a functional link between actin and the regulation of chromatin structure ( for reviews see olave et al . , 2002 ; bettinger et al . , 2004 ) . the molecular mechanisms by which actin and arps contribute to chromatin remodeling are not fully understood . the ubiquity of actin and arps in a large variety of chromatin remodeling complexes suggests that these proteins may be involved , directly or indirectly , in many different nuclear processes , including transcription ( for review see rando et al . , 2000 ) . in the case of the mammalian baf complex , which participates in transcription activation in response to external stimuli , , actin is necessary for the association of brg1 with chromatin and is required for the full activation of the brg1 's atpase activity ( zhao et al . , 1998 ) . as summarized in table i , actin can potentially be recruited to transcription complexes through different types of interactions . the presence of actin in some chromatin remodeling complexes suggests a possible mechanism for the recruitment of such complexes to active genes ( fig . binding partners for - actin in the eukaryotic transcription complexes models for the function of actin in chromatin regulation at class ii genes . ( a ) actin is a component of atp - dependent chromatin remodeling complexes ( crcs ) involved in transcriptional activation . ( b ) actin becomes incorporated into the growing pre - mrnp while transcription is taking place . an alternative mechanism , supported by the observed binding of actin to the ctd , is that actin is recruited to the transcription machinery via binding to the ctd and subsequently transferred from pol - ii to the nascent transcript . adaptor proteins , such as hrp65 - 2 in c. tentans and hnrnp u in mammals ( see the text for details ) , help actin recruit hats that acetylate histones along the gene and maintain the chromatin template in a transcription - competent state . ( c ) we speculate that actin mediates the cotranscriptional recruitment of chromatin remodeling complexes to active genes through interactions with pol - ii and / or with the nascent pre - mrnp . studies in the dipteran chironomus tentans suggest that actin can also influence chromatin structure through the recruitment of histone - modifying enzymes . a synthetic peptide that can disrupt the interaction between actin and hrp65 - 2 inhibits pol - ii transcription in living cells , which suggests that the actin hrp65 - 2 interaction is required for transcription in vivo ( percipalle et al . , 2003 ) . a recent study has shown that the inhibitory effect of the peptide can be counteracted by trichostatin a , which is a general inhibitor of histone deacetylases . this suggests that the actin hrp65 - 2 interaction is involved in acetylation / deacetylation events . this suggestion is supported by the observation that hrp65 - 2 binds directly to a histone acetyltransferase ( hat ) called p2d10 , and the interaction between actin and hrp65 - 2 is required for p2d10 to associate with the transcribed chromatin ( sjlinder et al . , 2005 ) . moreover , the association of p2d10 , actin , and hrp65 - 2 with chromatin is sensitive to ribonuclease digestion ( percipalle et al . , 2001 ; kiesler et al . , 2005 ; sjlinder et al . ,2005 ) , which indicates that these proteins are tethered to the transcribed genes by binding to the nascent transcript . in summary , these findings suggest that actin , hrp65 - 2 , and p2d10 become assembled into nascent pre - mrnps during transcription . based on these observations , it has been proposed that the actin hrp65 - 2p2d10 complex is part of the nascent pre - mrnp , and it can travel along the transcribed gene , allowing p2d10 to acetylate histone h3 ( sjlinder et al . , 2005 ) . according to this proposal , the actin hrp65 - 2p2d10 complex maintains the chromatin in a transcription - competent conformation ( fig . this model is supported by the observations that h3 acetylation is reduced ( sjlinder et al . , 2005 ) and transcription is inhibited ( percipalle et al . , 2003 ) when the interaction between actin and hrp65 - 2 is disrupted . a recent study by kukalev et al . ( 2005 ) suggests that the cotranscriptional binding of actin to mrna binding proteins with the concomitant recruitment of chromatin modifiers has been conserved throughout evolution . dnase i affinity chromatography has shown that in human cells there is a specific association between actin and heterogeneous nuclear rnp ( hnrnp ) u. in vitro reconstitution experiments with purified proteins have shown that the interaction between actin and hnrnp u is direct and that actin binds a short amino acid sequence that is similar to the actin binding motif of c. tentans hrp65 - 2 . moreover , actin must interact with hnrnp u for pol - ii transcription to take place ( kukalev et al . , 2005 ) . interestingly , hnrnp u associates with the transcription activator p300 / cbp , a potent hat ( martens et al . , 2002 ) . the hrp65 - 2p2d10 case in c. tentans is thus similar to the hnrnp uhnrnp complexes serve as molecular platforms for the recruitment and tethering of chromatin - modifying enzymes in both insect and mammalian cells . the investigations described in this section support the view that actin modulates the structure of the chromatin template during the transcription of class ii genes . in this context , actin functions as a platform for protein protein interactions through a mechanism that requires ongoing rna synthesis . this mechanism is coupled to transcription elongation and does not seem to require myosin or motor activity . the role of actin in the modulation of chromatin structure does not , however , exclude more direct actions of actin on the basal transcription apparatus . for both pol - i and - ii , anti - actin antibodies inhibit the transcription of naked dna templates in transcription systems containing partially purified polymerases and the necessary transcription factors ( hofmann et al . , 2004 ; philimonenko et al . , further , - actin is needed for the full activation of partially purified pol - iii preparations from hela cells , again when a pure dna template is used ( hu et al . , 2004 ) . these results demonstrate that actin plays a role in transcription even when chromatin is not present . this conclusion is supported by the findings that actin is associated with pol - i ( fomproix and percipalle , 2004 ; philimonenko et al . , 2004 ) , pol - ii ( hofmann et al . , 2004 ; kukalev et al . ,2005 ) , and pol - iii ( hu et al . , 2004 ) . the identities of the actin binding partners in each transcription machinery are not known , but coimmuno precipitation experiments in hela cells have identified three pol - iii subunits associated with actin ( hu et al . , 2004 ) . two of them , rpabc2 and -3 , are present in all three rna polymerases , and the solution of the crystal structure of pol - ii shows that these two subunits are located close to each other at the surface of the polymerase ( cramer et al . , 2001 ) . ( 2004 ) suggested that rpabc2 and -3 form an actin binding patch that is common to all three rna polymerases . on the other hand , coimmunoprecipitation experiments have also shown that actin binds to the cooh - terminal domain of the largest subunit of pol - ii ( ctd ; kukalev et al . , 2005 ) , a domain that is absent in pol - i and - iii . these findings lead us to propose that actin can interact with the eukaryotic rna polymerases in two different ways . the first way is general and is probably mediated by rpabc2 and -3 , whereas the second way is specific to pol - ii . the latter interaction takes place via the ctd , presumably in its phosphorylated state ( table i ) . we do not yet know how actin acts at a molecular level when it associates with the rna polymerases . actin binds to the three rna polymerases , as described in the previous paragraph , and anti - actin antibodies reduce pol - i , - ii , and - iii activities to a similar extent in transcription assays in vitro ( philimonenko et al . , 2004 ) . abortive transcription - initiation assays in a pol - i system have demonstrated that anti - actin antibodies do not affect the synthesis of a 3 - nt - long abortive transcript , whereas they do inhibit the subsequent elongation of the 3 - nt product . this suggests that actin is not involved in initiation per se but in a process that occurs shortly after transcription initiation . this process may be promoter clearance or elongation ( philimonenko et al . , 2004 ) . similar experiments performed in a pol - ii system at a lower resolution could not determine the exact stage of transcription at which actin acts , but these experiments confirmed that actin plays an early role in the transcription of class ii genes ( hofmann et al . , 2004 ) . copurification and colocalization studies have led researchers to propose that actin plays a role in the assembly of pol - ii preinitiation complexes ( hofmann et al . , 2004 ) . many questions about the mechanisms by which actin functions in transcription remain unanswered . the simplest model that is compatible with our current knowledge of nuclear actin places actin in three different scenarios . second , actin appears to be necessary in an early step of the transcription process , a step in which actin interacts directly with the transcription apparatus . this step is independent of chromatin structure and may be common for all three rna polymerases . third , actin becomes incorporated into the nascent mrnps , where it is involved in the recruitment of factors that regulate chromatin structure . the structure of actin is complex ( for review see pederson and aebi , 2002 ) , and actin can adopt several molecular conformations in a reversible and regulated manner ( page et al . , 1998 ) . it has been proposed that actin works as a conformational switch to control the assembly or the activity of chromatin remodeling machines ( boyer and peterson , 2000 ) . in agreement with this idea , it is tempting to suggest that the fundamental function of actin in transcription is to mediate dynamic protein protein interactions and to act as an allosteric factor in the remodeling of large multimolecular complexes , such as the transcriptional apparatus or the nascent mrnp . the transcription apparatus undergoes major conformational changes after assembly of the preinitiation complex , and these changes lead to transition into the elongation phase and to promoter clearance ( for review see dvir , 2002 ) . we speculate that actin acts in association with the eukaryotic rna polymerases as a molecular switch in these structural transitions . the involvement of actin in the recruitment of chromatin - modifying factors while it is part of the nascent mrnp is a more specialized function of actin in pol - ii transcription . we suggest that actin has the potential to trigger the release of chromatin modifiers from the mrnp concomitantly with the termination of transcription . the newly synthesized mrnp must undergo remodeling while the pre - mrna is processed , surveyed , and exported , and it will be interesting to determine whether actin plays a role in these events . finally , we note that actin is involved in signal transduction pathways in the cytoplasm , and it is therefore interesting to consider that actin - based mechanisms of transcription regulation may sense extracellular signals via cytoplasmic changes in the actin pools . the idea that actin plays a central role in the coordination of signal transduction is not new ( demali et al . , 2003 ; hall , 2005 ) . what is new is the suggestion that actin can modulate the overall transcriptional activity of the cell in response to extracellular signals .\noutput:\n" }, { "from": "agent", "value": "actin is not only a major cytoskeletal component in all eukaryotic cells but also a nuclear protein that plays a role in gene transcription . we put together data from in vitro and in vivo experiments that begin to provide insights into the molecular mechanisms by which actin functions in transcription . recent studies performed in vitro have suggested that actin , in direct contact with the transcription apparatus , is required in an early step of transcription that is common to all three eukaryotic rna polymerases . in addition , there is evidence from in vivo studies that actin is involved in the transcription elongation of class ii genes . in this case , actin is bound to a specific subset of premessenger rna binding proteins , and the actin messenger rnp complex may constitute a molecular platform for recruitment of histone - modifying enzymes . we discuss a general model for actin in rna polymerase ii transcription whereby actin works as a conformational switch in conjunction with specific adaptors to facilitate the remodeling of large macromolecular assemblies at the promoter and along the active gene ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the fracture toughness of bone varies depending on sampling site and the initial crack orientation of fracture test samples with respect to the applied load . the orientation of the specimen used in the fracture test was based on fracture propagation direction with respect to the long axis of the bone . according to crack orientation , there were two types of specimen considered for the measurement of fracture toughness : longitudinal cracking specimen and transverse cracking specimen . in the longitudinal cracking specimen , a crack propagates parallel to the long axis that is , along the collagen fiber through the bone matrix , whereas in the transverse cracking specimen , a crack propagates normal to the long axis , that is , across the long axis . in this study , circumferential - longitudinal ( cl ) and longitudinal - circumferential ( lc ) direction specimen are categorized as longitudinal cracking and transverse cracking specimen , respectively ( figure 1 ) . crack orientation of a specimen was classified according to crack plane during fracture toughness testing . the first letter represents a normal direction to the created crack plane ; the second letter represents the expected direction of crack propagation . there are many reports of plane strain mode i fracture toughness , kic , in different bone materials ( cortical and trabecular bones ) obtained under both quasistatic and dynamic loading conditions . typically , there is a large scatter in kic values because of nonuniformity in specimen microstructure , size , shape , and initial crack length . since the standard deviation , in the measurement of fracture toughness , has a similar magnitude to the average value , a single value fracture toughness is not a reliable parameter to predict fracture toughness for bone materials . fracture of a bone occurs where it is structurally weakest ( at the haversian and volkmann canals ) . hence , it is appropriate to use weibull statistics to analyze fracture test data . assuming that the fracture toughness distribution is describable using the two - parameter weibull equation , the probability distribution function is given by ( 1 ) f ( kic ) = 1e ( kic / k0 ) m , where kic is the fracture toughness and f ( kic ) is the failure probability . in ( 1 ) , m is the weibull modulus , which indicates scatterness of test data , and k0 is the characteristic fracture toughness or scale parameter ( fracture toughness value that includes 63.2 % of the test data , when kic = k0 ) . the objective of the present work was to determine the influence of the orientation of a cortical bone from which the test specimen was extracted on the values of the weibull modulus and the scale parameter of kic . power analysis was conducted to determine the appropriate test samples using the mean and standard deviation of fracture toughness of cortical bone in longitudinal and transverse direction found from lucksanasombool et al . . the analysis found that over 24 samples provide a 95 % confident estimate of fracture toughness for cl and lc specimens with an error of 0.04 from their population mean . therefore , more than 24 samples of cl and lc specimens were made during this study . fifty - three 20 mm 4 mm 2 mm dimension single edge - notch bend ( senb ) specimens were prepared from cortical bone harvested from the femur of an animal of 18 months old or less , with 28 and 25 cuts from the cl and lc orientations , respectively ( figure 1 ) . table 1 shows the dimensions of cl and lc specimens with their mean and standard deviation . the initial crack length was created at the center of the specimens by a buehler isomet 11 - 1180 - 160 diamond saw cutter with a thickness of 0.125 mm . nikon 's smz - 2500 stereo microscope was used to view the topography of the specimens and measure the dimensions of the specimens . a custom made three - point bending test apparatus ( see figure 2 ) was used in this study . the bone specimens were supported horizontally by two rollers located 16 mm apart , which is the spun length , s , for the senb test . a load cell ( futek , model l2920 ) with a digital display ( futek , model ibt 500 ) was used to measure the indention load that was applied at the midspan of the bone . a digital displacement gage ( mitutoyo , series 543 ) was used to measure the load point displacement . the crack initiation and propagation were observed using a stereomicroscope ( nikon 's smz - 2500 ) , focused at the midpoint of the bone during the tests . the critical loads for rapture , pcr , for the cl and the lc samples were extracted from the load - displacement graph . the value of kic was calculated using the following expression : ( 2 ) kic = pcrybw0 .5 , where b is the specimen thickness , w is the width , and y is the shape function at the initial crack length , a0 . for three - point bend testing , the values of ywere calculated using ( 3 ) y = ( 1 ) 2 ( 5.5819.57 +36.82234.953 + 12.774 ) , where is the normalized crack length defined as = a0 / w . the weibull method was used to calculate the weibull parameters ( m and k0 ) of the fracture toughness , kic , data for cl and lc specimens . according to the method , ( 1 ) can be expressed as ( 4 ) ln [ ln ( 11f ( kic ) ) ] = mlnkicmlnk0 . after sorting and numbering the kic values of all the cl and lc specimens in ascending order , the failure probabilities of f ( kic ) were estimated by ( j 0.3 ) / ( n + 0.4 ) , where j is the rank number of the specimen 's fracture toughness and n is the specimen sample size ( n = 28 for cl specimen and n = 25 for lc specimen ) . the f ( kic ) and kic data were used to generate the weibull statistic graphs [ lnln ( 1 / ( 1 f ( kic ) ) ) versus ln ( kic ) ] . univariate regression analyses of the f ( kic ) against the kic data was conducted to calculate m and ko using microsoft excel weibull analysis add - on . a one - way anova analysis was used to compare weibull modulus values as a function of orientation for bone specimens . the estimate for the scale parameter was calculated using ( 5 ) k0 = e | ( b / m ) | , where b was calculated as mlnk0 , which is the intercept of the weibull graph . the weibull statistical model equation ( 1 ) was applied to the fracture toughness ( k0 = kic ) to obtain the value of probability of failure of fracture toughness . the comparison of the load - displacement plots of a cl and lc specimen is shown in figure 3 . this figure shows that the slope of the load versus the displacement value is steeper at the initial stage of the experiment than at failure condition . this result means a higher load is required at the initial stage than later near failure for the same load point displacement . the increment of the load with displacement behaved linearly until the onset of cracking which is observed in the figure by the nonlinearity ( fracture initiation ) point of the load - displacement curve . also , figure 3 shows that for the same notch depth ratio , the lc specimen requires a higher initial fracture load than cl load . figure 4 shows the weibull statistic graphs [ lnln ( 1 / ( 1 f ( kic ) ) ) versus ln ( kic ) ] . the regression model coefficients for the least square fit of weibull graphs for both specimens are given in table 2 . results show that specimen direction had significant regressions of the transformed failure probability ( f ( kic ) ) ( ( 4 ) ) against ln ( kic ) ( p 0.001 , figure 4 ) , demonstrating that the two - parameter weibull model is applicable for the analysis . figure 5 shows the cumulative distribution functions of the fracture toughness value for the cl and lc specimens . figure 5 also shows a wider range of fracture stress for the lc specimens compared to the cl specimens . individual weibull strength moduli , m , and characteristic fracture toughness , k0 , were calculated for each group ( table 3 ) . the weibull strength moduli were significantly different ( anova , p 0.001 ) between the specimen groups , as expected because the slopes are related to the specimens ' material failure properties . the weibull modulus of the cl specimens is higher than that of the lc specimen . this means that the scatterness of the fracture toughness value was lower for the cl specimen compared to the lc specimen . since the scale parameter of the lc specimens is higher than that of the cl specimens , one expects to find that the fracture toughness is higher for the lc specimens than that for the cl specimens for a particular failure probability ( figure 5 ) . different distribution of structural types in front of the propagation crack in cl and lc directions specimens can be the reason for the difference of weibull parameters of kic between the two groups . the authors reported a different distribution of the structural types within different locations of the same bovine femur . they found that a different level of osteonal remodeling is directly related to the pattern of mechanical stress at the various fracture sites . the crack propagation in the cl specimens was parallel to the collagen fibers through the bone matrix , whereas in the lc specimen , the crack propagated across the collagen fibers . for lc specimens , the variation of the mechanical stress at the tip of the crack is due to high variation of the bone matrix and / or mineralized collagen fibrils and / or osteonal systems in the transverse direction . on the other hand , for cl specimens , the variation of the mechanical stress at the tip of the crack is due to variation of structural differences of the cement line , the boundary between secondary osteons and the surrounding lamellar matrix . the difference between the extrinsic toughening behavior for the lc and the cl specimens may be the source of a larger characteristic fracture toughness value in the lc specimens compared to the cl specimens . according to ritchie et al . , extrinsic toughening in front of the propagating crack tip in lc specimen occurs due to the collagen fiber bridging , crack deflection due to the cement line , uncracked ligament bridging , and microcracking , whereas extrinsic toughening in front of the crack tip in cl specimen occurs mainly by microcracking and uncracked ligament bridging . there are no publications on weibull parameters of fracture toughness data for bovine cortical bone in cl and lc to compare the results of this investigation . however , pithioux et al . applied the weibull distribution to bovine compact bone tension failure under quasistatic loading . the direction of fracture of the specimen was the same as the cl specimen used in this study . the weibull tensile strength modulus ( scatterness of tensile strength ) was found to be 5.77 by pithioux et al . , which is in close agreement with the weibull modulus of fracture toughness in this study ( 5.48 ) . this difference was reasonable since the bone type , age , size , loading , shape , and measurement properties used in this study were different from those of the test specimen used by pithioux et al . . the results of this study can be utilized to quantify the role of bone toughening mechanism on the failure probability of extremely diverse range of biomedical and nonbiomedical applications and has potential use for orthopedic bone cement . also , a failure model that considers the physiological process like remodeling , adaptation can be investigated . this study will enable biomedical researchers to predict more effectively the microdamage associated with bone damage and design bone - implant systems . the aim of this paper was to compare the bovine cortical bone fracture toughness in two different directions : cl and lc . weibull statistical law was used to analyze the fracture failure variation and characteristic fracture toughness values of cl and lc specimens . the results of this study are as follows.the individual fracture toughness data for each direction of specimen tested follow the two - parameter weibull distribution . each distribution was characterized by a different weibull modulus.lc direction cortical bone possesses greater fracture toughness than lc direction specimen for a particular failure probability level.there is a statistically significant difference of weibull modulus and characteristic fracture toughness for specimens of different orientation . the observed variability in the fracture of bovine cortical bone in cl and lc directions was explained by microstructural variables depending on the direction . the individual fracture toughness data for each direction of specimen tested follow the two - parameter weibull distribution . lc direction cortical bone possesses greater fracture toughness than lc direction specimen for a particular failure probability level . there is a statistically significant difference of weibull modulus and characteristic fracture toughness for specimens of different orientation . the observed variability in the fracture of bovine cortical bone in cl and lc directions was explained by microstructural variables depending on the direction .\noutput:\n" }, { "from": "agent", "value": "the fracture toughness , kic , of a cortical bone has been experimentally determined by several researchers . the variation of kic values occurs from the variation of specimen orientation , shape , and size during the experiment . the fracture toughness of a cortical bone is governed by the severest flaw and , hence , may be analyzed using weibull statistics . to the best of the authors ' knowledge , however , no studies of this aspect have been published . the motivation of the study is the evaluation of weibull parameters at the circumferential - longitudinal ( cl ) and longitudinal - circumferential ( lc ) directions . we hypothesized that weibull parameters vary depending on the bone microstructure . in the present work , a two - parameter weibull statistical model was applied to calculate the plane - strain fracture toughness of bovine femoral cortical bone obtained using specimens extracted from cl and lc directions of the bone . it was found that the weibull modulus of fracture toughness was larger for cl specimens compared to lc specimens , but the opposite trend was seen for the characteristic fracture toughness . the reason for these trends is the microstructural and extrinsic toughening mechanism differences between cl and lc directions bone . the weibull parameters found in this study can be applied to develop a damage - mechanics model for bone ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: protein intake during childhood has a paramount effect on growth and development ( 1 ) . it is an essential macronutrient necessary for building and repairing tissues , defending the immune system , coordinating cell activity , serving as a catalyst , and providing energy . factors including food availability and absorptive capacity affect the quantity and quality of a child 's intake of protein . animal sources of dietary protein include meat , eggs , cheese , fish , and dairy ( 2 ) . protein is also found in plant products such as nuts , seeds , grains , legumes , beans , and vegetables . in general , animal protein varies from plant protein in that it has higher saturated fat content and contains cholesterol . vegetarian diets , which are typically high in plant proteins , are associated with health advantages such as lower blood cholesterol levels , lower risk of heart disease , lower body mass index ( bmi ) , lower overall cancer rates , lower blood pressure levels , and lower risk of hypertension and type 2 diabetes ( 4 ) . scoring systems have been developed to determine the quality of a dietary protein source by quantifying the amino acids profile ( 5 ) . the protein digestibility - corrected amino acid score ( pdcaas ) is a measurement of the protein quality in human nutrition ( 6 ) . the higher the pdcaa score , the higher the amino acid profile and quality of protein . animal proteins ( i.e. , egg ) and purified plant proteins ( i.e. , soy ) have higher scores than plant proteins ( i.e. , wheat ) with intact cell walls . previous studies focusing on overall protein intake during infancy and early childhood showed that a high protein intake ( 15 % of energy ) during early childhood may increase the risk of obesity . furthermore , high protein intake during certain periods of childhood ( 12 months , 1824 months , and 56 years ) results in an increased bmi in subsequent years and even into adulthood . a child with a high bmi - for - age percentile has an increased risk of being overweight or obese in adulthood ( 710 ) . the present review article primarily focused to impart knowledge pertaining to crucial relationships among protein intake and future aspects of incorrect dietary inputs based on quality , quantity and time of protein intake . the review covered important aspects essential for the proper diet of young adolescents in order to secure their future from the lethal effects of obesity . the early protein hypothesis , initially identified by rolland - cachera , suggested that a high protein intake in early infancy increases the risk of obesity ( 11 ) . infancy and early childhood protein intakes are of interest because of differing macronutrient distribution found in infant formula versus human milk and the stimulating effect protein has on insulin - like growth factor - 1 ( igf - 1 ) and insulin secretion ( 12 ) . however , children breast - fed during infancy are taller and have higher igf - 1 concentrations later in life ( 13 ) . a low igf - 1 concentration later in life is associated with increased risk of non - communicable diseases ( ncds ) facilitated through igf - 1 . there is a concern that high protein intakes during the first years of life may cause obesity later by altering igf - 1 concentrations . it is thought that infants experience a rapid increase of protein intake when transitioning to solid foods , typically 3 - to 4-fold greater than the physiological requirements of the average infant ( 14 ) . the protein energy percentage is 78 % in infant formula , 20 % in full fat cow 's milk , ~ 5 % in breastfed infants , and 1520 % in the typical family diet . in turn , breast - fed infants are shorter , weigh less , and have a lower bmi than formula - fed infants . furthermore , an inverse relationship between igf - 1 measured in infancy and in late adolescence has been identified . for example , it has been shown that early intake of cow 's milk increases linear growth in well - nourished populations by stimulating circulating igf - 1 ( 15 ) . the risk factor for ncds later in life is associated more with a poor protein quality intake with no animal protein than with high intakes of total protein . a systematic literature review conducted by hrnellet al ( 10 ) aimed to assess the health effects of different intakes and sources of protein ( animal - or plant - based ) in infancy and childhood in a nordic setting ( 10 ) the above systematic review concluded that a high intake of protein in infancy and early childhood is associated with an increased risk of obesity later in life . a review by martorell et al ( 16 ) examined the relationship between overall nutrition in early life and the development of adiposity later in life . three hypotheses were posited : i ) overnutrition increases the risk of later obesity ; ii ) undernutrition is associated with increased risk of obesity ; and iii ) optimal nutrition during infancy , the gold standard being breastfeeding , is protective against future obesity . possible mechanisms for these outcomes include disruptions in organ function , increase in the number and / or size of fat cells or alterations in adipose tissue function , and dysfunction of the central nervous system resulting in appetite regulation disturbances . the authors of that study ( 16 ) reviewed observational , experimental , and quasi - experimental studies . birth weight and adult bmi were used to indicate the influence of fetal nutrition on adult obesity . the results from those studies are conflicting . some studies ( 17,18 ) identified a j - shaped relationship between birth weight and adult bmi , while others only found an association between high birth weight and increased adult bmi . a majority of the studies ( 19,20 ) found that higher birth weights , particularly birth weights 10 pounds , led to increased obesity in adulthood . in addition , intrauterine overnutrition is associated with a greater risk of obesity and may play a role in childhood obesity . a longitudinal study conducted by gunther et al ( 21 ) examinedwhether certain time points or periods of protein intake in infancy , early childhood , or the preschool years contribute to bmi at 7 years of age , and whether the association is attributed to distinct protein sources ( animal , vegetable , dairy , meat , or cereal protein ) . the aim of that study was to investigate the validity of the early protein hypothesis , which suggested that high protein intake during infancy increases the risk of obesity later in life . the early protein hypothesis is based on the consideration that infant formula has significantly higher protein content than human milk and that children experience a rapid increase in protein intake when transitioning to solid foods . previous studies ( 22,23 ) have failed to investigate whether distinct protein sources are associated with the early protein hypothesis . the study population was derived from the donald study ( 24 ) , an ongoing cohort study that follows subjects through young adulthood . an average of 4050 infants from dortmund , germany were recruited on an annual basis and examined at the age of 36 months . up until early adulthood , investigators intermittently collected information from participants on nutrition , growth , metabolism , and health status . a similar prospective study by scaglioni et al ( 8 ) examined the effects of the early intake of macronutrients on the development of overweight in healthy children . skinner et al ( 25 ) examined longitudinal growth and energy intake in children aged 28 years and identified factors associated with the children 's bmi . weight , height , and bmi percentiles were determined based on the center for disease control ( cdc ) growth charts . dietary intakes from 3 - day food records were averaged and analyzed using nutritionist iv , version 3.5 ( axxya systems llc , stafford , tx , usa ) . each child was assessed 1517 times by the end of the study and additional behavior information was obtained at certain time points . dietary fat and dietary protein had a positive relationship to bmi whereas a negative association was identified with dietary carbohydrate intake . thus , the quantity and quality of protein intake during childhood affects bmi and body fat percentage ( bf % ) subsequently in life . children with a higher bmi - for - age and children who subsequently became obese ages had a greater risk of adult obesity . childhood obesity also increases the risk of developing morbidities in adulthood . in a review , maffeis and tat ( 26 ) addressed the association between childhood and adult obesity and the effects of childhood obesity on morbidity and mortality . rates of diabetes , coronary heart disease , atherosclerosis , hip fracture , and gout were increased in individuals who were overweight as adolescents . moreover , cardiovascular risk factors such as total blood cholesterol , blood low - density lipoprotein - and high - density lipoprotein - cholesterol , and blood pressure levels and being overweight continued from childhood into adulthood . high bmi - for - age values can be a useful tool in identifying children and adolescents at increased risk of becoming overweight or obese in adulthood . furthermore , dietary factors such as protein sources affect childhood obesity and should be examined as potential contributors in the development of morbidities in adulthood . identifying dietary intake markers for increased bmi in children may assist with the development of dietary recommendations that may decrease the risk of developing obesity as an adult . for example , if a high intake of animal protein compared to plant protein predisposes children to obesity , dietary recommendations for increasing plant protein intake and decreasing animal protein intake may be developed . in the case that high intakes of animal protein is associated with a high bmi in children , parents can intervene during early childhood by providing adequate amounts of animal and plant protein for proper growth and weight maintenance . to ensure that healthy children are raised into healthy adults , it is important for the public to be aware of contributing factors to obesity . previous findings have shown that the association between dietary inputs and resultant obese conditions in children are multi - dimensional or multi - factorial in nature . possible mechanisms for the future outcomes of incorrect dietary habits include disruptions in organ function , increase in the number and / or size of fat cells or alterations in adipose tissue function , and dysfunction of the central nervous system resulting in appetite regulation disturbances . a majority of the studies found that higher birthweights , particularly birthweights 10 pounds , led to increased overweight and obesity in adulthood ( 21 ) . a proportion of the causes of high birthweight may be attributed to early exposure to famine or gestational diabetes . the fetuses of mothers with diabetes are exposed to high concentrations of blood glucose , which leads to hyperinsulinemia and increased growth of fat , lean body , glycogen stores , and overall birth weight . on the other hand , however , it has been suggested that individuals whose nutrient intake is scarce early in life move to abundance or excess in adulthood . in addition , intrauterine overnutrition is associated with a greater risk of overweight and obesity and may play a role in childhood obesity . a longitudinal study conducted by gnther et al ( 21 ) evaluatedwhether certain time points or periods of protein intake in infancy , early childhood , or the preschool years contribute to bmi at 7 years of age , and whether the association is attributed to distinct protein sources ( animal , vegetable , dairy , meat , or cereal protein ) . a previous study ( 8 ) confirmed an additional time period ( 56 years of age ) as a sensitivity period of total and animal protein intakes for later body obesity . thus , the quantity and quality of protein intake during childhood affects bmi and bf % in subsequent years . future studies are needed to compare protein intake later in childhood and bmi as predictors for adult obesity . erroneous methodology often limits dietary intake data in outcome evaluations . however , this information is essential for advancing dietary recommendations for overweight and obese children ( 27 ) . selection of the appropriate measuring tool or method for dietary intake in children proposes a challenge in itself , whether it is a total diet assessment , a targeted diet , or related behaviours assessment . each method depends on the dietary features of interest and the characteristics of the study population . the weight status of subjects and study design are important factors when selecting an appropriate methodology for dietary assessment ( 13,21 ) . dietary studies on children and adolescents have identified a positive association between under - reporting and increased body fatness . collectively , reports from large - scale surveys have shown a decrease in energy intake over time despite weight gain worldwide , suggesting energy expenditure has decreased and / or measurements of dietary intake are flawed ( 28 ) . one cross sectional study examined the extent of under - reporting of energy intake in children between the ages of 418 years ( 29 ) the results of that study showed that the target group is also a critical element when selecting a dietary intake method . different age groups have varying literacy and numeracy skills , memory capabilities , attention spans , and cognitive abilities . for example , children 8 years of age have limited competency in providing an accurate dietary recall and children 10 years of age lack the conceptual skills required for reporting usual intake , serving sizes , and frequency of behaviors . the dietary habits and level of structured eating environment should also be considered for different age groups , as older children tend to consume more meals away from home and follow a less stringent eating schedule . total dietary methods such as food records , 24 - hour recall , food frequency questionnaire , and targeted diet and / or behaviours methods have advantages and disadvantages ( table i ) . bmi is commonly used in clinical practice to represent adiposity status ( normal , overweight , and obese ) ( 30 ) . bmi , formulated from weight and height , is an inexpensive and convenient indicator of body fat mass for most children and shows the relative position of the child 's bmi among children of the same gender and age . bmi in children is often reported as a percentile ranking and subsequent weight status category . bmi is plotted on the cdc bmi - for - age gender - specific growth charts and is used to assess the size and growth patterns of children aged 2 years in the united states ( 31 ) . the relationship between bmi and adiposity was demonstrated in a study on italian children with a wide range in age ( 32 ) . although a strong positive relationship was found between bmi and total body fat , bmi compared across different age groups can be erroneous and results must be evaluated cautiously . total body fat was shown to increase with age while the percentage of body fat decreased with age . the association between childhood bmi and adult adiposity has been supported in some studies but refuted in other studies ( 33 ) . a large longitudinal study aimed to compare the accuracy of childhood levels of bmi and triceps skin - fold thickness in predicting adult adiposity . the study found that childhood bmi - for - age was significantly associated with adult levels of bmi . adult obesity and excessive body fat mass consistently increased as childhood bmi - for - age increased , even among young children . in conclusion , it is clear from the above citations that proper knowledge of dietary options is necessary to secure the future of young adolescents from the consequences of obesity .\noutput:\n" }, { "from": "agent", "value": "the abundance of protein and its functional diversity in living systems makes it essential for virtually all life processes . dietary protein and amino acid requirements are affected by age , body size , body composition , physiological state , and the level of energy output . the requirement for dietary protein is based on the indispensable amino acids under all conditions and under specific physiological and pathological conditions as well as the synthesis of dispensable amino acids and other nitrogen - containing compounds . previous findings have shown the influence of early intake of proteins on the development of overweight in healthy children . the present review focused on the possible association ( if any ) between protein intake and later development of obesity . the aim is to benefit physicians , dieticians as well as parents to understand future consequences of incorrect dietary habits in young adolescents and encourage healthy dietary habits to avoid obesity ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: torsion of the vascular pedicle of an ovary , fallopian tube , or paratubal cyst or of a fallopian tube alone results in ischemia and rapid onset of acute pelvic pain . the clinical presentation of ovarian torsion is non - specific , and its recognition and differentiation from other pathologies pose a diagnostic challenge . ovarian torsion has been described in all age groups from the fetal / neonatal period to elderly women , with 80 % of cases occurring in females under the age of 50 years . the 2 most common presenting features are lower abdominal pain ( 83 % ) and an adnexal mass ( 72 % ) . the diagnosis should be considered in women with lower abdominal pain , especially in the setting of ovarian cyst / mass and diminished or absent blood flow in the ovarian vessels , but the definitive diagnosis of ovarian torsion is based on surgical findings . we report an even more unusual case of bilateral torsion of the adnexa complicated by simultaneous bilateral adnexal entanglement . to the best of our knowledge , a 43 - year - old female , para 2 , was admitted to the gynecologic emergency department with the complaint of severe lower abdominal pain lasting for 2 days . the pain was cramping and not accompanied by nausea or vomiting . the patient was afebrile , her pulse rate was 107 / min regular , and her blood pressure was 123/61 mm hg . the abdominal examination was normal except for a slight tenderness on the right lower abdomen . speculum examination revealed no abnormality , and bimanual vaginal examination revealed that the uterus was normal in size , diverted to the right , mobile , and not tender . a smooth nontender 10 - cm cystic mass was palpated separate from the uterus in the douglas pouch . on ultrasonography , the uterus appeared to be normal in size and diverted to the right , and a multilocular cystic mass ( 11x8 cm ) was seen on the left side of the uterus . the ovaries could not be visualized separately because of the extent of their entanglement with one another . no free fluid was present in the douglas pouch . the hemoglobin count was 12.8 g / dl , the total leukocyte count was 8900 / ml and hcg in the urine was negativethe patient was diagnosed with ovarian torsion , and a laparoscopy was scheduled . at surgery , both adnexas were seen to be entangled with each other ( figure 1 ) . the left ovary was also enlarged ( 10 cm in diameter ) and cystic , and twisted twice around the ovarian proprii ligament . each ovary was displaced to the opposite side of the pelvis as a result of these entanglements . adnexa entangled with each other . to free both adnexas , we had to first fenestrate the right ovarian cyst and then use a grasper to return each adnexa to its correct anatomic position . the patient underwent left salpingo - oophorectomy and biopsy of the collapsed right ovarian cyst . the histopathological examination revealed a mucinous cyst adenoma in the left ovary and a simple cyst in the right ovary . we conducted a review of the literature by searching the world wide web for published reports on bilateral adnexal torsion , complex adnexal torsion , synchronous bilateral adnexal torsion , and adnexal entanglement . we found 2 case reports on increased risk for bilateral adnexal torsion after clomiphene citrate or other ovulation - inducing therapy , but the bilateral torsions were not entangled as they were in our patient . an earlier review of the 15 cases of bilateral adnexal torsion reported in the world literature5 revealed that fever ( 82 % ) , nausea or vomiting , or both together ( 73 % ) , and abdominal pain ( 93 % ) were the most common presenting symptoms . previous recurrent attacks of abdominal pain had occurred in 53 % of patients and that may be the only finding that is directly suggestive of this entity . the adnexas were histologically normal in 50 % of the specimens , and evidence existed of tubal infection ( hydrosalpinx and pyosalpinx ) in several cases . we describe a unique case of simultaneous torsion and entanglement of bilateral adnexas unassociated with prior ovulation induction treatment . elongation of ovarian proprii ligament or infundibulopelvic ligament could be attributed to the collagen type or connective tissue strength of the tissue . another likely cause in our patient is that both her ovaries were cystic and enlarged , and their being enlarged could explain the bilateral adnexal torsion . the additional finding of entanglement makes this a very unique case . although the usual presentation of adnexal torsion is unilateral pelvic pain , we recommend that the diagnosis of concomitant bilateral adnexal torsion and entanglement be considered when the presentation is diffuse , severe , lower abdominal pain .\noutput:\n" }, { "from": "agent", "value": "we report the first case of bilateral adnexal torsion complicated by concomitant entanglement of both adnexas . the clinical presenting symptoms and signs were similar to those described in unilateral adnexal torsion without adnexal entanglement . the final diagnosis was established by diagnostic laparoscopy , and aspiration of one of the ovarian cysts was required to disentangle the adnexas ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: clinical manifestations vary from localized nodules to debilitating lesions that can involve large areas of the body . there are 4 types of calcinosis cutis : idiopathic , dystrophic , metastatic , and iatrogenic . determining the type of calcinosis is very important for accurate management . here , we report the case of a 7 - year - old girl with idiopathic calcinosis , few cases of which have been described in early childhood . the unilateral distribution of calcinosis cutis has been previously reported in rare cases in the literature . furthermore , this is the first report that describes a unique unilateral presentation on the upper and lower limbs . a 7 - year - old healthy girl was referred to our dermatology clinic for an evaluation of asymptomatic skin lesions involving multiple sites exclusively on the right side of her body . medical history , family history , and social history were all negative . according to the parents of the patient , the lesions had enlarged minimally since they were first noted 2 years prior to the visit . the patient did not experience any restrictions in the movement of her joints , and she did not have any systemic symptoms . clinical examination revealed multiple skin - colored , nontender , firm - to - hard mobile nodules of various sizes ( 0.51.0 cm ) located over the right side of the patient 's body , mainly around her joints ( fig . a laboratory evaluation revealed a normal blood count and normal liver and renal function tests . serum calcium , phosphorus , uric acid , erythrocyte sedimentation rate , c - reactive protein , alkaline phosphatase , and creatine kinase were all normal . a hormonal workup , including calcitonin , parathyroid hormone , and thyroid hormone levels , was also within normal limits . to exclude connective tissue disorders , extensive immunological investigations were performed , including complement c3 and c4 , ana , anti - ds dna , rnp ab , ss - a ab , ss - b ab , and anti - sm ab . all values were normal . histological examination of one of the nodules revealed thick , cheesy material at the time of the procedure and microscopic massive calcium deposits ( fig . the patient had been seen by a pediatric rheumatologist for the calcifications , which had been managed conservatively with regular follow - up visits for the last year and no increase in the number of lesions or change in the patient 's general health status . based on the etiology , calcinosis cutis can be classified into 4 variants : idiopathic , dystrophic , metastatic , and iatrogenic . idiopathic calcinosis cutis is a skin calcification with no known etiology and an unclear pathogenesis , and serum calcium and phosphorus levels are normal . the dystrophic type of calcinosis cutis is associated with infection , inflammatory processes , cutaneous neoplasm , or connective tissue diseases in which preexisting damage to the skin results in calcium deposits . metastatic calcification results from systemic metabolic disorders and leads to elevated serum levels of calcium or phosphorus as well as calcium deposits in the skin and often other tissues . these types include calcinosis cutis circumscripta , calcinosis cutis universalis , tumoral calcinosis , subepidermal calcified nodule , and transplant - associated calcinosis cutis . only a small number of cases of idiopathic calcinosis have been reported in early childhood or adolescence . idiopathic calcinosis with unique unilateral presentation has been previously reported in the literature in only 2 cases : 1 in association with ipsilateral porokeratotic eccrine ostial and dermal duct nevus and 1 on the right elbow of a child . determining the exact type of calcinosis cutis is very important for selecting accurate management . it is recommended that patients be evaluated for abnormalities of calcium and phosphorus metabolism and that they be assessed for associated systemic conditions , such as collagen vascular diseases , renal insufficiency , and vitamin d poisoning . in our patient , there was no history of trauma or constitutional symptoms ; all of her blood samples fell within normal ranges . most medical measures , although beneficial in some cases , are not recommended for children because the risks outweigh the benefits . intralesional corticosteroid is a safe example that can be used in children and may be beneficial . aluminum hydroxide antacids may be effective phosphate binders in patients with hyperphosphatemia , but their use in renal insufficiency may result in toxicity . bisphosphonates may be helpful in some individuals by inhibiting bone resorption followed by reducing calcium turnover , which may be a source of further calcium deposition . however , treatment is prolonged , and paradoxical hyperphosphatemia may result . various beneficial effects reported with the use of the calcium channel blocker diltiazem have been reported . the therapeutic effect of this drug is believed to be antagonism of a calcium - sodium ion pump . unless the exact pathogenesis or dystrophic variant of calcinosis cutis is determined , the medical line of prevention after surgical excision has more potential complications in children . in our case , there was no evident defect in calcium metabolism , so no treatment was planned . in conclusion , after a clinical diagnosis of calcinosis cutis , a careful evaluation by history and laboratory workup should be performed to exclude possible associated abnormalities and correctly classify calcifying disorders . our patient was subject to regular follow - up for any new local or systemic symptoms . we did not encounter any new lesions , growth in the present lesions , or laboratory abnormalities at the 1 - year follow - up . excision of the lesion has been offered to the patient and could provide a successful resolution ; however , recurrence is possible . we confirm that the patient has provided written informed consent to use his photos for publications .\noutput:\n" }, { "from": "agent", "value": "calcinosis cutis is a rare disorder characterized by the deposition of calcium in the skin and subcutaneous tissue . unilateral idiopathic calcinosis cutis has only rarely been reported in the literature . here , we report the case of a 7 - year - old healthy girl who presented with multiple asymptomatic hard nodules on the right side of her body . histopathological , radiological , and extensive blood investigations confirmed the diagnosis of unilateral idiopathic calcinosis cutis ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: hybrid nanocomposites containing carbon nanotubes ( cnts ) have attracted much attention when each constituent component provides different functions for specific applications . although the properties of some cnt - containing nanocomposites have been investigated , the interface and transport issues in systems still remain a challenge , particularly in electrochemical ( ec ) systems . as shown from previous studies , cnts have great potential as electrode materials in direct methanol fuel cells ( dmfcs ) ; however , the surface of cnts is chemically inert and therefore the uniform dispersion of metal nanoparticles ( nps ) is impossible . it is necessary to modify the cnts prior to the support for capturing electrocatalysts such as pt - or pt - based nps . in general , the chemical modification is accomplished by acid oxidation using some oxygen - containing functional groups . recently , chemical doping of cnts is an attractive proposition for a wide range of potential applications . extrinsic doping of the tube surfaces can give rise to the formation of localized electronic states and makes the tubes chemical active ; hence , n - doped cnts are less stable than their pure carbon counterparts , breaking easily and oxidizing at lower temperature than undoped cnts due to the fact of nitrogen atoms as localized defects , which will be energetically less stable than a pure carbon lattice . their active surfaces mean they can be dispersed in a range of solvents not possible with undoped tubes . on the other hand , it is found that n - doped cnts only show the metallic behavior with a strong donor peak just above the fermi level , unlike undoped cnts which exhibit a variety of metallic and semiconducting behavior depending on their chirality . doping provides a way to activate regions along the tube wall and surface reactivity is increased . this opens up the possibility of doping techniques not available in traditional three - dimensional materials , notably chemical functionalization of tubes , tube coating with metal ions . accordingly , it suggests that the concept of n incorporation would be critical in chemical modifications of cnts . these properties possessed by n - doped cnts could render a new type of desirable catalyst support and electrode material in dmfcs . in this work , we have developed a simple chemical method to directly immobilize pt nps on n - doped cnts without any pre - surface modification . the electrocatalytic properties of pt - loaded n - doped cnts for methanol oxidation are examined and an obvious catalytic activity is obtained , indicating their potential ability in energy - generation applications . then , aligned cnts were grown on the pre - coated substrates by microwave plasma - enhanced chemical - vapor deposition ( mpecvd ) . the mpecvd growth was performed with microwave power at 2 kw ; ch4 , n2 , and h2 as source gases ; and the substrate temperature of 1000 c . to study n - doping effect , n2 gas was not fed into the chamber during cnts growth . for pt deposition , dc sputtering under ar gas flow was performed . for material analyses , a jeol 6700 field - emission scanning electron microscope ( fesem ) , a jeol jem - 2100f field - emission transmission electron microscope ( fetem ) , x - ray diffractometry ( xrd ) ( philips pw1700 ) , and x - ray photoelectron spectroscopy ( xps ) ( vg scientific escalab 250 ) were utilized . ec measurements were carried out using an autolab potentiostat system in a three - electrode set up using pt wire and reversible hydrogen electrode ( rhe ) as the counter and reference electrode , respectively . then , aligned cnts were grown on the pre - coated substrates by microwave plasma - enhanced chemical - vapor deposition ( mpecvd ) . the mpecvd growth was performed with microwave power at 2 kw ; ch4 , n2 , and h2 as source gases ; and the substrate temperature of 1000 c . to study n - doping effect , n2 gas was not fed into the chamber during cnts growth . for pt deposition , dc sputtering under ar gas flow was performed . for material analyses , a jeol 6700 field - emission scanning electron microscope ( fesem ) , a jeol jem - 2100f field - emission transmission electron microscope ( fetem ) , x - ray diffractometry ( xrd ) ( philips pw1700 ) , and x - ray photoelectron spectroscopy ( xps ) ( vg scientific escalab 250 ) were utilized . ec measurements were carried out using an autolab potentiostat system in a three - electrode set up using pt wire and reversible hydrogen electrode ( rhe ) as the counter and reference electrode , respectively . the xrd pattern of pt nps on n - doped and undoped cnts is shown in fig . it can be found that the peak ( 111 ) of pt nps on n - doped and undoped cnts is revealed . according to the debyescherrer equation , the grain size is inversely proportional to the full width at half maximum ( fwhm ) of diffraction peak in xrd pattern . therefore , the fwhm of n - doped cnts is broadened , which suggests that the grain size of pt nps on n - doped cnts is smaller than that on undoped ones . x - ray diffraction pattern of pt nanoparticles ( nps ) immobilized on n - doped carbon nanotubes ( cnts ) and undoped ones to understand the bonding of pt nps on n - doped and undoped cnts , the surface scan of xps spectrum is examined as shown in fig .2 . in the xps survey spectrum , four different bonding configurations of c 1s , pt 4d , and pt 4p in pt nps dispersed on n - doped and undoped cnts have been found . it shows that n bonding is present in pt nps dispersed on n - doped cnts , which suggests that n atom does incorporate with cnts and the relevant discussion would be performed in advance . surface scan of pt nps immobilized on n - doped cnts and undoped ones as seen in fig .3 a , 3c 1s xps spectrum of pt nps on n - doped and undoped cnts is measured . the binding energy of pt nps on n - doped and undoped cnts is 284.6 and 284.4 ev , respectively . from the report of matter et al . , the binding energy of c 1s xps spectrum for sp hybridization in pyridine ( c5h5n ) is located at 285.5 ev and it also appears in the nanostructured n - doped carbon [ 17 - 22 ] based on the above results , it is probably supposed that the c n bonding could be embedded within n - doped cnts . xps spectrum of pt nps immobilized on n - doped cnts and undoped ones however , pt 4f xps spectrum of pt nps on n - doped and undoped cnts looks the same , as depicted in fig . this means that no electron transfer of pt nps on n - doped cnts occurs ; accordingly , if the ec behavior of pt nps on n - doped cnts proceeds , the other possibility besides the electronic modification can be explained . to see the formation of n bonding , n 1s xps spectrum of pt nps on n - doped and undoped cntsit is found that the formation of n bonding is evident in pt nps deposited on n - doped cnts . in general , the n 1s xps spectrum can be deconvoluted with four n - based bonding configurations inclusive of pyridinic n ( 398.6 ev ) , pyrrolic n ( 400.5 ev ) , quaternary n ( 401.3 ev ) , and pyridinic no ( 402405 ev ) in n - doped cnts . among those n - induced bonding configurations , pyridinic and pyrrolicn are quite important in the enhancement of electrical properties of nts and dispersion of pt nps on n - doped cnts . figure 4 shows the cross - sectional fesem images of pt nps on n - doped and undoped cnts . it can be seen that both cnts look similar in terms of density or height . as shown in fig .4 a , pt nps are uniformly distributed on the sidewalls of n - doped cnts . by contrast , those pt nps agglomerate on the surface of undoped cnts in fig .4 b . from the sem images of pt nps on n - doped and undoped cnts , it can be seen that well - dispersed pt nps on cnts can be realized using n doping . cross - sectional scanning electron microscope images of pt nps immobilized on a n - doped cnts and b undoped ones to further see the deposition of pt nps on n - doped and undoped cnts , one - single n - doped and undoped cnt are shown in fig .5 a , the uniform dispersion of pt nps are immobilized on n - doped cnts due to the defects induced by n doping . on the contrary , if cnts do not contain n bonding , the interfacial energy of nts would be much higher . as a result , the degree of dispersion for pt nps on cnts is substantially reduced ; therefore , the pt nps will agglomerate as shown in fig . it provides the important information that pt nps are uniformly dispersed on the sidewalls of cnts incorporated with n. moreover , the particle - size distribution of pt nps dispersed on n - doped cnts is performed in fig .5 c . clearly , the particle diameter of pt nps ranges from 2 to 4.5 nm and the estimated average size is about 3.14 nm calculated from the depicted diagram , which infers that the ultrafine pt nps immobilized on cnts without any chemical modification can be achieved using n incorporation . transmission electron microscope ( tem ) images of pt nps immobilized on a n - doped cnts and b undoped . c the magnified tem image of ( a ) for ec activity characterization of pt nps on n - doped and undoped cnts , fig 6 exhibits the ec properties of pt nps on cnts under different conditions . it is examined at the scan rate of 50 mv / s in 1 m ch3oh and 0.5 m h2so4 . in fig .6 a , the cv diagram of pt nps dispersed on n - doped cnts shows the better performance compared with that of those nps on undoped ones .6 b also reveals that the onset potential of pt nps on n - doped cnts is lower than that of those nps on undoped ones . the weight of pt particles on undoped and n - doped cnts is estimated about 83 and 122 g / cm , respectively . from the resultant data , it is evident that the ec characteristics of pt nps on n - doped cnts are superior to that on undoped ones ; hence , the so - called n doping could efficiently promote the uniform dispersion of pt nps on cnts accompanied by the enhanced methanol - oxidation activity . a electrochemical activity of ptnps immobilized on n - doped cnts and undoped ones and bonset potential for methanol oxidation ec performance of pt particles immobilized on n - doped and undoped cnts from the above studies , n - incorporation effect has very important impact on the enhancement of ec properties for dmfc applications . the n - doping technique efficaciously immobilizes extrinsic electrocatalysts such as pt nps and put them regularly on the sidewalls of cnts as demonstrated from sem and tem images . to elaborate the mechanism ,7 a , the scheme shows that the n doping generates the two defects inclusive of pyrrolic and pyridinic n. pyrrolic n is on the surface of cnts and pyridinicin fact , pyrrolic n is highly correlated with dispersion degree of pt nps and ec activity performances . as shown in fig .7 b , if n atoms are not doped , the surface of cnts becoming quite stable and electrochemically inert give rise to the agglomerate formation of pt nps on cnts accompanied by inferior ec activity . however , the aggregate problem can be removed as n doping is fulfilled due to the hydrophilic interface generated by preferential defect sites in cnt surfaces . accordingly , it generates the high ec activity followed by the enhanced methanol oxidation property [ 23 - 27 ] . on the other hand , n - doped cnts show only the metallic behavior with a strong donor peak just above the fermi level , unlike undoped tubes which exhibit a variety of metallic and semiconducting behavior depending on their chirality . this is also helpful in the enhancement of energy - generation efficiency for dmfc applications . schematic diagram of a n - doping mechanism and b pt nps immobilized on n - doped cnts and undoped onesthe enhanced ec activity of pt nps immobilized on n - doped cnts directly grown on si substrate has been established . structural properties show the characteristic bonding peaks of n within cnts providing good support for uniform distribution of pt nps . in ec activity , n - doped cnts covered with pt nps show superior current density at the scan rate of 50 mv / s . this is due to the fact that the so - called n incorporation could be used to create preferential sites of cnts with low interfacial energy for grabbing pt nps . thus the substantially enhanced methanol oxidation activity produced by n - incorporation technique is very promising in energy - generation applications . the author is grateful for the support of the industrial technology research institute ( no .\noutput:\n" }, { "from": "agent", "value": "pt nanoparticles ( nps ) with the average size of 3.14 nm well dispersed on n - doped carbon nanotubes ( cnts ) without any pretreatment have been demonstrated . structural properties show the characteristic n bonding within cnts , which provide the good support for uniform distribution of pt nps . in electrochemical characteristics , n - doped cnts covered with pt nps show superior current density due to the fact that the so - called n incorporation could give rise to the formation of preferential sites within cnts accompanied by the low interfacial energy for immobilizing pt nps . therefore , the substantially enhanced methanol oxidation activity performed by n - incorporation technique is highly promising in energy - generation applications ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: world health organization ( who ) has reported that 5 % of males and 6 % of females of age 60 years or above are affected with alzheimer 's type dementia worldwide . oxidative stress has been a major cause of neurotoxicity in alzheimer 's disease and other neurodegenerative disorders . amyloid - ( a ) causes oxidative damage in brain which may lead to alzheimer 's disease . malva parviflora l. ( cheeseweed ) family malvaceae is a wonderful gift from nature for mankind . leaves are used in the management of wounds and swelling . a lotion made from the leavespharmacological studies show that malva parviflora possesses antibacterial , antidiabetic , antifungal , and other activities . based on the notion that antioxidant herbs and food are effective in the management of neurodegenerative diseases , we evaluated the neuroprotective effect of ethanol extract of the leaves of malva parviflora in this study . fresh leaves of malva parviflora l. were collected from khairpur , sindh , pakistan . a pharmacognosist of the department of pharmacognosy , federal urdu university , pakistan , authenticated the sample . voucher specimen ( rp / pharm / 1390 ) now , the powdered material was extracted using a percolator for 72 hours . in the subsequent step , the extract was filtered and made solvent - free using a rotary evaporator . in the final step , amyloid - protein fragment 2535 ( a4559 sigma ) and ethanol ( 46139 fluka ) were purchased from sigma - aldrich . swiss albino mice weighing between 25 and 30 g were used in this study . acute toxicity of ethanol extract of malva parviflora leaves was evaluated at a dose range of 2501000 mg / kg using litchfield and wilcoxon method . the dose of the extract was calculated according to the body weight of the mice . the extract was given at two different doses , namely , 250 mg / kg and 500 mg / kg . the dosing of the extract was done daily in normal doses according to the body weight of the animals . a total number of 40 healthy swiss albino mice weighing between 25 and 30 g were procured from the animal house of university of karachi , pakistan . six animals were kept per cage in polypropylene cages with a layer of sawdust litter under controlled conditions at room temperature 2530c , relative humidity 4555 % , and 12/12 hours light - dark cycle . the pellets and water were withdrawn six hours before the administration and during the experiments . the mice were divided into four groups , namely , group i : normal control , given normal saline 1 ml / kg ; group ii : alzheimer group , given amyloid - ( a ) protein 10 l / animal ; group iii : treatment group , given amyloid - ( a ) protein 10 l / animal and ethanol extract at the dose of 250 mg / kg ; group iv : treatment group , given amyloid - ( a ) protein 10 l / animal and ethanol extract at the dose of 500 mg / kg.the extract was administered to all animals by oral gavage once a day for 21 days prior to amyloid - protein injection and continued for a further 7 days . group i : normal control , given normal saline 1 ml / kg ; group ii : alzheimer group , given amyloid - ( a ) protein 10 l / animal ; group iii : treatment group , given amyloid - ( a ) protein 10 l / animal and ethanol extract at the dose of 250 mg / kg ; group iv : treatment group , given amyloid - ( a ) protein 10 l / animal and ethanol extract at the dose of 500 mg / kg . amyloid - ( 2535 ) protein mixed with normal saline and incubated for 4 days at 37c was given through intracerebroventricular ( icv ) injections to induce alzheimer 's disease in groups ii , iii , and iv on day 21 . in group i , control group , mice were given normal saline by intracerebroventricular injection route . a ( 2535 ) was administered at the bregma point with a 50 l hamilton microsyringe using a 26 - gauge needle that was inserted 2.4 mm deep . in other words , the needle was inserted unilaterally 1 mm to the right of the middle point equidistant from each eye slightly angled towards 45 perpendicular to the plane of the skull . mice showed normal behaviour within 1 min after injection and the injection volume was 10 l / mouse . for the assessment of the effect of the extract on memory of mice , morris water maze test was used . the scored parameters were escape latency ( el ) , the time taken by the animal to move from the starting quadrant to find the hidden platform in the target quadrant , and time spent in the target quadrant ( tstq ) . the mice were sacrificed by cervical dislocation on the 29th day of the study . biochemical assay was performed after washing the brains with ice - cold normal saline . at first , the tissues were homogenized in tris hcl and then centrifuged for 10 min at 10,000 g at 4c . for the assessment of neuroprotective activity of the extractcalorimetric techniques were used in the estimation of enzymes as per standard procedures for glutathione peroxidase ( gshx ) , glutathione reductase ( gshr ) , catalase ( cat ) , lipid peroxidation ( lpo ) , and superoxide dismutase ( sod ) . the data expressed are mean standard error of mean ( sem ) with 95 % confidence intervals ( ci ) . data were analysed by one - way anova followed by tukey 's post hoc test . all statistical analyses were carried out by using graph pad prism version 5.00 for windows , graph pad software , san diego , ca , usa . a probability level of 0.01 or less was accepted as significant . the results of the morris water maze test show that there was a significant increase in escape latency ( el ) of group ii ( alzheimer group ) mice when compared to group i ( normal control ) mice ( p 0.01 ) . however , the time taken by the mice to move from the starting quadrant to find the hidden platform in the target quadrant ( el ) was decreased significantly in group iii ( treatment group ; 250 mg / kg ) and group iv ( treatment group ; 500 mg / kg ) mice when compared to group ii ( alzheimer group ) mice ( p 0.01 ) figure 1 . in the morris water maze test , the results of time spent in the target quadrant ( tstq ) show that there was a significant decrease in time spent in the target quadrant ( tstq ) of group ii ( alzheimer group ) mice when compared to group i ( normal control ) mice ( p 0.01 ) . however , time spent in the target quadrant ( tstq ) was increased significantly in group iii ( treatment group ; 250 mg / kg ) and group iv ( treatment group ; 500 mg / kg ) mice when compared to group ii ( alzheimer group ) mice ( p 0.01 ) figure 2 . there was a significant reduction in the glutathione peroxidase , glutathione reductase , catalase , and sod levels of group ii ( alzheimer group ) mice when compared to group i ( normal control ) mice ( p 0.01 ) . the levels of aforesaid enzymes were increased significantly in group iii ( treatment group ; 250 mg / kg ) and group iv ( treatment group ; 500 mg / kg ) mice when compared to group ii ( alzheimer group ) mice ( p 0.01 ) . however , there was a significant increase in lipid peroxidase levels of group ii ( alzheimer group ) mice when compared to group i ( normal control ) mice ( p 0.01 ) . the levels of lipid peroxidase were decreased significantly in group iii ( treatment group ; 250 mg / kg ) and group iv ( treatment group ; 500 mg / kg ) mice when compared to group ii ( alzheimer group ) mice ( p 0.01 ) table 1 . in the present study , ethanol extract of the leaves of malva parviflora ( 250 and 500 mg / kg , p.o . ) has shown a significant neuroprotective effect in mice . to the best of our knowledge , the morris water maze model was used as a behavioural model to assess the effect of the extract on memory . the morris water maze model is widely used to assess the effects of drugs on learning and memory . in this model , a decrease in escape latency ( el ) and an increase in time spent in the target quadrant ( tstq ) indicate improvement of learning and memory . the extract of leaves of malva parviflora showed a significant decrease in el and a significant increase in tstq in a injected mice . the extract of malva parviflora leaves also showed positive effects on mouse brain . in our study , icv injection of a ( 2535 ) increased the levels of lipid peroxidation as indicated by increased levels of lipid peroxidase . increase in lipid peroxidase indicates the increased levels of reactive oxygen species ( ros ) because lipid peroxidation ( lpo ) is catalysed by ros . lpo may become very harmful due to the fact that a single - free radical can cause damage to a number of polyunsaturated fatty acid ( pufa ) molecules . oxidized polyunsaturated fatty acid ( pufa ) can produce more neurotoxic molecules such as malondialdehyde ( mda ) , 4 hydroxynonenal ( hne ) , and acrolein . the brain is specifically vulnerable to oxidative stress and lipid peroxidation . highly efficient mechanisms are needed to protect nerve cells because they have very restricted regeneration capacity . chain - braking antioxidants like vitamin e have the capability of terminating the lpo chain reaction . the results of our study show that after icv injection of a ( 2535 ) the activity of sod was decreased in brain which could be a result of inactivation of sod by h2o2 . this result intimated a compensatory response to oxidative stress due to an increase in the synthesis of endogenous h2o2 . therefore , the elevation in the level of sod in ethanol extract treated animals foretells that malva parviflora may possess free radical scavenging potential , which could be beneficial against the pathological alterations produced by the presence of o2 and oh . one of the most important antioxidants in mammalian cells is glutathione ( gsh ) . gsh - dependent detoxification involves glutathione peroxidase ( gshx ) , which has a pivotal role in the elimination of hydrogen and organic peroxides and leads to the formation of oxidized glutathione but is reduced back to its thiol form ( gsh ) by glutathione reductase ( gshr ) , leading to the consumption of nadph , which is chiefly formed by pentose phosphate pathway . gsh is involved in xenobiotic conjugation with the help of different glutathione s - transferase isoenzymes . the inhibition of gsh synthesis causes an increase in amyloid -- ( a - ) mediated cell death and intracellular a accumulation . various clinical trials have reported strong evidences that impairment in memory observed in rodents is linked with the altered levels of gsh in the brain and with the activities of antioxidant enzymes . elevation of brain oxidative status of amnesic rodents was similar as observed in the clinical pathology of alzheimer 's disease patients . amyloid -- ( a - ) mediated increase in lpo and decrease in glutathione ( gsh ) , a natural antioxidant , are one of the principal causes of neurodegeneration . in our study , amyloid - ( a ) administration caused a significant decrease in the activity of glutathione peroxidase ( gshx ) , glutathione reductase ( gshr ) , catalase , and superoxide dismutase ( sod ) in alzheimer group mice . the administration of ethanol extract of malva parviflora leaves restored the levels of aforesaid enzymes in a injected mice to similar levels as seen in normal control mice . the neuroprotective activity of malva parviflora can be attributed to the presence of flavonoids and polyphenolic compounds in the leaves of the plant . therefore , in future , we intend to conduct studies on isolated compounds of the leaves of this plant . the present study has shown significant neuroprotective effect of ethanol extract of the leaves of malva parviflora at 250 and 500 mg / kg doses in mice . to the best of our knowledge , this is the first study on the neuroprotective activity of the leaves of malva parviflora .\noutput:\n" }, { "from": "agent", "value": "malva parviflora l. possesses significant antioxidant potential . this study was conducted to evaluate the neuroprotective effect of ethanol extract of the leaves of malva parviflora against amyloid -- ( a - ) mediated alzheimer 's disease . in morris water maze model , the extract significantly restored the defected memory of amyloid - injected mice ( p < 0.01 ) . the reduced levels of brain antioxidant enzymes such as glutathione peroxidase , glutathione reductase , catalase , and superoxide dismutase were also restored significantly to similar levels as seen in normal control mice ( p < 0.01 ) . the levels of lipid peroxidase were decreased significantly in treatment group mice when compared to alzheimer group mice ( p < 0.01 ) . so , this study showed that ethanol extract of the leaves of malva parviflora possesses neuroprotective activity in mice ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: a systematic review of 56 population - based studies showed a decrease in the incidence rate of stroke in developed western countries , but not in developing countries1 . meanwhile , the disability caused by stroke has been on the rise . according to the disability - adjusted life years ( dalys ) reported by the global burden of disease study 2010 ( gbd 2010 ) , stroke is the third leading cause of dalys worldwide . in 1990 , it was the fifth leading cause , and similar rates were reported for the turkish population by the turkish ministry of health2 , 3 . stroke has been recognized as having significant deleterious outcomes , thereby limiting the patients quality of life4 ,5,6 . participation in rehabilitation programs following acute stroke has the greatest effect on reduction of disability7 . patient characteristics also have a critical effect on the efficacy of inpatient rehabilitation among stroke survivors8 . moreover , initiating post - stroke rehabilitation soon after the onset of an acute stroke appears to be the most important factor associated with early discharge from the hospital ; in addition , earlier admission is recognized as a relevant favorable prognostic factor9 , 10 . paolucci et al . reported that admission to inpatient rehabilitation in the first 20 days after stroke was associated with a better functional outcome11 . similarly , salter et al . reported that patients who underwent stroke rehabilitation within four weeks of stroke onset experienced greater functional gains and shorter lengths of hospital stay12 . accordingly , the american stroke association has recommended that in medically stable inpatients , rehabilitation can be initiated within two days following stroke onset4 , 5 . there is , however , no international consensus on the optimal timing for initiation of an inpatient rehabilitation program after discharge from an acute stroke care facility . in this context , defining the trends in admission timing to inpatient rehabilitation is essential for improving health outcomes . in particular , early admission to inpatient rehabilitation programs has not been identified among stroke survivors in turkey . the present study aimed to determine the timing of referral to inpatient rehabilitation among turkish stroke survivors and to identify factors affecting earlier admission . in this single - center retrospective study , medical and demographic data were tabulated for stroke survivors admitted to the ministry of health , ankara physical medicine and rehabilitation training and research hospital between january 2009 and december 2010 . located in turkey s capital , this institution is a center of excellence , as it is the largest inpatient rehabilitation hospital in turkey , where patients from all over the country are treated . only patients who have been previously diagnosed by a neurologist and whose findings have been confirmed by computed tomography or magnetic resonance imaging are admitted here for stroke rehabilitation . the present study enrolled stroke patients with relevant clinical identification codes from the international classification of diseases , 10th revision ( icd - 10 ) . stroke was defined as an acute cerebrovascular event associated with global or focal neurologic dysfunction lasting more than 24 hours13 . an experienced physical medicine and rehabilitation ( pmr ) specialist reviewed all clinical records and confirmed the icd - 10 coding . patients aged 35 years , who were admitted for the first time to a pmr program after stroke , were included in this study . patients who experienced stroke secondary to trauma , surgery , or malignancy were excluded from the study . the tabulated data included the following characteristics : patients demographic features , stroke date / time , type of stroke ( ischemic stroke , is ; or hemorrhagic stroke , hs ) , type of first acute stroke care center ( teaching hospital , university hospital , or training hospital ; or state hospital ) , presence of hypertension ( htn ; self - reported , antihypertensive use , or newly diagnosed at entry ) , diabetes mellitus ( dm ; self - reported , use of any hypoglycemic agents , or newly diagnosed at entry ) , coronary heart diseases ( chd ; self - reported or documented ) , carotid artery disease ( self - reported or documented ) , atrial fibrillation ( af ; self - reported or documented ) , hyperlipidemia ( hl ; self - reported , use of hypolipidemic medication , or newly diagnosed at entry ) and previous transient ischemic attack ( tia , self - reported or documented ) . detailed descriptions of current medications were obtained for all the enrollees . early onset of rehabilitation was defined as registering for an inpatient program within four weeks of experiencing an acute stroke12 . multiple morbidity was defined as presence of two or more accompanying diseases including htn , dm , chd , hl , af , and carotid artery disease . the spss version 20.0 ( spss inc . , chicago , il , usa ) software was used for the statistical analyses . student s t - test and mann - whitney test were used for inter - group comparisons . the results were expressed as mean standard deviation ( sd ) . the multiple binary logistic regression analyses were performed in the samples with information from the acute stroke care facility ( 77.6 percent of all samples ) . the dependent variable was earlier onset of the rehabilitation program ( coded as 1 = present , 0 = absent ) . dichotomous variables were used as independent variables . these included age ( 65 y vs. 65y ) , sex ( coded as 1 = male , 2 = female ) , etiology of stroke ( 1 = ischemic , 2 = hemorrhagic ) , type of acute stroke care center ( 0 = state hospital , 1 = teaching hospital ) , recurrent stroke ( 0 = non - recurrent , 1 = recurrent ) , bilateral hemiplegia ( 0 = no , 1 = yes ) , tia ( 0 = no , 1 = yes ) , htn ( 0 = no , 1 = yes ) , dm ( 0 = no , 1 = yes ) , chd ( 0 = no , 1 = yes ) , hl ( 0 = no , 1 = yes ) , af ( 0 = no , 1 = yes ) , carotid artery disease ( 0 = no , 1 = yes ) and multiple comorbid diseases ( 0 = no or one co - morbid disease , 1 = two or more comorbid diseases ) . two - tailed p values 0.05 were accepted as significant . in the present study , data from 1,002 patients diagnosed with stroke were screened , and 811 patients met the inclusion criteria . mean patient age was 69.0611.6 years , and 64.7 % of the patients were 65 years . slightly more female than male ( female , n = 433 ; male , n = 378 ) were included . in the study cohort , 88 % of the patients ( n = 714 ) were admitted to inpatient rehabilitation following their first stroke . is accounted for 83.2 % ( n = 673 ) of all confirmed stroke diagnoses . left - sided hemiplegia was diagnosed in 49.0 % of patients ( n = 397 ) , whereas bilateral hemiplegia was detected in 3.2 % ( n = 26 ) of the patients . table 1table 1 . characteristics of study participantsvariabletotal ( n = 811 ) male ( n = 378 ) female ( n = 433 ) age , mean ( sd ) , y69 .06 ( 11.6 ) 67.2 ( 11.8 ) 70.7 ( 11.2 ) *** young adult , n ( % ) 276 ( 34 ) 155 ( 41.0 ) 121 ( 27.9 ) *** elderly , n ( % ) 535 ( 66 ) 223 ( 59.0 ) 312 ( 71.2 ) *** stroke onset ( weeks ) , mean ( sd ) 9.8 ( 6.7 ) 9.5 ( 6.1 ) 10.1 ( 7.1 ) bilateral hemiplegic , n ( % ) 26 ( 3.2 ) 16 ( 4.3 ) 10 ( 2.3 ) ischemic stroke , n ( % ) 675 ( 83.2 ) 317 ( 83.9 ) 358 ( 82.7 ) recurrent stroke , n ( % ) 51 ( 12 ) 46 ( 13.6 ) 61 ( 10.6 ) tia , n ( % ) 49 ( 6.0 ) 23 ( 6.1 ) 26 ( 6.0 ) hypertension , n ( % ) 727 ( 89.6 ) 319 ( 84.4 ) 408 ( 92.2 ) *** coronary heart disease , n ( % ) 213 ( 26.3 ) 114 ( 30.2 ) 99 ( 22.9 ) * diabetes mellitus , n ( % ) 263 ( 32.4 ) 118 ( 31.2 ) 145 ( 33.5 ) atrial fibrillation , n ( % ) 176 ( 21.7 ) 66 ( 17.5 ) 110 ( 25.4 ) ** hyperlipidemia , n ( % ) 176 ( 21.7 ) 66 ( 17.5 ) 110 ( 25.4 ) ** carotid artery disease , n ( % ) 53 ( 6.5 ) 20 ( 5.3 ) 33 ( 7.6 ) comorbidities , n ( % ) 481 ( 59.3 ) 205 ( 54.2 ) 276 ( 63.7 ) * * * statistically significant at p 0.05 , * * statistically significant at p 0.01 , * * * statistically significant at p 0.001 mann - whitney test and test were used for other comparisons . the mean age among female was significantly higher than that among male ( 70.7211.19 vs. 67.1611.77 years , p 0.001 ) . females also had a higher incidence of htn ( 94.2 % vs. 84.4 % , p 0.001 ) , af ( 25.4 % vs. 17.5 % ; p = 0.006 ) and multiple morbidity ( 63.7 % vs. 54.2 % ; p = 0.008 ) than males , whereas chd was more frequent among men ( 30.2 % vs. 22.9 % ; p = 0.02 ) . no significant gender differences were observed regarding stroke recurrence , tia history , and the type of acute stroke care facility . * statistically significant at p 0.05 , * * statistically significant at p 0.01 , * * * statistically significant at p 0.001 mann - whitney test and test were used for other comparisons . sd : standard deviation , tia : transient ischemic attackthe duration between stroke onset and admission to a rehabilitation program is shown in table 2table 2 . comparison of stroke patients admitted to inpatient rehabilitation within 4 weeks of an acute stroke event ( early onset ) and those admitted later ( late onset ) variableearly onset ( n = 285 ) late onset ( n = 526 ) age , mean ( sd ) , y69 .59 ( 11.77 ) 68.77 ( 11.51 ) * young adult / elderly , % ( n ) 34.1 ( 94 ) / 35.7 ( 191 ) 65.9 ( 182 ) / 64.3 ( 344 ) male / female , % ( n ) 34.7 ( 131 ) / 35.6 ( 154 ) 65.3 ( 247 ) / 64.4 ( 279 ) bilateral / unilateral hemiplegia , % ( n ) 26.9 ( 7 ) / 35.8 ( 278 ) 73.1 ( 19 ) / 64.6 ( 507 ) ischemic / hemorrhagic , % ( n ) 37 ( 250 ) / 25.7 ( 35 ) 63 ( 425 ) / 74.3 ( 101 ) * recurrent / first stroke , % ( n ) 42.3 ( 41 ) / 34.2 ( 244 ) 57.7 ( 56 ) / 65.8 ( 470 ) teaching / state hospital , % ( n ) 40.0 ( 173 ) / 29.8 ( 67 ) 60 ( 259 ) / 70.2 ( 158 ) * transient ischemic attack , % ( n ) 30.6 ( 15 ) / 35.4 ( 270 ) 69.4 ( 34 ) / 64.6 ( 492 ) hypertension , % ( n ) 34.9 ( 254 ) / 36.9 ( 31 ) 65.1 ( 473 ) / 63.1 ( 53 ) coronary heart disease , n ( % ) 37.1 ( 79 ) / 34.4 ( 206 ) 62.9 ( 134 ) / 65.9 ( 392 ) diabetes mellitus , n ( % ) 36.5 ( 96 ) / 34.5 ( 189 ) 63.5 ( 167 ) / 65.5 ( 359 ) atrial fibrillation , n ( % ) 39.2 ( 69 ) / 34 ( 216 ) 60.8 ( 107 ) / 66 ( 419 ) hyperlipidemia , n ( % ) 39.6 ( 89 ) / 33.4 ( 196 ) 60.4 ( 136 ) / 66.6 ( 390 ) carotid artery disease , n ( % ) 37.7 ( 20 ) / 35 ( 265 ) 62.3 ( 33 ) / 65 ( 493 ) comorbidities , n ( % ) 36.4 ( 175 ) / 33.3 ( 110 ) 63.6 ( 306 ) / 66.7 ( 220 ) * statistically significant at p 0.05 , student s t - test and test were used for other comparisons.analysis were performed among 77.6 percent of all samples with acute stroke care center data . n : number , ns : not significant , sd : standard deviation , tia : transient ischemic attack . please see materials and methods for detailed definitions of comorbidities . . in the entire cohort , the duration between stroke onset and inpatient rehabilitation was 9.826.66 weeks ; it was 9.596.52 weeks in the is subgroup and 117.22 weeks in the hs subgroup ( p = 0.018 ) . rehabilitation was initiated 9.066.11 weeks following stroke at teaching hospitals and after 10.807.19 weeks at state hospitals ( p = 0.02 ) . similarly , attending a rehabilitation program in the first four weeks following stroke was significantly higher among patients who received acute stroke care at teaching hospitals vs. other hospitals ( 40.0 % vs. 29.8 % , p = 0.01 ) and among patients with is vs. hs ( 37 % vs. 25.7 % , p = 0.07 ) . the time period after stroke until admission to a rehabilitation program was not associated with multiple morbidities . * statistically significant at p 0.05 , student s t - test and test were used for other comparisons . analysis were performed among 77.6 percent of all samples with acute stroke care center data . n : number , ns : not significant , sd : standard deviation , tia : transient ischemic attack . multiple logistic regressions were performed with early start of rehabilitation ( 4 weeks ) as the dependent variable and age , etiology of stroke , type of acute stroke care center , recurrent stroke , bilateral hemiplegia , tia , htn , dm , chd , hl , af , carotid artery diseases , and multiple morbidity as the independent variables . as shown in table3table 3 . binary logistic regression analysis for the determinants of early onset of rehabilitation in stroke survivorsindependent variabledependent variable : early onset of rehabilitationor95 % ciage1 .0910.7571.572 gender1 .0030.7151.406 etiology of stroke0 .5790.3520.952 * acute stroke care center1 .5951.1212.271 *** recurrent stroke1 .5050.9132.482 bilateral hemiplegia0 .8570.3863.146 transient ischemic attack0 .6630.3281.341 hypertension1 .1710.6242.2 diabetes mellitus1 .1060.6951.761 coronary heart disease0 .7280.4921.077 hyperlipidemia1 .5531.0022.406 * carotid artery disease1 .1610.5982.254 atrial fibrillation1 .1860.7111.977 multiple comorbid disease0 .7570.4141.386 * statistically significant at p 0.05 , * * * statistically significant at p 0.001 , presence of is , no evidence of dyslipidemia , and admission to a teaching hospital for acute stroke treatment were significantly associated with early admission to an inpatient pmr program . * statistically significant at p 0.05 , * * * statistically significant at p 0.001 to the best of our knowledge , the present study is the first to evaluate the timing of admission to inpatient rehabilitation programs among turkish stroke survivors and to evaluate the conditions affecting early admission . in addition , the study reports the health characteristics of stroke patients , using a considerably large sample and based on well - organized records . we found that a majority of turkish stroke survivors began inpatient stroke rehabilitation after a significant delay following the onset . compared to the results of the present study , inpatient stroke rehabilitation began 13 days post - stroke in england ( uk ) , 22 days post - stroke in belgium , 19 days post - stroke in switzerland , 16 days post - stroke in germany , and 10.6 days post - stroke in the united states of america14 , 15 . sakurai et al . showed that the duration from stroke to the onset of inpatient rehabilitation in japan was approximately 30 days ; however , their results do not present the primary or secondary ends of the study , and their results may not represent the actual trend in inpatient rehabilitation admissions in japan16 . the putman et al . study reviewed six european stroke rehabilitation units in four european countries ( uk , belgium , germany , and switzerland ) , and granger et al . used a uniform data system for medical rehabilitation in the usa between 2000 and 2007 ; therefore , these results may better represent admission trends in the above - mentioned nations . our study sample size of 811 patients was larger than that of putman et al. s study , which was approximately 500 patients . the results of the present study also showed that patients who underwent acute stroke treatment in a teaching hospital were more likely to be admitted to an inpatient rehabilitation program within four weeks of a stroke event , while hs patients were more likely to be admitted later . later admission trends found among hs patients in the present study were consistent with trends reported in most but not all earlier studies11 , 17,18,19 . the observational designs of these earlier studies on hs patients were limited to factors that may have led to later inpatient rehabilitation admission . it is generally believed that hs patients have better neurological and functional prognoses than non - hs survivors20 . therefore , later admission to inpatient rehabilitation programs may be related with better neurological and functional prognoses among hs patients . an earlier study conducted in four european countries concluded that older age and presence of comorbid diseases were important criteria for referring stroke patients to a rehabilitation program in belgium but not in england , germany , or switzerland14 . granger et al . did not analyze the factors related to earlier admission . in the present studythis may be because of a relatively younger population and other health - related characteristics in our turkish sample . further studies should be conducted to identify the effects of age and comorbid disease on earlier admission of patients to inpatient stroke rehabilitation . women stroke survivors in the present study were nearly four years older than the men a result consistent with previous studies , which showed that stroke occurs in men at an earlier age21 . htn and af were more prevalent in women , whereas chd was predominant in men , which is similar to the findings of other studies21 , 22 . although the frequency of htn in the patients of the present study was consistent with a previous report23 , it was higher than the findings in many earlier studies21 , 22 . one of the causes of this discrepancy could be an already higher prevalence of htn in the turkish population . one study demonstrated that the prevalence of htn among elderly turkish individuals is approximately 6080 % 24 . moreover , optimum blood pressure ( bp ) rates in turkey were found in as little as 8.1 % of the population . data from the national health and nutrition examination survey ( nhanes ) 20072008 cohort revealed that bp is controlled in an estimated 50.1 % of all patients with htn25 . according to the bp control rate and cardiovascular risk profile ( bp - care ) study , bp control rates in eastern europe vary between 16 % and 51 % ( average , 27.1 % ) 26 . first , although our hospital is the biggest national inpatient rehabilitation hospital in turkey and admits patients from all over the country , our sample can not be considered as representative of the population of turkish stroke survivors . second , the study may not represent all patients with stroke admitted to our hospital , because the number of patients enrolled was dependent on the quality of icd - 10 coding in our hospital dataset . third , we lacked detailed information on whether the stroke patients enrolled in our study had not been referred to inpatient rehabilitation following acute stroke treatment earlier than when they actually began rehabilitation or whether the patients refused to be admitted to the inpatient rehabilitation program at an earlier time even if they were referred from an acute stroke treatment facility . fourth , we did not evaluate admission trends among stroke survivors . in conclusion , the present study confirms that turkish stroke survivors begin inpatient rehabilitation program later than patients in other countries . patients diagnosed with hs are unlikely to be admitted early to inpatient rehabilitation programs , whereas undergoing acute stroke care in a teaching hospital is positively associated with early referral to post - stroke inpatient rehabilitation .\noutput:\n" }, { "from": "agent", "value": "[ purpose ] early admission to inpatient rehabilitation is critical for reducing post - stroke disability . assessing admission timing and other trends in inpatient rehabilitation are essential for improving health outcomes . this study is the first to evaluate the timing of admission of stroke patients to inpatient rehabilitation in turkey . [ subjects and methods ] we retrospectively analyzed acute stroke survivors who were admitted to the inpatient rehabilitation program in the ministry of health , ankara physical medicine and rehabilitation training and research hospital between january 2009 and december 2010 . [ results ] the mean onset of inpatient rehabilitation was 9.8 6.7 weeks post - stroke in the entire cohort . occurrence of ischemic stroke and undergoing acute stroke care at a teaching hospital were most strongly associated with early admission . these results did not change after multivariate analysis . [ conclusion ] turkish stroke survivors begin inpatient rehabilitation later than patients in other countries . the type of stroke and type of hospital in which the patient undergoes acute stroke treatment affects early admission ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: periodontal diseases are a heterogeneous group of inflammatory conditions that involve the supporting tissues of the teeth and include gingivitis , in which only the gingivae are involved , and the various forms of periodontitis , chronic inflammatory conditions initiated by a polymicrobial infection that leads to gingival tissue destruction and alveolar bone resorption . gingivitis is the most prevalent form of periodontal disease that can be defined as a nonspecific inflammatory process of the gingivae ( gums ) without destruction of the supporting tissuesthis is a reversible condition as a return to meticulous dental hygiene practices will restore gingival health . several bacterial species have been implicated as aetiological agents of this disease : these include actinomyces israelii , actinomyces naeslundii , actinomyces odontolyticus , lactobacillus spp . , prevotella intermedia , treponema spp . , and fusobacterium nucleatum . bacteria and their products can directly damage periodontal tissues and / or initiate inflammation locally . the clinical outcomes of these events are determined by the host response to the infections . different experimental systems can be utilized to evaluate cellular responses to different bacteria or antibacterial agents , from fibroblasts derived from human periodontal ligaments to epithelial cells and fibroblasts derived from human gingivae . foodstuffs as a source to obtain agents / fractions that can improve oral health have been the focus of intensive research because such natural agents are likely to be nontoxic and edible ; for example , they can be used to supplement various oral hygiene products . in studies described elsewhere in this issue , it has been shown that low molecular mass ( lmm ) fractions obtained from extracts of raspberry , chicory , and mushrooms inhibit coaggregation , biofilm formation , and adhesion to hydroxyapatite and / or cultured gingival cells of oral bacteria involved in caries and / or gingivitis . to further evaluate the beneficiary effect on oral health of these dietary fractions , the present study was designed to determine the effect of the raspberry , chicory , and mushroom lmm fractions on the ability of gingivitis - associated bacteria to induce deleterious gene expression in the gingival kb cell line . bacteria were grown in brain heart infusion broth ( bhib , difco laboratories , detroit , mich . ) supplemented with haemin ( final concentration , 5 mg ml ) and vitamin k ( final concentration , 1 mg ml ) and incubated at 37c under anaerobic conditions . cells were harvested at stationary phase by centrifugation ( 5,000 g for 10 min at 4c ) and washed twice with 10 mm phosphate buffered saline , ph 7.0 . bacterial suspensions ( final concentration , 2510 cfu ml ) were prepared in pbs ( 0.1 m na2hpo4 , 0.1 m kh2po4 , 0.15 m nacl , ph 7.2 to 7.4 ) alone or suspensions containing different concentrations of test lmm fractions ( ph adjusted to 7 ) . aliquots ( 10100 l ) of the bacterial suspensions were suitably added to kb cell monolayers in order to reach a nominal bacteria : kb cell ratio of 50 and incubated at 37c for different periods of time in 5 % co2 atmosphere with gentle shaking . for each strain , untreated controls were included . in experiments with killed bacteria , bacteria were heat inactivated at 70c for 15 min , centrifuged at 10,000 g , and washed twice in pbs , before being adjusted to the appropriate density in the same buffer . briefly , aliquots of frozen mushroom ( lentinus edodes ) ( 400 g ) and fresh chicory ( cichorium intybus var . silvestre ) ( 500 g ) and fresh raspberry fruit ( rubus idaeus l. var . tulameen ) ( 200 g ) were homogenized and centrifuged ( 10 min , 8000 rpm ) . the juice , after separation from the solid part , was filtered on paper filter . mushroom and chicory extracts were then fractionated into low and high molecular weight ( lmm and hmm ) fractions using an ultradiafiltration system . the obtained lmm and hmm fractions contained all the compounds with molecular mass lower and higher than 5000 da , respectively . raspberry extract was fractionated by dialysis with cellulose ester membrane ( spectrum europe b.v . ) with a 3500 da mwco . the obtained lmm and hmm fractions contained all the compounds with molecular mass lower and higher than 3500 da , respectively . the gingival fibroblast kb cell line ( accession number iclc htl96014 ) obtained from cell bank interlab cell line collection ( iclc ) of ist - istituto dei tumori di genova ( genoa , italy ) was cultured in a complete medium consisting of dulbecco 's modified eagle 's medium ( dmem ) - high glucose , with 4.5 g l glucose and sodium bicarbonate supplemented with 10 % fetal calf serum , penicillin ( 100 u ml ) , streptomycin ( 100 g ml ) , and 2 mm l - glutamine . cells were incubated at 37c in a 5 % co2 atmosphere to about 90 % confluence and used after 510 passages . for mtt assay , cells were seeded in flat - bottom 96 - well plates , at a density of 210 cells per well , in 0.2 ml of complete medium without antibiotics in triplicate and incubated for 24 h at 37c . for rt - q - pcr analysis cellswere plated ( 310 cells ) in to 25 cm flasks in 5 ml of complete medium and incubated for 48 hrs at 37c . after 24 hrs of starvation in dmem without serum , cell monolayers were washed twice with pbs and then exposed to bacterial suspensions alone or suspensions containing lmm test fractions at the indicated concentrations . after each treatment mtt [ 3 - ( 4,5 - dimethyl -2-thiazolyl ) -2,5-diphenyl tetrazolium bromide ) ] solution in phosphate buffered saline ( pbs , ph 7.4 ) ( final concentration of 1 mg / ml ) was added to each well and incubated for 3 h at 37c . following incubation , 100 l of 0.04 n hcl isopropanol was added to each sample and the plates incubated for 10 minutes at room temperature . the absorbance at 550 nm was determined by a varian cary 50 - bio uv - visible spectrophotometer . the bacteria - induced changes in mrna expression of keratinocyte growth factor receptor ( kfgr ) , cytokeratin 18 ( ck18 ) , 4 integrin ( b4itg ) , and defensin 2 ( hd2 ) were evaluated by quantitative rt - pcr analysis . after harvesting , total cellular rna was isolated by the procedure of chomczynski and sacchi using tri - reagent ( sigma , milan , italy ) . rna purity was evaluated by measuring the 260/280 nm absorbance ratio , and only samples with od260 / 2801.8 were processed , resolved on a 1.5 % agarose gel , and stained with ethidium bromide , to check for purity . cdna synthesis was performed from 1.5 g of total dnasei ( fermentas , m - medical , italy ) treated rna using 200 units revertaid h minus m - mulv reverse transcriptase ( fermentas italy , m - medical , milan ) in presence of 201 pmoles oligo ( dt ) 18 ( tib molbiol , genova , italy ) , 40 units ribolock ( ribonuclease inhibitor ) , and 1 mm dntps ( fermentas italy , m - medical , milan ) at 42c for 60 min in a reaction volume of 20 l according to the manufacturer 's protocol .5 l of cdna was then used to amplify the genes of interest using a chromo 4 system real - time pcr apparatus ( biorad italy , segrate , milan ) in a final volume of 20 l containing 1x itaq sybr green supermix with rox ( biorad , milan , italy ) and 0.25 m of each primer ( tib molbiol , genoa , italy ) . the primer pairs were used , and their accession numbers are shown in table 1 . the primers for kfgr , ck18 , hd2 , and gapdh were designed with the primer3 ( v. 0.4.0 ) software , those for b4itg were from wang et al . . the thermal protocol consisted of 3 min initial denaturation at 95c , followed by 40 cycles : 15 s at 95c ; 30a melting curve of pcr products 5594c ) was also performed to ensure the absence of artefacts . gene expression was determined relative to the expression of the gene glyceraldehyde 3 - phosphate dehydrogenase ( gapdh ) by the comparative ct threshold method using the biorad software tool genex - gene expression macro . the normalized expression obtained was expressed as relative quantity of mrna with respect to control samples . data representing the mean sd of at least 4 experiments in triplicate were analysed by the mann - whitney u test ( p 0.05 ) . the effects of the gingivitis - associated p. intermedia and a. naeslundii and lmm fractions ( raspberry , chicory , mushroom ) alone on kb cell viability were first evaluated by the mtt assay . lmms were tested at different concentrations ( 0.2 x , 0.5 x , 1x ) and times of incubation with monolayers ( 4 and 6 h ) . the viability of kb cells treated with live bacteria alone ( at the nominal bacteria : kb cell ratio of 50 ) was not affected at 4 h ; the number of viable bacteria remained the same during the assay as evaluated by cfu counting . kb cell incubation for longer than 4 h or in the presence of 0.5 x and 1x concentrations of lmm fractions alone decreased by 2030 % ( data not shown ) . therefore , all subsequent experiments with live bacteria were performed by treating kb cells for 4 h with bacteria and 0.2 x lmm fractions , both alone and in combination . in these conditions , the effects of kb cell treatment for 4 h with p. intermedia and a. naeslundii and lmm fractions , alone and in combination , on the expression of different genes ( kgfr , ck18 , 4int and hd2 ) were evaluated . no appreciable changes could be detected in the expression of kgfr by kb cells in response to different treatments ( not shown ) . in contrast , p. intermedia and a. naeslundii alone decreased significantly the transcription of ck18 by 40 % and 18 % , respectively ( p 0.05 ) ( figure 2 ( a ) ) . no significant changes in ck 18 expression were noted in kb cells exposed to lmm fractions . nevertheless , raspberry and chicory lmm fractions prevented the downregulation of ck18 induced by both bacteria , whereas the lmm mushroom fraction did not . all bacteria and lmm fractions , when tested alone , induced a decrease in transcription of 4itg with respect to controls ( figure 2 ( b ) ) . the effect was significant for all treatments , with decreases in 4itg mrna level ranging from about 60 % ( p. intermedia ) to 40 % ( mushroom fraction ) ( p 0.05 ) . however , when kb cells were exposed to a mixture of bacteria and lmm fractions , raspberry , the decrease in 4itg expression was attenuated ; moreover , mushroom lmm fraction prevented the effect induced by a. naeslundii . the same experiments as above were carried out with heat - killed p. intermedia and a. naeslundii alone and in combination with lmm extracts . longer times of incubation and lower concentrations of lmm extracts ( 0.1 x ) were tested : however , from 8 to 20 hr incubation , decreases in cell viability were observed in different experimental conditions with both bacteria and test substances , with raspberry lmm extracts in particular . at 6 hr , stable cell viability was observed in all experimental conditions , and therefore this time of exposure was chosen for subsequent experiments ; however , since raspberry lmm still induced significant loss in cell viability , it was no longer utilized for subsequent experiments . in figure 3 , data on viability of kb cells exposed for 6 h to p. intermedia and a. naeslundii , alone and in combination with chicory and mushroom lmm fractions , are reported . possible changes in gene expression induced by kb cell exposure for 6 h to inactivated bacteria and lmm fractions , alone and in combination , were evaluated , and the results are reported in figure 4 . on the other hand , in these experimental conditions , chicory fraction caused a significant decrease ( 27 % ) and shiitake mushroom fraction an increase ( + 43 % ) in ck18 expression ( p 0.05 ) ( figure 4 ( a ) ) . in cells incubated with bacteria and lmm fractions , upregulations of ck18were observed : in the presence of p. intermedia , both chicory and mushroom fractions induced an increase in ck18 mrna levels with respect to control cells ( + 58 % and + 133 % , resp . ;p 0.05 ) ; a larger increase was observed in the presence of a. naeslundii which was induced by both chicory and mushroom ( + 269 % and + 247 % , resp . changes in 4itg expression were observed with heat - killed bacteria alone , with p. intermedia inducing an increase ( + 119 % ; p 0.05 ) , and a. naeslundii a decrease ( 30 % ; p 0.05 ) in the level of 4itg mrna ( figure 4 ( b ) ) . both chicory and mushroom lmmfractions alone caused a decrease in 4itg expression ( 39 % and 54 % , resp . ; however , both fractions prevented the upregulation of 4itg induced by p. intermedia and the downregulation of 4itg induced by a. naeslundii . in these experimental conditions , changes in expression of the defensin gene hd2p . intermedia alone induced a 2-fold increase in the level of hd2 mrna ; however , the effect was not significant due to large sample variability . in contrast , a. naeslundii alone induced a decrease in transcription of hd2 ( 52 % with respect to controls ; p 0.05 ) . even larger decreases were observed with chicory and shiitake mushroom lmm fractions alone ( 80 % and 70 % ; p 0.05 ) . when tested in combination with p. intermedia , both fractions prevented the increase in hd2 expression induced by bacteria . moreover , chicory fractions prevented the decrease in hd2 expression induced by a. naeslundii , whereas mushroom was ineffective . in this work , the effects of different fruit and vegetable lmm fractions , alone or in combination with the gingivitis - associated bacteria p. intermedia and a. naeslundii , on cell viability and gene expression by human kb gingival cells were evaluated . in preliminary experiments , different concentrations of lmm fractions and times of exposure with bacteria and fractions were tested ; however , since loss in cell viability was observed in different experimental conditions , assays with live bacteria were carried out at 4 h of exposure and at a concentration of lmm fractions of 0.2 x , whereas assays with heat - killed bacteria were carried out for longer times ( 6 h ) in the presence of lower concentrations of lmm fractions ( 0.1 x ) . in these conditions , no effects on cell viability were observed , as evaluated by the mtt assays , that measures the number of live and metabolically active cells . the possible effects of bacteria and lmm fractions , alone and in combination , on the expression of selected genes associated with cell differentiation , proliferation , and adhesion , and the production of antimicrobial peptides were evaluated . significant changes in expression of cyt18 , 4itg , and hd2 were observed in different experimental conditions . when expression of other genes such as kgfr ( keratinocyte growth factor receptor ) , 1 integrin , or 3 defensin ( hd3 ) was evaluated , no changes were induced by different bacteria and lmm fractions , alone and in combination ( data not shown ) . the lack of effect could be probably due to the short duration of the experiments ( 46 h ) that did not allow appreciable changes in the level of mrnas for these genes to be observed . cytokeratins belong to intermediate filament proteins and are characterized by remarkable biochemical diversity , represented in epithelial tissues by at least 20 different polypeptides . their expression varies with proliferation , differentiation , and the states of cell development and transformation ; cyt 18 in particular has been utilized as a marker for healthy gingival cells in culture . cytokeratins are connected through transmembrane cell - matrix junctional complexes , the hemidesmosomes , to the ecm . integrins , a component of hemidesmosomes , are heterodimeric transmembrane glycoproteins formed by the noncovalent association of and subunits .1 and 4 ( 4itg ) are also involved in apical migration of junctional epithelium during the periodontal attachment loss .4 itg is expressed in the basal side of cells cultured from rat oral epithelium . distinct changes in gene expression were observed in response to live and heat - killed bacteria , alone and in combination with lmm fractions . at 4 h incubation with live bacteria and fractions , when no changes in cell viability were observed , only changes in cyt18 e 4int could be detected in different experimental conditions . the effect was reduced by both raspberry and chicory lmm fractions , whereas mushroom was ineffective . interestingly , the effect of p. intermedia was prevented by raspberry fractions and that of a. naeslundii by raspberry and mushroom , whereas chicory was ineffective . this indicates that simultaneous exposure to bacteria and lmm fractions in certain combinations has a synergistic protective effect on the expression of 4int . overall , these data indicate a protective effect of lmm fractions ( raspberry chicory mushroom ) on the decrease in the expression of genes involved in gingival cell proliferation and differentiation , as well as in cell attachment and signalling , induced by live p. intermedia and a. naeslundii . distinct effects were observed in experiments carried out with heat - killed bacteria at longer times of incubation and lower concentrations of lmm chicory and mushroom fractions . heat - killed bacteria alone did not affect cyt18 expression at 6 h incubation , whereas small decreases and increases were observed with chicory and mushroom fractions , respectively . interestingly , combined exposure to bacteria and lmm fractions induced small upregulation of cyt18 expression . this synergistic action indicates a beneficial effect of chicory and mushroom fractions on cells exposed to heat killed bacteria . p. intermedia alone induced an increase in expression of 4int , whereas all the other individual treatments resulted in downregulation . moreover , combined exposure to a. naeslundii and lmm fractions abolished the downregulation induced by individual treatments , again indicating a synergistic effect between lmm fractions and heat - killed bacteria . in these experimental conditions , changes in expression of the antimicrobial peptide hd2antimicrobial peptides ( amps ) are components of the host innate immune defence system , exerting broad - spectrum antimicrobial activity via the binding and perforation of cell membranes , as well as exerting neutralising effects on the lps activity of gram negative bacteria , including periodontopathogens such as p. intermedia . human - defensins are small , cationic amps : - defensin 1 ( hd1 ) is expressed constitutively in epithelial tissues , whereas hd2 and hd3 are expressed in response to bacterial stimuli or inflammation . defensins , including hd2 , may also participate in epithelial differentiation and tissue damage repair in periodontal disease and contribute to the host defense by recruiting neutrophils to the site of inflammation and modulate the expression of cytokines , thus playing an important role in the control of oral health . gingival epithelial cells and tissue express hd2 mrna and peptide in response to inflammatory mediators and challenge from commensal bacteria naturally present in the oral cavity . in gingivalepithelial cells , hd2 mrna was induced in response to the supernatant from porphyromonas gingivalis , and this expression might be associated with periodontal health and disease . cell wall components of periodontal pathogens induce hd2 expression through activation map kinases ; such effect can be mediated by activation of fibronectin - integrin components . the results here obtained with heat - killed p. intermedia and a. naeslundii and with chicory and mushroom lmm fractions show that individual treatments induced changes in the level of hd2 mrna similar to those observed for that 4int , with upregulation by p. intermedia and downregulation by a. naeslundii and lmm fractions . both chicory and mushroom prevented the upregulation of hd2 induced by p. intermedia and combined exposure to a. naeslundii and lmm fractions abolished the downregulation induced by individual treatments . again , the results indicate a comparable effect of chicory and mushroom lmm fractions on the overall changes in gene expression induced by heat - killed gingivitis - associated bacteria . on the basis of the results of various assays , reported elsewhere in this issue , raspberry , chicory , and mushroom lmm fractions were chosen as the most active test materials towards the gingivitis - associated species p. intermedia and a. naeslundii . with respect to studies of coaggregation , biofilm formation , and adhesion to hydroxyapatite and cultured gingival cells , in this work lmm fractions were utilised at lower concentrations and longer times of exposure in order to maintain cell viability and allow for detection in changes in mrna transcription , respectively . our data indicate that both chicory and mushroom lmm fractions , at concentrations that do not affect viability of kb gingival cells , can modulate the expression of different genes induced by both live and heat - killed p. intermedia and a. naeslundii . this supports the hypothesis that chicory and mushroom lmm fractions can modulate the responses of gingival cells to periodontopathogens and can be used as source for obtaining agents to be included in toothpaste , mouthwashes , and other oral health care products .\noutput:\n" }, { "from": "agent", "value": "low molecular mass ( lmm ) fractions obtained from extracts of raspberry , red chicory , and shiitake mushrooms have been shown to be an useful source of specific antibacterial , antiadhesion / coaggregation , and antibiofilm agent ( s ) that might be used for protection towards caries and gingivitis . in this paper , the effects of such lmm fractions on human gingival kb cells exposed to the periodontal pathogens prevotella intermedia and actinomyces naeslundii were evaluated . expression of cytokeratin 18 ( ck18 ) and 4 integrin ( 4int ) genes , that are involved in cell proliferation / differentiation and adhesion , and of the antimicrobial peptide 2 defensin ( hd2 ) in kb cells was increased upon exposure to either live or heat - killed bacteria . all lmm fractions tested prevented or reduced the induction of gene expression by p. intermedia and a. naeslundii depending on the experimental conditions . overall , the results suggested that lmm fractions could modulate the effects of bacteria associated with periodontal disease in gingival cells ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: vanadium is actually known as a trace element , essential for higher organisms although deficiency symptoms in humans have not yet been clearly identified ( guevara 1996 ) . trapping free oxygen radicals that might cause cardiac problems , it acts as a biological antioxidant and shows antitumoral activity ( scior et al 2005 ) . bis - maltolato - oxovanadium ( iv ) ( bmov ) is under investigation in other pathological processes induced by uric acid , such as vascular endothelial dysfunction ( jindal et al 2007 ) . the development of innovative vanadium compounds against diabetes mellitus ( dm ) has attracted much pharmaceutical interest during the last decades ( saatchi et al 2005 ) . in the light of desired clinical advantages of a novel orally administered drug with selective insulin - like effects , a considerable impact on the patients health , their insulin injection - related long - term complications , or reduced side effects compared to other oral antidiabetics , can be expected ( zhang et al 2008 ) . besides our review with critical details on the protein tyrosine phosphatase ( ptpase ) inhibition , the pharmacodynamical behavior of organic vanadium compounds , their complex stabilities and inconclusive role as prodrugs for simpler inorganic vanadium ions in combination with toxicity data , it is noteworthy here to add newer reports on pharmacological findings ( scior et al 2005 ) . in 2007the action mechanism on a molecular level was studied in bmov - treated cell cultures . it was confirmed that bmov enhanced the tyrosine - phosphorylation of upstream insulin - signaling proteins including the insulin receptor ( bose et al 2007 ) . heinemann and colleagues ( 2003 ) examined the pharmacokinetics of insulin mimetic inorganic vanadium ions : mainly vanadate ( + v , 80 % ) and other oxidation states . their study in healthy humans after administration of a single intravenous dose revealed that the apparent volume of distribution was of the order of 0.6 l / kg . it is responsible for the typical heavy metal accumulation of vanadium in tissues such as liver , kidneys , bone , and spleen ( heinemann et al 2003 ) . most recently , another pharmacokinetics study in rats evaluated positively the therapeutical potential of bmov as an oral glucose - lowering drug candidate . bmov was rapidly absorbed , widely distributed in various tissues but only slowly eliminated from plasma due to accumulation to a greater extent in bone tissue . significant decrease of glucose concentrations in plasma was observed in hyperglycemic diabetic rats ( zhang et al 2008 ) . among the protein - tyrosine phosphatases , ptp1b has received much attention due to its role as a negative regulator of insulin signaling ( elchebly 1999 ; cheng et al 2002 ) . on one side the protein tyrosine phosphatase - 1b ( ptp - 1b ) is highly expressed in insulin - resistant persons . the absence of ptp - 1b in genetically modified mice , on the other side , immunizes them against obesity and diabetes , even with rich and fatty diets . clearly , a selective control of the biological function of ptp1b is a challenging task , and an inhibitor must not only efficiently bind to the specific target enzyme but also do so without impeding the catalytic behavior of closely related enzymes . in figure 4 of our reviewwe have already reported on the alignment studies to elucidate the regiospecificity of ptp1b ( scior et al 2005 ) . the design of small molecule ptp1b inhibitors to treat type ii diabetes has received considerable attention ( groves et al 1998 ; wang et al 2000 ; shen et al 2001 ; doman et al 2002 ; patankar and jurs 2003 ; sun et al 2003 ; szczepankiewicz et al 2003 ) . vanadium compounds have been known to mimic the effects of insulin by inhibition of tyrosine phosphatases . based on such observations that vanadate ( oxo complexes of vanadium with oxidation state + v ) electronically and structurally imitates phosphate , and phosphorylated proteins constitute the substrates of ptp - 1b , vanadium - coordinated compounds should be capable of blocking ptp - 1b upon competitive replacement of the natural substrates . this is one of the possible hypotheses of the reaction mechanisms for vanadium compounds with insulin - like activities ( scior et al 2005 ) . in addition , more recent papers explore these mechanisms in further detail ( zborowski et al 2005 ; adachi et al 2006 ) . the discovery of the insulin - like activity ( insulin - mimetics ) of vanadate ( [ vo4 ] or [ h2vo4 ] ) ( shechter and karlish 1980 ) , has ushered in a new era of antidiabetes research with new oxovanadium coordination complexes with inhibitory activities against protein - tyrosine phosphatases ( ptp - 1b ) ( huyer et al 1997 ) , albeit not selectively . the next generation compounds have been based on organic vanadium complexes in search of higher target selectivity or less toxicity . however , some vanadium compounds have a great plethora of intrinsic enzyme affinities because of their phosphate - like physicochemical behavior : bio - isosterism ( scior et al 2005 ) . hence , it is of paramount importance whether the insulin - mimetic effect can be dissociated from the unwanted side effects based on phosphate imitation ( scior et al 2005 ) . the insulin - mimetic activity of certain vanadium coordination compounds has been well documented ( thompson and orvig 2000 ) , in particular , the improved glucose uptake and biosynthesis of glycogen as well as the inhibition of gluconeogenesis or lipolysis ( shechter et al 1998 ) . in addition , specific biomolecular targets regarding the aforementioned effects have been identified as protein phosphatases ( posner et al 1994 ; crans and tracey 1998 ; cuncic et al 1999 ; tracey 2000 ) , whereas neither insulin receptor nor glut2 / glut4 pathways are directly concerned as targets ( goldwaser et al 2000 ) . in particular , bis - maltolato - oxovanadium ( iv ) ( bmov or [ vo ( ma ) 2 ] with central atom = v4 + ; and ma = monoanion maltolate ) has one of the highest antidiabetic activities among the known insulin - mimetics with vanadium coordination . syntheses in nonaqueous solvents always yield trans - bmov , while in water trans - and cis - aquo forms of bmov are present due to interconversion ( figure 1 ) . hence , the exact molecular mechanism of bmov still remains unknown ( liboiron 2005 ) . the work also aims at studying the rotational barrier with its transition state because so far , no crystal structure of bmov bound to ptp - 1b has been reported ( pdb last visited august 8th , 2008 ) . intriguingly , in 2003 a report presents the binding of a trigonal - bipyramidal vanadium oxide to the active site of ptp - 1b although bmov was incubated with the enzyme at the beginning of the crystallization ( peters et al 2003 ) . thus , whether bmov would constitute a sort of prodrug ( with an inorganic oxovanadium complex as its bioactive form ) or bmov itself might reach the binding cleft ( katherine et al 2006 ) , constitutes the scientific motivation for the present in silico simulations combining geometry prediction of the ligand and its docking into the suggested target . in this context we devised ab initio calculations to elucidate bmov geometries and related structures . the overall goal was to gain more insight about its possible bioactive structure by modeling an amenable binding mode of bmov and related oxovanadium complexes applying adapted force field techniques from the literature . the energy minimization and unbiased , manual docking of vanadium complex into the enzyme ptp - 1b was conducted in five steps on a sgi 02 work station with 126 mb ram ( silikon 2001 ) . in general , cundari and colleagues had already demonstrated good modeling accuracy using semiempirical quantum chemistry and even molecular mechanics mm2 force fields ( cundari et al 1997 , 1998 ) . other authors applied quantum chemical methods ( zborowski et al 2005 ) . since both have been used successfully , we combined them in our joint study . we adapted the available tripos force field ( ff ) ( sybyl ; tripos inc . , st . louis , mo , usa ) and validated it against cundari s test series , which also contains cis - and trans - bmov ( table 1 ) . the brookhaven pdb database ( berman et al 2000 ) was searched for crystal structures of ptp - 1b in active conformation ( the open state ) with docked ligands reflecting some structural patterns : tetraoxo - complexes or aromatic wings ( groves et al 1998 ) . the atoms of the target proteins were loaded with kollman_united pre - calculated charges ( tripos inc . ) while the charges of vanadium ligands were derived from our ab initio calculations ( gaussian 1998 ) . the geometry optimization was tailored to model the aqueous medium in a simplified approach by simulating the dumping effects of solvent molecules on electrostatic interaction in the binding groove : distance - dependent dielectric constant ( = 40 ) ; nonbonded cut off at 8 ; conjugate gradient algorithm : powell , and terminal criteria : energy change : of 0.2 kj / mol ( tripos inc . ) . the final docked poses were compared to tungstate ( wo4 sodium salt ) bound to human ptp - 1b ( barford et al 1994 ) . calculations of the cis - trans conversion were carried out on two dell - computers ( dimension 2400 , with pentium iv 2.8 ghz processors , 256 mb ram , and 40 gb hard discs ) , using the gaussian 98 electronic structure software ( gaussian , inc . , wallingford ct , usa ) , and the chemoffice 2000 program ( cambridgesoft , cambridge , ma , usa ) to visualize the results . in order to draw electronic - density and electrostatic - potential graphics , the arguslab software has been used ( arguslab 2005 ) . together with the chemoffice program , both bmov structures have been generated at the b3lyp ( becke 1993 ) dft level , choosing a quadratic convergence criterion ( scf = qc ) . with these initial geometries , sto - 3 g single - point energy calculations have been performed , yielding some reference parameters of both species . subsequently , a stepwise optimization of both chemical structures has been carried out by using the following basis sets : sto - 3 g , 3 - 21 g , 3 - 21 g * , and 6 - 31 g . having terminated the optimization process , frequency calculations for each structure characterized the corresponding energy minimum type ( ie , a global , local or intermediate minimum ) . considering the biological activity of bmovin addition , dft calculations using the b3lyp / 6 - 311 g * approach ( gaussian 03 program system ; gaussian inc . ) were carried out for trans - and cis - bmov as well as for the transition state connecting the both isomers , in order to determine the relative stabilities of these structures . to postulate a viable mechanism one has to cope with a principle obstacle : while cis - aquo - bmov is the observed active species , the isomeric trans - bmov is its administered solid form . the first part of our study simulates the blocking of ptp - 1b by either cis - or trans - bmov . the calculated active configuration ( cis or trans ) is thought to suppress the intracellular insulin effects , therein assisting the cells in need of an adequate insulin response . to avoid blind docking , we conducted a pdb search for the most related crystal structure to bmov and found a tetraoxo analogue to vanadate , called tungstate . it binds to the active site of the protein tyrosine phosphatase1b ( pdb code : 2hnq ) ( figure 2 ) . applying the adapted tripos ff ( tripos inc . ) , the geometric structures of the bmov and of some related complexes ( cundari et al 1997 , 1998 ) were predicted correctly ( table 1 ) . prior to the unbiased docking of bmov into the ptp - 1b targets ( pdb codes : 1bzc , 1bzh ) ( groves et al 1998 ) , the ligands were removed . in good agreement with reported data , trans - bmov meets steric hindrance whatever the docked poses around the central atom position . but for the central atom of cis - bmov , the computed pose is very similar to that described for tungstate . the final coordinates of the central atom on bmov and of inorganic vanadate resulted in practically identical coordinates as compared to the crystallographic position of tungstate ( pdb code : 2hnq ) ( barford et al 1994 ) : w in [ wo4 ] : x = 1.1596 , y = 0.0977 , z = + 9.2017 cf . v in [ vo4 ] : x = 1.5147 , y = 0.8434 , z = + 10.3426 . for validation purpose , tungstate was successfully docked back into its crystallographic position using the same force field conditions ( cf . this successful validation of the test system evidences that steric and electrostatic forces mainly control this anion binding . it is noteworthy that hydrophobic and solution effects ( entropy ) are not quantified during manual docking in the tripos ff . notwithstanding , the nonbonded electrostatic and van der waals terms were combined in a qualitative manner with the insight obtained from other docking tools ( ludi , flexx , autodock ) ( coupez and lewis 2006 ) . for instance , in autodock with it s a ( romatic ) atom type and solvation descriptors for hydrophobic effects , - and cation - interactions of neutral bmov were recognized even without a set of vanadium parameters at hand ( castellano et al 2003 ) . the calculated energy ( interpreted with precaution for its limited parameterization for bonded and nonbonded electrostatic / steric terms ) for docked cis - bmov was 136 kj / mol , which lies in good proximity to the peptide ligands found in 1bzc and 1bzh after crystal strain was released by full geometry optimization ( groves et al 1998 ) : 179 kj / mol and 203 kj / mol , respectively . the bioactivity pattern of bmov is a hybrid : on the one side , it has aromatic contacts in common with the peptide ligands , on the other side it establishes the typical hydrogen bon network of other nonpeptide small ligand complexes through the many oxo groups ( figure 3 ) . figure 8 is a schematic drawing of the binding - relevant amino acids ( pharmacophore ) : tyr46 , phe182 , ser216 , ala217 , gly218 , ile219 , gly220 , and arg221 . particularly , the residues ser216 , ala217 , gly218 , ile 219 , gly220 , and cationic arg221 participate in binding of [ wo4 ] as an inorganic tetraoxo - monoanion whereas some of them ( ser216 , ala217 , gly220 , arg221 ) and others ( anionic asp181 , aromatic phe182 and tyr46 ) interact with formally uncharged , aromatic cis - bmov . moreover , a - interaction can be observed between one maltolate ring on bmov with tyr46 ( figure 3 and 8 ) . in addition , positively charged arg221 attracts the other maltolate anion in a typical cation - interaction ( castellano et al 2003 ) . since both identical maltolate rings on docked bmov enhance binding strength , but in two different ways thiswing - symmetry can be broken up in future drug profiling in search of higher binding selectivity . in this respect , we had already aligned the ptp - 1b against other phosphatase family members and have reported the results of conserved and unique amino acids at the binding site elsewhere ( scior et al 2005 ) . as a final step in docking to confirm our working hypothesis , cis - and trans - bmovthere is computed evidence that cis - aquo - bmov can be favorably placed into the active site of the target enzyme , while trans - bmov can not enter there due to energetically high barriers ( figure 3 ) . due to the absence of imaginary frequencies , the ab initio optimization process for trans - bmov yielded a global minimum ( figure 4 ) on the potential energy surface . moreover , comparing both optimization results with and without solvent effects , respectively , we observed only marginal deviations . thus , we consider this structure to be stable . with respect to the cis - aquo - bmov geometry , generated by stepwise single - point energy optimization , we obtained two structures : the first one , termed closed - type cis - aquo - bmovtheoretically , this structure represents a local minimum , due to its three imaginary frequencies , which might stem from a geometrical distortion generated by the water ligand ; taking into consideration the solvent effect , this structure remains stable , too . the second structure ( the stepwise optimization result using the 6 - 31 g basis set ) is the so - called open - type cis - aquo - bmov ( figure 6 ) . showing the same energy as closed - type cis - aquo - bmov , this structure represents a global minimum , since no imaginary frequencies occurred . the solvent interaction option confirms that open - type cis - aquo - bmov can be considered being stable throughout , with a slight tendency towards the aqueous phase . energy values obtained for the three species indicate , that in aqueous solution and room temperature ( ie , under physiological conditions ) the conversion from trans - bmov to cis - aquo - bmov is thermodynamically possible . hereby seems to be the stable intermediate in kinetic equilibrium with the closed - type cis - aquo - bmov form . to find out which of the two species interacts with the enzyme we determined both corresponding electrostatic potential surfaces by means of the arguslab program ( arguslab 2005 ) . the result confirms that closed - type cis - aquo - bmov shows a negative electrostatic potential of higher absolute value at the vanadium position and its close environment ( figure 7 ) . open structure , with higher affinity to the catalytic center of the enzyme ptp - 1b . finally , the geometries of trans - and cis - aquo - bmov ( open - type ) were optimized at the b3lyp / 6 - 311 g * level of theory . subsequent frequency calculations demonstrated , that both forms represent minima , ie , stable structures , on the energy hypersurface . the cis isomer is lower in energy by 5.6 kj / mol as compared with the trans - bmov , thus being the global minimum . the search for a transition state connecting the both forms along the reaction coordinate resulted in a structure possessing one imaginary frequency , ie , a first order saddle point , being higher in energy by 21.1 kj / mol with respect to the global minimum . to avoid blind docking , we conducted a pdb search for the most related crystal structure to bmov and found a tetraoxo analogue to vanadate , called tungstate . it binds to the active site of the protein tyrosine phosphatase1b ( pdb code : 2hnq ) ( figure 2 ) . applying the adapted tripos ff ( tripos inc . ) , the geometric structures of the bmov and of some related complexes ( cundari et al 1997 , 1998 ) were predicted correctly ( table 1 ) . prior to the unbiased docking of bmov into the ptp - 1b targets ( pdb codes : 1bzc , 1bzh ) ( groves et al 1998 ) , the ligands were removed . in good agreement with reported data , trans - bmov meets steric hindrance whatever the docked poses around the central atom position . but for the central atom of cis - bmov , the computed pose is very similar to that described for tungstate . the final coordinates of the central atom on bmov and of inorganic vanadate resulted in practically identical coordinates as compared to the crystallographic position of tungstate ( pdb code : 2hnq ) ( barford et al 1994 ) : w in [ wo4 ] : x = 1.1596 , y = 0.0977 , z = + 9.2017 cf . v in [ vo4 ] : x = 1.5147 , y = 0.8434 , z = + 10.3426 . for validation purpose , tungstate was successfully docked back into its crystallographic position using the same force field conditions ( cf . this successful validation of the test system evidences that steric and electrostatic forces mainly control this anion binding . it is noteworthy that hydrophobic and solution effects ( entropy ) are not quantified during manual docking in the tripos ff . notwithstanding , the nonbonded electrostatic and van der waals terms were combined in a qualitative manner with the insight obtained from other docking tools ( ludi , flexx , autodock ) ( coupez and lewis 2006 ) . for instance , in autodock with it s a ( romatic ) atom type and solvation descriptors for hydrophobic effects , - and cation - interactions of neutral bmov were recognized even without a set of vanadium parameters at hand ( castellano et al 2003 ) . the calculated energy ( interpreted with precaution for its limited parameterization for bonded and nonbonded electrostatic / steric terms ) for docked cis - bmov was 136 kj / mol , which lies in good proximity to the peptide ligands found in 1bzc and 1bzh after crystal strain was released by full geometry optimization ( groves et al 1998 ) : 179 kj / mol and 203 kj / mol , respectively . the bioactivity pattern of bmov is a hybrid : on the one side , it has aromatic contacts in common with the peptide ligands , on the other side it establishes the typical hydrogen bon network of other nonpeptide small ligand complexes through the many oxo groups ( figure 3 ) . figure 8 is a schematic drawing of the binding - relevant amino acids ( pharmacophore ) : tyr46 , phe182 , ser216 , ala217 , gly218 , ile219 , gly220 , and arg221 . particularly , the residues ser216 , ala217 , gly218 , ile 219 , gly220 , and cationic arg221 participate in binding of [ wo4 ] as an inorganic tetraoxo - monoanion whereas some of them ( ser216 , ala217 , gly220 , arg221 ) and others ( anionic asp181 , aromatic phe182 and tyr46 ) interact with formally uncharged , aromatic cis - bmov . moreover , a - interaction can be observed between one maltolate ring on bmov with tyr46 ( figure 3 and 8 ) . in addition , positively charged arg221 attracts the other maltolate anion in a typical cation - interaction ( castellano et al 2003 ) . since both identical maltolate rings on docked bmov enhance binding strength , but in two different ways thiswing - symmetry can be broken up in future drug profiling in search of higher binding selectivity . in this respect , we had already aligned the ptp - 1b against other phosphatase family members and have reported the results of conserved and unique amino acids at the binding site elsewhere ( scior et al 2005 ) . as a final step in docking to confirm our working hypothesis , cis - and trans - bmov were docked into ptp - 1b . there is computed evidence that cis - aquo - bmov can be favorably placed into the active site of the target enzyme , while trans - bmov can not enter there due to energetically high barriers ( figure 3 ) . due to the absence of imaginary frequencies , the ab initio optimization process for trans - bmov yielded a global minimum ( figure 4 ) on the potential energy surface . moreover , comparing both optimization results with and without solvent effects , respectively , we observed only marginal deviations . thus , we consider this structure to be stable . with respect to the cis - aquo - bmov geometry , generated by stepwise single - point energy optimization , we obtained two structures : the first one , termed closed - type cis - aquo - bmovtheoretically , this structure represents a local minimum , due to its three imaginary frequencies , which might stem from a geometrical distortion generated by the water ligand ; taking into consideration the solvent effect , this structure remains stable , too . the vacuum structure , however , seems to be slightly preferred . the second structure ( the stepwise optimization result using the 6 - 31 g basis set ) is the so - called open - type cis - aquo - bmov ( figure 6 ) . showing the same energy as closed - type cis - aquo - bmov , this structure represents a global minimum , since no imaginary frequencies occurred . the solvent interaction option confirms that open - type cis - aquo - bmov can be considered being stable throughout , with a slight tendency towards the aqueous phase . energy values obtained for the three species indicate , that in aqueous solution and room temperature ( ie , under physiological conditions ) the conversion from trans - bmov to cis - aquo - bmov is thermodynamically possible . hereby seems to be the stable intermediate in kinetic equilibrium with the closed - type cis - aquo - bmov form . to find out which of the two species interacts with the enzyme we determined both corresponding electrostatic potential surfaces by means of the arguslab program ( arguslab 2005 ) . the result confirms that closed - type cis - aquo - bmov shows a negative electrostatic potential of higher absolute value at the vanadium position and its close environment ( figure 7 ) . open structure , with higher affinity to the catalytic center of the enzyme ptp - 1b . finally , the geometries of trans - and cis - aquo - bmov ( open - type ) were optimized at the b3lyp / 6 - 311 g * level of theory . subsequent frequency calculations demonstrated , that both forms represent minima , ie , stable structures , on the energy hypersurface . the cis isomer is lower in energy by 5.6 kj / mol as compared with the trans - bmov , thus being the global minimum . the search for a transition state connecting the both forms along the reaction coordinate resulted in a structure possessing one imaginary frequency , ie , a first order saddle point , being higher in energy by 21.1 kj / mol with respect to the global minimum . the goal of the present in silico study is to theoretically address the missing explanation of a trans - cis conversion of bmov . to our best knowledge , it generates the first molecular binding mode model concerning the insulin - mimetic activity of bmov . it also elucidates the stereochemical requirements of bmov as an inhibitor to the biomolecular target site . in aqueous solutionopen - type cis - aquo species of bmov , which itself is in equilibrium with another closed - type form of cis - aquo - bmov . the postulated binding mode for bmov , ie , closed - type cis - aquo - bmovcomplex , is fully consistent with in vivo studies on bmov activity with respect to enzyme activity of ptp - 1b : the group of mcneill reported that bmov treatment reduced the activity of ptp i b by 25 % in fatty treated rats ( mohammad et al 2002 ) . our present work may lead to the detection of the activated complex upon forming a complex of cis - bmov with a h2o moiety . our report may help other researchers to devise new calculations concerning this activated complex . to thisend our modeling input and output data can be obtained by email . in conclusion , we contribute with computed solutions to better understand the molecular recognition process and selectivity of nonpeptide insulin - mimetic vanadium complexes . to complete the picture , on a theoretical level it can not be discarded that vanadium coordinated organic compounds would also be prodrugs after re - arrangements with stronger chelators and following redox - reactions . thus , whether bmov or a simple ( inorganic ) tetraoxo compound is the final bioactive species acting on target structure remains an open question and disserves further investigation\noutput:\n" }, { "from": "agent", "value": "the postulated transition of bis - maltolato - oxovanadium ( iv ) ( bmov ) from its inactive trans - into its cis - aquo - bmov isomeric form in solution was simulated by means of computational molecular modeling . the rotational barrier was calculated with dft b3lyp under a stepwise optimization protocol with sto - 3 g , 3 - 21 g , 3 - 21 g * , and 6 - 31 g ab initio basis sets . our computed results are consistent with reports on the putative molecular mechanism of bmov triggering the insulin - like cellular response ( insulin mimetic ) as a potent inhibitor of the protein tyrosine phosphatase - 1b ( ptp - 1b ) . initially , trans - bmov is present in its solid dosage form but in aqueous solution , and during oral administration , it is readily converted into a mixture of open - type and closed - type complexes of cis - aquo - bmov under equilibrium conditions . however , in the same measure as the closed - type complex binds to the cytosolic ptp - 1b , it disappears from solution , and the equilibrium shifts towards the closed - type species . in full accordance , the computed binding mode of cis - bmov is energetically favored over sterically hindered trans - bmov . in view of our earlier report on prodrug hypothesis of vanadium organic compounds the present results suggest that cis - bmov is the bioactive species ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the social worlds of animals are filled with many different types of interactions , and social experience interacts with organismal stress on many levels . social stressors have proven to be potent across a wide range of species , and their study in rodents has led to greater understanding of the role of stressor type , timing , and other factors impacting physiology and behavior . while negative social interactions can be acutely damaging , social interaction can alsomoderate stressful experiences , buffering potentially adverse impacts and contributing to resilience . in this reviewwe consider three main classes of effects : the social environment as a stressor ; the effects of stress on subsequent social behavior ; and social buffering of stressful experience ( fig . 1 ) . we explore mechanisms that mediate links between stress and social behavior , and consider sex differences in these mechanisms and behavioral outcomes . finally , we discuss data from a wide variety of rodent species wherever possible , in order to explore the universality and specificity of findings in single species . responses to stress span a spectrum from detrimental immediate and long - term effects to resilience and protection against future stressors . the effects of stress exposure and consequent trajectory depend on the nature of the stressor , the severity , duration ( acute vs. chronic ) , sex / gender , genetics , timing of exposure ( early life , adolescence , adulthood or aging ) as well as the perception of the stressor by the individual for example , stressor controllability dramatically affects resilience versus vulnerability as an outcome ( maier and watkins , 2005 , amat et al . , 2010 , lucas et al . , 2014recently it was shown that even the gender of researchers can affect rodent stress levels and influence results of behavioral tests ( sorge et al . , 2014 ) . one of the most commonly measured immediate physiological responses to stress is activation of the hypothalamiccorticotropin releasing factor ( crf , also called crh ) is released from the hypothalamus , and is the primary trigger of adrenocorticotropic hormone ( acth ) secretion from the anterior pituitary . acth then triggers systemic release of glucocorticoids ( cort ) from the adrenal gland ( bale and vale , 2004 ) . we describe outcomes related to hpa - axis responsivity , as well as several additional neurochemical players including bdnf , serotonin , and multiple neuropeptides in the text below . social behavior is complex and varies with the behavioral test chosen , and whether focal individuals are tested with familiar or novel conspecifics , with same - or opposite - sex individuals , or with familiar or unfamiliar strains . the laboratory setting is a sparse environment compared to the complexity of nature , both physically and socially . some research aims to quantify social behavior in complex housing areas such as enriched caging with social groups ( e.g. , artificial , visible burrow systems ( blanchard et al . , 2001 ,2006 ) , and large , semi - natural enclosures ( e.g. king , 1956 , dewsbury , 1984 , ophir et al . , 2012 , margerum , 2013 ) . other research relies on constrained social interactions in tests designed to measure a few particular aspects of social behavior ( crawley , 2007 ) . for example social interaction tests typically measure the amount of time spent in social contact or investigation with a conspecific . social choice tests take place in multi - chambered apparatuses that allow investigation of either a conspecific or a non - living stimulus such as a novel object or empty restrainer ( moy et al . , 2007 ) . variations on this test involve a choice of a familiar versus unfamiliar individual , such as in the partner preference test ( williams et al . , 1992 ) . social habituation / dishabituation tests are often used to assess social recognition and memory for familiar individuals ( ferguson et al . , 2002 ; choleris et al . ,2003 ) . social motivation may be assessed by measures of effort expended to access another individual ( lee et al . , 1999 ) , or by conditioned place preference for a social environment ( panksepp and lahvis , 2007 ) . other tests measure specific aspects of social competency , such as memory and social inferences involved in hierarchy ( cordero and sandi , 2007 , grosenick et al . recent studies of pro - social behavior in rats have focused on latency to free a restrained rat under different scenarios ( ben - ami bartal et al . , 2011 , ben - ami bartal et al . , there is no peripheral hormonal indicator of sociability , but two neuropeptides have been highly implicated in many aspects of mammalian social behavior : oxytocin ( ot ) and arginine vasopressin ( vp ) . oxytocin is produced in the hypothalamus and facilitates a wide variety of processes related to social behavior , including maternal behavior , trust , anxiolysis , and sexual pair - bond formation ( reviewed in ross and young , 2009 , young et al . , 2008 , neumann , 2008 , zucker et al . , 1968 , carter et al . , vasopressin activity has been associated with aggression , anxiety , and social behavior ( reviewed in kelly and goodson , 2014 ) , as well partner preference formation in male prairie voles ( cho et al . , 1999 , young and wang , 2004 ) . the locations and densities of oxytocin receptors ( otr ) and vasopressin type 1a receptors ( v1ar ) have been associated with species variations , as well as with individual variations in social behavior from affiliation to aggression ( e.g. everts et al . , 1997 , young , 1999 , beery et al . many studies have also investigated the role of the mesolimbic dopamine system and opioid regulation of rewarding social behaviors such as pair - bonds between mates ( aragona , 2009 , resendez et al . , 2012 ) ; we describe these and additional research avenues throughout . in addition to considering how social behavior is assessed , we must consider the significance of the behavior to the species in which it is assessed . social behavior encompasses skills from social recognition to social memory , as well as many distinct types of interaction , including with peers , potential reproductive partners , competitors , and offspring . some of these interactions are better studied in some species than others ; for example biparental care is only present in a few rodent species that have been studied in laboratories , namely prairie voles ( microtus ochrogaster ) , california mice ( peromyscus californicus ) , and djungarian hamsters ( phodopus campbelli ) . monogamous pairing with mates is similarly rare among rodents , and is most studied in prairie voles and california mice . mechanisms supporting group living have been in explored in colonial rodents including naked mole - rats ( heterocephalus glaber ) , tuco - tucos ( ctenomys sociabilis ) , seasonally social meadow voles ( microtus pennsylvanicus ) , and others ( anacker and beery , 2013 ) . the idea that some problems are best studied in particular species is far from new ; this principle was promoted in 1929 by the late physiologist and nobel laureate august krogh ( krebs , 1975 ) . in contrast to krogh 's assertion that species should be selected for their suitability for studying particular problems , modern biological research is strongly biased towards rats and mice ; in 2009 rats and mice made up approximately 90 % of mammalian research subjects in physiology , up from 18 % at the time krogh 's principle was articulated ( beery and zucker , 2011 supplementary material ) . lab strains of mice and rats are highly inbred and in many ways quite different from their wild peers . use of multiple species allows researchers to compare and contrast mechanisms across the phylogenetic tree . while the depth of mechanistic information available for non - model organisms is much less than for rats and mice , the comparative perspective is essential for understanding to what extent mechanisms underlying social behavior are unique to particular species , common across broader groups , or are variations on a theme ( phelps et al . , 2010 , katz and lillvis , 2014 ; hofmann et al . , 2014 ) . in this reviewwe focus on rats and mice for which data on stress and social behavior are most abundant , but incorporate findings from other rodent species whenever possible . and although laboratory research in rodents is heavily male - biased ( beery and zucker , 2011 ) , we review a substantial body of findings on the interrelationship of stress and social behavior in females . , rodents may encounter competition for resources such as territory , food , and access to mates , and even solitary species interact with conspecifics and their chemical cues , if only to avoid them in the future . widely used models of social stress in rodents include social subordination , crowding , isolation , and social instability ( fig . 1 , left side ) . while most studies have been conducted in mice and rats , prairie voles and other social rodent species provide an opportunity to study the role of identity of the social partner , and how separation from a mate differs from isolation from a same - sex peer . in humans , social rejection is used as a potent experimental stressor ( kirschbaum et al . , 1993 ) , and decades of work in humans andnon - human primates have demonstrated that an individual 's position in the social hierarchy has profound implications for health and well - being ( adler et al . , 1994 , sapolsky , 2005 ) . in rodents , the most prominent model of stressful social interactionsocial defeat is typically induced by a version of the resident - intruder test in which a test subject is paired with a dominant resident in its home cage . dominance may be assured by size , prior history of winning , strain of the resident , and / or prior housing differences ( martinez et al . , 1998 ) . social defeat is typically used as a stressor in male rodents , for whom dominance is easier to quantify and aggressive interactions related to home territory are presumed more salient . a few studies report effects of social defeat on females , particularly in syrian hamsters in which females are highly aggressive and dominant to males ( payne and swanson , 1970 ) . in rats and mice , females do not always show a significant response to this task and the effect in males is far greater ( palanza , 2001 , huhman et al . , 2003 ) . thus , other stress paradigms such as social instability are more widely used with females ( haller et al . , 1999 ) . social defeat can have a more substantial impact on male rodent physiology and behavior than widely used stressors such as restraint , electric shock , and chronic variable mild stress ( koolhaas et al . , 1996 , blanchard et al . , 1998 , sgoifo et al . , 2014 ) . in the short - term , social defeat produces changes in heart rate , hormone secretion , and body temperature , with longer - term impacts on a wide variety of additional outcomes including activity , social behavior , drug preference , disease susceptibility and others ( martinez et al . , 1998 , sgoifo et alunlike physical stressors such as restraint , social defeat does not appear to be susceptible to habituation or sensitization ( tornatzky and miczek , 1993 , sgoifo et al . , 2002 ) , and can be used in groups housed with a single dominant individual ( nyuyki et al . , 2012 ) . social defeat stress has profound effects on hippocampal morphology and function ( reviewed in mcewen and magarinos , 2001 , buwalda et al . , 2005 , these effects include reduction in hippocampal volume ( czh et al . , 2001 ) related to dendritic remodeling and reduced neurogenesis ( magarios et al . , 1996 , gould et al . , 1998 ) , social defeat also alters the ratio of mineralocorticoid to glucocorticoid receptors in the hippocampus ( buwalda et al . , 2001 , veenema et al . , 2003 ) . aswith most of neurobiological research , attention has centered on neurons as the brain mediators of the biological embedding of the social world . however , following recent reports on the effects of stress ( in general , and particularly social stress ) on astrocytes , oligodendrocytes and microglial cells , it has become clear that glial cells are likely to play a role in this process , and deserve more attention in future studies ( braun et al . , 2009 , , 2011 , araya - calls et al . , 2012 , chetty et al . , social hierarchy has also been explored in settings where dominance is established through unstaged social interactions that occur on an ongoing basis ( e.g. blanchard et al . , 1995 , blanchard et al . , 2001 ) . a low position in the social ( and economic / resource ) hierarchy appears to be stressful across a wide range of species . negative health effects of low social status have been particularly well documented in non - human primates ( e.g. sapolsky , 1989 , sapolsky , 2005 , virgin and sapolsky , 1997 , wu et al . , 2014 ; shively review , 2015 ) . in humans , lower socioeconomic status ( ses ) predicts decreased mental and physical health in a graded fashion , and subjective perception of socioeconomic status may be an even more potent mediator than objective ses ( adler et al . , 1994 , kawachi and kennedy , 1999 , siegrist and marmot , 2004 , singh - manoux et al . , 2005 ) . while low social status appears stressful across all instances discussed thus far , several studies have demonstrated that low status is not always stressful , in part dependent on species - particular life - history traits . for example , subordinate status is most stressful in species with despotic hierarchies , and may not be a stressor inhigh status is more stressful in societies in which dominance must be continuously defended than in stable social hierarchies ( sapolsky , 2005 ) . in a meta - analysis of cortisol levels in primates , abbott et al . ( 2003 ) found that subordinates had higher basal cort levels only when exposed to higher rates of stressors due to subordinate status , and when subordinate status afforded them few opportunities for social contact . in naked mole rats , a highly social rodent species that lives in large underground colonies , all but a few animals in each colony are reproductively suppressed subordinates ( sherman et al . , 1991 ) . in this instance , subordinates are related to breeders and are non - aggressive except in the event of loss of the breeding queen or her mates ( clarke and faulkes , 1997 ) . reproductively suppressed subordinates do not have higher cort levels than breeders and may have lower levels ( clarke and faulkes , 1997 , clarke and faulkes , 2001 ) . while it is not yet clear how stress relates to status in this species , social subordination must be considered in the context of how it affects the individuals involved . housing density affects rodent behavior , and both crowded and isolated social environments have been used as stressors in rodents . crowding is a naturalistic stressor especially for social or gregarious species that relates to high population density and resource competition in the field . in house mice , several studies have shown that crowding can impair reproductive function and may be part of population size regulation ( christian and lemunyan , 1958 , christian , 1971 ) . in the highly social , group - living rodent species the degu ( octadon degus ) , increased group sizeis associated with greater dispersal consistent with a social competition hypothesis ( quirici et al . , 2011 ) . in the laboratory , crowding typically consists of large numbers of mice or rats ( e.g. 6 rats / cage ( brown and grunberg , 1995 , reiss et al . , 2007 ) ) with ad libitum access to resources such as food and water . crowding must be somewhat extreme to induce stressful outcomes , as group - housing ( e.g. 46 rats or 12 mice in a sufficiently large area ) is often used as a key component of environmental enrichment ( sztainberg and chen , 2010 , simpson and kelly , 2011 ) . social crowding has been shown to impact many different physiological outcomes in male mice , rats , and prairie voles . these include changes in organ weights , hormone secretion , hpa reactivity , pain sensitivity , telomere length , and cardiac outcomes ( gamallo et al . , 1986 , gadek - michalska and bugajski , 2003 , kotrschal et al . , 2007 , grippo et al . , 2010 , tramullas et al . , 2012 , puzserova et al . , crowding of pregnant dams also produces changes in the offspring birth weight , pubertal timing , and reproductive behavior ( e.g. harvey and chevins , 1987 , ward et al . , 1994 ) and may lead to lasting changes through a subsequent generation ( christian and lemunyan , 1958 ) . there appear to be important sex differences in the consequences of crowding , with one study in rats finding that crowding is a stressor for males but has the capacity to calm females ( brown and grunberg , 1995 ) . at the opposite extremesocial isolation is employed as a stressor in previously group - housed mice and rats ( heinrichs and koob , 2006 ) ; in both species , extended ( 213 week ) solitary housing produces an isolation syndrome particularly in females , consisting of hyperadrenocorticism , reduced body weight , altered blood composition , and enhanced pain responsiveness among other outcomes ( hatch et al . , 1965 , valzelli , 1973 ) . these changes coincide with alterations in behavior including aggression , mating behavior , learning , and pain sensitivity ( valzelli , 1973 ) . more recent studies have added a host of additional physiological outcomes related to stress and depressive behavior , including changes in dopamine signaling in different brain regions ( heidbreder et al . , 2000 ) , altered heart rate and cardiac function ( spni et al . , 2003 , carnevali et al . ,2012 ) , and neurogenesis ( stranahan et al . , 2006 , lieberwirth and wang , 2012 ) . which outcomes are affected by isolation depend in part on the age at which isolation occurs ( reviewed in hall , 1998 ) , and there are sex differences in the effects of social isolation . these suggest that isolation may be stressful for females but not necessarily to the same extent for males ( hatch et al . , 1965 , palanza , 2001 , palanza et al . ,2001 ) . assessing the impacts of both isolation and crowding share the problem of what to consider as the control comparison , as anxiety and other behavioral outcomes vary along a continuum of group sizes ( botelho et al . , 2007 ) . in recent decades , prairie voles have become a popular model for studying social behaviors because of their unusual capacity to form socially monogamous pair - bonds with opposite sex mates ( getz et al . , 1981 ) . an additional advantage of this species is that the effects of social manipulations can be contextualized in terms of findings from field populations and semi - natural settings ( e.g. ophir et al . , 2008 , mabry et al . , 2011 ) . in wild prairie voles , cohabitation with a mate or a mate and undispersed offspring is common ( getz and hofmann , 1986 ) , and reproductively nave prairie voles are affiliative towards their same - sex cage mates . in the lab , separation of adult prairie voles from a sibling cage - mate for 12 months reduced sucrose consumption ( a measure of anhedonia ) , and was associated with increased plasma levels of oxytocin , cort , and acth , as well as increased activity of oxytocin neurons in the hypothalamus following a resident intruder test . these effects were more profound in females ( grippo et al . , 2007 ) . further work has shown that social isolation from a sibling also leads to changes in cardiac function associated with cardiovascular disease ( grippo et al .2012 ) , and immobility in the forced swim test ( grippo et al . , 2008 ) considered a measure of depressive behavior . some physiological and behavioral sequelae were prevented or ameliorated by exposure to environmental enrichment , or by peripheral administration of oxytocin ( grippo et al . , 2009 , grippo et al . , 2014 ) , as has been demonstrated in rats ( hellemans et al . , social isolation of prairie voles from weaning has been associated with higher circulating cort , and greater crf immunoreactivity in the paraventricular nucleus ( pvn ) of the hypothalamus ( ruscio et al . , 2007 ) . while the majority of current studies have focused on social isolation from a non - reproductive partner , recent investigation into disruption of opposite - sex pairs takes advantage of this unusual feature of prairie vole behavior , and suggests that mate - pair disruption has substantial autonomic and behavioral consequences for both male and female prairie voles ( bosch et al . , 2009 ; mcneal et al . ,2014 ) . as the work in prairie voles illustrates , it is important to consider the natural history of species when social manipulations are performed . for example , male syrian hamsters housed in isolation are more aggressive than those housed in groups ( brain , 1972 ) , but that is not to suggest that isolation was distressing , or produced an unusual behavioral phenotype , as this species is naturally solitary ( gattermann et al . , conversely , crowding might be a particularly potent but unnatural stressor for this species , and it has been associated with increased mortality ( germann et al . , 1990 , marchleswska - koj , 1997 ) . social species provide good subjects for studying the influence of social interactions on health and related outcomes , and this has been demonstrated both in the laboratory and in the field . in a species of south american burrowing rodentthe colonial tuco tuco ( c. sociabilis ) females may live alone or share a burrow with several other adults members and their young ( lacey et al . , 1997 ) . yearling c. sociabilis that live alone ( whether via dispersal in the field or investigator manipulations in the lab ) , have significantly higher baseline fecal glucocorticoid metabolite levels than do group - living individuals in the same environments ( woodruff et al . , 2013 ) . in a putatively monogamous species of wild guinea pig ( galea monasteriensis ) , social separation induces increases in cortisol secretion that are only rectified by return of the social partner ( adrian et al . , 2008 ) . the study of species in the context of their natural behavior allows us to better understand stress - related outcomes in a variety of rodent species . some studies employ both crowding and isolation in alternation ( for example , 24 h of each for 2 weeks ) , as a model for chronic social instability ( e.g. haller et al . , 1999 , herzog et al . , 2009 ) . social instability has particularly been used as a social stressor for female rats , for whom crowding and social defeat are not always effective stressors ( palanza , 2001 ) . in the crowding phase , females exposed to this variable social environment show increased adrenal weight , increased corticosterone secretion , decreased thymus weight , and reduced weight gain relative to females housed in stable male female pairs ( haller et al . , 1999 ) . a second study replicated these findings and demonstrated that social instability also induced dysregulation of the hypothalmic pituitarygonadal ( hpg ) axis ( elevated luteinizing hormone , prolactin , and disrupted estrus cycles ) , and reduced sucrose preference and food intake ( herzog et al . , 2009 ) . this stressed phenotype persisted for several weeks without habituation and led to a depressive - like phenotype . prior history of social instability in the form of early - life separation from the mother also exacerbates vulnerability to later life chronic subordination stress ( veenema et al . , 2008 ) in humans , stressful situations can promote affiliative behavior ( zucker et al . , 1968 , teichman , 1974 , taylor , 2006 ) and anticipation of stressful events can promote group cohesion and liking for group members ( latan et al . all stress is not the same , however , and in some cases , social behavior is reduced after a stressor in fact social withdrawal is one of the diagnostic criteria for post - traumatic stress disorder ( dsm v , american psychiatric association , 2013 ) . while effects of stress on social behavior are evident in humans , most of our understanding of these impacts , and of the underlying molecular and cellular mechanisms , come from rodent studies . in rodents , several stressors and manipulations of the hypothalamicadrenal ( hpa ) hormonal axis have been shown to impact a variety of subsequent social behaviors . in this case , much of what we know comes from research on prairie voles for which there appear to be important differences between the sexes , with some outcomes dependent on whether the partners are same - sex siblings or opposite - sex mates . as previously mentioned , prairie voles provide an opportunity to study pair - bond formation between males and females , as this species forms reproductive pair bonds both in the laboratory and in the field . prairie voles also exhibit unusually high levels of circulating cort relative to other rodents including montane voles , rats , and mice ( devries et al. , 1995 ) moderated by reduced tissue sensitivity to glucocorticoids ( taymans et al . , 1997 , klein et al . , 1996 ) . stress has opposite effects on the formation of mate preferences in male and female prairie voles . in males , males do not typically form a partner preference for a female after 6 h of cohabitation , however they form significant preferences within this time interval when paired after a brief swim stress ( devries et al . , 1996 ) . preference formation is also facilitated by cort administration in male prairie voles , and impaired by adrenalectomy ( devries et al . some doses of central crf administration also facilitate partner preference formation in males ( devries et al . , 2002 ) . interestingly , cort decreases after pairing with a female , but partner preferences are not established during the early cohousing interval , and cort levels have returned to baseline by the time male preferences have been formed ( devries et al . , 1997 ) . in female prairie voles , stress impairs partner preference formation , but this effect is prevented in adrenalectomized voles ( devries et al . , 1996 ) . this phenomenon appears to be mediated by cort , as exposure to cort during ( but not after ) cohabitation with a novel male prevents partner preference formation , and adrenalectomized females form partner preferences after shorter cohabitation periods than are typically necessary ( devries et al . , 1995 ) . cort levels are naturally low immediately following cohousing with a male , and partner preferences are formed before they return to baseline ( devries et al . , 1995 ) . in rats , in particular , stress has been shown to inhibit mating behavior in males and in naturally cycling females , via elevation of the inhibitory hypothalamic hormone rf - amide related peptide 1 ( kirby et al . , 2009 , geraghty et al . , 2013 ) . same - sex interactions have not been as well explored in prairie voles as opposite - sex affiliative interactions have been , although some data suggest same - sex affiliative behavior in prairie voles may be enhanced following a stressor ( devries and carter , unpublished data referenced in carter , 1998 ) . same - sex affiliative behavior can be studied more broadly in rodent species that live in groups , so additional rodent species may be informative for this question . meadow voles are conditionally social rodents , with photoperiod - mediated seasonal variation in social huddling . while females are aggressive and territorial in summer months , they live in social groups and huddle with conspecifics in winter months or short day lengths in the laboratory ( madison et al . , 1984 , seasonal variations in huddling and partner preference formation allow for the study of the endocrine and neurobiological mechanisms underlying changes in social tolerance and peer affiliation outside the context of mate - pairing . in meadow voles , cort varies seasonally ( boonstra and boag , 1992 , galea and mcewen , 1999 , pyter et al . , crf / urocortin pathways may also link stress - reactivity and social behavior in this species , as crf1 and crf2 receptor densities change with day length and are associated with huddling behavior ( beery et al . , 2014 ) . stress exposure prior to pairing impairs preference formation for a same - sex individual in female of this species ( anacker et al . , 2014 ) . in addition , familiarity of the conspecific prior to the stressor may influence whether social behavior is increased or decreased . wild rats live in gregarious colonies , where social interactions may be beneficial for predator avoidance and under other stressful conditions ( macdonald et al . , 1999 ) . in male rats , social defeat stress leads to social avoidance less time spent in social contact with an unfamiliar non - aggressive rat ( meerlo et al . ,1996 ) and avoidance of the dominant rat ( lukas et al . , 2011 ) . non - social stressors may have the opposite effect , for example , in groups of familiar male rats , rats spend more time huddling in large groups during an immediate stressor ( cat fur or bright light ) . this effect has been termed defensive aggregation , and is facilitated by oxytocin ( bowen et al . , 2012 , bowen and mcgregor , 2014 ) . exposure to chronic social defeat stress leads to social avoidance , altered fear acquisition and elimination , anhedonia , changes in neural circuitry and transmission , neurogenesis and metabolism in groups of exposed versus unexposed subjects ( chou et al . however , looking at individual outcomes reveals a much more complex picture , even in inbred mice . for example , measuring social motivation after exposure to social defeat stress reveals a bimodal segregation of the group into affected and unaffected individuals . affected individuals spend less time interacting with conspecific peers in the social zone , while unaffected ( unsusceptible ) individuals spend time in the social zone similar to unstressed individuals . susceptibility to social aversion following social defeat is associated with a suite of other signs of stress including decreased sucrose preference , decreased body weight , and increased sensitivity to cocaine - induced conditioned place preference ( krishnan et al . , 2007 ) . what is the difference between responders and non - responders , or a resilient vs. vulnerable trajectory ? interestingly , this resilience phenotype did not correlate with social motivation pre - stress , nor with levels of circulating glucocorticoids ( krishnan et al . , 2007 ) . however , stress - susceptibility has been correlated with stress - induced increase in levels of brain derived neurotrophic factor ( bdnf ) , a key regulator of dopamine release in the nucleus accumbens ( nac ) . following 10 days of repeated social defeat , bdnf protein levels were persistently elevated in the nac of mice . reduction of bdnf levels in the ventral tegmental area ( vta ) via local bdnf knockdown provided an antidepressant - like effect relative to untreated , defeated mice and prevented social aversion ( berton et al . , 2006 ) . investigation of the individual differences between susceptible and unsusceptible mice revealed that susceptibility was characterized by increased nac bdnf , but reinforced the importance of bdnf release from the vta , as knockdown in the vta but not nac promoted resilience . susceptibility to defeat was further shown to be mediated by enhanced firing of vta dopamine neurons , with resilience characterized by a lack of activity - dependent bdnf release ( krishnan et al . , 2007 ) . interestingly , unsusceptible individuals were not lacking a neural response , but in fact showed greater change in gene expression patterns in the vta than susceptible individuals suggesting that behavioral non - responsiveness is an active process and not merely a lack of the pathological process . analysis of differential gene expression revealed significant down - regulation of several members of the wnt ( wingless ) - dishevelled signaling cascade , including phospho - gsk3 ( glycogen synthase kinase - 3 ) , in the nac of susceptible , but not resilient , mice ( wilkinson et al . regulation of hpa axis activity , and specifically reduced expression of crf ( regulated by stress - induced demethylation of regulatory areas of the gene crf1 ) was shown in the subset of vulnerable mice that displayed social avoidance ( elliott et al . , 2010 ) and in mice that displayed short latency to defeat in the resident / intruder paradigm ( wood et al . , 2010 ) . supporting this finding , knockdown of crf levels diminished stress - induced social avoidance ( elliott et al . , 2010 ) . in a separate model of chronic subordinate colony housing , mice selectively bred for low anxiety were behaviorally resilient to subordination stress , and showed distinct hpa axis responses ( fchsl et al . , 2013 ) . several neurotransmission systems are implicated in social - stress resilience vs. vulnerability : in addition to bdnf - control of dopamine mentioned above , differences in the nac dopaminergic system resulting from differential maternal behavior are correlated with increased preference for social interactions in a group of highly groomed rat offspring ( pea et al . , 2014 ) . vulnerable and resilient animals differ significantly in the expression of ampa receptors in the dorsal hippocampus , and activation of ampa receptor during the stress exposure prevented the physiological , neuroendocrine , and behavioral effects of chronic social stress exposure ( schmidt et al . , 2010 ) . knockout of serotonin transporter increases the vulnerability to social avoidance following social defeat ( bartolomucci et al . , 2010 ) . finally , supression of the gabaergic system is seen in the pre - frontal cortex of mice showing depressive symptoms following social defeat ( veeraiah et al . , 2014 ) , and in amygdala of mice exposed to peripubertal stress ( tzanoulinou et al . , 2014 ) . similar suppression is found in the cortex of human patients with ptsd ( meyerhoff et al . , 2014 ) . stress exposure not only alters social interaction , but that social interaction can in turn play a role in buffering or moderating the effects of that stressor , providing adaptive value of social networks for coping with stress exposure . we can think about stress - resilience in multiple layers : life - long programming of stress - resilient individuals originating from the early life environment and in particular through maternal interactions ( parker et al . , 2012 ; lyons et al . , 2010 , szyf et al . , 2007 ) ; short - term resilience after an acute moderate stressor promoting better functioning after a secondary stressor ( kirby et al . ,2013 ) ; or resilience that comes from mitigating ( buffering ) the effects of stress by positive , supportive social environment , or even by aggressive social interactions . for example , lower ranking baboons that show displacement of aggression on peers have lower cort levels ( virgin and sapolsky , 1997 ) . the effects of social buffering are far reaching , and in humans there is evidence that social relationships aid immune function , cardiovascular health , and other health - related outcomes ( reviewed in berkman and kawachi , 2000 ) . stable natural social relationships have even been associated with increased longevity in humans and other species ( humans : holt - lunstad et al . , 2010 ; baboons : silk et al . , the endocrine consequences of social buffering were first described in primates ( coe et al . , 1978 , mendoza et al . , 1978 ) andprimate studies continue to be important particularly for our understanding of natural social buffering in the context of stress . for example in female chacma baboons , loss of a partner results in elevated cort and also in enhanced social behaviors such as allogrooming which may help mediate the decline to baseline levels ( engh et al . , 2006 ) . studies of social manipulations in rodents have also played a pivotal role in our understanding of social support on a variety of behavioral , endocrine , and neurobiological outcomes ( reviewed in devries et al . , 2003 , kikusui et al . , 2006 ) . in rodents , most studies of social buffering have focused on the presence or absence of a conspecific such as the cage - mate after a stressor . as one might imagine , many different variables may affect whether social buffering occurs , including the familiarity of the conspecific , the relative hierarchy , presence or absence during stress exposure , whether the cage - mate was also stressed , sex of the individual and partner , sensory modalities of exposure to that individual , timing of the availability of social support and so forth . while these parameters have by no means been explored in all combinations , we summarize what is known for each variable across a variety of rodent species . rats temporarily housed in an open field spend more time together than expected by chance ( latan , 1969 ) , and stressed males are more likely to interact socially than non - stressed males ( taylor , 1981 ) . investigator - manipulated housing conditions ( solitary - , pair - , or group - housing ) also affect reactions to stress . conditioned avoidance of noxious stimuli is reduced in pair - housed animals ( hall , 1955 , baum , 1969 ) . pair - housed rats also show reduced impacts of stress exposure relative to rats housed alone in their response to white noise ( taylor , 1981 ) and foot shock ( davitz and mason , 1955 , kiyokawa et al . , 2004 ) . group - housed rats exposed to social defeat exhibit greater growth and less anxiety behavior in repeated open field exposure relative to solitary - housed rats ( ruis et al . , 1999 ) . solitary housing increases anxiety - like behaviors on its own ( see above section ) ; thus distinguishing between effects of isolation and effects of a stressor ( and their potential interactions ) requires that all housing conditions be paired with both the stressor and lack thereof . in studies wherethis has occurred , pair - housed animals do not show stress - induced anxiety behavior changes relative to control pair - housed animals , unlike solitary - housed individuals ( nakayasu and ishii , 2008 ) . more recent studies have examined novel behavioral outcomes , including social buffering effects on pain tolerance ( reviewed in martin et al . , 2014 ) and changes in alcohol consumption ( anacker et al . , 2011social housing impacts hpa axis responsiveness to a stressor or to hormonal stimulation via crf . following crf administration , male group - housed rats have reduced cort and acth relative to isolated males ( ruis et al . , 1999 ) . in young male guinea pigs , presence of the mother or an unfamiliar adult female attenuates increases in plasma acth , cortisol and vocalizations in response to a novel environment ( hennessy et al . , 2000 ) , with additional , subtly varying effects across the lifespan ( hennessy et al . , 2006 ) . studies in prairie voles allow for distinction between buffering by social peers and reproductive partners . in prairie voles , exposure to a novel individual of the opposite sex leads to a decline in serum cort over the following 1560 min in both males and females , while same - sex novel pairings did not influence serum cort ( devries et al . , 1997 , devries et al . , this decline in cort may be important for the ability of the female to form a partner preference , while it must pass in order for males to form ( cort - dependent ) partner preferences ( devries , 2002 ) . the nature of social buffering may be quite different within established social relationships : in prairie voles , female sibling pairs experienced elevated cort following separation and this effect was attenuated following reunion ( unpublished data referenced in carter et al . , 1995 ) . in males , loss of a female partner also resulted in increased circulating cort as well as increased adrenal weight ( bosch et al . , the presence of a partner may provide social buffering from a stressor ; female prairie voles that recovered alone from immobilization stress exhibited high levels of cort and increased anxiety behavior , while females recovering with their male partner showed no such elevation ( smith and wang , 2014 ) . while cort is an easily measured signal that often relates to stress level , it is worth noting that measurement of glucocorticoids is not always a clear indicator of either stress exposure or stressed affect , and stress may result in both enhanced and dampened cort profiles depending on timing and chronicity ( e.g. sapolsky et al . social companionship has been associated with outcomes beyond the hpa axis , although many of these changes may ultimately be related to common pathways . for example , in prairie voles , females recovering from immobilization stress with a male partner showed no cort elevation , coupled with evidence of increased oxytocin ( ot ) release in the paraventricular nucleus ( pvn ) of the hypothalamus . direct administration of ot to the pvn reduced cort responses to a stressor , while oxytocin receptor antagonist ( ota ) injection prevented the ameliorative effects of housing with the partner ( smith and wang , 2014 ) . this parallels research in humans in which ot and social buffering interact to reduce cort responses to a social stressor ( heinrichs et al . , 2003 ) . for example , the presence of a conspecific in an open - field test reduces peripheral prolactin in male rats ( wilson , 2000 ) . relative to isolated individuals , socially housed female siberian hamsters experience improved wound healing ; an effect which is mediated by oxytocin ( detillion et al . , 2004 ) . while little is known about the natural social organization of this hamster species ( wynne - edwards and lisk , 1989 ) , wound healing has also been studied in three species of peromyscus mice for which social organization is well characterized . in the two species of monogamous or facultatively monogamous peromyscus mice , wound healing was facilitated by social contact . this was not the case in the promiscuous species , and this species did not experience reduced cort with pair - housing ( glasper and devries , 2005 ) . this suggests that social housing was beneficial only to the species that normally resides with a partner . some recent findings in humans suggest that higher blood oxytocin and vasopressin levels may also be associated with faster wound healing in our species ( gouin et al . , 2010 ) . social environment during stress has been shown to impact gastric ulcer formation in male rats following a stressor , however , only the social environment at the time of testing and not prior housing affected ulcer frequency ( conger et al . , 1958 ) . ( 2005 ) found that group - housed chronically stressed female rats had less adrenal hypertrophy than solitary - housed , stressed females . social housing and support , social support reduces heart rate and alters the ratio of systolic to diastolic blood pressure after performing stressful tasks ( lepore et al . , 1993 , thorsteinsson et al . , 1998 ) . in mice and prairie voles , , 2003 , grippo et al . , 2007 ) , as well as other measures of cardiovascular health ( grippo et al . , 2011 ) . not all social interactions are equal , and the effects of social companionship may differ by partner familiarity , sex , age , species , and affective state . most studies of social buffering have explored one or two of these contexts at a time , but some evidence suggests that each of these can , but does not necessarily , impact the social buffering provided . in guinea pigs , the presence of both familiar and unfamiliar adults reduces hpa activation in response to a novel environment ; however for young ( pre - weaning ) guinea pigs , this effect is greater with the mother ( graves and hennessy , 2000 ) , and the salience of different individuals changes over the life course and varies with sex ( kaiser et al . , 2003 ) . in a pair of studies in male rats , armario et al . found the surprising result that cort levels in an open field were higher when paired with a familiar versus an unfamiliar individual ( armario et al . in prairie voles , brief separation from a mate , but not from a same - sex sibling , increased depressive - like behavior ( bosch et al . , 2009 ) . partner identity / familiarity was also found to be critical in a recently developed paradigm in which helping behavior is measured in rats . in this study , rats were motivated to rescue a trapped rat from restraint only if it was matched to their own strain , or a strain they had exposure to from birth ; they were uninterested in freeing rats of an unfamiliar strain ( ben - ami bartal et al . , exposure to nave , unshocked individuals can lessen stress responses relative to exposure to shocked individuals ( kiyokawa et al . , 2004 ) , similar to earlier findings in fear - conditioned rats ( davitz and mason , 1955 ) . future research on social buffering in rodents will hopefully make progress into questions of how and when social support is helpful , and what the optimal timing and type of that support is . in contrast , anxiety is a lasting state that is not an immediate response to the external environment . while stressful events can have impacts on social behavior , individual differences in anxiety also relate to variation in social behavior . for example , in humans , extraverted personality is associated with lower trait anxiety ( jylh and isomets , 2006 , naragon - gainey et al . , 2014 ) . in rodents , the social interaction test in which social interaction with a familiar or an unfamiliar individual are measured in an open arena was initially developed to be an ethologically relevant measure of anxiety behavior ( file and hyde , 1978 ) . social interaction times of individual male and female rats are positively correlated with exploratory behavior in classic tests of anxiety - like behaviors . for example , individuals that spend more time in social interaction are more likely to spend more time in the center region of an open field or the light portion of a light - dark box ( starr - phillips and beery , 2014 ) . maternal care , particularly maternal grooming behavior , has lasting effects on offspring anxiety behavior . high levels of maternal grooming are associated with reduced anxiety behavior in two paradigms : pup reunion after brief separation and / or handling , and natural , individual variation in maternal care ( reviewed in gonzalez et al . natural variations in the amount of time dams spend licking and grooming their new pups in the first week of life impacts their offspring in many ways that persist into adulthood . reduction in stress - reactivity in rats reared by high - licking dams appears to be mediated by increased glucocorticoid receptor expression in the hippocampus ( liu et al . , 1997 , weaver et al . , 2004 ) which enhances negative feedback on the hpa axis ( sapolsky et al . , 1985 , recent studies have shown that natural variation in maternal care affects a wide range of outcomes beyond anxiety behavior , including social behaviors . high levels of early maternal grooming are associated with increased play behavior in juvenile male rats ( parent and meaney , 2008 , van hasselt et al . , 2012 ) , increased social interaction in adult offspring of both sexes ( starr - phillips and beery , 2014 ) , and altered play dominance rank in adult female rats ( parent et al . , 2013 ) . effects of maternal contact have also been described in other species ; for example in prairie voles , maternal care and family structure have been associated with social investigation in adolescence , and changes in parental and mate - directed behaviors in adulthood ( ahern and young , 2009 , perkeybile et al . , 2013 ) . early experience of maternal care is sometimes associated with changes in oxytocin and vasopressin system regulation ( reviewed in veenema , 2012 ) , although it is not yet clear whether such changes underlie the known differences in social behavior . in a synthesis of findings across rodents , primates , and human studies , shelly taylor proposed that in addition to flight - or - flight responses to stress , females show pronounced tend and befriend responses to a stressor ( taylor et al . , 2000 ) . taylor related tending to parental nurturing behaviors , based on evidence that rat dams lick their pups ( tending ) following separation , that oxytocin appears to be more elevated in females following a stressor , and that oxytocin can act both as an anxiolytic and to promote affiliative behavior . befriending was related to the adaptive value of social support under stressful conditions , and its particular value for females that might be more vulnerable than males . whether or not shared history of maternal care - giving and defensive social behaviors best explains distinct female responses to stress , the existence of such sex differences in stress / social behavior interactions has been demonstrated repeatedly . we have discussed several examples in this review ; first , we described sex differences in the potency of particular stressors , for example crowding is particularly stressful for males , but is either calming to females or does not have major effects on physiological endpoints ( brown and grunberg , 1995 , kotrschal et al . , 2007 ) . even when the same event is stressful to both males and females , the sequelae of stress exposure may differ , for example stress impairs classical conditioning in females , which is the opposite of the effect found in males ( wood and shors , 1998 ) . sex differences are also present in social behavior responses to stress : conditions of stress , high cort , and high crf facilitate pair - bonding in male prairie voles , while the same conditions impair pair - bonding in females voles ( devries et al . , even where both sexes appear to be supported by their same - sex peers , male and female rats exhibit anxiety responses and adrenal reactions under different combinations of conditions ( westenbroek et al . , 2005 ) . some of these differences may relate to neurochemical variation in the brains of males and females . both oxytocin and vasopressin are important for social behavior , and there are sex differences in the production and release of these neuropeptides , the location and density of their receptors , and their roles in social behavior ( bales and carter , 2003 , carter , 2007 ) . there are many sex differences in human psychiatric disorders , most notably anxiety and depression , which some argue are based on sex differences in responses to stress ( bangasser and valentino , 2014 ) . one consequence of these findings is that we must study the interactions of stress and social behavior in both sexes in order to make meaningful conclusions about each sex . this idea is gaining greater appreciation within the scientific and funding communities ( mogil and chanda , 2005 , cahill , 2006 , zucker and beery , 2010 , couzin - frankel , 2014 , clayton and collins , 2014 , woodruff et al . , 2014 ) . the social environment can cause stress or ameliorate the impacts of stress , and social behavior responds to stress . these effects may happen all together or at different times , and vary with individual genetic background , experience , sex , species , and other factors . while it is not feasible to study all such factors in a single study , almost a century of research has helped to show which stressors are most impactful in males and females , and how such stress is reflected in neurochemistry . interaction time is a longstanding measure of social behavior , but recent studies have begun to employ more nuanced approaches for instance measuring helping behavior and distinguishing preferences for familiar versus unfamiliar individuals . while adverse social conditions ( from subordination to isolation ) are potent stressors , the interactions between stress and social behavior also offer multiple entry points into the study of stress resilience . stress resilience varies with early life social environment in particular with experience of maternal behavior and life history of exposure to mildly stressful experiences . resilience can also arise from the mitigating or buffering effects of positive ( or negative ) social interactions . there is a vast body of literature linking stress and social behavior and their roles in resilience . we may learn the most from these studies when we consider the social life of the organism , and look beyond group averages to individual variability .\noutput:\n" }, { "from": "agent", "value": "the neurobiology of stress and the neurobiology of social behavior are deeply intertwined . the social environment interacts with stress on almost every front : social interactions can be potent stressors ; they can buffer the response to an external stressor ; and social behavior often changes in response to stressful life experience . this review explores mechanistic and behavioral links between stress , anxiety , resilience , and social behavior in rodents , with particular attention to different social contexts . we consider variation between several different rodent species and make connections to research on humans and non - human primates ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: an increasing number of shortages in different drug classes has been reported globally over the last decade in various clinical settings , including oncology .119 a drug shortage is defined by the united states food and drug administration ( fda ) as a situation in which the total supply of all clinically interchangeable versions of an fda - regulated drug is inadequate to meet the current or projected demand at the user level .2 the american society of health - system pharmacists ( ashp ) considers a drug shortage as a supply issue that affects how the pharmacy prepares or dispenses a drug product or influences patient care when prescribers must use an alternative agent .3 in the united states , an increased number of new drug shortages of 211 , 267 , and 204 new drugs , were recorded in 2010 , 2011 , and 2012 , respectively , compared with 58 reported in 2004 . as of the third quarter of 2013 ,294 active drug shortages had been recorded by the university of utah drug information service ( uudis ) , which identifies drug shortages according to the fda definition .2 a call to action has been raised by the fda , the ashp , and the american society of clinical oncology ( asco ) among the professional societies actively involved in addressing this serious challenge . to raise awareness and assist health care providers in managing drug shortages , the fda provides on its website an updated national listing of drugs in short supply , as well as the number of new drug shortages prevented each year . similarly , acute and chronic shortages of key pharmaceutical products are being reported in the european union ( eu ) , and the european medicines agency ( ema ) currently publishes on its website a catalog of the drug shortages assessed by the agency , with information on the cause of the drug shortage and the status of the drug supply . as noted by the ema , such a list is not complete , because a substantial number of shortages are being actively managed at the country level , and specific information may be available from the appropriate national authorities in the local language .1416 in canada , the canadian pharmacists association , the canadian medical association , and the canadian society of hospital pharmacists are prompting discussion and management of this serious challenge .17,18 at the institutional level , analysis of survey data collected by the american hospital association in the united states , from 820 non - federal , short - term , acute care hospitals showed that almost all ( 99.5 % ) of the hospitals surveyed had experienced one or more drug shortages in the preceding 6 months , with at least half of the hospitals reporting shortages of 21 drugs .7 oncology was among the therapeutic areas most affected . rationing and restrictions resulting from short drug supplies had to be implemented by 78 % of the hospitals . the majority of hospitals ( 77 % ) reported not being informed in advance of a drug shortage by the drug manufacturers , wholesalers , or distributors , nor being informed of its cause ( 67 % ) or duration ( 56 % ) . shortages were frequently associated with increased expenditures because of higher drug costs , more expensive treatment alternatives , or purchase of excess inventory .7 chemotherapeutic agents , such as liposomal doxorubicin , 5 - fluorouracil , bleomycin , cytarabine , and fludarabine , as well as analgesics , antibiotics , and parenteral nutrition products , which are often used in patients with cancer , represent current examples of first - choice and essential drugs or products that may be critically affected by shortages .1,3,6,7 the purpose of this article is to review the literature regarding the causes of drug shortages and their impact on patient care , ethical concerns , and management strategies , specifically in the therapeutic area of oncology . we will then provide an assessment of how biosimilars may magnify or mitigate biopharmaceutical shortages . according to the ashp , there are many factors that contribute to drug shortages , including limitations in the availability of active or inactive ingredients , manufacturing delays , or poor compliance with current good manufacturing practice ( gmp ) guidelines .20 other causes may be related to an increased demand for a specific pharmaceutical product , including changes in clinical standards and inventory practices .3,14,19,20 it is important to note that many of these causes are interrelated . for example , if it becomes known that a manufacturer is exiting the market for a drug , this may cause hoarding and result in a worsened shortage .20 according to the results of an fda review released in 2011 , the most frequent causes of drug shortages are manufacturing problems ( 43 % ) , followed by manufacturing or shipping delays ( 15 % ) , and lack of availability of the active pharmaceutical ingredient ( 10 % ) .2 a similar finding has been reported by ema , which found that disruptions in manufacturing supply had caused acute and chronic shortages of key pharmaceutical products in the eu , leading to changes in prescriptions and patient allocation . consequently , the ema has underscored the responsibility of marketing authorization holders to ensure appropriate and continued availability of medicinal products for human use , to meet the needs of patients , by following current gmps and resolving any related compliance issues .14 a recent report from the international society of pharmaceutical engineering ( ispe ) provided further details on the manufacturing steps potentially involved in generating drug shortages on a global scale , particularly of sterile injectable products .19 after analysis of the six key manufacturing and testing systems known as quality systems ( qs ) , they concluded that drug shortages were frequently associated with aseptic processing equipment problems and production system issues during product development or technology transfers .19 shortages of first - choice or essential drugs have a substantial negative impact on patient management , safety , and overall clinical outcomes , as summarized in table 1 . delays in treatment , as well as the use of alternative , suboptimal treatment options , increased medication errors , increased length and number of hospitalizations , increased case management burden for health care professionals , increased health care costs , and limitations for clinical trials are all negative consequences found to be associated with drug shortages .1,35,2128 recent data published in the new england journal of medicine showed that 83 % of the 214 surveyed physicians who routinely prescribe cancer drugs could not give the chemotherapeutic agent of choice to their patients , at least once in a period of 6 months , because of a drug shortage .1 the most frequent shortages reported in this survey involved leucovorin ( experienced by 66 % of physicians ) and liposomal doxorubicin ( 62 % ) . as a consequence , switching from the preferred chemotherapy regimen to an alternative optionapproximately 43 % of physicians indicated delays in treatment ; in addition , 29 % and 20 % of them reported omitted or reduced doses , respectively . in addition , 37 % of the responders had to choose which patients would be excluded from the standard - of - care regimen .1 for medications used in oncology , a detailed analysis of a survey conducted at a new york city hospital on the effects of drug shortages on outpatient use showed that a shortage of 12 medications was reported in 2010 and of up to 22 products in 2011 , according to the ashp definition of shortage . one - third of the shortage - related treatment changes involved use of less effective treatment regimens or of more toxic alternative options .22 similarly , results from another recent survey conducted among ashp members , focused on injectable drugs prescribed to patients with cancer , revealed that almost all ( 98 % ) of the 358 surveyed pharmacy directors had experienced a drug shortage in the previous 12 months , 62 % of them reported use of alternative regimens , and 25 % had noted adverse events associated with a drug shortage .26 clinical trials based on evaluation of new agents in combination with standard - of - care treatments may also be significantly affected by drug shortages , thus hampering development of new therapeutic agents for patients with cancer in need of more effective treatment options .1,27,28 in their survey , gogineni et al reported delays in study drug administration and patient enrollment owing to a drug shortage in 12 % of clinical trials analyzed .1 other investigators have confirmed that drug shortages may substantially compromise clinical trial recruitment in oncology .27,28 about half of the 400 trials funded by the national cancer institute , which were actively enrolling patients , encountered shortage of one of the 22 anticancer drugs listed by the fda as in short supply in 2012 . in addition , shortages involving eight anticancer drugs were reported for 23 different protocols evaluated by the cancer and leukemia group b in seven different cancer types , between the end of 2010 and march 2012 . choosing treatment options for patients in need of medications in short supply raises a number of ethical implications that may be challenging for all stakeholders , including clinicians , patients , pharmacists , nurses , health systems administrators , and payers .2932 multiple factors are being identified that may help with prioritizing treatment for patients whose care and clinical outcomes are challenged by drug shortages , including goals of care , drug indication , treatment cycle , and availability of suitable alternatives . overall , treatment allocation decisions should be based on clinical considerations rather than on a patient s insurance status and / or financial resources . patients may be prioritized for treatment with a drug in short supply 1 ) if their condition matches a medication s indication ; 2 ) if the goal of care is curative rather than palliative ; 3 ) if a patient is to receive the drug as a first - line rather that second - or third - line treatment ; 4 ) if treatment is ongoing rather than a new start ; and / or 5 ) if no other suitable , alternative options are available . fair strategies and proactive measures for the management of potential drug shortages are advocated by clinicians and the health care systems or practices in which they operate to provide the best care possible for all of their patients .2932 in view of the serious consequences associated with drugs in short supply , a number of strategies are being devised and implemented on a global scale by regulatory authorities , health care providers , professional societies , and manufacturers to prevent and manage drug shortages , and in particular , short supplies of essential medications .20,3341 the us fda safety and innovation act mandated drug manufacturers to communicate impending drug shortages with at least a 6 - month advance notice or as soon as possible ahead of the actual shortage .33 in the more recent strategic plan for preventing and mitigating drug shortages , released in 2013 , the fda expanded the early notification requirements for temporary drug shortages and product discontinuations , and added medically important biologic agents to the list of relevant products .34 according to the fda , a product is considered a medically necessary product when it is used to treat or prevent a serious disease or medical condition for which there is no alternative drug in adequate supply that is judged by medical staff to be an appropriate substitute .35,36 immune gamma - globulin preparations for intravenous use produced by different manufacturers represent a recent example of a biologic product reported to be in short supply in the united states and actively monitored by the fda for potential shortage . in addition , in its strategic plan for preventing and mitigating drug shortages , the fda communicated plans to address the manufacturing and product quality issues often underlying drug shortages , with a broader use of manufacturing metrics and incentives to support high - quality manufacturing , as well as the evaluation of risk - based approaches to identify early signs of manufacturing and quality issues .34 asco has reiterated in a recent statement its concern for the high number of drug shortages currently reported , particularly those involving sterile , injectable products , and has expressed support for adoption of measures that can facilitate drug supply monitoring by the fda and ensure adequate supply of key drugs for the treatment of patients with cancer .37 this communication follows a letter to the fda in concert with the national coalition for cancer research , supporting the fda proposed rule on drug manufacturing interruptions , the provision that requires manufacturers of approved drugs or biologic products to notify the fda of any discontinuation or manufacturing interruption that may compromise the drug supply to patients in the united states .38 in europe , a study led by the european society of medical oncology ( esmo ) , in collaboration with the world health organization ( who ) and other professional societies , is collecting data on actual availability and affordability of approved anticancer drugs in europe to identify current challenges , and to provide the eu and ema with information on current drug supply for patients with cancer . once a drug is in short supply , determination by the health care providers of the extent , cause ( s ) , and estimated duration of the drug shortage , evaluation of the available stock , limitation of waste , and the selection of appropriate , alternative formulations or identification of potential supply from alternative , reliable sources are all operational strategies that may help in limiting negative impacts on patient outcomes and health care costs .30 the results of the surveys and cases discussed in this review indicate that the pharmaceutical products most vulnerable to a shortage are typically sterile injectable products . further , products whose exclusivity has expired ( and thus , generic versions are available ) are particularly at risk of a shortage , likely because smaller profit margins make these products highly sensitive to changes in economic and market forces . notably , biologic products ( innovators ) are not typically associated with shortages . however , with the emergence of an abbreviated approval pathway for biosimilars , it is reasonable to question whether these products may also be vulnerable to shortages . nevertheless , a shortage of monoclonal antibodies ( mabs ) could have devastating consequences for cancer patients , with a far greater impact than previously reported shortages . the term biosimilar is defined as a biologic product that is highly similar to the reference biologic product , notwithstanding minor differences in clinically inactive components , as stated in section 351 ( i ) of the us public health service act .42 according to the guidelines released by the regulatory authorities , similarity in safety , purity , and potency encompass the criteria set by the fda for the development and approval of biosimilars in the united states ; quality , safety , and efficacy are the biosimilarity criteria set by the ema for evaluation and approval in europe .4348 the characteristics of biologic drugs such as mabs , summarized in table 2 in comparison with those of conventional small - molecule drugs , underscore the complexity of these pharmaceutical products and the need for extensive evaluations in the development and production of biosimilar mabs .44 a number of essential , widely used biologic agents , such as the mabs trastuzumab ( herceptin ) , rituximab ( rituxan / mabthera ) , bevacizumab ( avastin ) , and cetuximab ( erbitux ) will lose market exclusivity within the next few years in the united states and in europe ( table 3 ) , thus potentially creating significant changes in their availability . in the united states , rituximab will lose exclusivity in 2017 , and both trastuzumab and bevacizumab in 2019.48 examples of emerging potential biosimilars , which are being actively developed according to guidelines and with substantial investments for patients with cancer , include trastuzumab ( eg , pf - 05280014 [ pfizer inc , new york , ny , usa ] , ct - p6 [ celltrion , incheon city , south korea ] , abp 980 [ amgen inc , thousand oaks , ca , usa ] , and bcd - 022 [ biocad , moscow , russia ] in breast cancer ) ; rituximab ( eg , pf - 05280586 [ pfizer inc ] , gp2013 [ novartis international ag , basel , switzerland ] , bcd - 020 [ biocad ] , and rtxm83 [ mabxience sa , lugano , switzerland ] in non - hodgkin s lymphoma ) ; and bevacizumab ( eg , pf - 06439535 [ pfizer inc ] and bcd - 021 [ biocad ] ) .4959 the potential biosimilar mab pf - 05280014 ( pfizer inc ) has a structure comparable to that of trastuzumab , and similar physicochemical and functional characteristics in in vitro assays .50,51 results from a double - blind , three - arm study ( reflections b327 - 01 ) conducted in healthy male volunteers demonstrated similarity in pharmacokinetic and safety profiles between pf - 05280014 , trastuzumab sourced in the us , and trastuzumab sourced in the eu ( trastuzumab - eu ) .50 the potential biosimilar mab ct - p6 ( celltrion ) has demonstrated similarity to trastuzumab in pharmacokinetic and safety profile analyses , and comparable response rates in patients with her2 - overexpressing metastatic breast cancer in combination with paclitaxel .52 pf - 05280586 ( pfizer inc ) has demonstrated similarity to rituximab - eu ( mabthera ) in preclinical studies , including tryptic peptide maps and complement - dependent cytotoxicity assays .54 similarity was also observed in the pharmacokinetic and pharmacodynamic profiles between these two biologic agents . pf - 05280586 has been evaluated in a phase i study in patients with rheumatoid arthritis .55 in vitro evaluation of mab gp2013 ( novartis international ag ) demonstrated physicochemical properties similar to those of the originator rituximab in primary and secondary structure , post - translational modifications , and size variants .56 functional , non - clinical studies , including in vitro cell - based bioassays and binding assays , indicated biological properties similar to those of the reference mab . potential causes of future shortages of biologics , specifically mabs , produced by non - originator manufacturers might be linked to demand that exceeds supply , problems in the supply chain ( eg , reduced yields resulting in a reduction in supply availability ) , product quality issues ( eg , contamination by exogenous microorganisms of injectable preparations ) , facility delays associated with other products , capacity and scheduling constraints , distribution delays , or outright discontinuation , as observed for conventional pharmaceutical products .2,14,19 further issues , not reported with generic drugs or other small - molecule parenteral products , may specifically affect production of mabs when manufacturing facilities are transferred during a product lifecycle , owing to the complex multi - chain structure and the post - translational modifications occurring during production of mabs in in vitro systems , which may add significant risk to a manufacturer s ability to produce high - quality biologics and meet existing clinical demand . there are measures that biologics manufacturers can implement to reduce the risk of incurring a shortage of their product . in addition to compliance with good manufacturing processes , it has been recommended that strategies such as inventory and raw material management , maintenance of multiple facilities , and preservation of the distribution network be adopted as best practices . furthermore , health care providers should assess a manufacturer s capability to supply the product as one of the criteria included in the formulary review process .60 it remains to be seen whether , in the future , there will be interruptions in the supply of key biologics , and whether the introduction of an abbreviated biosimilar approval pathway will compound the issue . for example , a shortage of a biosimilar for filgrastim was observed in europe , and one may wonder whether this was an anomaly or if it was a symptom of a more systematic problem .61 there are differences in the processes and associated complexities between small molecules and biologics , with regard to manufacturing of active pharmaceutical ingredients , drug substances , and drug products . the authors do not stipulate that the individual or combined complexities associated with manufacturing of either small molecules or biologics are greater than the other , or debate which complexities have the greater potential to disrupt supply availability and induce shortages . biosimilars are equally susceptible to aseptic manufacturing challenges and associated potential batch failures as originator biologics and sterile small molecule originator and generic products . however , it is important to note that biosimilar shortages present clinical challenges different from those involving small - molecule drugs , such as concerns about safety due to the presence of potential aggregates , fragments , or contaminants from the expression systems , as well as concerns related to potency due to potential changes in binding specificity or effector functions of the biologic . stability upon storage of complex molecules such as mabs and immunogenicity related to the switching of biologic products represent further important challenges in the use of biologics that may influence biosimilar shortages .44,47 many originator and generic products are produced in an interdependent supply chain model with aone : one : many relationship for active pharmaceutical ingredients manufacturing , drug product manufacturing , and final branded product , respectively . in an interdependent supply chain , a disruption in manufacturing has the potential to limit supply availability of several interchangeable products concomitantly , thereby inducing a shortage . in the current eraone : one : one relationship for drug substance manufacturing , drug product manufacturing , and final branded product , respectively . in an independent supply chain model , a disruption in one supply chain limits the impact to one product , and if the impacted product is not interchangeable with another , then there is a shortage . the introduction of biosimilars with the potential for interchangeability with innovator biologics would mitigate the risk of shortages associated with disruption of supply in an independent supply chain for either innovator biologics or biosimilars . currently , a few manufacturers are accelerating development of potential biosimilar mabs to full commercial scale production , in compliance with the fda / ema standards for biosimilarity , gmp guidelines , and other regulatory requirements .5059 as recommended , the complexity of biologics and the need to produce them in host - cell systems require careful validation of the multi - step manufacturing process and accurate analytical and biological testing beyond their initial characterization , to ensure consistent safety and efficacy for biosimilars . in addition , monitoring of the final product quality is of particular importance when changes are made in the manufacturing process , the site of production , packaging , or the delivery device . as indicated by the fda , evaluation of the functional activity of a biosimilar may provide an estimate of its stability as well as an indication of the consistency achieved in the manufacturing process .45,46 in considering the therapeutic potential of emerging , new products in the biologics field , it is also important to differentiate biosimilar mabs from intended copies , which are not developed according to fda / ema standards and are marketed outside of recognized biosimilar approval pathways , thus creating safety and / or efficacy concerns for their clinical use . as proposed by the ema working party on similar biological medicinal products , biologics for which there is no demonstrated similarity in physicochemical characteristics , safety , and efficacy to a licensed , reference biologic product should not be referred to as biosimilars , but as me - too biologics or noninnovator biologics .62,63 following approval for use in patients with cancer of biosimilar mabs developed according to fda / ema standards , future availability of high - quality biosimilars will depend on compliance with gmp guidelines by the biosimilar manufacturers , as recommended by the regulatory agencies , together with implementation of a reliable supply chain and the ability to scale up production in case of supply disruption in other manufacturers supply chains . in this regard , the ispe survey found that key success factors for the prevention of drug shortages include robust qs to ensure compliance with manufacturing regulations , a strong qs track record and gmp inspection history , the ability and the resources to quickly react to a potential risk of shortage , as well as effective communications with the regulatory authorities .19 significant progress is being made in the development and evaluation of potential biosimilar mabs for patients with cancer , with promising results in preclinical and clinical studies . in addition , the first anti - inflammatory biosimilar mab ( infliximab ) has been recently approved in europe and in canada .64,65 accelerated development of potential biosimilar mabs to full commercial - scale production , through substantial , long - term investments by reliable manufacturers , may contribute to minimize some of the potential causes of recent or current drug shortages , such as limitations in supply , delays in the supply chain , issues with quality of the manufactured pharmaceutical products , or discontinuations . the future availability of well characterized and fda - / ema - approved biosimilars , developed by manufacturers that comply with good manufacturing process and follow best practices for reducing the risk of shortage , may thus help in preventing potential shortages of essential biologic therapeutic agents , and ensure patient access to effective and safe treatment options , according to the recommended standards of care .\noutput:\n" }, { "from": "agent", "value": "acute and chronic shortages of various pharmaceuticals and particularly of sterile injectable products are being reported on a global scale , prompting evaluation of more effective strategies to manage current shortages and development of new , high - quality pharmaceutical products to mitigate the risk of potential future shortages . oncology drugs such as liposomal doxorubicin and 5 - fluorouracil represent examples of first - choice drugs critically affected by shortages . survey results indicate that the majority of hospitals and practicing oncologists have experienced drug shortages , which may have compromised patient safety and clinical outcomes , and increased health care costs , due to delays or changes in treatment regimens . clinical trials evaluating novel agents in combination with standard - of - care drugs are also being affected by drug shortages . clinical and ethical considerations on treatment objectives , drug indication , and availability of alternative options may help in prioritizing cancer patients involved in active drug shortages . the united states food and drug administration and the european medicines agency have identified manufacturing problems , delays in supply , and lack of available active ingredients as the most frequent causes of recent or ongoing drug shortages , and have released specific guidance to monitor , manage , and reduce the risk of shortages . the upcoming loss of exclusivity for a number of anticancer biologics , together with the introduction of an abbreviated approval pathway for biosimilars , raises the question of whether these products will be vulnerable to shortages . future supply by reliable manufacturers of well characterized biosimilar monoclonal antibodies , developed in compliance with regulatory and manufacturing guidelines and with substantial investments , may contribute to prevent future biologics shortages and ensure access to effective and safe treatment options for patients with cancer . preclinical and clinical characterization is ongoing for potential biosimilars of trastuzumab , rituximab , and bevacizumab , with promising results ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: evidence suggests that the glucagon - like peptide - 1 receptor ( glp - 1r ) agonist exendin - 4 ( ex-4 ) , used in the treatment of type 2 diabetes mellitus , also displays neuroprotective properties in multiple cellular and in vivo models of neurodegenerative disorders . evidence of its potential for the treatment of these neuropathologies has been accumulated rapidly . the drug appears to be well tolerated and its use in the clinic , albeit for a different indication , obviates many of the obstacles seen with other putative treatments for pd . a key factor with ex-4 is that despite being a relatively large peptide it readily enters the cns . ex-4 is a potent agonist at mammalian glp - 1rs and promotes insulin secretion from beta islet cells . additionally , ex-4 protects beta cells from cytotoxic insults and also promotes their proliferation and neogenesis from precursors . this suggests that similar mechanisms could be responsible for neuronal cell survival in animal models of neurodegenerative disorders in which ex-4 has been shown to be effective . neuroprotective effects have been shown in vitro to be glp - 1r dependent by the use of the glp - 1r selective antagonist ex - ( 9 - 39 ) and also more recently in glp - 1r knockout mice . a possible mechanism of action for ex-4 is that it causes a reduction of deleterious inflammation . however , ex-4 has also been shown to stimulate neurogenesis in the adult rat , which constitutes a possible means by which the peptide might restore function in a damaged system . in the context of pd , a potential influence could also be activation of da d3 receptors , which are thought to be involved in stimulation of neurogenesis , as demonstrated in the rat 6 - ohda model of pd . we have , therefore , decided to determine whether the neuroprotective effect of ex-4 is selectively glp - 1r mediated by use of ex - ( 9 - 39 ) in our 6 - ohda model . secondly , since stimulation of da d3 receptors has been shown to protect da neurons against 6 - ohda - induced damage and promote neuronal survival as well as stimulate neurogenesis in the subventricular zone ( svz ) , we wanted to evaluate the possible role of d3 receptors in ex-4-mediated neuroprotection by using nafadotride ( naf ) , a selective d3 receptor antagonist . finally , we wished to determine the effects of ex-4 on brdu + cell numbers in the svz and sn of 6 - ohda - lesioned rats and how this might be altered by ex - ( 9 - 39 ) or naf . all drugs and reagents were purchased from sigma - aldrich ltd . , uk , unless otherwise specified . male wistar rats ( 250300 g ) were purchased from harlan , uk , and housed under standard conditions in an animal care facility with controlled temperature , humidity , and fixed light / dark cycles . all experimental procedures were carried out in accordance with institutional and home office regulations ( 1986 scientific procedures act , uk ) and the helsinki agreement . rats were anaesthetised using 5 % isoflurane ( abbott , uk ) v / v in o2 for induction ( 1.5 % for maintenance ) and then secured on a stereotaxic frame ( david kopf , usa ) . prior to surgery , animals were injected with pargyline ( 50 mg / kg ) and desipramine ( 25 mg / kg ) intraperitoneally ( i.p . ) . this was done to minimize the metabolism of 6 - ohda and to preserve the noradrenergic system , respectively . the animals were , then , injected with 6 - ohda hydrochloride ( 8 g / 2 l ) dissolved in saline containing 0.2 % ascorbic acid into the left medial forebrain bundle ( from bregma in mm ; a 4.3 , l 1.4 , and v 8.2 ) . infusion was performed at a rate of 1 l per minute , and a 5 - minute period was allowed for diffusion of the toxin after which the syringe was slowly retracted . ( 0.5 g / kg ) or saline twice a day ( 10 am and 5 pm ) , for a period of one week , seven days after the administration of 6 - ohda . injections of the compound 1 g / kg or saline twice a day 5 min prior to ex-4 injection . in another group of rats ( 1 mg / kg ) , a dose that is very largely d3 selective , or saline twice daily , also 5 min prior to ex-4 . the dose of naf was based upon studies also using this dose with apparent d3 selectivity . in a separate set of treatment groups brduwas injected to investigate if lesions and treatment with ex-4 altered cell proliferation in the svz . brdu is a brominated thymidine analog able to incorporate into the dna of actively dividing cells and is currently a frequently used measure of presumed neurogenesis . injections of the compound ( 50 mg / kg twice a day ) 10 min after injection of ex-4 and the antagonists . these groups were used exclusively for brdu immunohistochemistry and at the end of the brdu treatment were allowed a 4 - day washout period to excrete unincorporated brdu . fourteen days after surgery , animals were injected with 0.05 mg / kg of apomorphine subcutaneously ( s.c . ) in saline , and after 15 minutes each rat was placed in a circular test arena . we have used longer assessment periods in the past but found that these simply revealed quantitatively larger but qualitatively very similar numbers of turns between groups and were , therefore , deemed an unnecessary use of time . this accords with procedures we have tested and used previously . animals were anaesthetised with isoflurane ( 5 % induction v / v in o2 and 1.5 % maintenance ) and then secured in a stereotaxic frame . microdialysis probes , constructed as described previously and with a membrane length of 4 mm ( whitton et al . , 1991 ) , were bilaterally implanted into the striatum ( mm from bregma a + 0.2 , l 3 , and v 8 ) ; dental screws were placed within but not penetrating the skull ; the assembly was fixed solidly with dental acrylic ( duralay , reliance dental mfg . after surgery , animals were placed in individual microdialysis cages and allowed to recover for 24 hours before dialysis . the following day rats were perfused with artificial cerebrospinal fluid ( acsf ) ( 2.5 mm kcl , 125 mm nacl , 1.18 mm mgcl26h2o , and 1.26 mm cacl2 ) ph 7.4 at a rate of 1 l / min using harvard apparatus model 22 syringe infusion pumps . after a stable baselinewas established , around 1 hour , samples were collected every 30 minutes and after sample four normal acsf was switched to one containing 100 mm kcl , with na concentration reduction to maintain osmolarity , for 30 minutes before returning to normal acsf for the rest of the experiment . samples were frozen immediately at 80c and analysed for da within one week using high - performance liquid chromatography ( hplc ) with electrochemical detection . the hplc system comprised a p580 dionex , piston pump ( mobile phase : sodium acetate ; 90 mm , citric acid ; 35 mm , edta , 0.34 mm ; 1 - octane - sulfonic acid , 0.06 mm and 5.5 % methanol with ph was adjusted to 4.2 using citric acid , flow rate of 0.65 ml / min ) connected to a triathlon refrigerated ( 4c ) autosampler ( spark - holland , the netherlands ) and a c18 reverse phase column maintained at 35c ( ods 3 wm , 4.6 mm i.d . usa ) and protected by a microsorb guard column ( c185 wm , 4.6 mm i.d . detection was made with an antec - intro electrochemical detector ( antec leyden bv , the netherlands ) fitted with a vto3 flow cell ( vcell + 625 mv filtered to 5 abu with range set on 0.5 na / volt ) . data capture was achieved and analysed by a pc system ( dell corporation , usa ) equipped with chromperfect for windows software ( justice innovations chromatography data systems , ca , usa ) . da peak areas were converted to amounts using the external standard method . animals were always sacrificed on completion of microdialysis ( two weeks after 6 - ohda surgery ) . rats were lightly anaesthetised with 5 % isoflurane v / v in o2 in order to minimise stress and decapitated , and the brains were rapidly removed , flash frozen on dry ice , and stored at 80c until use . one day before histology , frozen brains were taken from 80c storage and stored at 20c overnight to facilitate dissection and cryostat sectioning . striata were removed using a stainless steel punch , placed into microcentrifuge tubes containing 1 ml ice cold 0.01 m pbs and homogenised for da determination . homogenates were centrifuged at 9000 g for 15 minutes , and duplicates of 50 l aliquots of the supernatant were treated with 0.2 m perchloric acid containing ascorbic acid ( 0.2 m ) and edta ( 0.2 m ) to precipitate the cell debris . the 50 l homogenate and 10 l perchloric acid mixtures were centrifuged again at 9000 g for 15 minutes at 4c , and 25 l of this supernatant was injected in the hplc system to determine tissue da concentration in pg / gram of striatal tissue . slide mounted 12 m thick cryostat sections from frozen brain blocks were removed from the freezer and allowed to equilibrate to room temperature for 30 minutes before fixation in 4 % w / v paraformaldehyde containing 1 % w / v glutaraldehyde in deionised water for 5 minutes at 0c . following rinsing in 0.01 m pbs for 5 minutes , sections were dehydrated through graded ethyl alcohol concentrations , and endogenous peroxidase activity was blocked by incubation in 0.3 % h2o2 in methanol for 10 minutes . the sections were then rehydrated , and nonspecific immunoreactivity was blocked using 10 % swine serum in 0.01 m. pbs for 10 minutes . sections were then incubated in primary antibody ( anti - th igg raised in rabbit at 1 : 1000 in 0.01 m pbs ) for 15 hours at 4c . after rinsing , the sections were incubated sequentially in biotinylated swine anti - rabbit antibody 1 : 500 in 0.01 m. pbs and abc ( vector labs ltd . ) immunoreactivity was visualized through incubation in 0.5 mg / ml 3,3 - diaminobenzidine ( dab ) , containing 0.009 % h2o2 in 20 ml of dab solution , for 2 minutes at room temperature . the sections were counterstained in harris haematoxylin , dehydrated , cleared , and mounted for examination . digital images were captured using a leica dc500 system and the manufacturer 's software . for brdu histology , slide mounted 12 m thick cryostat sections from frozen brain blocks were removed from the freezer and allowed to dry for 24 hours before fixation in 75 % acetone and 25 % absolute alcohol for 5 minutes . slides intended for brdu immunodetection were also preincubated in 2 m hcl for 30 min at 37c to facilitate antigen retrieval . the brdu antibody used was a goat monoclonal raised against brdu ( 1/1000 ) followed by a secondary rabbit anti goat - polyclonal antibody with a biotin tag ( 1/500 ) . brdu staining was quantified , by an investigator unaware of the treatment protocol , by manually counting cells over a set distance along the lateral ventricular wall viewing sagittal sections . data obtained from apomorphine tests , tissue da , th , and brdu immunohistochemistry were subjected to one - way analysis of variance ( anova ) and post hoc bonferroni multiple comparison tests to compare difference between selected treatments . microdialysis data were subjected to a two - way anova with a post hoc bonferroni multiple comparison test . in both cases , the 6 - ohda - lesioned rats treated with apomorphine two weeks after surgery made intensive turning behavior compared to sham animals that do not show turns ( figure 1 ) . circlingwas significantly reduced by cotreatment with ex-4 , an effect attenuated by both ex-9 - 39 and naf ( figure 1 ) . neither of the antagonists or ex-4 administered alone to nave animals had any effect on apomorphine circling . in sham groupsthe mean da content was 6.81.1 pg / g of tissue while in 6 - ohda - only groups there was a substantial reduction in da levels ( 0.770.2 pg / g ) . in groups cotreated with ex-4 tissue da was restored to 5.20.33 pg / g , an effect reversed by both ex-9 - 39 ( 0.190.1 pg / g ) and , to a lesser extent at the doses employed here , by naf ( 2.60.53 pg / g ) ; both results were significantly different from 6 - ohda + ex-4 ( figure 2 ) . animals treated with either ex-4 , ex-9 - 39 , or naf alone did not show significant changes in their striatal da tissue content compared to control groups . basal and k - evoked striatal extracellular da were assessed using in vivo microdialysis , with da release shown as fmol / 10 l of sample . basal da levels in control groups were 391.2 fmol / 10 l , increasing to 1108113 fmol / 10 l when stimulated with 100 mm kcl and rapidly returning to baseline on removal of this stimulus ( figure 3 ) . in 6 - ohda - only - treated rats basal da was reduced to 83 and k - induced da release decreased to 18834 fmol / 10 l . it is noteworthy that the decrease in extracellular da was proportionately less than tissue da in lesioned animals . rats given 6 - ohda and then cotreated with ex-4 displayed a significant restoration of both basal ( 289 fmol / 10 l ) and k - evoked ( 78087 fmol / 10 l ) extracellular da ( figure 3 ) .6 - ohda rats cotreated with ex-9 - 39 + ex-4 displayed drastically reduced levels of both basal and k - induced extracellular da compared with 6 - ohda and ex-4 groups ( figure 3 ) , as did ex-4 rats cotreated with naf ( basal 51 fmol / 10 l and k - induced 12521 fmol / 10 l ; figure 3 ) . da levels in sham animals treated with ex-4 , ex-9 - 39 , or naf only were statistically not different from the sham groups ( data not shown ) . th staining is shown both qualitatively ( photomicrographs ) and quantitatively ( figures 4 ( a ) and 4 ( b ) ) . control groups had a high level of th expression ( colour intensities of 215322853 ) while groups treated with 6 - ohda and tested after two weeks showed an approximate 80 % decrease in th content compared to controls ( figure 4 ) , an effect reversed by ex-4 ( 182932620 units ) . in 6 - ohda and ex-4 groups which also received ex-9 - 39 , thdecreased to 32251893 units , while after cotreatment with naf intensities were decreased to 56802854 units ( figure 4 ) . groups which were treated with ex-4 , ex-9 - 39 , or naf only were not significantly different from controls ( data not shown ) . brdu was coadministered to treatment groups to investigate cell proliferation in the rat svz and sn while dab staining was used to visualise brdu antibody binding . results were expressed as numerical density calculated as numbers of dab positive cells per section . in the svz , 6 - ohda - only - treated animals showed a significant increase in brdu + cells , which was reversed by ex-4 . in turn , the effects of ex-4 were markedly attenuated by ex - ( 9 - 39 ) ( figures 5 and 6 ) . in the sn , the reverse was seen .6 - 0hda dramatically reduced the count of brdu + cells , and this was largely reversed by ex-4 . both antagonists decreased the effect of ex-4 , resulting in reductions in brdu + cells similar to that seen with 6 - ohda alone ( figures 5 and 6 ) . many studies , both in vitro and now in vivo , strongly indicate the therapeutic potential of ex-4 in neurodegenerative disorders where glp - 1rs appear to be the key in mediating these effects . the present report indicates that glp - 1rs as well as da d3 receptors are required for neuroprotective effect of ex-4 in the 6 - ohda rat model of pd . thus , when the specific antagonist of glp - 1r ex - ( 9 - 39 ) was coadministered with ex-4 in 6 - ohda rats , animals displayed increased contralateral circling , reduced extracellular as well as tissue da levels , and also decreased snc th expression , a complete reversal of the previously observed effects of ex-4 . glp - 1rs are also expressed throughout the central nervous system , with binding sites identified in both the human and the rat brain , and are produced by neuronal cells in discrete regions of the cns . more recently , the neuroprotective role of glp - 1rs was demonstrated in an mptp mouse model of pd . ex-4 was able to protect normal mice against mptp - induced damage of the sn , whereas no effect was observed in glp - 1r deficient mice , indicating that the glp - 1r is instrumental for ex-4-mediated neuroprotection . however , broadly , it seems that there may be a rescue of dying neurons that are not yet fatally damaged , quite possibly as a result of the well - known anti - inflammatory properties of these molecules . alternatively , it has been suggested that glp - 1 and ex-4 are able to promote de novo neurogenesis as indicated by the findings of bertilsson et al . . in our studies we have observed increased accumulation of brdu + cells in the svz of 6 - ohda - treated animals , an effect which was reduced significantly when animals were given ex-4 , while in the sn the opposite effect was seen with reduced brdu + cells in 6 - ohda - treated rats and a reversal with ex-4 . the effects of ex-4 were themselves completely reversed by ex - ( 9 - 39 ) , indicating a glp - 1 receptor specific primary action . additionally , the effects of ex-4 in the svz and sn were attenuated by naf , indicating that da d3 receptors play a role in the overall process . d3 receptors are localized on da neurons of the adult sn as well as upon the surface of progenitor cells in the svz , where their stimulation appears to elicit maturation and migration of these cells . these observations underpinned our interest in the possible role of these receptors as facilitators of glp - 1r - mediated neuroprotection . interestingly , evidence has been accumulated from animal models suggesting that d3 receptor stimulation is neuroprotective . selective agonists of this receptor subtype are effective in both mptp - treated mice and 6 - ohda rat models of pd . neuroprotective effects of these agents are abrogated in the presence of the d3 antagonist a-437203 and also in mice lacking d3 receptors . evidence from both in vitro and in vivo studies suggests that protective effect of pramipexole , which is a preferential d3 agonist used in the treatment of early pd , is dependent on brain - derived neurotrophic factor ( bdnf ) signaling . in vivo evidencedemonstrates that infusion of a d3 preferring agonist into lateral ventricles doubled cell proliferation in the svz and the olfactory bulb whereas no such effect was observed with a d1 preferring agonist or in the presence of a d3 antagonist . in addition , proliferation of cultured svz cells treated with various da agonists correlated with affinity of the agonist for the d3 receptor and was reduced in the presence of an antagonist of this receptor subtype . d3 receptor stimulation not only results in svz cell proliferation but stimulated cells also display neuron specific markers in both svz and the rostral migratory stream . moreover , a 2 - week infusion of a d3 preferring agonist into the third ventricle resulted in a sixfold increase in brdu - labeled cells in the sn which were also th positive and displayed a neuronal phenotype . the linkage between glp - 1r and d3 receptors has not been studied directly as far as we are aware but is of obvious interest and has been tentatively suggested . our choice of the naf dose was based upon previous studies where there was a clear selectivity for the use of a 1.0 mg / kg . indeed , in one study a question raised was whether this dose is sufficient to determine the effect of d3 receptor blockade . the effects of 6 - ohda on brdu incorporation into cells in the svz are themselves somewhat controversial . progenitor cell numbers in the svz have been observed to decrease in response to dopaminergic denervation while in other studies increases are observed . evidence for neurogenesis in the sn is also controversial with some studies reporting increased levels of this phenomenon in mptp models while others using 6 - ohda - treated rats report no evidence of sn neurogenesis . results obtained from human pd patients demonstrate reduced cell proliferation in the svz , and changes in adult neurogenesis resulting from neurodegenerative disorders likely depend on selected neuronal populations affected ; and the role of neurogenesis needs further clarification . the effects we observe here could be explained by alterations in the migration of brdu + cells between the svz and sn . these structures are linked by a dopaminergic pathway , stimulation of which would presumably increase da tone on progenitor cells and augment their proliferation and / or migration . presumably the converse may occur if the pathway is damaged , such as by daergic denervation , leading to a potential accumulation of progenitor cells in the svz and a decrease in the sn . this is exactly what we have observed and is reversed by ex-4 , which is efficacious in preclinical pd models . whether this contributes to the positive effect of ex-4is unclear but at the very least , in theory , could play some role in the neuroprotective actions of ex-4 in these models . more recently evidence suggests that ex-4 has actual therapeutic efficacy , as indicated in a small scale clinical trial . these observations have naturally led to understanding the mechanism of action of ex-4 being of intense interest . the present data suggest that ex-4 reverses the decrease in brdu + cells in the sn of lesioned rats . this is blocked by da d3 receptor stimulation one possibility may be that ex-4 alters the migration and / or maturation of progenitor cells . moreover , our findings with ex-9 - 39 unambiguously show that these effects are primarily mediated by the glp - 1r .\noutput:\n" }, { "from": "agent", "value": "glucagon - like peptide - 1 receptor ( glp - 1r ) activation by exendin - 4 ( ex-4 ) is effective in preclinical models of parkinson 's disease ( pd ) and appears to promote neurogenesis even in severely lesioned rats . in the present study , we determined the effects of ex-4 on cellular brdu incorporation in the rat subventricular zone ( svz ) and substantia nigra ( sn ) . we also determined the specificity of this effect with the glp - 1r antagonist ex - ( 9 - 39 ) as well as the potential role of dopamine ( da ) d3 receptors . rats were administered 6 - ohda and 1 week later given ex-4 alone , with ex - ( 9 - 39 ) or nafadotride ( d3 antagonist ) and brdu . seven days later , rats were challenged with apomorphine to evaluate circling . extracellular da was measured using striatal microdialysis and subsequently tissue da measured . tyrosine hydroxylase and brdu were verified using immunohistochemistry . apomorphine circling was reversed by ex-4 in lesioned rats , an effect reduced by ex-4 , while both ex - ( 9 - 39 ) and naf attenuated this . 6 - ohda decreased extracellular and tissue da , both reversed by ex-4 but again attenuated by ex - ( 9 - 39 ) or naf . analysis of brdu + cells in the svz revealed increases in 6 - ohda - treated rats which were reversed by ex-4 and antagonised by either ex - ( 9 - 39 ) or naf , while in the sn the opposite profile was seen ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we began an epidemiologic investigation in osaka on may 17 , 2009 , and conducted face - to - face interviews . the definition of a confirmed case - patient was a person with influenza - like illness ( ili ) and laboratory confirmation of pandemic ( h1n1 ) 2009 virus infection by real - time reverse transcription pcr . ili was defined as the presence of a fever ( 38.0 c ) and acute respiratory symptoms ( cough or sore throat ) . local public health staff also conducted face - to - face or telephone interviews , or both , with other patients and persons in close contact with the case - patients until the end of may , when the local epidemic appeared to wane ( 1,6 ) . interviews were conducted by using a standard questionnaire to collect data on patient demographics , clinical course of illness , patient behavior , and history of patient contacts . by analyzing these data and careful investigation of contact history and epidemiologic links , we found 3 clusters in which disease transmission could have occurred before symptom onset in the index case - patients ( figure ) . three clusters of pandemic ( h1n1 ) 2009 presymptomatic transmission in may 2009 in osaka , japan . all cases were confirmed as pandemic ( h1n1 ) 2009 virus infection by real - time reverse transcription pcr . colors of the squares and circles denote the similar or different schools the students attended . the first outbreak in osaka occurred in 1 high school , and no community transmission had been verified in mid - may . case - patient 1 , a student at the high school , had symptoms on may 13 . case - patient 2 , the sister of case - patient 1 , had no symptoms while she was at school , according to her answer on the self - report survey as well as face - to - face interview carried out with a classmate who sat right behind her ( case - patient 3 ) . symptoms developed in the evening of may 15 after she returned home , and the school was closed proactively the following day . for case - patient 3 , who sat immediately behind case - patient 2 in class and chatted with her , influenza - related symptoms developed on may 17 . our investigation suggested that transmission of infection from case - patient 2 to case - patient 3 occurred during the presymptomatic phase of infection in case - patient 2 . case - patients 4 , 5 , and 6 were previously healthy boys and schoolmates of case - patients 2 and 3 . they played video games together in a small room on may 18 for several hours . he may have been infected by case - patient 2 at school , but we can not confirm this . they had no opportunity to be in contact with symptomatic persons other than case - patient 4 . thus , we concluded that case - patients 5 and 6 were likely infected by case - patient 4 before symptom onset . even if transmission from case - patient 2 were the reason that case - patients 5 and 6 became ill , transmission from a presymptomatic person likely occurred because case - patient 2 would have been asymptomatic when she met case - patients 5 or 6 , or both , at school . case - patient 8 was an elementary school pupil who lived in a different region from case - patients 17 . no cases of pandemic ( h1n1 ) 2009 had been reported in the area where he lived , including at his school , in mid - may . investigation results indicate that case - patient 7 was infected by a classmate other than case - patients 18 around may 16 ; this classmate was infected by a student at the same high school that case - patient 1 attended . on may 17 , 20 persons , including case - patients 7 and 8 , went on a 1 - day trip to okayama prefecture , which is 180 km west of osaka . no positive results were reported by active surveillance for ili in okayama in mid - may . case - patients 7 and 8 stayed close together during the trip . in the evening of may 18 , case - patient 7 had a sore throat and cough , and he became febrile on may 19 . case - patient 8 had symptoms on may 21 , 3 days after case - patient 7 exhibited symptoms . the trip was the only opportunity for case - patient 8 to have been exposed to the virus . this indicates that transmission from case - patient 7 to case - patient 8 occurred on the day before symptom onset . our epidemiologic investigation results indicate that pandemic influenza virus ( h1n1 ) 2009 is infectious during the presymptomatic phase . our investigation was conducted in the early phase of the outbreak in japan . during this period , almost all persons with reported cases in osaka were students and their close contacts ( 1 ) . the institute had been conducting active surveillance for patients with ili and suspected pandemic ( h1n1 ) 2009 virus infection since april 2009 ( 7 ) . since mid - june , many community - transmitted cases had been reported in japan , thereby limiting the ability to find single exposure cases . , our results are valuable in terms of collecting information before the community spread of the virus . the mode of transmission of pandemic ( h1n1 ) 2009 is considered to be similar to that of seasonal influenza . the infectious period of seasonal influenza is measured from 1 day before symptom onset to 57 days after onset or until symptoms resolve ; this period is mainly based on experimental data on viral shedding ( 4,5 ) . regarding seasonal influenza , we found only 1 report documenting that a transmission took place during the presymptomatic phase , but the index case - patient of the report could have been in apresymptomatic , state because this case - patient did not feel completely well when the transmission took place ( 8 ) . our epidemiologic results provide useful clues for understanding the transmission of pandemic ( h1n1 ) 2009 virus . this finding of presymptomatic transmission has critical implications for public health because it indicates that viral transmission in communities can not be completely prevented solely by isolating symptomatic case - patients . two possible limitations of this report are the presence of unidentified case - patients and asymptomatic infected persons because our epidemiologic investigation was based on interviews with symptomatic patients and their close contacts . however , we could not find any cases that suggested infection from these kinds of cases during the early phase of the outbreak in japan . , our epidemiologic investigation results suggest that pandemic ( h1n1 ) 2009 is probably infectious during the presymptomatic period , at least 1 day before symptom onset .\noutput:\n" }, { "from": "agent", "value": "during an epidemiologic investigation of pandemic influenza ( h1n1 ) 2009 virus infection in may 2009 in osaka , japan , we found 3 clusters in which virus transmission occurred during the presymptomatic phase . this finding has public health implications because it indicates that viral transmission in communities can not be prevented solely by isolating symptomatic case - patients ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: worldwide , it is estimated that 366 million people have diabetes , with half unaware they have the disease .1 of the ten countries with the highest prevalence of diabetes , six are in the middle east ( kuwait , lebanon , qatar , saudi arabia , bahrain , and the united arab emirates ) . in the 20 arab countries for which data are available , nearly 20.5 million people are living with diabetes and another 13.7 million are in the prediabetes stage , having impaired glucose tolerance . in contrast with developed countries , in which most people with diabetes are over the age of retirement , nearly three quarters ( 73.4 % ) of diabetics in arab countries are under 60 years of age and hence in their most productive years , further increasing the burden of disability due to diabetes .1 in 2009 , an international committee for the diagnosis of diabetes recommended use of glycated hemoglobin ( hba1c ) , an index of average plasma glucose over several weeks , as a marker for the disease .2 this recommendation was also made by the american diabetes association ( ada ) in 2010,3 which suggested that hba1c 6.5 % ( 48 mmol / mol ) be considered diagnostic of diabetes . hba1c is considered equal to fasting plasma glucose ( fpg ) as a predictor of diabetes .4 assessments of fpg concentrations have been associated with methodological , procedural , and practical problems , and the oral glucose tolerance test is tedious to perform . measurements of hba1c are considered an alternative diagnostic test , overcoming many of the problems associated with other tests .5 moreover , a diagnosis of diabetes can be confirmed by measuring fpg and hba1c at the same time .6 a comparison of the association of diabetic retinopathy with the results of three diagnostic tests ( hba1c , fpg , and 2 - hour glucose ) in 44,623 individuals showed that fpg ( 117 mg / dl [ 6.5 mmol / l ] ) and hba1c ( 6.5 % [ 48 mmol / mol ] ) were associated with retinopathy , whereas 2 - hour glucose concentrations were not .7 the ada does not recommend testing both fpg and hba1c , because these tests are not completely ( 100 % ) concordant , which can lead to confusion . in contrast , the japan diabetes society has recommended that individuals be simultaneously tested for fpg and hba1c for the diagnosis of diabetes .6 early diagnosis is important for effective management , significantly reducing the risk of complications such as diabetic nephropathy and diabetic retinopathy , but not mortality .8,9 the objective of this investigation was to assess the prevalence of diabetes mellitus in basrah , southern iraq . basrah is a governorate located in southern iraq , 550 km from the iraqi capital , baghdad , with a total population of 3 million . a population - based , cross - sectional , simple random study was performed to screen for diabetes in basrah between january 2011 and october 2012 . using a google map , we screened people from the dur nuwab al dubat , duran naft , dur al - dhabaat , yaseen khrebit , al hayy almarkazi , al iskan , al - abelah , dur alhindia , hateen , al hadi , and al gzaiza districts of basrah . the study was approved by the ethics committee of the basrah directorate of health and written informed consent was taken from each study participant . subjects were invited via the media and during home visits performed as part of a vaccination program to come to the center to be screened for diabetes . prior to screening , the participants were informed about the importance of establishing a database for diabetes in iraq . the participants were invited to undergo examination at the al - faiha diabetes endocrine and metabolism center in basrah , southern iraq . information was collected using a structured , interviewer - administered questionnaire , followed by a physical examination . age , sex , education level , smoking , and family history of diabetes ( first - degree and / or second - degree relatives ) were recorded . kg / m ) , overweight ( 2529.9 kg / m ) , or obese ( 30 kg / m ) . smokers were defined as those who reported smoking 100 cigarettes during their lifetime and were currently smoking every day or some days . hypertension was defined as either a resting systolic blood pressure 140 mmhg or a resting diastolic blood pressure 90 mmhg recorded at a single visit or being prescribed an antihypertensive medication . a blood sample was obtained after an overnight fast and parameters were measured at the center s laboratory . plasma glucose concentrations were measured using an automated glucose oxidase method ( biolyzer 300 ; analyticon biotechnologies ag , lichtenfels , germany ) . in subjects unable to fast , hba1c was measured by high - performance liquid chromatography ( variant hemoglobin testing system ; bio - rad laboratories inc . , hercules , ca , usa ) . this minority agreed to come the next day fasting to do proper oral glucose tolerance test with 75 g anhydrous glucose powder dissolved into 250300 ml of water . subjects were classified according to ada criteria , with normal fpg being 100 mg / dl ( 5.6 mmol / l ) , impaired fasting glucose being fpg ranging from 100 mg / dl ( 5.6 mmol / l ) to 125 mg / dl ( 6.9 mmol / l ) , and diabetes being fpg 126 mg / dl ( 7.0 mmol / l ) .2 hba1c concentrations 5.7 % were considered normal , those ranging from 5.7 % ( 39 mmol / mol ) to 6.4 % ( 46 mmol / mol ) were considered prediabetes , and those 6.5 % ( 48 mmol / mol ) were considered to indicate diabetes . on an oral glucose tolerance test , diabetes was diagnosed if 2 - hour plasma glucose was 200 mg / dl ( 11.1 mmol / l ) , and the impaired glucose tolerance test was considered in those with plasma glucose 140199 mg / dl ( 7.711 mmol / l ) . persons with impaired fasting glucose or the impaired glucose tolerance test and prediabetes on hba1c were considered to have prediabetes according to the ada classification . study participants were asked if they had ever been told by a physician that they had diabetes ; if so , blood tests were performed to assess diabetes control . continuous variables are presented as the mean standard deviation , and categorical data as frequencies and percentages . all statistical analyses were performed using statistical package for the social sciences version 15 software ( spss inc . , chicago , il , usa ) . a p - value 0.05 was considered to be statistically significant . basrah is a governorate located in southern iraq , 550 km from the iraqi capital , baghdad , with a total population of 3 million . a population - based , cross - sectional , simple random study was performed to screen for diabetes in basrah between january 2011 and october 2012 . using a google map , we screened people from the dur nuwab al dubat , duran naft , dur al - dhabaat , yaseen khrebit , al hayy almarkazi , al iskan , al - abelah , dur alhindia , hateen , al hadi , and al gzaiza districts of basrah . the study was approved by the ethics committee of the basrah directorate of health and written informed consent was taken from each study participant . subjects were invited via the media and during home visits performed as part of a vaccination program to come to the center to be screened for diabetes . prior to screening , the participants were informed about the importance of establishing a database for diabetes in iraq . the participants were invited to undergo examination at the al - faiha diabetes endocrine and metabolism center in basrah , southern iraq . information was collected using a structured , interviewer - administered questionnaire , followed by a physical examination . age , sex , education level , smoking , and family history of diabetes ( first - degree and / or second - degree relatives ) were recorded . participants were categorized according to world health organization bmi criteria as normal ( 25 kg / m ) , overweight ( 2529.9 kg / m ) , or obese ( 30 kg / m ) . smokers were defined as those who reported smoking 100 cigarettes during their lifetime and were currently smoking every day or some days . hypertension was defined as either a resting systolic blood pressure 140 mmhg or a resting diastolic blood pressure 90 mmhg recorded at a single visit or being prescribed an antihypertensive medication . a blood sample was obtained after an overnight fast and parameters were measured at the center s laboratory . plasma glucose concentrations were measured using an automated glucose oxidase method ( biolyzer 300 ; analyticon biotechnologies ag , lichtenfels , germany ) . in subjects unable to fast , hba1c was measured by high - performance liquid chromatography ( variant hemoglobin testing system ; bio - rad laboratories inc . , hercules , ca , usa ) . this minority agreed to come the next day fasting to do proper oral glucose tolerance test with 75 g anhydrous glucose powder dissolved into 250300 ml of water . subjects were classified according to ada criteria , with normal fpg being 100 mg / dl ( 5.6 mmol / l ) , impaired fasting glucose being fpg ranging from 100 mg / dl ( 5.6 mmol / l ) to 125 mg / dl ( 6.9 mmol / l ) , and diabetes being fpg 126 mg / dl ( 7.0 mmol / l ) .2 hba1c concentrations 5.7 % were considered normal , those ranging from 5.7 % ( 39 mmol / mol ) to 6.4 % ( 46 mmol / mol ) were considered prediabetes , and those 6.5 % ( 48 mmol / mol ) were considered to indicate diabetes . on an oral glucose tolerance test , diabetes was diagnosed if 2 - hour plasma glucose was 200 mg / dl ( 11.1 mmol / l ) , and the impaired glucose tolerance test was considered in those with plasma glucose 140199 mg / dl ( 7.711 mmol / l ) . persons with impaired fasting glucose or the impaired glucose tolerance test and prediabetes on hba1c were considered to have prediabetes according to the ada classification . study participants were asked if they had ever been told by a physician that they had diabetes ; if so , blood tests were performed to assess diabetes control . continuous variables are presented as the mean standard deviation , and categorical data as frequencies and percentages . all statistical analyses were performed using statistical package for the social sciences version 15 software ( spss inc . , chicago , il , usa ) . a p - value 0.05 was considered to be statistically significant . demographic characteristics of the study population are shown in table 1 . of the 5,445 individuals screened , 52.6 % were women and 47.3 % were men . their mean age was 46.714.3 ( range 1994 ) years and their mean bmi was 27.46.4 kg / m ; 40.5 % had a family history of diabetes , 16.9 % were smokers , and 11.2 % were hypertensive . screening was by hba1c measurement in 88.3 % of the study subjects , followed by fpg in 18.7 % . of the study subjects , 8.7 % had been previously diagnosed with diabetes , whereas 11 % were found by screening to have diabetes , resulting in an age - adjusted prevalence of diabetes of 19.7 % . of those with diabetes , 55.7 % were previously undiagnosed . in addition , 29.1 % were found to have prediabetes , indicating that dysglycemia was present in 48.8 % of the study population , with only 51.2 % being normoglycemic ( figure 1 ) . table 2 shows the prevalence rates of diagnosed and undiagnosed diabetes according to subject age . the prevalence of diabetes in both sexes peaked at age 4660 years ( figure 2 ) , with 41.7 % of men and 43.9 % of women having diabetes . prediabetes peaked at age 3145 years in men and at age 4660 years in women . the prevalence of diabetes was higher in women than in men ( 19.8 % versus 19.6 % ; p 0.0001 ) , as was the prevalence of prediabetes ( 29.5 % versus 28.6 % ; p 0.0001 ) . the mean age and bmi of those with diabetes and prediabetes was higher than that in those with normoglycemia . hypertension and family history of diabetes were higher in the combined diabetes and prediabetes groups than in the normoglycemic group . the prevalence of smoking was lower in the diabetes group , but 44.4 % of smokers had prediabetes or diabetes . iraq has undergone rapid economic development in the last 10 years . in december 2011 , the international diabetes federation reported that , of the ten countries with the highest prevalence of diabetes in adults aged 2079 years , six were in the middle east , ie , kuwait ( 21.1 % ) , lebanon ( 20.2 % ) , qatar ( 20.2 % ) , saudi arabia ( 20.0 % ) , bahrain ( 19.9 % ) , and the united arab emirates ( 19.2 % ) .1 iraq is considered as having a medium prevalence ( 9.3 % ) of diabetes in the middle east based on surveys from 2006 to 2007.1,1012 diabetes was also found to affect 21.9 % of iraqis living in sweden in 2010.13 in the present study of adults in basrah , southern iraq , we found that one in five subjects had diabetes . we found that the peak age of diabetes in both sexes was in the fourth through sixth decades of life . studies in saudi arabia found that the age - adjusted prevalence of type 2 diabetes mellitus was 30.0 % 31.6 % , with the highest prevalence in those aged 4660 years .14,15 high diabetes prevalence rates have been observed in other gulf region countries , including bahrain ( 25.7 % ) and oman ( 16.1 % ) .16,17 in lebanon , the combined prevalence of previously diagnosed and newly diagnosed diabetes was 15.8 % , with 17.6 % in men and 13.4 % in women .18 in iran , 5.5 % of individuals have diabetes , with one third of adults in tehran having impaired glucose tolerance or diabetes ,19,20 while in jordan the age - standardized prevalence of diabetes and impaired fasting glucose was found to be 17.1 % and 7.8 % , respectively .21 in developed countries , in which most people are of european descent , diabetes affects mainly those older than 65 years of age . similar findings were observed in iran , where diabetes was more common among older people , with 10.9 % of those aged 60 years having the disease .22 however , in most developing countries , the peak incidence of diabetes is between 45 and 64 years . we also observed an association between diabetes and bmi , with 70.3 % of iraqis with diabetes having a bmi 25 kg / m , compared with 85.7 % of saudis with diabetes .14 slightly more than half of those with diabetes in our study were undiagnosed at the time of screening , similar to findings in the united arab emirates .23 reported rates of undiagnosed diabetes in the middle east and north africa region have been found to vary , with rates of 29 % in iraq , 50 % in algeria and iran , 56 % among women in pakistan , and 86 % in tunisia .24 we found that diabetes was more prevalent in women than in men , similar to findings in iran , but in jordan there was no difference between sexes .19,21 in contrast , the prevalence was higher in men in saudi arabia and lebanon .14,18 the present study had several limitations . first , the boundaries between rural and urban areas became blurred following the 2003 iraq war . many people from rural areas migrated to cities , especially when the government of iraq could no longer control migration . thus , dividing people into those living in rural and urban areas is no longer feasible . duplicate measurements of fpg are required for a diagnosis of diabetes due to day - to - day variations .25 for epidemiological studies , however , estimation of diabetes prevalence and incidence using a single elevated hba1c or fpg measurement is considered acceptable .26,27 third , this work has the limitations inherent to cross - sectional studies . first , the boundaries between rural and urban areas became blurred following the 2003 iraq war . many people from rural areas migrated to cities , especially when the government of iraq could no longer control migration . thus , dividing people into those living in rural and urban areas is no longer feasible . duplicate measurements of fpg are required for a diagnosis of diabetes due to day - to - day variations .25 for epidemiological studies , however , estimation of diabetes prevalence and incidence using a single elevated hba1c or fpg measurement is considered acceptable .26,27 third , this work has the limitations inherent to cross - sectional studies . the prevalence of diabetes in basrah , iraq , is very high , affecting one in five adults . this epidemic of diabetes will result in strain on the financial resources of health care systems .\noutput:\n" }, { "from": "agent", "value": "backgroundsix of the top ten countries in the world with the highest prevalence of diabetes mellitus are in the middle east . the objective of this investigation was to evaluate the prevalence of diabetes in basrah , southern iraq.methodsa population - based , cross - sectional , simple random study screened 5,445 persons aged 1994 years in basrah , with glycated hemoglobin measured in 88.3 % of the population and fasting plasma glucose in 18.7 % . body mass index and other demographic parameters were also measured.resultsof the 5,445 persons screened , 8.7 % had already been diagnosed with diabetes and 11 % were found by screening to have undiscovered diabetes , giving an age - adjusted prevalence of diabetes of 19.7 % , with 55.7 % of those with diabetes being previously undiagnosed . in addition , 29.1 % of the screened population had prediabetes , giving a prevalence of dysglycemia of 48.8 % , with only 51.2 % of the persons screened being normoglycemic . the prevalence of diabetes in both sexes peaked at age 4660 years . diabetes was slightly more prevalent in females than in males , and about 70.3 % of diabetic individuals had a body mass index 25 kg / m2.conclusionthe prevalence of diabetes in basrah , iraq , is very high , affecting one in five adults . the epidemic of diabetes will result in strain on the financial resources of health care systems ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: reactive hyperplasia comprises a group of fibrous connective tissue lesions that commonly occur in the oral mucosa as a result of injury the terminology used in this study is by neville classifying the common gingival overgrowth lesions under the following categories : ( 1 ) pyogenic granuloma ( pg ) ( including pregnancy tumor ) ; ( 2 ) peripheral ossifying fibroma ( pof ) ( also referred to as ossifying fibroid epulis , peripheral fibroma with calcification , calcifying fibroblastic granuloma , and peripheral odontogenic ossifying fibroma ) ; ( 3 ) peripheral fibroma also referred to as ( focal fibrous hyperplasia ( ffh ) , fibrous epulis ) ; and ( 4 ) peripheral giant cell granuloma ( pgcg ) . earlier , the term epulis was used clinically to describe any localized growth on the gingiva , but histological examination of such lesions indicate that the majority of them are ffh , pg , pgcg , and pof . their histopathological features are quite distinct but considerable overlap still exists among these lesions . for this reason , some authors have postulated that inflammatory hyperplasia may be the same lesion at different stages of maturation . eversole and rovin speculated that the different histological entities of inflammatory hyperplasia may be due to connective tissue response to varied intensities of mucosal irritation . although benign in nature they do have tendency toward recurrence with incomplete removal of the lesion or the local irritants involved at the site . the treatment in each case is surgical excision ; however , different treatment modalities may offer better outcomes with less frequency of recurrence . review of the literature reveals that there are controversies among the findings of previous studies , and that all reactive hyperplastic lesions have rarely been evaluated in one study . the aim of this survey was to evaluate oral connective tissue reactive hyperplastic lesions and to compare the results with those of similar studies . this retrospective cross - sectional study was performed on the archives of the department of oral pathology at st joseph dental college for the period of one and half years . data including the type of the lesion , age , gender , and the affected site were collected using prepared forms . descriptive statistical methods were applied to data , and analysis of variance ( anova ) test was employed to assess mean differences . from a total of 240 records evaluated , 100 ( 41.6 % ) of the lesions were reactive hyperplasia . of these , 59 % cases were in females and 40.7 % cases were in males . there was no statistically significant difference in mean age between genders ( p = 0.005 ) . mandibular anterior region ( anterior to premolars ) was the most common site with 29 cases ( 69.05 % ) and rest of the cases ( 30.95 % ) occurred in maxillary anterior and posterior gingival region . females were mostly affected than men with a ratio of 2:1 and with average age of 34 years . the most common cause was the presence of local deposits in approximately 70 % of cases and rest included minor trauma , abrasion , hormonal imbalance , overhanging restorations , and ill fitting dentures . other lesions in the descending order of prevalence were ffh ( 35 % ) , pof ( 18 % ) , and pgcg ( 10 % ) [ graph 1 ] . distribution of reactive lesions in males and females ffh constituted 35 % of the reactive hyperplasias with age ranging from 16 to 59 years . the most common site affected was buccal mucosa ( 51.43 % ) along the line of occlusion plane followed by gingiva ( 34.29 % ) and tongue ( 14.29 % ) . pof presented 18 % of all the lesions with average age of 39 years and trauma being the most common cause . pgcg accounted 10 % of the total lesions with equal sex distribution and average age of 33 years . the reactive lesions are common in the oral cavity because of the frequency with which the tissues are injured . esmeili et al . in their review stated that hyperplastic reactive lesions represent as a group of the most common oral lesions , excluding caries , periodontal and periapical inflammatory disease . in this group , the second most common group is represented by hyperplastic reactive gingival / alveolar lesions , including inflammatory gingival hyperplasia , oral pg , peripheral giant cell lesion and peripheral cemento - ossifying fibroma . it has been referred to by a variety of other names such as granuloma pediculatum benignum , benign vascular tumor , pregnancy tumor , vascular epulis , crocker and hartzell 's disease . it was given its present name by crocker in 1903 however , some researchers believe that hartzell in 1904 introduced the term pyogenic granuloma , which is widely used in literature , although , it does not express accurately the clinical or histopathologic features . clinically , the young lesions are highly vascular , red or reddish purple , often elevated and ulcerated , and bleed easily , whereas older lesions tend to be more collagenized and pink in appearance . the histological appearance is characterized by vast numbers of endothelium lined vascular spaces infiltrated with lymphocytes , plasma cells , and neutrophils [ figure 1 ] . the lesion is covered by a thin , often ulcerated layer of stratified squamous epithelium . despite the name , no pyogenic material or pusour study shows prevalence of pg in females than in males ( f : mthe most common site was mandibular anterior ( 69.05 % ) lingual aspect compared with maxillary anteriors labial aspect ( 30.95 % ) . out of 42 cases of pg , 28 appeared to be reddish in color and 14 cases appeared pink , clinically thereby signifying that there were short and long duration of presentation . our study is in correlation with a study carried out by saravna where oral pg was more common in females than in males . photomicrograph of pg showing numerous budding capillaries along with the inflammatory cells the term focal fibrous hyperplasia implies a reactive tissue response and is therefore preferable to the term fibroma , which implies incorrectly , a benign neoplastic proliferation of fibrous connective tissue . the lesion appears as a raised mass that is pedunculated or sessile with a smooth surface , and is usually the same color as the surrounding mucosa . the most common site is the buccal mucosa along the line of occlusion and sessile lesion on the gingiva , commonly in the interdental papilla of the anterior teeth in adults ( fourth to sixth decade of life ) with a slight female predilection . the tissue mass consists of bundles of collagen fibers often arranged in radiating , circular or haphazard fashion [ figure 2 ] . the vast majority is exceedingly dense fibrous connective tissue with poor vascularity and few chronic inflammatory cells present . in the present study ffhthe peak incidence was observed during third and fourth decade with a mean of 35 years with buccal mucosa being the most common site . this result was in concurrent with saravna et al . who found fibroma to be the most common gingival reactive lesion . photomicrograph of ffh showing stratified squamous epithelium with dense collagenous connective tissue pof , the nomenclature for this lesion , however , has been confusing and is often reported as a peripheral fibroma with calcification or a peripheral odontogenic fibroma . the issue has become more clouded since the world health organization ( who ) classification system recognized a peripheral odontogenic fibroma as a distinct and different entity from the pof . current literature refers to this lesion as the pof ( who type ) and it is recognized separately from the pof of gingiva . the pof is thought to originate from the superficial periodontal ligament and is found most often in the anterior maxilla . the clinical appearance may be identical to the peripheral fibroma and both are associated with local irritating factors . histologically , fibrous proliferation with large numbers of fibroblasts are seen associated with formation of mineralized product that may include bone , cementum - like material , dystrophic calcification , or a combination of both [ figure 3 ] . the peak incidence for the pof was in the third decade followed by a definite decline , which is concurrent with the present study . pof has a marked predilection for the younger age - group . eversole and rovin suggested that the loss of periodontium that accompany tooth loss in old age may explain the greater occurrence of pof in the younger age group . photomicrograph of pof showing calcifying material resembling bone within the connective tissue pgcg is one of the most frequent giant cell lesions of the jaws and originates from the connective tissue of the periosteum or the periodontal membrane . it is not a true neoplasm but rather a benign hyperplastic reactive lesion occurred in response to local irritation such as tooth extraction , poor dental restorations , ill - fitting dentures , plaque , calculus , food impaction , and chronic trauma . other names of this lesion are peripheral giant cell tumor , osteoclastoma , reparative giant cell granuloma , giant cell epulis and giant cell hyperplasia of the oral mucosa . clinically , it manifests as a firm , soft , bright nodule or as a sessile or pedunculated mass and with occasionally ulcerated surface . it is located in the interdental papilla , edentulous alveolar margin or at the marginal gingival level histologically , it shows a nonencapsulated mass of tissue , containing numerous multinucleated osteoclast - like giant cells lying in a very cellular and vascular stroma [ figure 4 ] . in our resultphotomicrograph of pgcg showing numerous multinucleated giant cells in the connective tissue considerable overlap exists among the different histological entities of the localized inflammatory hyperplasia but whether or not they represent the same lesion at different developmental stages as suggested by some authors is debatable . the predominantly vascular component of pg may be subsequently replaced partially or completely by fibrous tissue and , hence , diagnosed as organizing pg or a fibroma . the frequent location of the inflammatory hyperplasia on the gingiva appears to support the notion that they are the same lesion at different stages of histological maturation . however , if this is true , then a definite age grouping for the different histological entities should be obvious . the mean ages for various lesions should reflect the progressive development of the lesion through the different histological stages , but this was not the case in our studies or any of the previous reports . our study suggests that pg , ffh , pgcg , and pof are mucosal responses to chronic , low grade irritation caused by plaque and calculus , or any other irritant . however , the histological appearance of each entity may be influenced by the intensity of the irritation , duration of the lesion and possibly the metabolic effects of serum concentrations of hormones , such as estrogen and progesterone . despite the similarities , all reactive gingival lesions show some differences in sex , type , location , duration , and histologic features . imperative in the treatment of reactive gingival lesions is the complete removal of local irritants with follow - up care , as well as dental hygiene maintenance to prevent or treat recurrence .\noutput:\n" }, { "from": "agent", "value": "aim : reactive lesions of the oral cavity are associated with injuries of soft tissue and have high prevalence rates and different involvement patterns in different parts of the world . this study reviews the pathogenesis and analyzes demographic data , histopathological features and compares the clinico - pathologic profiles of the diseases to those previously reported.materials and methods : patient records of the department of oral pathology during one and half year period were reviewed for diagnosis of oral connective tissue reactive hyperplastic lesion . data including the area involved and the type of lesion were collected and analyzed using descriptive statistical methods and anova test.results : 100 cases ( mean age 36 years , male : female ratio 1:2 ) matched study criterion . the most common affected site was mandibular anterior region and buccal mucosa and the most common lesion was pyogenic granuloma and focal fibrous hyperplasia . all the lesions were more common in the mandible than in the maxilla . pgcg was seen to be equally distributed in males and females.conclusion : reactive hyperplastic lesions of the oral connective tissue are more common in females and the majority of the lesions occur in gingiva . this study supports previous assertions that pg and ffh may occur on any oral mucosal site with special preference for the mandibular anterior gingiva and buccal mucosa while pgcg and pof occur exclusively on the mandibular gingiva ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: obesity in adults and in adolescents significantly increases the risk for several chronic diseases including cardiovascular diseases ( cvd ) and type 2 diabetes ( t2d ) . excess accumulation of fat inside the abdominal cavity ( visceral adipose tissue : vat ) is associated with altered insulin sensitivity , blood pressure ( bp ) , and plasma lipid profile . clustering of cvd risk factors including accumulation of abdominal fat , impaired glucose tolerance , dyslipidemia , and hypertension defines the metabolic syndrome ( mets ) . not all obese individuals develop the mets , and as much as 20 % of the obese population could have normal metabolic parameters even in the presence of extensive adipose tissue accumulation . our knowledge of the factors involved in the etiology of obesity - related metabolic disturbances , either alone or clustered under the mets designation , remains largely incomplete , with evidence pointing to a potential implication of immunity and inflammatory processes as well as oxidative stress . there is also strong evidence for genetic components in the development of these perturbations . in a previous transcriptomic study aimed at the identification of genes predisposing to mets in established obesity , we have identified 489 differentially expressed genes in vat of nondiabetic obese men with the mets ( mets + ) in comparison with obese men without the mets ( mets ) . dusp1 , also known as mkp1 , is a member of the dual - specificity phosphatase family involved in the regulation of the innate immune function . following p53 - mediated transcription , dusp1 targets p38 , mapks , and jnks which are important players in the expression of inflammatory mediators . dusp1 overexpression has been reported in breast , gastric , and lung cancers . in contrast , downregulation was significantly correlated to increased tumor aggressiveness and reduced patient survival in hepatocellular carcinoma ( hcc ) , urothelial , prostate , and liver cancers . downregulation of dusp1 with concomitant promoter hypermethylation and loss of heterozygosity at the dusp1 locus was reported in hcc , and epigenetic regulation of dusp1 expression was suggested in prostate cancer . based on the functions of dusp1 in innate immune function , inflammation , and apoptosis and its implication in various disorders and differential expression we have shown in vat of mets + versus mets obese individuals , we postulated that dusp1 gene variations may contribute to partially explain interindividual variability observed in obesity - related metabolic complication among obese individuals through the regulation of gene methylation and expression . an extensive molecular analysis of the human dusp1 gene was undertaken to test for associations between dusp1 polymorphisms and obesity - related metabolic complications in a cohort of severely obese patients undergoing a bariatric surgery . the impact of the snps associated with metabolic complications on gene methylation and expression in vat was thereafter analyzed . between june 2000 and july 2012 , 1906 severely obese men ( n = 597 ) and women ( n = 1309 ) have been recruited . these caucasian patients from the eastern part of the quebec province , canada , underwent biliopancreatic diversion with duodenal switch at the quebec cardiology and pulmonology institute ( quebec city , quebec , canada ) . the study was approved by the universit laval ethics committee , and all individuals provided written informed consent before their inclusion . body weight , height , waist girth , resting bp [ systolic ( sbp ) and diastolic ( dbp ) , blood lipid , and glucose concentrations were measured preoperatively using standardized procedures . body mass index ( bmi ) was calculated as weight in kilograms divided by height in meters squared . the presence of mets was determined using the national cholesterol education program adult treatment panel iii ( ncep - atpiii ) guidelines when an individual fulfilled three or more criteria . in a previous study , a subset of 14 obese men ( bmi 40 kg / m ) not taking any medication to treat mets features were selected from our cohort for gene expression profiling using oligonucleotide microarrays . seven of them were affected by the mets ( mets + group ) and were matched for age , bmi , and smoking status to obese individuals without mets ( mets group , n = 7 ) . characteristics of these individuals stratified by mets group as well as procedures for expression profiling are available elsewhere . following data correction and normalization , the dusp1 gene was identified as part of a list of 489 genes differentially expressed in vat between the two groups . to validate the microarray results , dusp1 gene expression was measured by real - time pcr ( rt - pcr ) ( applied biosystems gene expression assays ; applied biosystems , foster city , ca , usa ) in the same 14 adipose tissue samples selected for the original microarray experiment using custom primers overlapping the first two coding exons . these samples were analyzed in triplicate and calibrated to the gapdh housekeeping gene ( endogenous control ; gapdh : hs99999905_m1 ) . relative quantification estimations were performed on an applied biosystems 7500 fast real - time pcr system following the manufacturer 's recommendations , and the ct calculation method was used to evaluate the mean fold expression difference ( mfed ) between mets and mets + groups . genomic dna was extracted from the blood buffy coat using the genelute blood genomic dna kit ( sigma , st . the promoter region ( ~ 1500 bp ) , exons , and intronic flanking regions of the dusp1 gene were first amplified and sequenced with primers designed using human dusp1 public sequence ( accession number : nc_000005 ) in a subset of 25 severely obese men ( mets + = 12 ; mets = 13 ) including the 14 individuals selected for gene expression profiling . mets status was taken into account to include similar proportions of mets + and mets individuals for dusp1 sequencing . the bigdye terminator 3.1 kit was used for sequencing , and samples were run on an abi 3730 / xl dna analyzer automated sequencer ( applied biosystems ) . from the snps identified by direct sequencing , five tagging single nucleotide polymorphisms ( tsnp ) ( minor allele frequency 5 % ; maf ) were selected using the tagger selection algorithm of the haploview software . selected tsnps were genotyped using validated primers and taqman probes ( applied biosystems ) . the rs201026723 polymorphism , resulting in amino acid change ( p.met60ile ) , was also included in our analysis and genotyped in the whole cohort ( 1906 obese individuals ) using the same method . genotypes were determined using applied biosystems 7500 fast real - time pcr system and analyzed using abi prism sds version 1.2.3 software ( applied biosystems ) . validation of genotyping data was conducted for the snp rs88150 demonstrating overrepresentation of rare homozygote individuals . pcr amplification and direct sequencing of dusp1 promoter region were performed on a subset of 91 consecutively recruited individuals from our cohort ( 4.8 % of the whole cohort ) . dna methylation analysis was conducted on the 14 obese men initially selected from our cohort for gene expression profiling . genomic dna was extracted from 200 mg of vat using the dneasy blood & tissue kit ( qiagen , mississauga , ontario , canada ) , as recommended by the manufacturer . bisulfite conversion was conducted on 1 g of dna , and quantitative dna methylation analysis was carried out at the mcgill university and gnome qubec innovation centre ( montreal , canada ) . infinium humanmethylation450 beadchip ( illumina inc . , san diego , ca ) was processed according to the manufacturer 's instructions . methylation data was visualized and analyzed using the genomestudio software version 2011.1 ( illumina inc . ) and the methylation module . methylation levels ( beta values ; ) were estimated as the ratio of signal intensity of the methylated alleles to the sum of methylated and unmethylated intensity signals of the alleles ( value = c / ( t + c ) ) . data correction ( background subtraction and normalization ) was applied using internal control probe pairs . methylation ratios ( values ) of cpg sites located within the dusp1 locus and promoter region ( ~ 2 kb upstream transcription start site ( tss ) ) were extracted using the genomestudio methylation module , thus leading to a total of 36 cpg sites analyzed in this study . phenotypic data ( untransformed and unadjusted values ) were reported as mean sd . gene expression microarray analysis was conducted using unpaired student 's t - test to identify differentially expressed genes between mets + and mets groups . hardy - weinberg equilibrium ( hwe ) , linkage disequilibrium ( r ) , and selection of tsnps ( minor allele frequency ; maf 5 % ) were conducted using the haploview software and the tagger selection algorithm . after genotyping , homozygotes for the minor allele of the snp rs201026723 were merged to heterozygotes due to genotype frequency below 5 % . phenotypic differences between genotype groups were tested for the whole cohort ( 1906 individuals ) using analysis of variance ( general linear model , type iii sum of squares ) and adjusted for the effects of age , sex , and bmi . transformations were applied to nonnormally distributed variables to meet the criteria for normality ( inverse transformed : triglycerides ( tg ) and hdl - cholesterol ( hdl - c ) ; log 10 transformed : fasting glucose and total - c ( total cholesterol ) / hdl - c ratio ) . when a significant snp effect was identified , all pairwise comparisons among genotype groups were performed using ls - means and student 's t - tests . pairwise pearson correlations between methylation and expression levels and between microarray and rt - pcr data were computed . statistical analyses were performed using sas software version 9.2 ( sas institute , cary , nc , usa ) . the potential functional impact of cvd risk factor - associated snps was assessed using two different programs . the matinspector program was used to analyze the impact of promoter snps on transcription factors binding sites while intronic snps were evaluated using the nnsplice 0.9 programs . the present study included 1906 severely obese individuals ( 597 men and 1309 women ) undergoing bariatric surgery who were consecutively recruited . from these individuals , 1899 were successfully classified either as mets + ( n = 1549 ) or mets ( n = 350 or 18.4 % ) . as shown in table 1 , this cohort of middle - aged , severely obese individuals demonstrates high mean fasting plasma glucose and tg levels , as well as elevated sbp according to mets criteria defined by the ncep - atpiii . as previously reported , microarray analysis of 14 obese men ( mets + , n = 7 ; mets , n = 7 ) revealed 489 differentially expressed genes between mets + and mets groups . although not listed at the time , the dusp1 gene was significantly underexpressed ( 3.77-fold ; p = 0.02 ) in vat of mets + versus mets obese men . validation of microarray data for the dusp1 gene was conducted in the same subset of individuals using rt - pcr . according to rt - pcr results , the dusp1 gene was found to be underexpressed in vat of mets + obese men ( mfed = 6.02 ; p = 0.04 ) . dusp1 gene expression levels obtained by rt - pcr were highly correlated to those obtained by microarrays ( r = 0.984 ; p 0.0001 ) . more details on rt - pcr and microarray results are available in supplementary table 1 available online at http://dx.doi.org/10.1155/2013/609748 . promoter region , exons , and intronic flanking sequences of the dusp1 gene were first analyzed in a subset of 25 severely obese individuals and led to the identification of 16 gene variations ( table 2 and supplementary figure 1 ) . from these snps ,12 were reported in the snp database ( dbsnp build 137 ) and 7 displayed a maf 5 % . common snps ( maf 5 % ) were found in individuals from mets and mets + groups . rare snps ( maf 5 % ) were mostly found in mets individuals with c. 648g t being identified in a mets + individual . among the 16 snps identified , the remaining 5 were exonic polymorphisms , 4 located in the first exon and the other located in exon 3 . three of the exonic snps resulted in amino acid changes ( p.asn36his ; p.arg53leu ; p.met60ile ) . five snps were selected and allowed us to cover 85 % of the sequence - derived genetic variability of the common polymorphisms ( maf 5 % ) at the dusp1 locus . these 5 tsnps ( rs13184134 , rs322382 , rs881150 , rs28372789 , and rs7702178 ) and the rs201026723 ( p.met60ile ) were further genotyped in the whole cohort of 1906 severely obese individuals . one of these snps ( rs881150 , c. 950a t ) displays deviation from hwe with an overrepresentation of rare homozygotes . validation of taqman genotyping results for rs881150 was conducted in a subset of 91 individuals via direct sequencing . associations between fasting plasma glucose , lipid profile bp - related variables ( systolic and diastolic blood pressure ) , and genotype groups were tested . following adjustment for the effects of age , sex , and bmi , rs881150 was associated with plasma hdl - c levels ( p = 0.01 ) , with the heterozygotes exhibiting lower levels ( table 4 ) and minor allele homozygotes having the lower values . snps rs13184134 and rs7702178 were associated with fasting glucose levels ( p = 0.04 and 0.01 , resp . ) , homozygotes for the minor allele of rs13184134 or rs7702178 having increased fasting glucose levels ( table 4 ) . further analyses were conducted for the three snps associated with cvd risk factors ( rs881150 , rs13184134 , and rs7702178 ) . prediction models have been used to assess the potential impact of cvd risk factor - associated snps . analysis of the potential effect of the rs7702178 intronic snp on splicing revealed that it slightly reduces the strength of an acceptor site located on the reverse strand ( 0.53 to 0.47 ) , thus unlikely impacting on mrna splicing for which junction between intron 2 and exon 3 scored 0.88 . the matinspector program was used to analyze the impact of the two cvd risk factor - associated promoter snps ( rs13184134 , rs881150 ) on binding of transcription factors . both snps demonstrated potential impact ( disruption or creation ) on transcription factor binding sites based on matrix similarities ( supplementary table 2 ) . these two promoter variants could thus result in differences in gene expression and contribute to the difference of dusp1 expression reported in the current study . to explore potential mechanisms underlying the relation between dusp1 snps and cardiometabolic risk factors , associations between cvd risk factor - associated snps ( rs881150 , rs13184134 , and rs7702178 ) and gene methylation levels were tested . of the 36 cpg sites analyzed , 25 were located within the promoter region , 8 in exons , and 3 in introns . the list of cpg sites analyzed with corresponding localization is provided in supplementary table 3 . significant associations between cpg site methylation levels and genotype groups were identified for 10 cpg sites . a trend towards an association ( p 0.10 ) a high proportion of these cpg sites ( 14/15 ) was located within the promoter region , with 7 ( cg25108022 , cg23002268 , cg14968860 , cg19537645 , cg09799633 , cg21121138 , and cg09493150 ) being located 11101402 bp upstream the tss ( 1359 - 1651 bp from first codon ) . high level of correlation ( mean pairwise correlation ; r = 0.642 ) was found between these 7 cpg sites . the link between gene methylation and gene expression was then assessed for snp - associated cpg sites . from the 10 snp - associated cpg sites analyzed , 4were inversely correlated with gene expression levels while a trend toward a significant association was identified for 3 other sites ( table 6 ) . furthermore , mean methylation level of the group of 7 cpg sites located 11001402 bp upstream the tss demonstrated inverse correlation with expression levels ( r = 0.624 ; p = 0.02 ) . over the past years , differences in dusp1 gene expression have been reported in various types of cancers . the current study reports underexpression of dusp1 in vat of severely obese individuals with the mets , thus extending the potential pathophysiological importance of this gene to obesity - related metabolic disease . following dusp1 sequencing and identification of tsnps , associations of dusp1 snps with cvd risk factors were identified , namely , hdl - c and fasting glucose levels . to provide potential explanation for these associations , further analyses were conducted on the three cvd risk factor - associated snps ( rs881150 , rs13184134 , and rs7702178 ) . results presented here suggest that dusp1 snps modulate plasma glucose and hdl - c levels in severely obese patients and that this effect is potentially mediated through alterations of gene methylation and expression . our analysis of differentially expressed genes in vat of severely obese individuals with and without mets revealed a potential implication of the dusp1 gene in the interindividual variability observed in obesity - related metabolic complications . a gene dosage effect of dusp1 on il - 10 levels has been reported in response to lipopolysaccharide at the systemic level in mice and on macrophage stimulation . this supports the hypothesis that differential expression of dusp1 in vat may have a physiological impact . with genetic variations potentially having an impact on gene expression , assessment of snpswas conducted and associations between selected snps and cvd risk factors ( blood pressure , glucose , and lipid levels ) were tested . two snps ( rs13184134 and rs7702178 ) were found to be associated with fasting glucose levels with a third one associated with hdl - c levels . dusp1 is known to be involved in the regulation of innate immune function , inflammation , and cellular response to oxidative stress . oxidative stress to endothelial cells and the subsequent decrease in glucose uptake and utilization have been shown to be responsible for insulin resistance . large - scale prospective studies have demonstrated that markers of inflammation predict incidence of t2d . oxidative stress in adipocytes results in dysregulated expression of inflammation - related adipocytokines and is characterized by decreased secretion of adiponectin and increased proinflammatory adipocytokines . in addition , an inverse relationship between elevated inflammation and low hdl - c has been demonstrated . with obesity being characterized by low - grade inflammation , the impact of phenotype - associated snps identified here may be exerted through a modulation of dusp1 antioxidative and anti - inflammatory functions . further analyses were performed to better understand the potential underlying mechanism for the difference in dusp1 gene expression levels and the associations identified for rs881150 , rs13184134 , and rs7702178 . with snps having an impact on the binding of transcription factors with consequent impact on transcriptional activity and gene expression levels , the first attempt assessed the impact of snps associated with cardiometabolic risk factors on transcription factor binding . the matinspector program revealed that dusp1 promoter snps may potentially affect the binding of transcription factors and promoter transcriptional activity . with snps potentially having an impact on gene methylation leading to differences in gene expression , the link between cardiometabolic risk factor - associated - snps , dna methylation , and gene expression levels was assessed . the three snps associated with cvd risk factors ( rs13184134 , rs7702178 , and rs881150 ) demonstrated associations with methylation levels of 10 different cpg sites . most of the associations were found for rs881150 ( 702 bp upstream tss ) which associates with methylation levels of two cpg sites located in its vicinity ( cg18121420 and cg02352687 ) and with 6 cpg sites located 11101402 bp upstream tss . a trend toward an association with another cpg site ( cg21121138 ) from this regioninterestingly , it contains the glucocorticoid - responsive region shown to be involved in the anti - inflammatory effects of glucocorticoids ( ~ 1300 bp from tss ) . in regard to these results and the correlations found between dusp1 gene methylation and expression levels , it is tempting to speculate that associations identified here between dusp1 snps and cardiometabolic risk factors may be mediated through differences in cpg sites methylation and expression . gene expression and dna methylation analyses were conducted in a relatively small number of selected individuals from our larger cohort . however , individuals from this subset were free of metabolic diseases such as type 2 diabetes , cardiomyopathy , or endocrine disorders and were matched for age , bmi , and smoking status to patients with , on average , none of the recognized features of the mets except high waist girth ( mets + group , n = 7 ; mets group , n = 7 ) . it is possible that other cell types found within adipose tissue such as endothelial cells , fibroblasts , or macrophages impact on tissue profiles . differences observed here may be the result of differences in these cells or their proportion . studies using isolated cell fractions and culture techniques will be required to elucidate this question . dusp1 resequencing and tsnps selection were conducted in 25 individuals including the highly selected subset . associations were thereafter tested in the whole cohort of 1906 individuals to identify snps explaining interindividual variability in obesity - related metabolic complications among severely obese patients . looking at snps having a small impact on the phenotypes of interest , we deliberately chose to exclude testing the association of rare snps with obesity - related metabolic complications as our study had a limited power . results presented here demonstrate an impact of dusp1 gene variations on obesity - related complications . although the impact is of small effect size , these results might partially explain interindividual variability observed in metabolic complications among obese individuals and thus highlight a potential new mets candidate gene . the present findings were obtained in a cohort of severely obese individuals . because inflammation is found in severely obese individuals , the impact of dusp1 snps through altered regulation of the innate immune functionthus , results from the present study can not be extrapolated to individuals with less pronounced obesity levels or to the general population . it would be relevant to conduct similar studies in the general population or in a cohort of normal weight individuals showing low or moderate levels of inflammation . in summary , the results obtained from the analysis of dusp1 promoter methylation and gene expression levels argue for an impact of dusp1 promoter snps on gene expression possibly mediated through alterations in specific cpg sites methylation levels . combined with the associations identified here between snps and cardiometabolic risk factors , these results provide a potential novel contributor to the modulation of plasma glucose and hdl - c levels in obese patients . it would be interesting to identify pathways mediating the impact of dusp1 snps and to investigate how epigenetic differences at the human dusp1 locus relate to the large - interindividual variability observed in metabolic complications among obese individuals .\noutput:\n" }, { "from": "agent", "value": "the dusp1 gene encodes a member of the dual - specificity phosphatase family previously identified as being differentially expressed in visceral adipose tissue ( vat ) of severely obese men with versus without the metabolic syndrome . objective . to test the association between dusp1 polymorphisms , obesity - related metabolic complications , gene methylation , and expression levels in vat . methods . the dusp1 locus and promoter region were sequenced in 25 individuals . snps were tested for association with obesity - related complications in a cohort of more than 1900 severely obese individuals . the impact of snps on methylation levels of 36 cpg sites and correlations between dna methylation and gene expression levels in vat were computed in a subset of 14 samples . results . heterozygotes for rs881150 had lower hdl - cholesterol levels ( hdl - c ; p = 0.01 ) , and homozygotes for the minor allele of rs13184134 and rs7702178 had increased fasting glucose levels ( p = 0.04 and 0.01 , resp . ) . rs881150 was associated with methylation levels of cpg sites located ~ 1250 bp upstream the transcription start site . methylation levels of 4 cpg sites were inversely correlated with dusp1 gene expression . conclusion . these results suggest that dusp1 polymorphisms modulate plasma glucose and hdl - c levels in obese patients possibly through alterations of dna methylation and gene expression levels ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: boron - doped diamond ( bdd ) 1 electrodes , which are produced by chemical vapour deposition , represent an interesting alternative carbon - based electrode material for use in electrochemistry . the electrode shows advantageous electrochemical properties including low pseudocapacitive background currents , a wide operating potential window and excellent electrochemical stability in comparison to traditional carbon materials . as - grown thin film diamond is largely hydrogen terminated and the alkane - like surface is thus hydrophobic .2 upon treatments such as anodic polarisation,2a - 3 potential cycling ,4 and oxygen plasma ,2 b oxygen - containing groups can be introduced onto the diamond surface , consequently rendering it hydrophilic . the surface - chemical composition can therefore be altered to influence properties such as hydrophobicity and the electron - transfer kinetics .2 b ,5 to impart additional functionality to the diamond , the surface of the substrate can be modified with electrocatalytic materials . the common approaches towards the attachment of such materials onto diamond electrodes include electrochemical deposition ,6 photochemical reaction ,7 electropolymerisation ,8 and ion implantation .9 these typically involve at least some level of instrumentation or covalent linkage . the relatively simple technique of dropcasting a coating onto diamond is rather limited however , but some examples from the literature are listed in table 1.10 these modifiers are predominantly particulate in nature . the limited use of such physical immobilisation is likely due to the general notion of diamond having greater chemical inertness relative to common carbon electrodes . nevertheless , a few recent reports on diamond have described the observation of adsorptive behaviour of molecular compounds such as quinizarin ,11 methyl viologen ,12 and anthraquinonedisulfonate12b from solution . therefore , in this paper we explore the attachment of molecular modifiers , in the form of microcrystals on diamond , using copper phthalocyanine as an exemplar . some examples of modification of boron - doped diamond ( bdd ) via dropcasting . there have been only several reports of the modification of diamond film electrodes with metallophthalocyanines . these were performed by vacuum deposition13 or after photochemical modification with 4 - vinylpyridine .14 we demonstrate that a simple dropcast method can be effective for the immobilisation of metallophthalocyanine onto diamond as well . in particular , we compare the influence of two different commonly used surface terminations , namely hydrogen and oxygen , on the interaction of metallophthalocyanine with diamond . moreover , we show that the dropcasting leads to an array of microcrystals of copper phthalocyanine on the bdd surface . metallophthalocyanines are well known as catalysts for homogeneous and heterogeneous chemical reactions ,15 amongst which is the capability to lower the overpotential for the oxygen reduction reaction ; 16 hence , this process is chosen to examine the metallophthalocyanine diamond system in this work . moreover the reduction of oxygen is of considerable technological importance , for instance in the development of fuel cells .17 in respect of oxygen reduction , diamond is especially useful for studying cathodic reactions without interference from water electrolysis owing to its large overpotential for hydrogen evolution1b ,1 e and its outstanding stability under reductive conditions . in this section , oxygen reduction is first investigated at unmodified bdd electrodes to provide a starting point for studying the reaction . next , the cathodic process is examined at copper - phthalocyanine - modified diamond to compare the effects of differing surface terminations . included is also a study of the behaviour of the modified hydrogen - terminated diamond towards the reduction of hydrogen peroxide . the electrochemical reduction of oxygen in aqueous solutions can proceed by the following two general pathways : either a direct four - electron route or a two - electron hydrogen peroxide mechanism .18 both pathways are described below for neutral conditions at ph 7 . direct 4 - electron pathway 1 the direct four - electron process is expected to exhibit a single voltammetric wave . for the peroxide route , there are two possibilities : a ) the potentials for the sequential electron transfers could be well separated , resulting in two distinct voltammetric waves , or b ) the reduction of peroxide could occur at or near the oxygen reduction potential , leading to a single voltammetric wave . cyclic voltammetry was first carried out on the unmodified boron - doped diamond with surface terminations of hydrogen and oxygen , in both o2 - and n2 - saturated phosphate buffer solution ( pbs ) at ph 7 , to provide a basis for understanding the oxygen reduction at these electrodes . the cyclic voltammograms obtained are shown in figure 1 . in the n2 - saturated solution , however , in the o2 - saturated solution , the two types of surfaces gave rise to a different response . at the o - terminated surface there was no apparent peak , whereas at the h - terminated surface , a large and irreversible voltammetric peak was observed with a peak potential at 1.09 v ( vs. ag / agcl ) , which can be attributed to the irreversible reduction of oxygen to hydrogen peroxide ,19 as given by equation 2 . the two - electron reduction of oxygen on the h - terminated diamond is typical of the peroxide pathway commonly seen on carbon electrodes .18 b ,20 cyclic voltammograms for h - terminated ( h - bdd , solid line ) and o - terminated ( o - bdd , dashed line ) bdd electrodes in n2 - saturated ( above ) and o2 - saturated ( below ) 0.1 m pbs ph 7 . scan rate : 100 mv s. the potential was swept in a negative direction from 0 v. the standard potential for the two - electron reduction of oxygen is + 0.281 v ( she ) at ph 7 and the large overpotential on the h - terminated surface is consistent with the work of yano et al. 19 which found the oxygen reduction to be highly inhibited on as - grown diamond . this was attributed to a lack of adsorption sites for oxygen and / or reduced intermediates , a low density of states , or a potential drop within a thin ( 2 nm ) surface layer . as the reduction of oxygen involves the addition of hydrogen , and the cathodic reactionis only observed on the h - terminated surface but not the o - terminated surface , there exists the possibility of the surface hydrogen providing the stoichiometric source . the surface density of carbon bonds on diamond and , hence , the maximum coverage of h , is 10 cm . assuming an electron transfer for each h reacted , the charge required to exhaust the surface h in this case is 710c . the charge passed on the cathodic sweep for the h - terminated surface in o2 - saturated solution is 1.110 c , therefore , a single scan should exhaust the surface h if it is reacting . consecutive cyclic voltammetric scans were thus carried out , and the voltammograms are shown in figure 2 . the second scan showed a decrease in the peak current , which can be attributed to the slow removal of reaction products from the reaction sites . after the solution was stirred by bubbling with oxygen , the subsequent voltammogram showed a restoration of the peak current to that of the initial value . this confirms that the h - terminated diamond is indeed electrocatalytic compared to the o - terminated surface . cyclic voltammograms for h - terminated bdd electrode in o2 - saturated 0.1 m pbs ph 7 showing initial scan ( solid line ) , second scan ( dashed line ) , and subsequent scan after stirring ( dotted line ) . scan rate : 100 mv s. a simple dropcast technique was used to immobilise copper phthalocyanine onto the diamond electrode as described in the experimental section , and the surface morphology of the modified h - and o - terminated electrodes were characterised by scanning electron microscopy ( sem ) . as revealed by the sem micrographs in figure 3 , the structure of the modified electrodes both consisted of microcrystalline deposits of varying sizes up to about 7 m in length across the diamond surface . sem micrographs of copper - phthalocyanine - modified a ) h - terminated , b ) o - terminated bdd . the scale bars represented by dotted lines are 15.0 m ( a ) and 15.8 m ( b ) . frame dimensions ( hw ) are 6958 m ( a ) and 7361 m ( b ) . the cyclic voltammograms on the modified h - terminated surface in both o2 - and n2 - saturated pbs are shown in figure 4 . while the curve obtained in the n2 - saturated solutionis relatively featureless , a large and irreversible cathodic peak was observed at 0.58 v ( vs. ag / agcl ) in the o2 - saturated solution attributed to the reduction of oxygen . this represents a significant decrease in overpotential of over 500 mv compared to the unmodified h - terminated electrode and demonstrates the substantial electrocatalytic effect as a result of copper - phthalocyanine modification . the behaviour for the modified o - terminated diamond is very different , however , as shown in figure 5 . cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in n2 - saturated ( above ) and o2 - saturated ( below ) 0.1 m pbs ph 7 . scan rate : 100 mv s. cyclic voltammogram for copper - phthalocyanine - modified o - terminated bdd in o2 - saturated 0.1 m pbs ph 7 . scan rate : 100 mv s. based on the results above , it is clear that the surface chemical termination has an effect on the interaction between copper phthalocyanine and diamond . only on the h - terminated surface is there significant interaction with the metallophthalocyanine based on the observation of its positive impact on the electrocatalysis of oxygen reduction . this is likely due to the hydrophobic interaction between copper phthalocyanine and the ( hydrophobic ) h - terminated surface .12 a as for the oxidised diamond electrode , the hydrophilic surface is expected to have much weaker interaction with the nonpolar compound . from the absence of a voltammetric peak in an o2 - saturated solution , it can be inferred that the electrical connection of copper phthalocyanine microcrystallites to the o - terminated diamond is therefore inferior to the case of the h - termination . figure 6 a displays the voltammetric data obtained at scan rates from 10 to 400 mv s , and the linear dependence of the peak current on the square root of the scan rate is shown in figure 6 b , indicating the reduction of oxygen on the modified surface is a diffusion - controlled process at the modified h - terminated surface . the peak current for the transport - limited irreversible n - electron - transfer reaction is described in equation 4 : 4 a ) cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in o2 - saturated 0.1 m pbs ph 7 at scan rates from 10400 mv s. b ) plot of peak current against square root of scan rate . where ipeak is the peak current , n is the number of electron transferred before the rate limiting step , is the transfer coefficient of the rate determining step , f is the faraday constant , a is the electrode area , [ o2 ] is the oxygen concentration , is the scan rate , d is the diffusion coefficient , r is the gas constant , and t is the absolute temperature . tafel analyses on the above data are shown in figure 7 , and an average value for of 0.46 was derived from the gradients of the plots . the concentration of oxygen in a saturated solution is 1.3 mm ,21 and the diffusion coefficient for oxygen is 2.110 cm s. 22 using these values and the gradient of the linear plot in figure 6 b , the number of electrons transferred is calculated using equation 4 to be 2 , indicating the reduction of oxygen to hydrogen peroxide . tafel plots of cathodic current for o2 - saturated 0.1 m pbs ph 7 at scan rates from 50200 mv s. from the results above , the copper - phthalocyanine - modified h - terminated diamond exhibits a two - electron reduction in o2 - saturated solution . it has been reported that oxygen can undergo a four - electron reduction at certain metallophthalocyanines .16 c16e therefore , the possibility of the electrochemical reduction of the hydrogen peroxide on the modified diamond surface was further investigated . the unmodified h - terminated diamond surface was examined by cyclic voltammetry in an n2 - saturated solution , and the measurement was featureless for the reduction of hydrogen peroxide . standard addition of hydrogen peroxide was then conducted on the copper - phthalocyanine - modified h - terminated diamond in an n2 - saturated pbs to study the reaction without contribution from dioxygen . figure 8 a shows the cyclic voltammograms of hydrogen peroxide for concentrations of 0.0 to 2.0 mm , with a peak potential of 0.57 v ( vs. ag / agcl ) at 0.1 mm . the magnitude of the peak current increases linearly with the hydrogen peroxide concentration , as shown in figure 8 b , and the gradient of the calibration plot is 121.4 a mm . a ) cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in n2 - saturated 0.1 m pbs ph 7 containing 0.02.0 mm h2o2 ( dashed line : 0.0 mm ) . scan rate : 100 mv s. b ) plot of peak current against concentration of h2o2 . tafel analyses on the descending portion of the voltammetric curve yielded an average value of to be 0.30 . together with the gradient of the calibration plot and the diffusion coefficient of hydrogen peroxide ( 8.310 cm s ) ,23 the number of electrons per molecule transferred can be calculated using equation 4 , giving a value close to 2 . this indicates that the reaction as described by equation 3 is taking place at the copper - phthalocyanine - modified h - terminated diamond . the cathodic peak potential for the reduction of hydrogen peroxide is very similar to that for the reduction of oxygen , and the reactions of both compounds have been demonstrated on the modified h - terminated diamond as above . therefore , this suggests that the reduction of oxygen should in principle be able to undergo an overall four - electron reaction via the stepwise mechanism with hydrogen peroxide as the intermediate , as described earlier . however , it is clear that oxygen reduction progresses according to equation 2 with no further electrochemical reduction of hydrogen peroxide . the key to this apparent conundrum likely lies in the structure of the surface deposition . as illustrated in figure 9 , the dropcast modification of molecular compounds could result in the formation of a continuous film or an array of microcrystallites on the electrode surface . in the former case . however , the results above are suggestive of the case for the microcrystalline array , in which the charge transfer is thought to occur at the triple phase boundary formed between the copper phthalocyanine microcrystallite , the diamond , and the aqueous solution .24 at the junction of contact of the three phases , the catalyst , electrons , and reactants are all present in adequate proximity for the reaction to occur . the fact that the reduction of oxygen is an overall two - electron process probably has to do with the microcrystallites behaving in effect as a random array of microelectrodes ( figure 10 ) , allowing the hydrogen peroxide formed in this instance to diffuse radially into the bulk phase at a rapid rate before it can undergo further conversion according to equation 3 . indeed the presence of microcrystallites on the modified diamond surface has been evidenced earlier by sem in figure 3 , and this supports our inference of a triple - boundary process . schematic diagram showing possible outcomes of h2o2 during o2 reduction at the triple phase boundary . the electrochemical reduction of oxygen in aqueous solutions can proceed by the following two general pathways : either a direct four - electron route or a two - electron hydrogen peroxide mechanism .18 both pathways are described below for neutral conditions at ph 7 . direct 4 - electron pathway 1 the direct four - electron process is expected to exhibit a single voltammetric wave . for the peroxide route , there are two possibilities : a ) the potentials for the sequential electron transfers could be well separated , resulting in two distinct voltammetric waves , or b ) the reduction of peroxide could occur at or near the oxygen reduction potential , leading to a single voltammetric wave . cyclic voltammetry was first carried out on the unmodified boron - doped diamond with surface terminations of hydrogen and oxygen , in both o2 - and n2 - saturated phosphate buffer solution ( pbs ) at ph 7 , to provide a basis for understanding the oxygen reduction at these electrodes . the cyclic voltammograms obtained are shown in figure 1 . in the n2 - saturated solution , however , in the o2 - saturated solution , the two types of surfaces gave rise to a different response . at the o - terminated surface there was no apparent peak , whereas at the h - terminated surface , a large and irreversible voltammetric peak was observed with a peak potential at 1.09 v ( vs. ag / agcl ) , which can be attributed to the irreversible reduction of oxygen to hydrogen peroxide ,19 as given by equation 2 . the two - electron reduction of oxygen on the h - terminated diamond is typical of the peroxide pathway commonly seen on carbon electrodes .18 b ,20 cyclic voltammograms for h - terminated ( h - bdd , solid line ) and o - terminated ( o - bdd , dashed line ) bdd electrodes in n2 - saturated ( above ) and o2 - saturated ( below ) 0.1 m pbs ph 7 . scan rate : 100 mv s. the potential was swept in a negative direction from 0 v. the standard potential for the two - electron reduction of oxygen is + 0.281 v ( she ) at ph 7 and the large overpotential on the h - terminated surface is consistent with the work of yano et al. 19 which found the oxygen reduction to be highly inhibited on as - grown diamond . this was attributed to a lack of adsorption sites for oxygen and / or reduced intermediates , a low density of states , or a potential drop within a thin ( 2 nm ) surface layer . as the reduction of oxygen involves the addition of hydrogen , and the cathodic reaction is only observed on the h - terminated surface but not the o - terminated surface , there exists the possibility of the surface hydrogen providing the stoichiometric source . the surface density of carbon bonds on diamond and , hence , the maximum coverage of h , is 10 cm . assuming an electron transfer for each h reacted , the charge required to exhaust the surface h in this case is 710c . the charge passed on the cathodic sweep for the h - terminated surface in o2 - saturated solution is 1.110 c , therefore , a single scan should exhaust the surface h if it is reacting . consecutive cyclic voltammetric scans were thus carried out , and the voltammograms are shown in figure 2 . the second scan showed a decrease in the peak current , which can be attributed to the slow removal of reaction products from the reaction sites . after the solution was stirred by bubbling with oxygen , the subsequent voltammogram showed a restoration of the peak current to that of the initial value . this confirms that the h - terminated diamond is indeed electrocatalytic compared to the o - terminated surface . cyclic voltammograms for h - terminated bdd electrode in o2 - saturated 0.1 m pbs ph 7 showing initial scan ( solid line ) , second scan ( dashed line ) , and subsequent scan after stirring ( dotted line ) . a simple dropcast technique was used to immobilise copper phthalocyanine onto the diamond electrode as described in the experimental section , and the surface morphology of the modified h - and o - terminated electrodes were characterised by scanning electron microscopy ( sem ) . as revealed by the sem micrographs in figure 3 , the structure of the modified electrodes both consisted of microcrystalline deposits of varying sizes up to about 7 m in length across the diamond surface . sem micrographs of copper - phthalocyanine - modified a ) h - terminated , b ) o - terminated bdd . the scale bars represented by dotted lines are 15.0 m ( a ) and 15.8 m ( b ) . frame dimensions ( hw ) are 6958 m ( a ) and 7361 m ( b ) . the cyclic voltammograms on the modified h - terminated surface in both o2 - and n2 - saturated pbs are shown in figure 4 . while the curve obtained in the n2 - saturated solutionis relatively featureless , a large and irreversible cathodic peak was observed at 0.58 v ( vs. ag / agcl ) in the o2 - saturated solution attributed to the reduction of oxygen . this represents a significant decrease in overpotential of over 500 mv compared to the unmodified h - terminated electrode and demonstrates the substantial electrocatalytic effect as a result of copper - phthalocyanine modification . the behaviour for the modified o - terminated diamond is very different , however , as shown in figure 5 . cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in n2 - saturated ( above ) and o2 - saturated ( below ) 0.1 m pbs ph 7 . scan rate : 100 mv s. cyclic voltammogram for copper - phthalocyanine - modified o - terminated bdd in o2 - saturated 0.1 m pbs ph 7 . scan rate : 100 mv s. based on the results above , it is clear that the surface chemical termination has an effect on the interaction between copper phthalocyanine and diamond . only onthe h - terminated surface is there significant interaction with the metallophthalocyanine based on the observation of its positive impact on the electrocatalysis of oxygen reduction . this is likely due to the hydrophobic interaction between copper phthalocyanine and the ( hydrophobic ) h - terminated surface .12 a as for the oxidised diamond electrode , the hydrophilic surface is expected to have much weaker interaction with the nonpolar compound . from the absence of a voltammetric peak in an o2 - saturated solution , it can be inferred that the electrical connection of copper phthalocyanine microcrystallites to the o - terminated diamond is therefore inferior to the case of the h - termination . figure 6 a displays the voltammetric data obtained at scan rates from 10 to 400 mv s , and the linear dependence of the peak current on the square root of the scan rate is shown in figure 6 b , indicating the reduction of oxygen on the modified surface is a diffusion - controlled process at the modified h - terminated surface . the peak current for the transport - limited irreversible n - electron - transfer reaction is described in equation 4 : 4 a ) cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in o2 - saturated 0.1 m pbs ph 7 at scan rates from 10400 mv s. b ) plot of peak current against square root of scan rate . where ipeak is the peak current , n is the number of electron transferred before the rate limiting step , is the transfer coefficient of the rate determining step , f is the faraday constant , a is the electrode area , [ o2 ] is the oxygen concentration , is the scan rate , d is the diffusion coefficient , r is the gas constant , and t is the absolute temperature . tafel analyses on the above data are shown in figure 7 , and an average value for of 0.46 was derived from the gradients of the plots . the concentration of oxygen in a saturated solution is 1.3 mm ,21 and the diffusion coefficient for oxygen is 2.110 cm s. 22 using these values and the gradient of the linear plot in figure 6 b , the number of electrons transferred is calculated using equation 4 to be 2 , indicating the reduction of oxygen to hydrogen peroxide . tafel plots of cathodic current for o2 - saturated 0.1 m pbs ph 7 at scan rates from 50200 mv s.from the results above , the copper - phthalocyanine - modified h - terminated diamond exhibits a two - electron reduction in o2 - saturated solution . it has been reported that oxygen can undergo a four - electron reduction at certain metallophthalocyanines .16 c16e therefore , the possibility of the electrochemical reduction of the hydrogen peroxide on the modified diamond surface was further investigated . the unmodified h - terminated diamond surface was examined by cyclic voltammetry in an n2 - saturated solution , and the measurement was featureless for the reduction of hydrogen peroxide . standard addition of hydrogen peroxide was then conducted on the copper - phthalocyanine - modified h - terminated diamond in an n2 - saturated pbs to study the reaction without contribution from dioxygen . figure 8 a shows the cyclic voltammograms of hydrogen peroxide for concentrations of 0.0 to 2.0 mm , with a peak potential of 0.57 v ( vs. ag / agcl ) at 0.1 mm . the magnitude of the peak current increases linearly with the hydrogen peroxide concentration , as shown in figure 8 b , and the gradient of the calibration plot is 121.4 a mm . a ) cyclic voltammograms for copper - phthalocyanine - modified h - terminated bdd in n2 - saturated 0.1 m pbs ph 7 containing 0.02.0 mm h2o2 ( dashed line : 0.0 mm ) . scan rate : 100 mv s. b ) plot of peak current against concentration of h2o2 . tafel analyses on the descending portion of the voltammetric curve yielded an average value of to be 0.30 . together with the gradient of the calibration plot and the diffusion coefficient of hydrogen peroxide ( 8.310 cm s ) ,23 the number of electrons per molecule transferred can be calculated using equation 4 , giving a value close to 2 . this indicates that the reaction as described by equation 3 is taking place at the copper - phthalocyanine - modified h - terminated diamond . the cathodic peak potential for the reduction of hydrogen peroxide is very similar to that for the reduction of oxygen , and the reactions of both compounds have been demonstrated on the modified h - terminated diamond as above . therefore , this suggests that the reduction of oxygen should in principle be able to undergo an overall four - electron reaction via the stepwise mechanism with hydrogen peroxide as the intermediate , as described earlier . however , it is clear that oxygen reduction progresses according to equation 2 with no further electrochemical reduction of hydrogen peroxide . the key to this apparent conundrum likely lies in the structure of the surface deposition . as illustrated in figure 9 , the dropcast modification of molecular compounds could result in the formation of a continuous film or an array of microcrystallites on the electrode surface . in the former casehowever , the results above are suggestive of the case for the microcrystalline array , in which the charge transfer is thought to occur at the triple phase boundary formed between the copper phthalocyanine microcrystallite , the diamond , and the aqueous solution .24 at the junction of contact of the three phases , the catalyst , electrons , and reactants are all present in adequate proximity for the reaction to occur . the fact that the reduction of oxygen is an overall two - electron process probably has to do with the microcrystallites behaving in effect as a random array of microelectrodes ( figure 10 ) , allowing the hydrogen peroxide formed in this instance to diffuse radially into the bulk phase at a rapid rate before it can undergo further conversion according to equation 3 . indeed the presence of microcrystallites on the modified diamond surface has been evidenced earlier by sem in figure 3 , and this supports our inference of a triple - boundary process . schematic diagram of the possible surface formation via dropcast modification . schematic diagram showing possible outcomes of h2o2 during o2 reduction at the triple phase boundary . the dropcast coating of boron - doped diamond electrodes has been studied as a facile method for the surface modification of diamond with molecular materials . the electrochemical behaviour of unmodified and copper - phthalocyanine - modified diamond electrodes was examined via the reduction of oxygen , a reaction known to be catalysed by metallophthalocyanines . hydrogenated diamond modified in such a manner was able to significantly decrease the overpotential for the cathodic reaction by about 500 mv when compared to the unmodified electrode . oxidised diamond , however , displayed no such electrocatalysis even after modification by the copper macrocycle . these effects may be attributable to the greater interaction between the nonpolar molecular modifier and the alkane - like hydrogen - terminated surface , through forces such as hydrophobic interaction . on the modified h - terminated diamond , the electrochemical reduction of oxygen occurred through a diffusion - control two - electron cathodic process via the peroxide pathway . in addition , the modified electrode showed activity for the electrochemical reduction of hydrogen peroxide at similar potentials as well . the role of microcrystallites is proposed to lead to the curtailment of the oxygen reduction at the peroxide stage due to the rapid diffusion of the reaction product away from the triple phase boundary at where the reaction is thought to occur . sem characterisation of the surface morphology confirmed the presence of microcrystallites on the modified h - terminated diamond . materials : copper ( ii ) phthalocyanine ( dye content 99 % , aldrich ) , ch3cn ( 99.7 % , rathburn ) , h2o2 ( 35 wt % , alfa aesar ) , kh2po4 ( 99.0 % , sigma aldrich ) , and k2hpo43 h2o ( 99.0 % , sigma aldrich ) were used as received . all aqueous solutions were prepared using ultrapure h2o ( 18.2 m cm at 25 c ) . o2 andgases were bubbled through for at least 15 min to saturate the solution , and an o2 or n2 atmosphere was kept over the solution during the experiment . apparatus : electrochemical experiments were conducted at 221 c using a - autolab iii potentiostat ( eco - chemie , utrecht , netherlands ) , with a standard three - electrode configuration comprising a platinum coil counter electrode , and an ag / agcl ( 1 m kcl ) reference electrode , against which working electrode potentials are referred , along with the working electrode . hydrogen plasma treatment of the electrode surface was carried out with a microwave plasma system . surface morphology was characterised by a hitachi 520 sem ( tokyo , japan ) operating at an accelerating voltage of 20 kv . electrode preparation : boron - doped polycrystalline diamond ( element six co. ) with a b doping concentration of 510 cm was used as the working electrode , which was mounted in a home - built polytetrafluoroethylene ( ptfe ) holder with an area of 0.44 cm being exposed to the electrolyte . an oxidised ( o - terminated ) diamond electrode was prepared by potential cycling in 0.1 mol dm hno3 between potentials of 1.5 v and + 2.5 v until a stable scan was observed . to produce a hydrophobic h - terminated surface , the electrode was exposed to a hydrogen plasma at 60 mbar pressure , 1.5 kw microwave power at a temperature of 600 c for 30 min . after this treatment , the substrate heater was switched off , and the sample was left exposed to the hydrogen plasma which was gradually reduced in power until the plasma extinguished and the sample cooled to rt under flowing hydrogen . this procedure yielded an electrode surface which x - ray photoelectron spectroscopy ( xps ) confirmed was largely free of adsorbed hydrocarbons or sp material which can adsorb if thecool - down period is not carefully controlled . to modify the diamond electrode , 50 l of copper phthalocyanine ( 1 mg in 1 ml acetonitrile ) was pipetted onto the electrode surface in aliquots of 23 l and allowed to dry in air between aliquots . this volume was found to give maximal voltammetric response , indicating the optimal coverage of the electrode . blank voltammograms were run in o2 - saturated pbs ph 7 ( 0.1 m ) to equilibrate each freshly prepared electrode before further experiments were conducted . the electrode - to - electrode response was generally reproducible and stable at least over the length of the experiments .\noutput:\n" }, { "from": "agent", "value": "surface modification of boron - doped diamond ( bdd ) with copper phthalocyanine was achieved using a simple and convenient dropcast deposition , giving rise to a microcrystalline structure . both unmodified and modified bdd electrodes of different surface terminations ( namely hydrogen and oxygen ) were compared via the electrochemical reduction of oxygen in aqueous solution . a significant lowering of the cathodic overpotential by about 500 mv was observed after modification of hydrogen - terminated ( hydrophobic ) diamond , while no voltammetric peak was seen on modified oxidised ( hydrophilic ) diamond , signifying greater interaction between copper phthalocyanine and the hydrogen - terminated bdd . oxygen reduction was found to undergo a two - electron process on the modified hydrogen - terminated diamond , which was shown to be also active for the reduction of hydrogen peroxide . the lack of a further conversion of the peroxide was attributed to its rapid diffusion away from the triple phase boundary at which the reaction is expected to exclusively occur ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: summarize the initial experience with the program , including its adoption and reception by small businesses . identify the characteristics of participating employees , and discuss the potential benefits of extending worksite health promotion programs to smaller companies . this study focuses on baseline recruitment and health risk profile data gathered from small businesses and their employees as part of a 5 - year , prospective , longitudinal casepinnacol assurance , a workers ' compensation insurer in the state of colorado , the united states , offered its policyholders access to a free hrm program described below . although outside the scope of this article , the larger goal of the ongoing longitudinal study was to compare rates of workers ' compensation claims and costs in companies that participate in the hrm program with matched companies that do not participate , hypothesizing that health risk reductions can lead to reductions in workers ' compensation claims and costs . before one can test such a hypothesis , it is necessary to demonstrate that it is feasible to recruit and retain small businesses to offer hrm to their employees . as such , this article and the remainder of the methods section focus on strategies used for recruitment of small businesses , description of the hrm intervention , and survey methods used to assess the types of organizations recruited and the health risk profiles of the employees participating in the study . in 2010 , pinnacol assurance , a colorado - based workers ' compensation insurance provider , began offering its employer - policyholders access to the hrm program . pinnacol 's decision to offer this program and engage in research was based on a belief that poor health has a negative effect on workers ' compensation costs . strategically , pinnacol assurance leadership was of the opinion that health risk management will become as fundamental to managing risks as safety management is currently . nevertheless , because of a paucity of reliable data , pinnacol had no actuarial basis for establishing the financial effect of hrm . as such , pinnacol made a commitment to an external evaluation . to comply with state workers ' compensation insurance regulations , . nevertheless , the initial pilot of this program allowed capping if recruitment goals were met . the program was capped at 300 businesses of any size . as a result , it is not possible for us to calculate a corporation participation rate . pinnacol assurance partnered with the trotter wellness ( sheboygan , wi ) , an administrator of employee wellness programs nationwide , to administer its hrm program . pinnacol assurance also contracted with the segue consulting ( denver , co ) to create its hrm program and the integrated benefits institute ( ibi ) ( san francisco , ca ) , a nonprofit employee health and productivity research organization , to advise on measurement and process data for the research study . for employees , the hrm program includes an hra questionnaire , a feedback report , advice on developing an action plan for improving wellness and reducing health risks , access to health educational materials , and unlimited telephonic coaching . for employers , the hrm program includes summary reports on employee needs , development of an action plan on the basis of employee health goals , ongoing feedback regarding employee participation and progress , educational content for distribution to employees , and advice on program enhancements . employers also receive a formal risk and recommendations report , which includes industry baseline comparisons and cohort reporting when applicable . employers with fewer than 50 employees receive a condensed version of the risks and recommendations report . employers were actively recruited to enroll in the hrm program through insurance agents and through joint hrm training sessions conducted by the trotter wellness and pinnacol assurance team members . the pinnacol hrm program was made available to all pinnacol assurance policyholders and offered at no direct cost to policyholders to enroll their employees in the program . pinnacol assurance encouraged policyholders to actively promote the program to their employees and support a culture of wellness . employers who enrolled in the hrm program completed a new policyholder information enrollment form and corresponding privacy agreement . the new policyholder information form captured essential employer information used by the trotter wellness to activate the employer , and for pinnacol assurance to monitor the characteristics of the employer enrolled in the program . once enrolled , employers received a welcome packet that contained information on the hra start and end dates , the telephonic health coaching start date , and instructions for accessing the employer web portal . the portal also contained information regarding rollout and implementation of the hrm program , as well as instructions that each enrolled hra employee participant used to access the online hra . employers who indicated that they have english - and spanish - speaking employees received welcome packets in both languages . employers subsequently participated in a wellness program orientation , conducted via webinar by the trotter wellness or in - person by pinnacol assurance . this webinar provides additional information on topics such as communications , leadership involvement , incentives , and participation goals , as well as information on other resources available through employer and employee portals . the hra served as the primary modality of risk assessment and data collection for the pinnacol hrm program . an online hra questionnaire was administered as part of the hrm program to assess health risks . the questionnaire used in this studywas provided by the trotter wellness and was certified by the national committee for quality assurance .20 the trotter wellness hra includes questions in the following categories : biographical information , health history , medical care , physical activity , nutrition , substance use , mental / social health , injury prevention practices , readiness to change , and job satisfaction . for this study , the trotter wellness hra questionnaire was supplemented with 58 additional selected questions from the world health organization health and work performance questionnaire ( hpq ) 21 and a modified version of the hpq , the hpq select which were provided by the ibi .22 these additional survey questions further elucidated health and lost - time information to assess lost productivity as measured by attendance , absence , and job performance . in total , the data presented below provide an analysis of participating employees ' overall health status and health risks on completion of an initial hra , prior to health promotion interventions ( eg , health coaching and education ) . to better understand the reasons why small businesses chose to participate in the hrm program and the aspects they value most highly , pinnacol assurance conducted a survey of employers . questions probed the reasons driving their decision to participate in the hrm program , what they hoped to achieve by participating , and their valuation of various aspects of the program . participants were also provided an open text response option , where they could indicate what they would improve about the program . employee participation rates were calculated using the following two measures : ( 1 ) using the number of participants who completed an hra , divided by the number of eligible employee participants as defined by the individual employer , and ( 2 ) using the number of participants who completed an hra , divided by employee counts as defined by pinnacol assurance . employee - level data were obtained from employees ' self - reported responses to the trotter wellness hra questionnaire and hpq - select questions . scheduled biannual data transfers from the trotter wellnessadditional employer and workers ' compensation data were provided by pinnacol assurance . all primary data described in this study were transferred to the ibi for participant matching and de - identification according to the health insurance portability and accountability act guidelines . de - identified data were provided to the center for worker health and environment ( cwhe ) at the university of colorado for analysis . the institutional review boards for the university of colorado ( colorado multiple institutional review board ) and the colorado state university reviewed this study and considered it to be exempt ( nonhuman subjects ' research ) . for this study , most results are presented as frequencies of individual characteristics within the employer and employee cohorts . this score is calculated for each participant on the basis of the individuals ' responses to questions within the hra . the ows each individual receives falls into one of the following categories : excellent ( score 80 ) , doing well ( 60 to 79 ) , needs improving ( 20 to 59 ) , orbody mass index was calculated according to the standard formula [ weight ( pounds ) / [ height ( inches ) ] 703 ] using self - reported height and weight data . body mass index classification was reported according to the world health organization 's international classification scale . alcohol consumption guidelines for males and females were based on the national institute on alcohol abuse and alcoholism guidelines and state that moderate to low risk consumption for men is 14 drinks / week and for women 8 drinks / week . nevertheless , those guidelines also include single - day alcohol consumption limits for men and women , which the hra questionnaire did not assess . for purposes of this study , employee stress was characterized as low or moderate / high on the basis of responses to three individual questions included in the hra . sometimes experienced stress at home or at work and also responded that their stress over finances was little or none were classified as having low stress . employees who responded that they had often or permanent or continual stress at home or work or had moderate oremployer and employee data were reported as frequencies , with means and standard deviations reported for some measures . all data analysis was performed by the cwhe at the university of colorado using stata 12 data analysis software ( statacorp , college station , tx ) . in 2010 , pinnacol assurance , a colorado - based workers ' compensation insurance provider , began offering its employer - policyholders access to the hrm program . pinnacol 's decision to offer this program and engage in research was based on a belief that poor health has a negative effect on workers ' compensation costs . strategically , pinnacol assurance leadership was of the opinion that health risk management will become as fundamental to managing risks as safety management is currently . nevertheless , because of a paucity of reliable data , pinnacol had no actuarial basis for establishing the financial effect of hrm . as such , pinnacol made a commitment to an external evaluation . to comply with state workers ' compensation insurance regulations , the program was offered to all approximately 55,000 policyholders in the pinnacol book of business . nevertheless , the initial pilot of this program allowed capping if recruitment goals were met . the program was capped at 300 businesses of any size . as a result , it is not possible for us to calculate a corporation participation rate . pinnacol assurance partnered with the trotter wellness ( sheboygan , wi ) , an administrator of employee wellness programs nationwide , to administer its hrm program . pinnacol assurance also contracted with the segue consulting ( denver , co ) to create its hrm program and the integrated benefits institute ( ibi ) ( san francisco , ca ) , a nonprofit employee health and productivity research organization , to advise on measurement and process data for the research study . for employees , the hrm program includes an hra questionnaire , a feedback report , advice on developing an action plan for improving wellness and reducing health risks , access to health educational materials , and unlimited telephonic coaching . for employers , the hrm program includes summary reports on employee needs , development of an action plan on the basis of employee health goals , ongoing feedback regarding employee participation and progress , educational content for distribution to employees , and advice on program enhancements . employers also receive a formal risk and recommendations report , which includes industry baseline comparisons and cohort reporting when applicable . employers with fewer than 50 employees receive a condensed version of the risks and recommendations report . employers were actively recruited to enroll in the hrm program through insurance agents and through joint hrm training sessions conducted by the trotter wellness and pinnacol assurance team members . the pinnacol hrm program was made available to all pinnacol assurance policyholders and offered at no direct cost to policyholders to enroll their employees in the program . pinnacol assurance encouraged policyholders to actively promote the program to their employees and support a culture of wellness . employers who enrolled in the hrm program completed a new policyholder information enrollment form and corresponding privacy agreement . the new policyholder information form captured essential employer information used by the trotter wellness to activate the employer , and for pinnacol assurance to monitor the characteristics of the employer enrolled in the program . once enrolled , employers received a welcome packet that contained information on the hra start and end dates , the telephonic health coaching start date , and instructions for accessing the employer web portal . the portal also contained information regarding rollout and implementation of the hrm program , as well as instructions that each enrolled hra employee participant used to access the online hra . employers who indicated that they have english - and spanish - speaking employees received welcome packets in both languages . employers subsequently participated in a wellness program orientation , conducted via webinar by the trotter wellness or in - person by pinnacol assurance . this webinar provides additional information on topics such as communications , leadership involvement , incentives , and participation goals , as well as information on other resources available through employer and employee portals . the hra served as the primary modality of risk assessment and data collection for the pinnacol hrm program . an online hra questionnaire was administered as part of the hrm program to assess health risks . the questionnaire used in this studywas provided by the trotter wellness and was certified by the national committee for quality assurance .20 the trotter wellness hra includes questions in the following categories : biographical information , health history , medical care , physical activity , nutrition , substance use , mental / social health , injury prevention practices , readiness to change , and job satisfaction . for this study , the trotter wellness hra questionnaire was supplemented with 58 additional selected questions from the world health organization health and work performance questionnaire ( hpq ) 21 and a modified version of the hpq , the hpq select which were provided by the ibi .22 these additional survey questions further elucidated health and lost - time information to assess lost productivity as measured by attendance , absence , and job performance . in total , the hra took approximately 20 to 30 minutes to complete . the data presented below provide an analysis of participating employees ' overall health status and health risks on completion of an initial hra , prior to health promotion interventions ( eg , health coaching and education ) . to better understand the reasons why small businesses chose to participate in the hrm program and the aspects they value most highly , pinnacol assurance conducted a survey of employers . questions probed the reasons driving their decision to participate in the hrm program , what they hoped to achieve by participating , and their valuation of various aspects of the program . participants were also provided an open text response option , where they could indicate what they would improve about the program . employee participation rates were calculated using the following two measures : ( 1 ) using the number of participants who completed an hra , divided by the number of eligible employee participants as defined by the individual employer , and ( 2 ) using the number of participants who completed an hra , divided by employee counts as defined by pinnacol assurance . employee - level data were obtained from employees ' self - reported responses to the trotter wellness hra questionnaire and hpq - select questions . scheduled biannual data transfers from the trotter wellnessadditional employer and workers ' compensation data were provided by pinnacol assurance . all primary data described in this study were transferred to the ibi for participant matching and de - identification according to the health insurance portability and accountability act guidelines . de - identified data were provided to the center for worker health and environment ( cwhe ) at the university of colorado for analysis . the institutional review boards for the university of colorado ( colorado multiple institutional review board ) and the colorado state university reviewed this study and considered it to be exempt ( nonhuman subjects ' research ) . for this study , most results are presented as frequencies of individual characteristics within the employer and employee cohorts . this score is calculated for each participant on the basis of the individuals ' responses to questions within the hra . the ows each individual receives falls into one of the following categories : excellent ( score 80 ) , doing well ( 60 to 79 ) , needs improving ( 20 to 59 ) , orbody mass index was calculated according to the standard formula [ weight ( pounds ) / [ height ( inches ) ] 703 ] using self - reported height and weight data . body mass index classification was reported according to the world health organization 's international classification scale . alcohol consumption guidelines for males and females were based on the national institute on alcohol abuse and alcoholism guidelines and state that moderate to low risk consumption for men is 14 drinks / week and for women 8 drinks / week . nevertheless , those guidelines also include single - day alcohol consumption limits for men and women , which the hra questionnaire did not assess . for purposes of this study , employee stress was characterized as low or moderate / high on the basis of responses to three individual questions included in the hra . sometimes experienced stress at home or at work and also responded that their stress over finances was little or none were classified as having low stress . employees who responded that they had often or permanent or continual stress at home or work or had moderate oremployer and employee data were reported as frequencies , with means and standard deviations reported for some measures . all data analysis was performed by the cwhe at the university of colorado using stata 12 data analysis software ( statacorp , college station , tx ) . a total of 276 employers of all sizes enrolled in the hrm program between may 15 , 2010 , and may 15 , 2013 . in this articlewe excluded 16 large employers from this analysis to focus on small businesses , which we have defined as having fewer than 500 employees . the ongoing recruitment of small employers into the program since its inception in may 2010 is illustrated by the yearly employer participation data shown in table 1 . in the first , second , and third full years of the program ,75 , 114 , and 71 small businesses with fewer than 500 employees enrolled , respectively . although there was some variation in the geographic and industry type characteristics of employers enrolling in individual years , this likely represents eligibility and timing of recruitment ( eg , a business newly insured by pinnacol would become eligible in the year it obtained a policy ) . the 260 employers represented a range of business sizes from microbusinesses with fewer than 10 employees ( 18.8 % ) to those with more than 250 employees ( 8.5 % ) . more than half ( 53.4 % ) of employers had fewer than 50 employees . because pinnacol assurance primarily provides workers ' compensation insurance to businesses operating in colorado , the geographic regions listed in table 1 are for colorado , with non - colorado businesses comprising less than 1.0 % of the total , which matches the percentage of the pinnacol 's non - colorado book of business overall . the majority of participating businesses , more than 70.0 % , were located in the urban front range . the more rural western slope region , which includes among its more populated areas the cities of grand junction , montrose , glenwood springs , aspen , and vail , comprised 18.0 % of employer policyholders . of the 260 companies that enrolled in the hrmof those who continued with the hrm , 82 % remained with the program through the end of the second year . a total of 6507 small business employees enrolled in the hrm program between may 15 , 2010 , and may 15 , 2013 , and completed a baseline hra questionnaire . employee participation as defined by completing a baseline hra represents 47.9 % of eligible employees , with a range of 0.8 % to 100 % participation , and 44.4 % of total employees , with a range of 0.5 % to 100 % . overall , the mean age of hrm participants was 41.413 years , with a predominance of married ( 74.3 % ) , white ( 80.6 % ) , male ( 55.7 % ) , and full - time employees ( 86.2 % ) ( table 2 ) . more than 40 % of all employees ( 41.7 % ) completed a 4 - year college degree , and 40 % of the college graduates had additional postgraduate education . three fourths of employees ( 75.3 % ) had at least some education beyond high school . the professional job category , which includes engineers , accountants , and systems analysts , accounted for 28.6 % of employees ' self - reported job descriptions , the most frequently reported ( table 2 ) . nearly one quarter of employees ( 24.9 % ) reported an annual income of less than $ 25,000 and nearly two thirds ( 65.8 % ) reported an annual income of less than $ 50,000 . part - time employees ( 9.9 % ) and those who listed their employment type as other ( 0.9 % ) were included in these calculations . ceo , chief executive officer ; ged , general education diploma ; hra , health risk assessment ; vp , vice president . as part of the hra survey , employees classified their overall health as excellent ( 15.1 % ) , very good ( 39.5 % ) , good ( 37.2 % ) , fair ( 7.4 % ) , or poor ( 0.5 % ) . for comparison , excellent ( 17.6 % ) , 60 to 79 doing well ( 53.7 % ) , 20 to 59 or needs improving ( 28.7 % ) , and 0 to 19 orthe average ows for the entire employee group was 66.7 ( 13.3 ) , with a range of 5 to 100 . of the 6507 employees , 38.9 % were classified as normal weight , 34.3 % as overweight , and 25.6 % as obese ( table 3 ) . no data were available on the use of other forms of tobacco , marijuana , or illicit drugs . the majority ( 81.7 % ) of female employees reported consuming seven or fewer servings of alcohol per week . more than 98 % of male employees reported consuming 14 or fewer alcoholic drinks per week . for female employees , this means 18.3 % consume alcohol at levels considered high risk by national institute on alcohol abuse and alcoholism guidelines , whereas only 1.9 % of males are at high risk ( table 3 ) . approximately one in 10 employers were sedentary ( 11.5 % ) , reporting no significant exercise during the week , and 4.3 % reported no daily consumption of fruits or vegetables . nevertheless , more than 60 % of employees reported exercising at least three times per week ( 62.0 % ) , and 82.1 % reported eating at least three servings of fruit or vegetables daily ( table 3 ) . more than half of employees ( 53.7 % ) reported getting seven or more hours of sleep daily . as a group , 71.5 % reported moderate or high stress in their lives over work , home , or finances . table 4 includes a list of the most common health conditions and risk factors reported by hrm participants . more than one third of hrm participants reported being overweight ( 37.8 % ) and experiencing seasonal allergies ( 34.8 % ) . other common health conditions affecting 15 % or more of the total enrollees include chronic fatigue ( 20.4 % ) , chronic sleeping problems ( 18.4 % ) , headaches ( 17.2 % ) , arthritis ( 16.3 % ) , high cholesterol ( 15.7 % ) , and hypertension ( 15.3 % ) . chronic and long - term health conditions reported , including diabetes ( 3.8 % ) , cancer ( 3.3 % ) , osteoporosis ( 2.9 % ) , coronary heart disease ( 1.7 % ) , and chronic lung disease ( 0.7 % ) , are reported by fewer than 5 % of study participants . twenty - one percent of policyholders who have ever participated in hrm completed a follow - up survey to determine how they learned about the hrm program , reasons why they elected to participate in the hrm , and how they valued various aspects of the program . the vast majority ( 97 % ) indicated that they believed that wellness is an important aspect of improving workplace safety . the top - ranked priority for participating in hrm was to improve employee health status , followed by a desire to reduce costs . the drivers for policyholders ' decision to participate fell into the following three broad categories : agent recommendation , pinnacol 's recommendation , and the policyholder searching for a wellness program . more than 6 % cited a preference to work with a company other than their health insurance provider as their primary driver to selecting hrm . there was high satisfaction noted for the wide range of tools and support provided , although the single most frequent suggestion for improvement was more on - site support for implementing and maintaining the hrm program . it should be noted that this survey did not ask specifically if employers chose the hrm because it was free of charge , because that option was not provided in the survey after an earlier pilot survey found that less than 8 % of employers considered this to be a factor in deciding to participate . this is the first field - based study that examines a broad - scale implementation of a worksite wellness program in a large number of small businesses . we have demonstrated that colorado small businesses are prepared to adopt worksite wellness programs , if the program is provided free of charge and are given company - specific advice in program design and execution . the cohort 's self - reported health risks and disease rates suggest that there are opportunities to address important modifiable health risks in the small business workforce . in this study , we found that small businesses with fewer than 500 employees were willing and able to adopt a worksite wellness program . despite the many potential barriers to adoption of health promotion programs that have been reported in the literature for small businesses ,18,2325 even the smallest companies and their employees across many industrial sectors demonstrated the ability and willingness to participate , when provided with guidance and access to resources . a key factor in the success of this program may be that the hrm is offered at no direct cost to employers . program costs are frequently cited as a primary reason why small businesses do not offer health promotion programs .18,23 the program described herein also provides employers with the added benefit of offering a well - established hrm program to their employees , without necessitating the investment of company resources into vetting various different hrm program options . lack of resources for and lack of expertise about hrm programs are also cited as barriers for small businesses to adopt worksite wellness programs ,18,23 and the plug and play nature of this program helps overcome both , as well as the extensive assistance provided by both the trotter wellness and pinnacol assurance . nevertheless , despite the successful enrollment of 260 small businesses in this program , there are limitations that need to be addressed . although all policyholders were deemed eligible for enrollment and all received at least one direct communication from pinnacol about the program , it is not known how many small businesses were simply unaware of the program or directly declined participation , thus introducing potential bias regarding the 260 businesses enrolled . thus , we are unable to assess the effectiveness of program communication and recruitment efforts . because the study was capped at 300 businesses of any size and was offered to all 55,000 policyholders , we are unable to calculate the rate of small business adoption . in addition to the employer - level barriers to worksite health promotion , there are potential barriers to participation at the employee level . future research is needed to identify the factors that determine the percentage of companies that choose to participate . in our future research , we intend to examine factors associated with employee participation in small businesses . working with 260 companies introduces substantial variability in the types of businesses and employees and could easily affect participation . furthermore , many hrm programs offer participation incentives to employees for completion of an hra and program engagement . one limitation of this study is that we do not know the exact nature of the incentives which the participating employers offered to their employees for hra participation . nevertheless , the trotter wellness data , which track incentives offered , as self - reported by the employer , indicated that about 60 % offered some sort of incentive for taking the hra . only a quarter of the employers with fewer than 15 employees offered an incentive , although they achieved the highest participation rates . also , as with all studies of this type , there is the potential for introduction of self - selection bias for those who chose to participate . linnan and colleagues18 have reported that low participation on the part of high - risk employees is an additional perceived barrier to implementation of hrm programs in small businesses . we were not able to address whether a healthy worker bias occurred among participating employees in our small business cohort , although our data suggest that participants were comparable with colorado adults in many of their self - reported health risks and medical conditions .26 this study has a number of unique characteristics that may help address gaps in the current literature . the majority of published reports on worksite hrm programs include only medium to large businesses . evaluating the collective effect of the hrm program in these small and microbusinesses will help inform future efforts in worksite health promotion for such employers , which include more than 95 % of all us businesses .27 specifically , it will be valuable to understand what benefits recognized for larger corporations can be extrapolated to small businesses . a limitation of this study is that 21 % of companies responded to the follow - up survey regarding their reasons for participating . our results suggest that future research should more thoroughly examine the motivations of small employers to adopt hrm programs . importantly , efforts at broad - scale introduction of hrm programs to small business should include multiple approaches to engagement , including insurance brokers , direct communication by insurers , and health and wellness education sessions . our data provide an early indication that such programs may be sustainable even in a small business culture . although we did not systematically examine the effect of pinnacol 's retention efforts , anecdotally we observed activities such as annual planning to create actionable goals , monthly communications and challenges provided to the employers for easy distribution to their employees , a simple online portal , and easily accessed personalized support , which may help small businesses remain engaged . providing an hrm program to employers and employees whose commonality is obtaining workers ' compensation insurance from a single carrier is another unique aspect of this study . the idea of an alternative model of workers ' compensation insurers , rather than health insurers , offering such programs may prove to be an appealing alternative , especially for smaller businesses . most previously reported studies of health promotion interventions have evaluated employees of a single , large enterprise , which may influence whether results can be applied to a more diverse group . studies of small businesses have also been limited to either single or small numbers of study sites . the results of this study may be more generalizable than previous studies because all participating businesses share a single workers ' compensation carrier , regardless of business type , employee job , or geographic location . to our own knowledge , this is the first example of a workers ' compensation carrier providing such services . importantly , through this approach , we were successful in attracting small businesses from a range of economic sectors . our data strongly support the need for effective interventions to address modifiable health risks among people who work in small businesses . participants in the pinnacol assurance hrm program were almost exclusively employed by businesses in colorado , which comprised 99.6 % of enrolled employers . in general , colorado is viewed as a relatively healthy state , with the prevalence of many chronic illnesses below the national average . for example , obesity is an acknowledged factor influencing many aspects of health and wellness , including costs and workers ' compensation ,10,11 and colorado is currently the leanest state in the nation .28 nevertheless , the small business employees who participated in the hrm study had a rate of obesity of 25.6 % , which aligns more closely with the national average of 28.1 % than the colorado rate ( 20.1 % ) .28 the burden of chronic illness and health risk factors in this study of more than 6500 small business workers is substantial . furthermore , when we take into consideration the possibility that primarily healthier workers may choose to complete an hra ,18 the estimated health risks and chronic illnesses in the small business community reported here may underestimate the true extent of the problem . in conclusion , we have demonstrated that small businesses can overcome barriers to adoption of worksite wellness programs . when such programs are offered to their employees , small business workers are willing to complete online hras at rates that are within the range seen in larger corporations . importantly , the modifiable health risks detected in the small business workforce are substantial and warrant public health consideration . this described study represents the foundation of ongoing analyses of the pinnacol assurance hrm study population . further longitudinal analyses will address whether the hrm program results in measurable changes in health risks , workers ' compensation costs , and employee productivity .\noutput:\n" }, { "from": "agent", "value": "objective : to assess small business adoption and need for a worksite wellness program in a longitudinal study of health risks , productivity , workers ' compensation rates , and claims costs.methods : health risk assessment data from 6507 employees in 260 companies were examined . employer and employee data are reported as frequencies , with means and standard deviations reported when applicable.results : of the 260 companies enrolled in the health risk management program , 71 % continued more than 1 year , with 97 % reporting that worker wellness improves worker safety . of 6507 participating employees , 34.3 % were overweight and 25.6 % obese . approximately one in five participants reported depression . potentially modifiable conditions affecting 15 % or more of enrollees include chronic fatigue , sleeping problems , headaches , arthritis , hypercholesterolemia , and hypertension.conclusions : small businesses are a suitable target for the introduction of health promotion programs ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: thrombin is the central protease in the cascade of blood coagulation proteases . structurally , thrombin consists of a double - barrel core surrounded by connecting loops and helices . genetic analysis of the clotting factor genes demonstrates that the clotting proteases of the chymotrypsinogen superfamily have evolved as a result of several gene duplications , exon shuffling , and intron sliding events . prothrombin has a unique exon organization and is thought to be the ancestral gene of the clotting factor family . the extended active site loops in thrombin are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity . thrombin is produced in a low - activity zymogen form that requires proteolytic cleavage to attain full activity . this cleavage event results in small overall changes to the molecular architecture but results in a large change in dynamics wherein one - barrel becomes more dynamic and the other becomes less dynamic . the result is a more perfectly formed active site for rapid proteolytic cleavage activity . despite the highly specific nature of thrombin activity , in association with allosteric modulators , in addition , allostery is key to thrombin regulation , and misregulation can lead to bleeding disorders or thrombosis . although , traditionally , allostery was defined as occurring among subunits in a multisubunit system such as hemoglobin , the phenomenon of altered activity resulting from binding of a regulatory molecule on the opposite side of a monomeric enzyme is now also recognized as a form of allostery . several experimental and computational approaches have hinted that the solution structure of thrombin is a broad and malleable dynamic ensemble . h / d exchange mass spectrometry showed that d - phe - pro - arg chloromethylketone ( ppack ) occupation of the active site not only protected the active site loops but also propagated to decreased exchange in several regions of the protein distant from the active site . thrombin has two binding sites distal to the active site ; exosite 1 is where thrombomodulin binds , and exosite 2 is where heparin binds . isothermal titration calorimetry ( itc ) experiments showed alteration of thermodynamic parameters of ligands binding to thrombin exosites when the active site was occupied . binding of active site ligands altered the balance of enthalpic and entropic contributions to binding of exosite 1 ligands and vice versa . such thermodynamic compensation phenomena are more likely if the allosteric mechanism is entropic rather than enthalpic , suggesting that differences in the dynamic properties of the system affect the ligand binding mechanism . indeed , x - ray crystallography shows no significant changes in the thrombin structure upon ligand binding , providing further evidence that it may exist as a malleable dynamic ensemble . nmr studies and md simulations remain the most direct approaches to investigating protein dynamics . a recent nmr / md study on ppack - thrombin revealed a large degree of dynamic motions , particularly in the active site loops , spanning time scales from picoseconds to milliseconds . a computational exploration revealed a strong dynamic component in the allosteric regulation of thrombin by tm . in the work presented here , we combine conventional md , nmr - calibrated accelerated md ( amd ) , and analysis of the residual local frustration to further explore the dynamics of thrombin , with particular interest in changes that occur upon active site ligation . the combined approach allows us to analyze a broad range of motional time scales . atomic coordinates for thrombin were obtained from the protein data bank 1.9 x - ray crystal structure [ pdb i d : 1ppb ] . both systems were placed at the center of a periodically repeating box , and the simulation cell size was defined such that the distance between the edge of the simulation box and the surface of the solute was at least 12 . all simulations were performed in explicit solvent , and three cl counterions were introduced to obtain cell neutrality . six 20 ns conventional md simulations were performed using a different random seed generator for the maxwellian distribution of atomic velocities following standard energy minimization and equilibration procedures . electrostatic interactions were treated using the particle mesh ewald ( pme ) method with a direct space sum limit of 10 . the ff99sb force field was used for the solute residues , and the tip3p water force field was employed for the solvent molecules . in the case of ppack - thrombin simulations , the conventional md simulations were analyzed in the community analysis and also constituted the starting point for the amd simulations . these simulations also provided the average ( unbiased ) dihedral angle energy , v0 ( dih ) and total energy v0 ( tot ) values used to define the acceleration parameters in the amd simulations described below . allosteric networks were characterized using a community network analysis approach previously applied to investigate allostery in trna / protein complexes and other protein systems . this approach constructs a dynamic contact map consisting of a network graph in which each residue is treated as atwo residues are deemed to be in contact throughout the majority of the simulation . clusters of residues ) of highly intraconnected but loosely interconnected nodes using the girvancentral to this method is the calculation of edge betweenness , the number of shortest paths that cross an edge . the edge betweenness is calculated for all edges , and the edge with the greatest betweenness is removed . this process is repeated , and a modularity score is tracked to identify the division that results in the optimal community structure . amd simulations were performed as described previously using an in - house modified version of the amber 10 code . amd approach is used , in which two acceleration potentials are applied simultaneously to the system ; the first acceleration potential is applied to the torsional terms only , and a second , weaker acceleration is applied across the entire potential . this dual boost amd protocol represents a unified approach facilitating the efficient sampling of both the torsional degrees of freedom and slow diffusive motions in the solute . in total , six independent dual boost amd simulations were performed for 10000000 steps ( the equivalent of 20 ns of md ) for each system . the physical conditions , force fields , and all other simulation parameters employed were identical to those described for the conventional md simulations . the specific acceleration parameters used in this study were [ eb ( dih ) v0 ( dih ) ] = [ 4 kcal / mol no . of solute residues ] and ( dih ) = [ 0.8 kcal / mol no . v0 ( tot ) ] = ( tot ) = [ 0.16 kcal / mol no . of atoms in the simulation cell ] for the background total acceleration . these acceleration parameters had been previously identified as the optimal acceleration parameters for the reproduction of experimental rdcs in ppack - thrombin , accessing configurational dynamics on time scales up to 10s100s of microseconds . for each amd simulation , a corrected canonical ensemble was obtained by reweighting each point in the configuration space on the modified potential by the strength of the boltzmann factor of the bias energy , exp [ v ( rt ( i ) ) ] at that particular point , and the bias potential block averaging method was employed to remove statistical noise errors . the internal dynamics present in the different amd simulations of apo - thrombin and ppack - thrombin were assessed by calculating order parameters , s , from the free - energy weighted amd ensembles . members of each ensemble were superimposed onto the backbone atoms ( n , c , c ) of all heavy chain residues for the appropriate average structure , and order parameters , s were calculated aswhere i are the cartesian coordinates of the normalized internuclear vector of interest . others have shown that s values calculated from standard md simulations in this way were in excellent agreement with experimental s values calculated using the liparithe order parameters presented here are averaged over all six amd trajectories for each system . residue - by - residue cross - correlations for the free - energy - weighted amd ensembles were calculated using the generalized cross - correlation approach applied to all backbone c atomic coordinates based on the mutual information method developed by the grubmller group using the g_correlation module in gromacs 3.3.3 . an algorithm for determining residual local frustration , that is , whether a contact between amino acid residues is energetically optimized or not in the folded state , was developed by the wolynes and komives groups some time ago . residue interactions by systematically perturbing the identity of individual residues and evaluating the resulting total energy change . for the work presented hereindex , in which the decoy set involves randomizing not just the identities but also the distance and densities of the interacting amino acids i , j. this scheme effectively evaluates the native pair with respect to a set of structural decoys that might be encountered in the folding process . after constructing a histogram of the energy of the decoys and comparing the distribution to the native energy , cutoffsenergetically favorable contacts between residues are minimally frustrated , whereas highly frustrated contacts are energetically unfavorable in the native state . depictions of the contacts on structural models typically show minimally frustrated contacts in green and highly frustrated contacts in red . the average of the frustration scores over all of the contacts made by a particular residue are also plotted in a per - residue format . a webserver is now available for performing these computations . for the work presented here , the minimally and highly frustrated contacts are depicted on the lowest - energy structure from the boltzmann - reweighted ensemble of structures from the amd simulations . to compute the average per - residue frustration , we clustered the boltzmann reweighted ensemble and averaged the frustration scores of all contacts made by each residue in the representative structure from the three most populated clusters . it is interesting to note that the residual local frustration varied between members of the ensemble , and the error bars on the residual local frustration plots represent one standard deviation . note : thrombin has several numbering schemes ; the chymotrypsin numbering scheme is used in the text because it is used in pdb files . this numbering scheme creates problems for the data presentation in this paper ; therefore , sequential numbering ( of the light chain or a - chain followed by the heavy chain ) is used in the plots , and sequential residue numbers are given in parentheses throughout the paper for reference . we performed a set of six independent 20 ns conventional md simulations for both apo - thrombin and ppack - thrombin . during the equilibration procedure , a rather large conformational transition in the active site loops was observed for apo - thrombin that involved a reorientation of both the - loop ( 178195 ) and the na binding loop ( 264271 ) , forming a more open active site pocket . a community network analysis approach was applied to identify groups of residues undergoing correlated motions in ppack - thrombin and apo - thrombin . representative community network analyses obtained from conventional md simulations are shown in figure 1 . the flow of information in the physical network of the protein was measured by the edge betweenness , defined as the number of shortest paths that pass through the edge in the network , and is a direct measure of the strength of intercommunity communication within the network ( black lines in figure 1a and b ) . ppack ligation causes consolidation of the community structure including the two active site communities most proximal to the ppack binding site ( green and brown , figure 1 ) . the community that includes part of the na binding loop in apo - thrombin ( figure 1c , brown ) consolidates with the active site serine195ct ( 241 ) , the 70s loop ( 98113 ) , residues 191194ct of the - loop ( 237240 ) , and the n - terminal residues 1719ct ( 3840 ) in the ppack - liganded form ( brown , figure 1d ) . ppack ligation also acts to consolidate the n - terminal - barrel , which is formed by two separate communities in apo - thrombin and forms a large community that also contains the 30s loop ( 5562 ) and part of the 60s loop ( 8294 ) ( orange , figure 1d ) . in summary , the community analysis revealed consolidation of the na binding site , the base of the - loop , and the n - terminus of the heavy chain into one community and most of the active site loops into a second community upon ppack binding . these two communities , which are strongly connected in ppack - thrombin , unite the residues required for proteolytic catalysis . the a - chain community also becomes more strongly connected to the active site and the community containing the 70s loop . on the basis ofthe substantial consolidation observed in the community analysis upon ppack binding , we set out to examine whether there were concomitant changes in dynamics . community analysis of apo - thrombin ( a , c ) and ppack - thrombin ( b , d ) . the two - dimensional view of the communities in panels ( a ) and ( b ) depicts the relative size of the communities ( based on the number of residues ) as colored circles of varying sizes with the thickness of the connecting lines representing the relative interconnectivity among communities . panels ( c ) and ( d ) are structural representations of communities superimposed on pdb 1ppb . residual dipolar couplings ( rdcs ) , which report on an ensemble average over all orientations of the magnetic dipole interaction vector up to the chemical shift coalescence limit , provide useful experimental data for determining the ensemble of structures that best represents the dynamic properties of a protein . when the experimentally derived rdcs are compared to rdcs that are back - calculated from ensembles of structures generated from amd simulations , the acceleration level that provides the most realistic representative structural ensemble can be identified . we previously demonstrated that the rdcs measured on ppack - thrombin did not agree well with the available crystal structures ( r = 0.72 ) .80 ) when the rdcs were back - calculated from an ensemble of structures obtained by conventional md . however , remarkable agreement was obtained between the experimental rdcs and the rdcs back - calculated from the ensemble of structures obtained from an amd simulation at the optimal acceleration level ( r = 0.92 ) . the ensembles obtained from such amd simulations of both ppack - thrombin and apo - thrombin are shown in figure 2 , with the loops colored according to the scheme shown below the structure . ensemble of the 10 representative structures of the rmsd clusters from the boltzmann reweighted structures from the rdc - calibrated amd for apo - thrombin ( left ) and ppack - thrombin ( right ) . the loops are colored according to the schematic under the structures . for ppack - thrombin , order parameters ( s ) from conventional md simulationsagreed extremely well with those measured by nmr relaxation experiments that are limited to the picosecondhowever , the fact that ensembles obtained from amd were required for good agreement with the rdc measurements suggested that motions on longer time scales are contributing to the solution structure . therefore , order parameters for the n h bond vectors were calculated from the amd ensembles ( samd2 ) . a comparison of samd2 for apo - thrombin to those obtained previously for ppack - thrombin is shown in figure 3a . most of the active site loops in both forms are highly flexible , yet a marked decrease in flexibility is observed upon active site ligation with ppack ( figure 3b ) . as expected , ppack ligation caused significant ordering ( s 0.1 ) of residues that directly contact the ppack arg side chain . the loops that surround the active site also experience significant ordering , including the 60s loop ( 8294 ) , the - loop , and the 180s loop ( 225239 ) . some regions distal to the ppack also showed significant ordering upon ppack ligation , including the a - chain , the 30s loop , residue 221ct ( 269 ) of the sodium binding loop , and residues in the c - terminal helix ( figure 3c ) . ( a ) order parameters calculated from amd simulations of apo - thrombin ( red ) and ppack - thrombin ( black ) . ( b ) differences in order parameters between the forms : s = sppack2 sapo2 from amd order parameters . ( c ) those residues with a s + 0.1 are marked with red spheres on the structure of thrombin ( pdb code 1ppb ) , indicating stabilization upon active site occupation by ppack . the schematic of important surface loops is provided above the graph . to identify residues undergoing correlated motions on longer time scales , amd simulations were performed that were optimized based on previous work comparing experimental rdcs to those back calculated from amd simulations carried out at different acceleration levels . the analysis of apo - thrombin revealed correlated motions between the active site loops , exosite 1 , and other distal sites . in particular , the entire - loop appears to undergo strongly correlated motions with the a - chain residues 1h1dct and 1214cct ( 15 and 2025 ) , the catalytic triad , h57ct , d102ct , s195ct ( 79 , 135 , 241 ) , the 60s loop , the 70s loop , the 90s loop ( 127133 ) , the surface strand under the 70s loop ( 145151 ) , the 170s loop ( 204219 ) , and the 180s loop ( figure 4 , lower triangle ) . whereas these correlated motions appeared to involve the entire - loop in apo - thrombin , only the tip of the - loop ( residues 146149ect ( 182190 ) ) appears to be undergoing the same set of motions in ppack - thrombin ( figure 4 , upper triangle ) . in apo - thrombin , the 170s and , to a lesser extent , the 180s loop , which are strongly correlated to the - loop , are also correlated with the a - chain and catalytic residues . upon ppack , the 30s loop and the 60s loop are weakly correlated , but the 30s loop is not correlated to the 70s and 90s loops . correlated motions between the 30s and 60s loops are stronger in ppack - thrombin , and these extend to the 70s and 90s loops ( figure 4 ) . analysis of correlated motions performed on the amd trajectories of ppack - thrombin ( top triangle ) and apo - thrombin ( bottom triangle ) . the motions range from 0.0 ( no correlation , white ) to 1.0 ( completely correlated , black ) . the schematic diagram indicating the location of surface loops is inserted above the correlated motions plot . the black boxes indicate correlations of the 170s and 180s loops with the a - chain and surface loops that are stronger in apo - thrombin than in ppack - thrombin . the blue boxes indicate correlations of the 30s loop with the 60s , 70s , and 90s loops that are stronger in ppack thrombin than in apo - thrombin . we applied a previously derived algorithm to identify the residual local frustration in representative structures from rmsd clusters of the boltzmann reweighted amd simulation results . according to the principle of minimal frustration , contacts made in the folded native state should be minimally frustrated , meaning that they are energetically favorable . we previously showed that while most contacts made in the native state are , indeed , minimally frustrated , some 1015 % of contacts are energetically unfavorable ( i.e. , highly frustrated ) in the native state . these highly frustrated contacts map to functional sites and are thought to have been preserved in evolution . both apo - and ppack - thrombin show regions of high frustration in many of the surface loops ( figure 5 ) . to discover whether regions of high frustration also map to dynamic regions , we compared the average residual frustration across representative structures from the three most populated rmsd clusters derived from the amd simulations to the order parameters . the order parameters derived from conventional md simulations ( sns2 ) agree very well with order parameters derived from nmr relaxation experiments on thrombin and reveal the disorder resulting from motions in the nanosecond time regime . the order parameters derived from the rdc - calibrated amd simulations ( samd2 ) reveal the disorder resulting from motions on longer time scales . the sns2 did not correspond well to the regions of high residual frustration ; however , the correspondence with the samd2 is remarkable ( figure 6 ) . these results highlight that regions of high residual frustration may have evolved to allow slow time scale motions to occur with relative energetic ease , as previously suggested by wolynes and colleagues . analysis of residual local frustration in the lowest - energy structure from the rdc - calibrated amd ensemble of apo - thrombin ( left ) and ppack - thrombin ( right ) . the contacts that are minimally frustrated are shown in green , and the contacts that are highly frustrated are shown in red . thin lines represent water - mediated contacts . the active site catalytic residues are shown in magenta . comparison of the order parameters reflecting nanosecond time scale motions versus longer time scale motions ( samd2 ) , with the average per residue fraction of highly frustrated contacts for the three lowest - energy structures from the amd simulation . ( a ) the sns ( gray ) and samd ( red ) for apo - thrombin are compared to the average fraction of highly frustrated contacts ( cyan ) . ( b ) the sns2 ( gray ) and samd2 ( black ) for ppack - thrombin are compared to the average fraction of highly frustrated contacts ( blue ) . we used a combination of community network analysis , rdc - calibrated amd simulations , and analysis of residual frustration to explore the dynamic ensemble of thrombin in solution from the nanosecond to the microsecond time regime . comparative analysis of apo - thrombin and the active - site - ligated thrombin systems identified differences in the dynamic fluctuations and changes in correlated motions upon active site ligation . analysis of thrombin complexed with the relatively small substrate analogue ppack showed a substantial rearrangement of the community structure . ppack binding consolidated the two active site communities most proximal to the ppack binding site as well as the na binding loop with the active site serine , the 70s loop , part of the - loop , and part of the a - chain . interestingly , this consolidation resulted in more residual local frustration near the active site ( figure 5 ) . the generalized cross - correlation analysis predicted that many of the thrombin surface loops are undergoing correlated motions ( figure 4 ) . the analysis of residual local frustration revealed that all of these loops are highly frustrated in the native structure of thrombin ( figure 5 ) . the striking correlation between the long timescale dynamics and the residual local frustration suggests that evolution has selected for energetically unfavorable contacts within the surface loops in order to facilitate larger amplitude slower motions . upon ppack binding , many of the loops retain dynamics and also remain highly frustrated . the surface loops exhibiting correlated motions are not necessarily structurally proximal , hinting at how allosteric regulation by binding of ligands at sites distal to the active site might occur . upon ppack binding , the active site community consolidates with the 70s loop where fibrinogen binds to stimulate its own cleavage and where thrombomodulin binds to alter substrate specificity . indeed , previous experiments have demonstrated a thermodynamic coupling between the 70s loop and the active site . another loop that is distal to the active site but that differs between apo - and ppack - thrombin is the - loop . residues leading up to the - loop are highly frustrated and highly dynamic in apo - thrombin but become much less dynamic in the ppack - bound form , with only the tip of the - loop remaining dynamic . although the strongly correlated motions in apo - thrombin between the - loop and the 170s loop almost completely disappear upon ppack ligation , correlations are strengthened between the tip of the loop and nearly every other loop in thrombin , including the 30s loop , the 60s loop , the 70s loop , the - strand connecting the 60s and 70s loops , and the 90s loop . thus , we can speculate that the reduced dynamics result from the binding of ppack , causing these regions to sample a more restricted conformational space , and that this reduced sampling leads to stronger correlated motions extending between the active site and the surface loops involved in allosteric regulation . the order parameter analysis revealed , as expected , that active site occupation decreases the microsecond motions in the surface loops ( figure 3 ) , consistent with amide h / d exchange experiments that showed that binding of ppack dampened exchange in all of the surface loops including those distal to the active site . millisecond time scale could explain how active site occupation lowers the entropic penalty for binding an exosite 1 allosteric modulator . thermodynamic measurements of binding show that the allosteric pathway between these two sites operates in both directions and changes in order parameters in the thrombin surface loops upon ppack binding to the active site are similar to those seen upon tm56 binding to exosite 1 . the serine protease architecture is that of a double - barrel fold in which the - strands are connected by surface loops . the active site is between the two - barrels , each of which has several - strands connected by the surface loops . such a - strand architecture provides a direct connection between distal surface loops , allowing transmission of allosteric information by subtle redistribution of the dynamic ensemble . such local unfolding or crackingwas predicted some time ago to be the fundamental mechanism of allostery , and residual local frustration is indeed found at such sites . it will be interesting to see if dynamic allostery is present in other proteins with mostly - strand structures similar to thrombin .\noutput:\n" }, { "from": "agent", "value": "thrombin is the central protease in the cascade of blood coagulation proteases . the structure of thrombin consists of a double - barrel core surrounded by connecting loops and helices . compared to chymotrypsin , thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity . previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites . we present a combined approach of molecular dynamics ( md ) , accelerated molecular dynamics ( amd ) , and analysis of the residual local frustration of apo - thrombin and active - site - bound ( ppack - thrombin ) . community analysis of the md ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts . amd simulations , calibrated on measured residual dipolar couplings , reveal that upon active site ligation , correlated loop motions are quenched , but new ones connecting the active site with distal sites where allosteric regulators bind emerge . residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics . the results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we aim to semiautomate the updating of systematic reviews , meta - analyses , and field synopses , thereby reducing reviewers ' efforts and the associated costs . as an example , we describe the application of data mining methods from computer science to facilitate updating four field synopses . field synopses are continuously updated and manually curated collections of publications that synthesize a broad field . first , one searches databases , such as medline , to retrieve potentially relevant studies . second , she or he screens the titles and abstracts of all retrieved citations to identify those that meet predefined eligibility criteria . these are exactly the same steps one would follow to update a systematic review or meta - analysis . therefore , to avoid confusion , from here on we refer to all literature databases that are updated following the above protocol as systematic reviews . we used citations published through 2009 to train a classification model to distinguish relevant from irrelevant citations ( i.e. , to discern citations likely to be ultimately included in the systematic review from those likely to be excluded ) . we then used this trained classification model ( classifier ) to automatically screen articles published in 2010 ( i.e. , the articles that would be considered when updating the systematic review ) . all articles designated as irrelevant would be excluded from further consideration , thereby saving human effort . we assessed the performance of the system with respect to the studies that were ultimately included by the researchers in the 2010 update of the systematic reviews . three synthesize genetic association studies , investigating parkinson disease ( pdgene ) , alzheimer disease ( alzgene ) , and schizophrenia ( szgene ) , respectively ( table 1 ) . the fourth is the tufts cost - effectiveness analysis registry ( cea registry ) , which summarizes information from published cost - effectiveness analyses . we added this fourth field synopsis to gain insights on the generalizability of our approach to nongenetic synopses . the protocol and methods for our four data sets are available on their respective websites ( table 1 ) . in contrast to typical systematic reviews , these address much broader questions and are updated on a weekly or monthly basis . for example , the alzgene review evaluates the strength of the association between alzheimer disease and genetic variations across the whole genome , whereas a typical systematic review would probably evaluate only a subset of such genetic variations ( e.g. , in the apoe gene ) . note that attaining perfect ( 100 % ) sensitivity with semiautomated updating is much more difficult when all reported variations across thousands of genes are of interest rather than only apoe variations . to simulate a prospective test of our semiautomated system , we segmented each of the data sets into a training set comprising all citations published through 31 december 2009 and an update ( validation ) set composed of citations published between 1 january 2010 and 31 december 2010 ( supplementary figure s1 online ) . this is equivalent to a prospective evaluation of our semiautomated system throughout 2010 . for each of the four databasesthere are two components to operationalizing this : a method to encode text in an analyzable format and a classification method . we created computer - friendly representations of the titles , abstracts ( when available ) , and medical subject heading terms ( mesh ; when available ) of citations using a standard encoding scheme . specifically , we created a long list that includes all words present in at least three citations in the set of abstracts screened for the original review . the length of the list ( which corresponds to the number of words encoded ) depends on the data set , but is typically in the tens of thousands . each document was then represented simply as a vector with elements 1 and 0 , denoting whether the citation contained the corresponding word in this long list . this encoding scheme is known as the bag - of - words representation . briefly , we used support vector machines ( svms ) , which are state - of - the - science methods for text classification . svms in their canonical form perform poorly when there are far fewer examples ( in our case , citations ) from one class ( relevant citations ) than the other ( irrelevant citations ) . this is known as class imbalance , and it is the norm in literature searches conducted for systematic reviews . further , in systematic reviews false negatives ( relevant citations misclassified as irrelevant ) are much more costly than false positives ( irrelevant citations misclassified as relevant ) . first , we modified the svms to emphasize sensitivity ( we penalized more severely for false negatives compared with false positives ) . second , we did not train svms on the entire training set , but instead on a balanced sample comprising an equal number of relevant and irrelevant examples . this was accomplished by using all relevant examples and a randomly selected sample of the irrelevant examples and is analogous to performing a nested casealthough undersampling discards information , empirical evidence shows that it yields classifiers with higher sensitivity . however , undersampling introduces randomness ( the random sampling of the irrelevant citations in the training set ) . to reduce random variation in the model 's predictions , we used an ensemble of 11 sets of svm classifiers trained independently ( an approach called bagging ) . the final classification decision was taken as a majority vote over this ensemble ( see figure 1 ) . we used an odd number of classifiers in the ensemble to avoid ties ( the exact choice of 11 was motivated by our previous experimental work , in which this value worked well across many data sets ) . for each dataset , we calculated the sensitivity and specificity of the classifiers on the update set . the reference standard was whether a citation was ultimately included in the systematic review ( based on manual screening ) . we report the number of citations that reviewers would have needed to screen , had they been using the proposed semiautomated system to update reviews in 2010 , versus the number of citations they actually screened . we assessed the variability of overall results by repeating all analyses 20 times using different random number seeds . we arbitrarily considered the first run the main analysis and report minimum and maximum results from the other 19 . analyses of misclassifications : our classification model does not provide rationales for its predictions . to provide some intuition as to whether the model and the human experts tend to make the same mistakes , we performed the following analysis . for each data set , we asked our experts to manually rescreen false - positive citations ( i.e. , citations not included in the final database but predicted to be relevant by the classifier based only on titles and abstracts and not on the full text ) . the experts then categorized the rescreened citations as clearly irrelevant , unclear , or clearly relevant ( scoring them as 0 , 1 , or 2 , respectively ) . for these same false - positive citations , we measured the confidence of the classification model in its ( mistaken ) predictions , as described below . an association between higher scores in human rescreening and higher confidence in the classification models predictions suggests that model and human experts tend to make the same mistakes . we took the proportion of votes in agreement with the majority vote as a measure of the model 's confidence in its predictions . for example , in figure 1 , 7 of the 11 base classifiers predict that the citation is relevant , and the confidence of the classification is 7/11 ( 0.64 ) . thus , confidence ranges from 6/11 ( 0.54 ) to 11/11 ( 1.0 ) . to test for an association between human rescreening and model confidence , we compared the distribution of human scores across the extreme quartiles of the distribution of confidence scores over false - positive citations using fisher 's exact test . in the case of the smaller cea registry , we performed this comparison across the top and bottom halves of the confidence score distributions . to also quantify the direction of the association , we used a proportional odds ordinal logistic regression to calculate the odds ratio for a human assigning a higher score ( from 0 to 1 or from 1 to 2 ) . statistical analyses were performed in stata se , version 11 ( stata , college station , tx ) . we aim to semiautomate the updating of systematic reviews , meta - analyses , and field synopses , thereby reducing reviewers ' efforts and the associated costs . as an example , we describe the application of data mining methods from computer science to facilitate updating four field synopses . field synopses are continuously updated and manually curated collections of publications that synthesize a broad field . first , one searches databases , such as medline , to retrieve potentially relevant studies . second , she or he screens the titles and abstracts of all retrieved citations to identify those that meet predefined eligibility criteria . these are exactly the same steps one would follow to update a systematic review or meta - analysis . therefore , to avoid confusion , from here on we refer to all literature databases that are updated following the above protocol as systematic reviews . we used citations published through 2009 to train a classification model to distinguish relevant from irrelevant citations ( i.e. , to discern citations likely to be ultimately included in the systematic review from those likely to be excluded ) . we then used this trained classification model ( classifier ) to automatically screen articles published in 2010 ( i.e. , the articles that would be considered when updating the systematic review ) . all articles designated as irrelevant would be excluded from further consideration , thereby saving human effort . we assessed the performance of the system with respect to the studies that were ultimately included by the researchers in the 2010 update of the systematic reviews . three synthesize genetic association studies , investigating parkinson disease ( pdgene ) , alzheimer disease ( alzgene ) , and schizophrenia ( szgene ) , respectively ( table 1 ) . the fourth is the tufts cost - effectiveness analysis registry ( cea registry ) , which summarizes information from published cost - effectiveness analyses . we added this fourth field synopsis to gain insights on the generalizability of our approach to nongenetic synopses . the protocol and methods for our four data sets are available on their respective websites ( table 1 ) . in contrast to typical systematic reviews , these address much broader questions and are updated on a weekly or monthly basis . for example , the alzgene review evaluates the strength of the association between alzheimer disease and genetic variations across the whole genome , whereas a typical systematic review would probably evaluate only a subset of such genetic variations ( e.g. , in the apoe gene ) . note that attaining perfect ( 100 % ) sensitivity with semiautomated updating is much more difficult when all reported variations across thousands of genes are of interest rather than only apoe variations . to simulate a prospective test of our semiautomated system , we segmented each of the data sets into a training set comprising all citations published through 31 december 2009 and an update ( validation ) set composed of citations published between 1 january 2010 and 31 december 2010 ( supplementary figure s1 online ) . for each of the four databases , we aim to train a classifier to discriminate relevant from irrelevant citations . there are two components to operationalizing this : a method to encode text in an analyzable format and a classification method . we created computer - friendly representations of the titles , abstracts ( when available ) , and medical subject heading terms ( mesh ; when available ) of citations using a standard encoding scheme . specifically , we created a long list that includes all words present in at least three citations in the set of abstracts screened for the original review . the length of the list ( which corresponds to the number of words encoded ) depends on the data set , but is typically in the tens of thousands . each document was then represented simply as a vector with elements 1 and 0 , denoting whether the citation contained the corresponding word in this long list . this encoding scheme is known as the bag - of - words representation . briefly , we used support vector machines ( svms ) , which are state - of - the - science methods for text classification . svms in their canonical form perform poorly when there are far fewer examples ( in our case , citations ) from one class ( relevant citations ) than the other ( irrelevant citations ) . this is known as class imbalance , and it is the norm in literature searches conducted for systematic reviews . further , in systematic reviews false negatives ( relevant citations misclassified as irrelevant ) are much more costly than false positives ( irrelevant citations misclassified as relevant ) . first , we modified the svms to emphasize sensitivity ( we penalized more severely for false negatives compared with false positives ) . second , we did not train svms on the entire training set , but instead on a balanced sample comprising an equal number of relevant and irrelevant examples . this was accomplished by using all relevant examples and a randomly selected sample of the irrelevant examples and is analogous to performing a nested casealthough undersampling discards information , empirical evidence shows that it yields classifiers with higher sensitivity . however , undersampling introduces randomness ( the random sampling of the irrelevant citations in the training set ) . to reduce random variation in the model 's predictions , we used an ensemble of 11 sets of svm classifiers trained independently ( an approach called bagging ) . the final classification decision was taken as a majority vote over this ensemble ( see figure 1 ) . we used an odd number of classifiers in the ensemble to avoid ties ( the exact choice of 11 was motivated by our previous experimental work , in which this value worked well across many data sets ) . for each data set , we calculated the sensitivity and specificity of the classifiers on the update set . the reference standard was whether a citation was ultimately included in the systematic review ( based on manual screening ) . we report the number of citations that reviewers would have needed to screen , had they been using the proposed semiautomated system to update reviews in 2010 , versus the number of citations they actually screened . we assessed the variability of overall results by repeating all analyses 20 times using different random number seeds . we arbitrarily considered the first run the main analysis and report minimum and maximum results from the other 19 . analyses of misclassifications : our classification model does not provide rationales for its predictions . to provide some intuition as to whether the model and the human experts tend to make the same mistakes , we performed the following analysis . for each data set , we asked our experts to manually rescreen false - positive citations ( i.e. , citations not included in the final database but predicted to be relevant by the classifier based only on titles and abstracts and not on the full text ) . the experts then categorized the rescreened citations as clearly irrelevant , unclear , or clearly relevant ( scoring them as 0 , 1 , or 2 , respectively ) . for these same false - positive citations , we measured the confidence of the classification model in its ( mistaken ) predictions , as described below . an association between higher scores in human rescreening and higher confidence in the classification models predictions suggests that model and human experts tend to make the same mistakes . we took the proportion of votes in agreement with the majority vote as a measure of the model 's confidence in its predictions . for example , in figure 1 , 7 of the 11 base classifiers predict that the citation is relevant , and the confidence of the classification is 7/11 ( 0.64 ) . thus , confidence ranges from 6/11 ( 0.54 ) to 11/11 ( 1.0 ) . to test for an association between human rescreening and model confidence , we compared the distribution of human scores across the extreme quartiles of the distribution of confidence scores over false - positive citations using fisher 's exact test . in the case of the smaller cea registry , we performed this comparison across the top and bottom halves of the confidence score distributions . to also quantify the direction of the association , we used a proportional odds ordinal logistic regression to calculate the odds ratio for a human assigning a higher score ( from 0 to 1 or from 1 to 2 ) . statistical analyses were performed in stata se , version 11 ( stata , college station , tx ) . table 2 lists the size of the initial ( training ) and update ( validation ) sets in the four databases , as well as the proportion of citations that were finally included upon full - text review . researchers screened between ~ 25,000 and 50,000 citations for the three genetic synopses and a total of 6,129 for the cea registry ( from inception through 2010 ; these comprise the training sets ) . of these , for example , during 2010 , 0.9 to 3.3 % of citations reviewed were included in the genetic databases , and 7.8 % were included in the cea registry . the proposed semiautomated strategy correctly identified all citations that were included in the systematic reviews in 2010 ( 100 % sensitivity ) and considered relevant only ~ 10 % of the papers that were excluded by the human experts ( specificity of about 90 % ) . had the semiautomated system been used in 2010 , the human experts would have needed to screen only 605 ( pdgene ) , 555 ( alzgene ) , and 717 ( szgene ) titles and abstracts compared with the 5,616 , 7,298 , and 5,381 citations they manually screened for the three data sets ( table 3 ) . this translates to reductions in labor of ~ 81 , 92 , and 87 % , respectively . in the case of the cea registry , the classifier missed only 1 eligible article ( sensitivity about 99 % ) , and incorrectly considered relevant ~ 28 % of the papers that were excluded by human reviewers in 2010 ( specificity around 73 % ) . relying on the semiautomated system throughout 2010 , researchers would have needed to screen only 334 of 1,015 citations ( a reduction in labor of ~ 67 % ) . all results were robust when we repeated the entire analysis an additional 19 times using different random number seeds . no eligible papers were missed in the three genetic topics , and the same eligible paper was always missed in the cea registry . the specificity of the classifiers was practically identical to that of the main analyses ( table 2 ) . as mentioned above , only a single citation in one data set ( cea registry ) would have been a false negative ( i.e. , missed if the semiautomated system was actually in use during 2010 ) . the confidence of the classification model in that prediction was high because 10 of 11 base classifiers categorized the citation as irrelevant . upon re - review , human experts deemed that this citation might also have been missed by an inexperienced reviewer : only a single sentence in the abstract suggests that a cost - effectiveness ( or cost - utility ) analysis might have been performed . table 4 describes the results of human rescreening of citations that were not included in the systematic reviews , but were suggested as relevant by the classifier ( false positives ) for different strata of classifier confidence . classifier confidence appears to be associated with human experts ' dispositions upon re - review . based on ordinal logistic regressions , false positives in the highest 25 % ( 50 % for the cea registry ) had between 1.9 and 6.1 higher odds of being deemed clearly relevant rather than maybe or maybe rather than clearly irrelevant upon re - review by human experts . if we are ever to keep up with the information overload while adhering to the current demanding standards , we must modernize the methodology and conduct of systematic reviews , meta - analyses , and field synopses without compromising their scientific validity . this is particularly relevant to genetics and genomics , in which data accumulate rapidly . to this end , we demonstrated that data mining methodologies can reduce the burden of updating of systematic reviews without sacrificing their comprehensiveness . indeed , only a single citation of the many dozens that were included in each topic 's 2010 update would have been missed by the semiautomated method . this is directly comparable to the performance of individual human screeners : in empirical explorations , human experts missed on average 8 % of eligible citations ( ranging from 0 to 24 % ) . to minimize the likelihood of overlooking eligible studies , current recommendations suggest using two independent screenersthus , computer - assisted screening could replace full manual screening for both screeners , replace one screener , or be used in addition to both screeners to further increase the sensitivity of the overall process . to refine the role of the semiautomated process in real - life settings , we must evaluate their utility using study designs similar to those used for evaluating medical tests . the most robust design would entail a randomized comparison of using versus not using the semiautomated system during the conduct of systematic reviews . apart from quantifying the utility of the semiautomated system , such an experiment would potentially allow one to detect unforeseen detrimental consequences ( e.g. , sloppiness during manual screening as a result of overreliance on the computer ) . we note that semiautomating the updating of systematic reviews is different than semiautomating the screening of citations when performing a new systematic review . the main difference is that when updating an existing review , one has access to the set of citations that were manually screened for the original review . these citations can be used to train a classifier ; the larger this set is , the better the classifier will likely perform , because it has more data from which to learn . by contrast , when performing a new review , no such training data set is available at the outset , and the problem is more challenging . methods for new systematic reviews are still in development and remain to be empirically validated on a large scale . allowing for some caveats , our results are applicable to the general case of updating typical systematic reviews and meta - analyses . first , the scope of key questions in the updates should be identical to ( or at worst a subset of ) the scope in the original review . if the update is on one part of the original review , we would expect a decrease in the specificity of the predictions ( some citations that would be eligible for the original review would be out of scope for the update ) , but no effect on the sensitivity . further , there is a tacit assumption that there is no abrupt shift in the typical vocabulary of the field , as may happen , for example , in the case of an experimental drug or a disease or condition being referred to with a new name . finally , the initial review should have a large enough number of citations to train a robust model . ultimately , systematic reviewers must make a decision regarding the applicability of a model trained on the original review to the citations retrieved for the update ; no hard and fast rules currently exist . the latter observation is perhaps the most important concern when assessing the applicability of our results to updating typical systematic reviews . specifically , in the three genetic topics , the initial set was an order of magnitude larger than most systematic reviews . however , in our previous work on semiautomating citation screening in new systematic reviews , we have consistently attained 100 % sensitivity with training sets of 1,7002,500 citations in all examined examples . if anything , the systematic reviews ( field synopses ) in our examples have broader inclusion criteria than most systematic reviews and thus likely represent a more difficult problem : there are more eligible papers and thus more opportunities to miss them . furthermore , there is greater diversity among the eligible papers . moreover , in practice one can assess the likely performance that a classification model will achieve when semiautomating a review update by performing an analysis called cross - fold validation on the citations manually screened for the original review . this analysis involves splitting the original database into , for example , 10 parts and sequentially training a model on 9/10 of the data and then assessing its performance on the remaining 1/10 . this is repeated 10 times , and an estimate of performance is taken as average of these 10 tests . if the estimated performance is deemed acceptable ( i.e. , very high sensitivity is consistently achieved ) , then the researchers undertaking the update may opt to use the semiautomated approach . finally , another limitation is that the computer is a black box because no readily interpretable explanation is provided for the classifications . however , a detailed rationale for excluding the citations during screening is not necessarily critical . for example , we do not really provide rationales for the millions of citations that are excluded by the search strategy in the first place . in the end , trusting computer algorithms to semiautomate abstract screening in routine settings is contingent on their empirical performance : if there are consistently acceptable empirical results , this criticism is less important . we find it intuitively agreeable that upon re - reviewing false positives ( i.e. , citations ultimately not included in the respective synopses but denoted relevant by the model ) , experts tended to have trouble with the same citations that our model did . this is an indirect indication that the models rely at least on similar patterns of terms as humans do , of course lacking a human 's semantic comprehension . the semiautomated system reduced the number of citations that would have needed to be screened by a human expert by 7090 % , a substantial reduction in workload , without sacrificing comprehensiveness . regularly updated systematic reviews and meta - analysesthe novel approach developed here is an important and practical step toward reaching that goal . in addition to making the process of updating systematic reviews substantially more efficient , application of our method may also improve the quality of evidence - based medicine .\noutput:\n" }, { "from": "agent", "value": "purpose : the aim of this study was to demonstrate that modern data mining tools can be used as one step in reducing the labor necessary to produce and maintain systematic reviews.methods : we used four continuously updated , manually curated resources that summarize medline - indexed articles in entire fields using systematic review methods ( pdgene , alzgene , and szgene for genetic determinants of parkinson disease , alzheimer disease , and schizophrenia , respectively ; and the tufts cost - effectiveness analysis ( cea ) registry for cost - effectiveness analyses ) . in each data set , we trained a classification model on citations screened up until 2009 . we then evaluated the ability of the model to classify citations published in 2010 as relevant or irrelevant using human screening as the gold standard.results : classification models did not miss any of the 104 , 65 , and 179 eligible citations in pdgene , alzgene , and szgene , respectively , and missed only 1 of 79 in the cea registry ( 100 % sensitivity for the first three and 99 % for the fourth ) . the respective specificities were 90 , 93 , 90 , and 73 % . had the semiautomated system been used in 2010 , a human would have needed to read only 605/5 ,616 citations to update the pdgene registry ( 11 % ) and 555/7 ,298 ( 8 % ) , 717/5 ,381 ( 13 % ) , and 334/1 ,015 ( 33 % ) for the other three databases.conclusion : data mining methodologies can reduce the burden of updating systematic reviews , without missing more papers than humans ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the survey addressed information on antimicrobial drug resistance testing , phage typing , or both . since most countries do not routinely apply these typing methods , the questionnaire was not simply sent to all world health organization ( who ) member states . instead , an invitation to participate in the survey was distributed through the who global salm - surv ( gss ) network ( 25 ) and directly to all enter - net ( 26 ) network countries , plus a group of large countries known or assumed to have resistance testing or phage typing as an integrated part of their national salmonella surveillance system . a total of 52 questionnaires were sent out in june and july 2002 . of these , 44 were sent directly to countries known or assumed to have resistance testing or phage typing , and 8 were sent out to member states responding to the gss invitation . of the 52 questionnaires ,32 were sent to countries in the european region , 6 to the american region , 7 to the asian region , 5 to the african region , and 2 to the oceania region . country names and names of geographic regions and subregions are used as described in the united nations classification system ( 27 ) . each country was requested to give information on the total annual number of laboratory - verified episodes of nontyphoidal salmonellosis , s. typhimurium , mdr s. typhimurium , and s. typhimurium dt104 from 1992 to 2001 . the participating countries were also asked to give details on whether the reported number of salmonella isolates that formed the basis for further phage typing or antimicrobial drug susceptibility testing included all national isolates or if they were a subset of isolates . if only a subset of isolates were tested , the countries were asked to state the proportion of s. typhimurium strains tested and what the criteria for choosing the isolates were . we also asked participants to describe methods used for antimicrobial drug resistance testing and the drugs included in their tests . multidrug - resistance was defined as isolates being resistant or intermediately susceptible towards 4 separate classes of drugs . this group includes isolates of r - type acssut , the so - called classical penta - resistant phenotype . when information was available , participants were asked to give the numbers of isolates exhibiting r - types extending the acssut - complex and the number of isolates resistant to clinically relevant antimicrobial drugs ( quinolones , trimethoprim , and cephalosporins ) . in countries where only a subset of salmonella isolates had been submitted for phage typing , antimicrobial drug - resistance testing , or both , the total number of dt104 or mdr s. typhimurium isolates was extrapolated from the reported numbers of isolates and the proportion of tested isolates . the survey addressed information on antimicrobial drug resistance testing , phage typing , or both . since most countries do not routinely apply these typing methods , the questionnaire was not simply sent to all world health organization ( who ) member states . instead , an invitation to participate in the survey was distributed through the who global salm - surv ( gss ) network ( 25 ) and directly to all enter - net ( 26 ) network countries , plus a group of large countries known or assumed to have resistance testing or phage typing as an integrated part of their national salmonella surveillance system . a total of 52 questionnaires were sent out in june and july 2002 . of these , 44 were sent directly to countries known or assumed to have resistance testing or phage typing , and 8 were sent out to member states responding to the gss invitation . of the 52 questionnaires ,32 were sent to countries in the european region , 6 to the american region , 7 to the asian region , 5 to the african region , and 2 to the oceania region . country names and names of geographic regions and subregions are used as described in the united nations classification system ( 27 ) . each country was requested to give information on the total annual number of laboratory - verified episodes of nontyphoidal salmonellosis , s. typhimurium , mdr s. typhimurium , and s. typhimurium dt104 from 1992 to 2001 . the participating countries were also asked to give details on whether the reported number of salmonella isolates that formed the basis for further phage typing or antimicrobial drug susceptibility testing included all national isolates or if they were a subset of isolates . if only a subset of isolates were tested , the countries were asked to state the proportion of s. typhimurium strains tested and what the criteria for choosing the isolates were . we also asked participants to describe methods used for antimicrobial drug resistance testing and the drugs included in their tests . multidrug - resistance was defined as isolates being resistant or intermediately susceptible towards 4 separate classes of drugs . this group includes isolates of r - type acssut , the so - called classical penta - resistant phenotype . when information was available , participants were asked to give the numbers of isolates exhibiting r - types extending the acssut - complex and the number of isolates resistant to clinically relevant antimicrobial drugs ( quinolones , trimethoprim , and cephalosporins ) . in countries where only a subset of salmonella isolates had been submitted for phage typing , antimicrobial drug - resistance testing , or both , the total number of dt104 or mdr s. typhimurium isolates was extrapolated from the reported numbers of isolates and the proportion of tested isolates . the questionnaire was sent to 52 countries , and a completed questionnaire was received from 29 , a response rate of 56 % ( figure 1 ) . of the 52 invited countries ,23 were members of or affiliated with enter - net ; from these a positive feedback was received from 20 ( 87 % ) . these countries were australia , austria , belgium , canada , denmark , england and wales , finland , germany , greece , ireland , japan , luxembourg , the netherlands , new zealand , norway , scotland , south africa , spain , sweden , and switzerland . the 8 countries and 1 regional center ( 31 % response rate ) that participated in the survey that were not associated with enter - net when data were collected were brazil , the czech republic , hungary , israel , latvia , malta , republic of south korea , united states , and the caribbean epidemiology centre ( carec ) , a regional center that represents 21 countries in the caribbean ( anguilla , antigua and barbuda , aruba , bahamas , barbados , belize , bermuda , british virgin islands , cayman islands , dominica , grenada , guyana , jamaica , montserrat , netherlands antilles , st . kitts and nevis , st . vincent and the grenadines , suriname , trinidad and tobago , and turks and caicos ) . for the purpose of this study , participating countries in the survey of multidrug - resistant salmonella enterica serotype typhimurium , 19922001 , internationally ( a ) and in europe ( b ) . the proportion of salmonella isolates forwarded from local health laboratories to national or regional institutions varied from 5 % to 100 % . none of the participating countries restricted the submission of isolates to strains from selected patients , e.g. , in case of septicemia or outbreak situations . all 29 participating countries performed serotyping on 85 % to 100 % of salmonella isolates received at the national reference laboratory . table 1 shows the number of nontyphoidal salmonella isolates and the proportion hereof that were s. typhimurium in each country from 1992 to 2001 presented as 2 - year intervals . the table also shows the estimated incidence of laboratory - confirmed cases of s. typhimurium in 2001 . throughout the study period , the proportion of s. typhimurium among nontyphoidal salmonellae has been relatively stable . in 1992 , 16 % of isolateswere s. typhimurium , compared to 17 % in 2001 . however , large differences between countries and variations from year to year within each country made comparison difficult . nevertheless , some trends emerged when the countries were aggregated into geographic regions . in the caribbean region , south america , eastern asia , and europe , a general decrease in the proportion of s. typhimurium was observed . in north america , on the other hand , the situation has remained relatively stable , whereas both australia and new zealand have seen an increase in the number and proportion of s. typhimurium cases from 1992 to 2001 . * pop . , population 10 ; ist , incidence of s. typhimurium per 10 population . data on s. typhimurium and incidence are based on data from the new federal states of germany and the city of berlin . submission of strains for serotyping at the central laboratory was not compulsory in switzerland at the time of data collection . # according to the united nations classification , israel belongs to the western asian region . in this studyphage typing was carried out in 6 of the participating countries ; by 2001 , this number had risen to 22 . five countries ( brazil , japan , norway , switzerland , and the united states ) only performed phage typing when an mdr strain was found or in outbreak situations . although not all countries performed phage typing in accordance with the colindale scheme ( 28 ) , the countries using different standards provided information that allowed for comparison with results obtained using the colindale scheme ( 2931 ) . the proportion of s. typhimurium strains that were dt104 and the proportion thereof that were found to be mdr are shown for each country in table 2 . in general , the incidence and proportion of dt104 increased throughout the period . in 1992 , 8.7 % of s. typhimurium isolates were dt104 , but in 2001 this proportion had increased to 33 % . again , the incidence peaked in 1996 and then decreased . in most other european countries and north america , the relative numbers of dt104 strains had increased throughout the period . in australia and new zealand , the proportion of s. typhimurium strains that were dt104 is depicted in figure 2 ( the countries are aggregated into 8 regions ) . * mdr , multidrug - resistant ; na , data not available . ; no . of dt104 ; and no . of dt104 that are mdr . according to the united nations classification , israel belongs to the western asian region . in this study , israel has been grouped with southern european countries . salmonella enterica serovar typhimurium dt104 as percentage of all s. typhimurium in 8 world regions , 19922001 . only countries that had data available for 2 or more 2 - year periods are included : united kingdom and ireland : england and wales , scotland , ireland ; scandinavia : denmark , finland , norway , sweden ; western europe : austria , germany , and the netherlands ; eastern europe : czech republic and hungary ; southern europe : spain and israel ; north america : canada , united states ; eastern asia : the republic of korea ; oceania : australia and new zealand . antimicrobial susceptibility testing became an increasingly common constituent of the surveillance during the study period . in 1992 , susceptibility testing was performed in 14 of the 29 participating countries and in all but one in 2000 . all countries routinely tested a minimum of 6 antimicrobial drugs , all belonging to different drug classes . the majority of countries ( 73 % ) used disc diffusion testing according to nccls standards . listed by frequency , the most common antimicrobial drug classes included in the test panel were ( fluoro ) quinolones , broad - spectrum penicillins , phenicols , aminoglycosides , tetracyclines , cephalosporins , sulfonamides , and trimethoprim . in 21 countries , antimicrobial susceptibility testing was performed independently of phage typing results , but in 2 countries ( finland until 1999 and new zealand ) , testing was only performed on strains found to be dt104 . table 2 shows the distribution of mdr s. typhimurium presented as 2 - year time - bands . figure 3 depicts the general trend , with countries divided into 9 different regions . in 199215 % of all s. typhimurium isolates were mdr ; by 2001 , this percentage had increased 3-fold to 42 % . once again , large variations occurred between countries and within countries from year to year . in most european countries and northamerica , mdr s. typhimurium was common and , with the exception of the united kingdom and ireland , multidrug resistance increased from the mid-1990s to the end of the study period . for example , in 2001 multidrug resistance ranged from 22 % ( greece ) to 72 % ( ireland ) . only limited data were available from brazil , the caribbean region , south africa , and the republic of korea . however , in these regions multidrug resistance was far less common , ranging from zero in the caribbean region to 19 % in the republic of korea . in australia , multidrug resistance remained low throughout the period , with 1.0 % of strains in 1997 and 3.6 % in 2001 . multidrug - resistant salmonella enterica serovar typhimurium as a percentage of all s. typhimurium in 9 world regions , 19922001 . only countries that had data available for 2 or more 2 - year periods are included : united kingdom and ireland : scotland and ireland ; scandinavia and the baltics : denmark , finland , norway , and latvia ; western europe : austria , germany , luxembourg , and the netherlands ; eastern europe : czech republic and hungary ; southern europe : greece , malta , and spain ; north america : canada , united states ; south america : brazil ; eastern asia : the republic of korea ; oceania : australia . mdr dt104 was a frequent subtype of mdr s. typhimurium in most of the countries . in 1992 , between 11 % ( germany ) and 77 % ( scotland ) of the mdr strains were dt104 ; in 2001 this ranged from 22 % ( australia ) to 94 % ( the netherlands ) . overall , the proportion of mdr dt104 of all dt104 has remained fairly stable ; 84 % of dt104 were classified as mdr in 2001 , compared with 72 % in 1992 . among mdr dt104 , the classical penta - resistant phenotype , r - type acssut , was by far the most common phenotype throughout the period . it was found in 99 % of mdr dt104 strains in 1992 and in 94 % of such strains in 2001 ( data not shown ) . finally , we looked at trends in development of additional resistance in the classical penta - resistant phenotype ( r - type acssut ) , with focus on 3 clinically important antimicrobial drug classes : quinolones , cephalosporins , and trimethoprim . both quinolone and trimethoprim resistance increased in mdr dt104 throughout the study period . in 1992 , nalidixic acid susceptibility testing was performed on a total of 194 mdr dt104 isolates in 4 different countries ; no resistant isolates were found . in 2001 , nalidixic acid susceptibility testing of 1,812 mdr dt104 strains in 11 countries identified 109 ( 6.0 % ) resistant strains . similarly , trimethoprim resistance was found in 1.2 % of the 180 mdr dt104 strains tested in 1992 , but in 6.6 % of 1,855 mdr dt104 strains tested in 2001 . cephalosporin - resistant mdr dt104 remained rare , with only 0.5 % resistant strains in 2001 , and no clear trend observable . figure 4 shows the overall trend of resistance to quinolone , trimethoprim , and cephalosporins from 1992 to 2001 . the increase in quinolone resistance seen in 1996 and in 1998 was caused by a general increase in quinolone - resistant mdr dt104 in scotland and an outbreak of quinolone - resistant mdr dt104 in denmark ( 14 ) , respectively . the increase in trimethoprim resistance from 1995 to 1996 was also caused by a general increase in trimethoprim - resistant mdr dt104 in scotland . proportion of multidrug - resistant salmonella enterica serovar typhimurium with additional resistance to quinolones , cephalosporin , or trimethoprim , 19922001 . the proportion of salmonella isolates forwarded from local health laboratories to national or regional institutions varied from 5 % to 100 % . none of the participating countries restricted the submission of isolates to strains from selected patients , e.g. , in case of septicemia or outbreak situations . all 29 participating countries performed serotyping on 85 % to 100 % of salmonella isolates received at the national reference laboratory . table 1 shows the number of nontyphoidal salmonella isolates and the proportion hereof that were s. typhimurium in each country from 1992 to 2001 presented as 2 - year intervals . the table also shows the estimated incidence of laboratory - confirmed cases of s. typhimurium in 2001 . throughout the study period , the proportion of s. typhimurium among nontyphoidal salmonellae has been relatively stable . in 1992 , 16 % of isolateswere s. typhimurium , compared to 17 % in 2001 . however , large differences between countries and variations from year to year within each country made comparison difficult . nevertheless , some trends emerged when the countries were aggregated into geographic regions . in the caribbean region , southamerica , eastern asia , and europe , a general decrease in the proportion of s. typhimurium was observed . in north america , on the other hand , the situation has remained relatively stable , whereas both australia and new zealand have seen an increase in the number and proportion of s. typhimurium cases from 1992 to 2001 . * pop . , population 10 ; ist , incidence of s. typhimurium per 10 population . data on s. typhimurium and incidence are based on data from the new federal states of germany and the city of berlin . submission of strains for serotyping at the central laboratory was not compulsory in switzerland at the time of data collection . # according to the united nations classification , israel belongs to the western asian region . in this studyin 1992 , phage typing was carried out in 6 of the participating countries ; by 2001 , this number had risen to 22 . five countries ( brazil , japan , norway , switzerland , and the united states ) only performed phage typing when an mdr strain was found or in outbreak situations . although not all countries performed phage typing in accordance with the colindale scheme ( 28 ) , the countries using different standards provided information that allowed for comparison with results obtained using the colindale scheme ( 2931 ) . the proportion of s. typhimurium strains that were dt104 and the proportion thereof that were found to be mdr are shown for each country in table 2 . in general , the incidence and proportion of dt104 increased throughout the period . in 1992 , 8.7 % of s. typhimuriumthe incidence peaked in 1996 and then decreased . in most other european countries and northamerica , the relative numbers of dt104 strains had increased throughout the period . in australia and new zealand , the proportion of s. typhimurium strains that were dt104 is depicted in figure 2 ( the countries are aggregated into 8 regions ) . * ; no . of dt104 ; and no . of dt104 that are mdr . according to the united nations classification , israel belongs to the western asian region . in this studysalmonella enterica serovar typhimurium dt104 as percentage of all s. typhimurium in 8 world regions , 19922001 . only countries that had data available for 2 or more 2 - year periods are included : united kingdom and ireland : england and wales , scotland , ireland ; scandinavia : denmark , finland , norway , sweden ; western europe : austria , germany , and the netherlands ; eastern europe : czech republic and hungary ; southern europe : spain and israel ; north america : canada , united states ; eastern asia : the republic of korea ; oceania : australia and new zealand . antimicrobial susceptibility testing became an increasingly common constituent of the surveillance during the study period . in 1992 , susceptibility testing was performed in 14 of the 29 participating countries and in all but one in 2000 . all countries routinely tested a minimum of 6 antimicrobial drugs , all belonging to different drug classes . the majority of countries ( 73 % ) used disc diffusion testing according to nccls standards . listed by frequency , the most common antimicrobial drug classes included in the test panel were ( fluoro ) quinolones , broad - spectrum penicillins , phenicols , aminoglycosides , tetracyclines , cephalosporins , sulfonamides , and trimethoprim . in 21 countries , antimicrobial susceptibility testing was performed independently of phage typing results , but in 2 countries ( finland until 1999 and new zealand ) , testing was only performed on strains found to be dt104 . table 2 shows the distribution of mdr s. typhimurium presented as 2 - year time - bands . figure 3 depicts the general trend , with countries divided into 9 different regions . in 199215 % of all s. typhimurium isolates were mdr ; by 2001 , this percentage had increased 3-fold to 42 % . once again , large variations occurred between countries and within countries from year to year . in most european countries and northamerica , mdr s. typhimurium was common and , with the exception of the united kingdom and ireland , multidrug resistance increased from the mid-1990s to the end of the study period . for example , in 2001 multidrug resistance ranged from 22 % ( greece ) to 72 % ( ireland ) . only limited data were available from brazil , the caribbean region , south africa , and the republic of korea . however , in these regions multidrug resistance was far less common , ranging from zero in the caribbean region to 19 % in the republic of korea . in australia , multidrug resistance remained low throughout the period , with 1.0 % of strains in 1997 and 3.6 % in 2001 . multidrug - resistant salmonella enterica serovar typhimurium as a percentage of all s. typhimurium in 9 world regions , 19922001 . only countries that had data available for 2 or more 2 - year periods are included : united kingdom and ireland : scotland and ireland ; scandinavia and the baltics : denmark , finland , norway , and latvia ; western europe : austria , germany , luxembourg , and the netherlands ; eastern europe : czech republic and hungary ; southern europe : greece , malta , and spain ; north america : canada , united states ; south america : brazil ; eastern asia : the republic of korea ; oceania : australia . mdr dt104 was a frequent subtype of mdr s. typhimurium in most of the countries . in 1992 , between 11 % ( germany ) and 77 % ( scotland ) of the mdr strains were dt104 ; in 2001 this ranged from 22 % ( australia ) to 94 % ( the netherlands ) . overall , the proportion of mdr dt104 of all dt104 has remained fairly stable ; 84 % of dt104 were classified as mdr in 2001 , compared with 72 % in 1992 . among mdr dt104 , the classical penta - resistant phenotype , r - type acssut , was by far the most common phenotype throughout the period . it was found in 99 % of mdr dt104 strains in 1992 and in 94 % of such strains in 2001 ( data not shown ) . finally , we looked at trends in development of additional resistance in the classical penta - resistant phenotype ( r - type acssut ) , with focus on 3 clinically important antimicrobial drug classes : quinolones , cephalosporins , and trimethoprim . both quinolone and trimethoprim resistance increased in mdr dt104 throughout the study period . in 1992 , nalidixic acid susceptibility testing was performed on a total of 194 mdr dt104 isolates in 4 different countries ; no resistant isolates were found . in 2001 , nalidixic acid susceptibility testing of 1,812 mdr dt104 strains in 11 countries identified 109 ( 6.0 % ) resistant strains . similarly , trimethoprim resistance was found in 1.2 % of the 180 mdr dt104 strains tested in 1992 , but in 6.6 % of 1,855 mdr dt104 strains tested in 2001 . cephalosporin - resistant mdr dt104 remained rare , with only 0.5 % resistant strains in 2001 , and no clear trend observable . figure 4 shows the overall trend of resistance to quinolone , trimethoprim , and cephalosporins from 1992 to 2001 . the increase in quinolone resistance seen in 1996 and in 1998 was caused by a general increase in quinolone - resistant mdr dt104 in scotland and an outbreak of quinolone - resistant mdr dt104 in denmark ( 14 ) , respectively . the increase in trimethoprim resistance from 1995 to 1996 was also caused by a general increase in trimethoprim - resistant mdr dt104 in scotland . proportion of multidrug - resistant salmonella enterica serovar typhimurium with additional resistance to quinolones , cephalosporin , or trimethoprim , 19922001 . the present survey was conducted to gain a better understanding of the global impact of dt104 and mdr s. typhimurium , given the severity of illness than can result from infection with s. typhimurium and mdr strains in particular . the survey 's primary findings are that during the period 19922001 , the total number of mdr s. typhimurium and s. typhimurium dt104 cases increased , while that of other types of s. typhimurium decreasedthe collected data also may not always accurately describe the real national incidence or be directly comparable between countries . the total number of isolates of nontyphoidal salmonellae registered at the national level decreased from 1992 to 2001 . this result may be biased because of changes in surveillance practices . since the survey indicated that surveillance systems generally improved throughout the study period , this trend is most likely correct , however . concurrent with this decrease , an overall decrease in the number of s. typhimurium isolates was observed , thus keeping the proportion of s. typhimurium cases among total salmonella cases constant . the decrease was primarily seen in europe and north america , whereas australia and new zealand saw an increase in both the number of cases of s. typhimurium and of the total number of nontyphoidal salmonella cases . in germanythe total number of nontyphoidal salmonella cases is available for the whole country , but for administrative reasons data on serotypes , antimicrobial susceptibility , and phage types are based only on results from the new federal states of germany ( formerly east germany ) and the city of berlin . however , german studies have shown that serotype distribution and drug resistance are comparable between former west and east germany ( 32 ) ( w. rabsch , pers . mdr s. typhimurium has increased in the past decades in almost all the regions covered in this study . most of this increase is due to the concurrent upsurge of dt104 , whereas other phage types , such as u302 , dt120 , dt12 , and dt193 , were reported to play a smaller role in this development . a high proportion of mdr s. typhimurium was primarily observed in europe and north america . because of the low coverage of participating countries in asia , south america , and africa , the situation in these areas was difficult to assess . both australia and new zealand , however , reported high incidence of s. typhimurium , but mdr strains of s. typhimurium and dt104 were largely absent . the isolated increase in mdr s. typhimurium in australia in 2001can be explained by a large outbreak of mdr dt104 associated with consumption of halva ( dessert made of sesame seeds ) ( 33 ) . that dt104 has not spread markedly in australia and new zealand may be explained both by geography and the very strict food and livestock import restrictions in force in these countries , which prevent any large - scale introduction and spread of foreign salmonella types in the food animal production chain ( 34 ) . although high and generally increasing levels of mdr s. typhimurium were observed in europe , the united kingdom presents a special case . it and germany had an increase in dt104 in the beginning of the 1990s , before most other countries ( 5,35 ) . in fact , dt104 was first isolated in the united kingdom in the early 1980s , years before it was isolated in other countries ( 5 ) . in the united kingdom , the incidence of dt104 peaked in 1996 and has since declined ( and this study ) . possible explanations for this finding include the management of bovine spongiform encephalitis in the united kingdom , associated general improvements in farm hygiene , and an overall decline in cattle production ( 36 ) . although multidrug - resistance and dt104 were closely linked , large country - specific differences were seen , even between neighboring countries . most pronounced was the difference between germany and the netherlands in 2001 , where 64 % and 94 % , respectively , of mdr isolates were dt104 . such differences probably reflect both real differences and biases resulting from , for instance , different laboratory reporting practices . for example , some of the countries in this survey ( new zealand , norway , and the united states ) performed antimicrobial susceptibility tests on all their dt104 isolates but only on a subset of non - dt104 strains . in australia and in scandinavia , where the incidence of domestically acquired salmonellosis is generally low , many cases appeared to be imported . in a recent study of australian dt104isolates , 37 % were associated with travel abroad , particularly to southeast asia ( d. lightfoot , pers . complete data on travel association of mdr s. typhimurium cases were available for norway and finland and showed that most mdr s. typhimurium patients were infected abroad . in sweden , where information on dt104 but not mdr was available , most dt104 patients were infected abroad . a special issue concerns the possibility of acquisition , with time , of resistance traits additional to the classical penta - resistant pattern . of particular concern is the additional acquisition of quinolone resistance by mdr dt104 , since fluoroquinolones are often the drugs of first choice when treating severe salmonellosis . as mentioned , several studies have now shown that multidrug resistance and quinolone resistance may be associated with particular adverse health effects . when seen in the light of the ability of dt104 to spread and establish itself in a large variety of food animal lines ( cattle , pigs , poultry ) , the increase in the number of mdr s. typhimurium strains that include quinolone resistance becomes particularly problematic . quinolone , and in particular the fluoroquinolones , have been part of human medicine since the 1980s , resulting in no or very limited resistance in salmonellae . it was not until the license of fluoroquinolones for food animal production in the early 1990s that resistant salmonella strains emerged ( 37 ) . the use of fluoroquinolones for food production animals should therefore be discontinued or at least severely restricted as quickly as possible . first , it was limited to countries with relatively sophisticated surveillance systems in place , since only countries performing phage typing or resistance testing in addition to serotyping were eligible . therefore , the survey contains no representative data on the situation in these regions . who global salm - surv seeks to enhance the capacity of countries to provide such data . second , the collection of isolates at the national level is likely to vary from country to country , depending on a number of factors such as sampling frequency at the local level , availability of laboratory reagents , and the degree to which isolates and results are forwarded to the national level . local practice , the priority given to foodborne illnesses , and financial factors will influence on how often a physician will request a fecal sample . furthermore , many countries stated that strains and information were not always routinely collected centrally , while in some of the countries strains were never forwarded from certain local laboratories . for these reasons , care should be taken in the interpretation of results of this survey ; in particular when comparing incidence rates between countries . however , these limitations are inherent to surveillance in general and do not apply only to this survey . cross - checking these survey data with available published surveillance data showed them to be in line with each other in the united states ( 38 ) , the netherlands ( 39 ) , and denmark ( 40 ) . in summary , on a global scale , only a small number of countries perform antimicrobial susceptibility testing or phage typing , although the number of countries doing so more than doubled throughout the study period . despite its limitations , the survey showed that the incidence of both mdr s. typhimurium and mdr s. typhimurium dt104 increased markedly worldwide during the 1990s , although the problem has primarily affected europe and north america . the survey implies that mdr s. typhimurium poses a serious and increasing public health problem in large parts of the world . surveillance and control programs such as the global salm - surv international network recently launched by who should therefore be reinforced .\noutput:\n" }, { "from": "agent", "value": "the incidence of multidrug - resistant ( mdr ) salmonella typhimurium infections in humans , and in particular mdr definitive phage type 104 ( dt104 ) , has increased substantially in many countries in the last 2 decades , often associated with increased illness . to examine the magnitude of this problem , a survey was conducted among countries with available antimicrobial resistance or phage typing surveillance data . a total of 29 , primarily industrialized , countries participated in the survey , which covered the years 19922001 . overall , the incidence of mdr s. typhimurium and dt104 increased continuously during this period , although the problem affected primarily europe and north america . the increase appeared to have peaked in the united kingdom but not in other countries . also , the incidence of quinolone - resistant s. typhimurium was increasing . this survey implies that mdr s. typhimurium constitutes an increasing public health problem in large parts of the world and emphasizes the importance of surveillance and control programs ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: there have been questions about its class i versus ii versus iii classification , or it being a lever in the first place and the loading assumptions . but it is the lever model , coupled with the bending beam analogy of the mandible that form the foundation of the generally accepted ( longitudinal ) stress distribution pattern depicted in figure 1 ( a ) and its variant , figure 1 ( b ) . the lever is an oversimplified structural representation of the jaw , so biomechanical concepts derived from it should be suspect . in the present context , the lever 's intrinsic vertical - only occlusal force is its primary drawback . thus , the principal purposes of this paper are to demonstrate , with basic analytical engineering mechanics , but barebones mathematics , the shortcomings of the lever / beam model - based concepts that relate to the surgery of the mandible . more specifically , the central issues involve ( 1 ) the relationship between occlusal force direction and the associated stress distributions within an intact mandible and ( 2 ) the extrapolation of those stress fields to a plated fractured mandible . figure 2 ( a ) is a partial ( because dimensions irrelevant to this discussion are omitted ) free - body diagram ( fbd ) of the frame - ( versus lever - , figure 1 ) idealized mandible . an fbd , used in equilibrium analysis , shows all external loads ( forces and moments ) that act on an isolated object ( i.e. , the mandible or a portion of it ) of interest . for the purposes of this project , the crucial difference between the lever ( figure 1 ) and the frame model is that in the latter , the direction of force vector t is not necessarily vertical , figures 2 and 3 . the fbd in figure 2 ( b ) is of an imaginary or real ( i.e. , fractured ) segment of the mandible that is anterior to the arbitrarily defined ( at distance from the occlusal contact ) circle , , on the approximated centroidal axis ( dashed line ) of the mandible . and represent the internal shear and normal ( perpendicular ) forces , respectively , and represents the internal moment . , , and symbolize the net internal loads at the interface ( real or imaginary ) that are necessary to maintain the static equilibrium of the anterior segment when occlusal force t acts on it . applying static equilibrium conditions to the fbd in figure 2 ( b ) yields ( 1 ) forcesvertical = 0 : ty = 0 or = ty , forceshorizontal = 0 : + tx = 0 or = tx , moments abouto = 0 : tytx = 0or = tytx . the right hand sides of the equations are known because they are specified or calculated . for the purposes of this project , it is important only to recognize that and are determined by ty and tx , respectively , and that is a function of both ty and tx , as well as anatomy ( ) and the horizontal distance ( ) between the section and the occlusal contact . the analysis is based on the range of occlusal force directions represented in figure 3 ( a ) . occlusal contact can occur between a maxillary cusp distal incline and a mandibular cusp mesial incline ( t0 , t1 , and t2 ) , a maxillary cusp mesial incline against a mandibular cusp distal incline ( t4 ) or flat - plane occlusion ( t3 , also in figure 1 ) . ( according to classic friction principles , assuming frictionless contact , the direction of a contact force between surfaces must be perpendicular to their common tangent . t 04 can be characterized by the positions of their lines - of - action ( loa ) relative to the circle , . t1 passes above ( or equivalently , behind ) it , thus requiring a clockwise ( cw ) moment , , for equilibrium . equilibrium dictates that must be counterclockwise ( ccw ) with t2 , t3 , and t4 , because they pass below or in front of . the second relevant characteristic of a t is the direction of its horizontal component . t0 , t1 , and t2 are directed posteriorly ; therefore , for equilibrium , must be to the right . because t3 ( the lever analogue ) is vertical , = 0 . thus , the 5 ts generically represent the permutations of the loa orientations relative to and the horizontal force component directions . it is emphasized that ( 1 ) ) and figures 24 ( essentially , , , and ) apply identically to the imaginary anterior segment of an intact mandible and to an actual fractured - off section , but that is where the similarity ends . the physical manifestations of , , and in the two scenarios are fundamentally distinct . the system that is equivalent to , , and is produced by the stresses within the bone . in the plated mandible , it is produced by the loads in the plates and by contact between the fractured bone surfaces . elementary engineering beam theory is used to determine the stress systems ( figure 5 ) that are equivalent to a specific set of + , , and ( figure 4 ) . ( the identical engineering principles are implicitly behind the generally accepted as obvious figure 1 stresses . ) a uniform compression is the equivalent to an anteriorly directed ( c in figures 5 ( a ) , 5 ( b ) , and 5 ( c ) ) . similarly , uniform tensile stress , t , is the equivalent to the posteriorly directed in figure 5 ( e ) . ( there is no uniform tension or compression associated with t3 , figure 5 ( d ) , because t3 , being vertical , requires that = 0 for equilibrium . ) the equivalents of a cw ( figure 5 ( b ) ) and a ccw ( figures 5 ( c ) , 5 ( d ) , and 5 ( e ) ) are stress gradients with compression - on - top / tension - on - bottom ( c on top / t on bottom ) and the opposite , respectively . ( a uniform stress , without a gradient , is sufficient for t0 equilibrium , figure 5 ( a ) . ) for completeness , the shear stress equivalent of is included in figure 5 , but as generally done in the literature , it is henceforth ignored . as noted above , figures 24 and ( 1 ) ) also apply exactly to a plated fractured mandible ( figure 6 ( a ) ) . however , the system that is equivalent to a specific set of + , , and ( figure 4 ) is provided by the loads ( hu , vu , mu , hl , vl , ml , , and ) identified in the fbd of the plated fractured segment in figure 6 ( b ) not the distributed bone stresses at the imaginary section ( figures 1 and 5 ) . h ( ) , v ( ) , and m ( ) are the unknown forces and moments acting within the upper and lower plates directly overlying the bone fracture , figure 6 ( b ) . and are representative of the normal ( perpendicular ) and shear contact forces , respectively , on the fractured bone surface if the two segments touch . ( according to basic friction theory , the maximum , max = , where is the coefficient of friction between bones . this is likely to influence the results of experimental studies in which the mandible analogue plastic has a different than bone . ) similar to the derivation of ( 1 ) ) , three independent simultaneous equations of static equilibrium , based on the fbd in figure 6 ( b ) , can be obtained by summing forces in the vertical ( 2 ) and horizontal ( 3 ) directions and by summing moments ( ( 4 ) about the tooth contact point ( 2 ) ty + + vu + vl = 0 , ( 3 ) tx + huhl = 0 , ( 4 ) duhuvu + mudlhlvl + ml = 0 . because there are fewer independent equations than unknown forces and moments ( only tx and ty are known ) , this ( statically indeterminate ) problem can not be solved using only the principles of static equilibrium . fortunately , solving the problem is not a goal . equations ( 2 ) ( 4 ) serve as explicit evidence of the complexity of plating biomechanics . as consequence of loa position ( figure 3 ) , t1 produces a counterclockwise ( ccw ) moment ( rotation ) about the circle ; t0 does not cause a rotation ; t2 , t3 , and t4 produce clockwise ( cw ) rotations . for the equilibrium of the intact or fractured mandible , these moments , and t 's horizontal and vertical components , must be opposed by the internal loads , , and , respectively , figures 2 ( b ) and 4 and ( 1 ) ) . in the intact mandible , , , and are expressed as equivalent stress distributions , figure 5 . the sums , according to the superposition principle , of those individual stress distributions ( excluding the - associated shear stress ) yield the net longitudinal tension / compression stress gradients shown in figure 7 . ( the result in figure 7 ( d ) is identical to that depicted in figure 1 ( a ) . ) in a plated mandible , the load system that is equivalent to , and is supplied by the loads on the plates and by the contacts between bone fragments . but even a simplified plated assembly ( figure 6 ) is far too intricate to solve with the methods of basic static equilibrium . equations ( 1 ) ( 4 ) clearly indicate the complex relationships between what is known / given and what is unknown . three - dimensional ( 3d ) numerical and experimental models often lead to questions about the prevailing lever - based ( tot / cob ) stress distribution dogma . however , those previous criticisms involve the location of occlusal forces ; the focus of this paper is on the direction of those forces . specifically , the lever - based two - dimensional ( 2d ) model , figure 1 , consists of one force component direction ( vertical ) and one moment component direction ( perpendicular to the page by the right - hand rule ) . the model in figure 2 , the basis for the presented analysis , adds the horizontal force component . this is the most general 2d model that is possible , and it is used to demonstrate serious deficiencies in the lever method without having to resort to the complexities of a 3d approach . for convenience , and / or perhaps because of the lever model legacy , studies have generally been limited to occlusal forces in one ( usually vertical , t3 ) direction . ( in some experimental setups , the occlusal plane is slightly canted , so with a vertical force , the effect is similar to t4 . ) but there is no reason to believe that a bolus of food would necessarily elicit a vertical , or any particular , occlusal force direction . if , instead , crown - crown contact is assumed , then the vertical force assumption restricts analyses solely to frictionless flat - plane or edge - to - edge occlusions . this study is framed in the context of crown - crown contacts , so the specified contact angle ( i.e. , cusp incline angulation or incisal guidance ) generally defines a nonvertical orientation of the occlusal force . some readers may prefer to attribute nonvertical occlusal forces to the interactions of muscle activity with the presence of a bolus of food . in either case , there is no compelling justification for the vertical occlusal force simplification , and as demonstrated , occlusal force direction is a critical determinant of the mechanical environment , , , and , within a mandible . the fbd in figure 3 ( b ) can serve the same purpose as the fbd in figure 2 ( b ) . however , the former is presented to emphasize that without the ( entirely superfluous ) mandible outline , this is actually a mundane static equilibrium problem in which a force , t , is being applied at a point located in a specified ( by and ) position relative to another point , , where the reactions , and are of interest . therefore , for this aspect of the analysis , the only things that matter are the direction of t 's loa and its position relative to ( i.e. , distance from ) . for specific quantitative values of , , and , the magnitude of t would also be needed . but for the qualitative analysis , the relative magnitudes of , , and are sufficient , and because this is a linear model , these relative magnitudes do not change with changes in t magnitude . another purpose for presenting figure 3 ( b ) as an alternative is to illustrate that the human mandible drawing in figure 2 ( b ) could easily be replaced with a nonhuman mandible , a machine part , and so forth . without any effects on , , and . the 5 occlusal forces , t04 , but instead of a continuum of directions , it is more practical to consider categories of force directions defined by the positions of their loa 's relative to , combined with the directions of their horizontal components . for example , whenever the loa of a force passes through , generically represented by t0 , the results presented herein for t0 apply . naturally , the angulation of t0 ( defined by and ) would be different for incisal versus molar contact , nonetheless , qualitatively , the stress distributions would be identical . this concept is already being taken for granted with t3 , because the stress distribution in figure 1 is not specified for any particular contact location . t2 's loa is bounded by t3 and t0 , shaded region in figure 5 ( c ) , so the associated stress distribution can be seen to morph , left to right in figure 7 ( c ) , from the tot / cob of t3 ( figure 7 ( d ) ) to the complete compression of t0 , ( figure 7 ( a ) ) . similar trends , but with less defined endpoints , occur with t1 and t4 because their loa 's are bound only on one side by t0 and t3 , respectively . the stress distribution within the body of the mandible , there is a decreasing tension gradient from the gingival height , and near the mid - level , there is a reversal to an increasing gradient of compression toward the inferior border . this tension on top compression on bottom ( tot / cob ) stress distribution is consistent with the inherent vertical occlusal force of the lever . but in reality , in general , there must also be a nonzero horizontal bite force component , figure 3 , whenever inclined planes ( cusps ) contact each other . andas demonstrated , its presence has the potential to profoundly alter the stress distribution within the mandible from the generally accepted tot / cob ( figures 1 , 5 ( d ) , and 7 ( d ) ) to , as an example , exactly the opposite ( figure 7 ( b ) , left ) . the depictions of the relative magnitudes of the stress distributions in figures 5 and 7 are not drawn to scale because the mathematical complexities of the governing equations , necessary for quantitative results , are being circumvented and because such detail would be unnecessarily obfuscating . serendipitously , the simplifications are perfectly suited to the mathematics - minimized approach of this paper , because the critical nuances of figure 7 can be examined without resorting to rigorous mathematics . if t acts through the circle , t0 , then the longitudinal stress in the body of the mandible is entirely a uniform compression , figures 5 ( a ) and 7 ( a ) . ( as illustrated in figure 4 ( a ) , t0 requires that = 0 for equilibrium , hence the uniform stress . ) that , of course , is contrary to the tot / cob lever - based stress distribution , figures 1 and 7 ( d ) . the sums of the 1 associated uniform compression ( c ) and the cw 1 associated c t gradients of t1 , figures 4 ( b ) and 5 ( b ) , can combine to produce 3 different net stress distribution patterns , figure 7 ( b ) . because both 1 and 1 are associated with compression in the top part of the mandible ( c and c , respectively ) , there is no doubt that the top part will be in compression . in the bottom part of the mandible , 1 is associated with compression ( c ) , but 1 is associated with tension ( t ) . thus , depending on the relative magnitudes of c and t , the net longitudinal stress in the bottom part of the mandible can be tensile , zero or compressive ( left , middle , and right , respectively , in figure 7 ( b ) ) . to determine which of the three stress patterns reflects the actual stress , the governing beam equations would have to be solved . but for the present purposes , it suffices simply to note that all 3 potential t1 results are at variance with the lever 's tot / cob stress distribution . t 2 ( figures 4 ( c ) and 5 ( c ) ) , like t1 , produces a uniform compression consistent with 2 , but because 2 is ccw , its associated gradient is t c. so , when these 2 longitudinal stress distributions are superimposed , figure 7 ( c ) , it is certain that the bottom part of the mandible is in compression , but depending on the position of t2 's loa within the shaded region in figure 5 ( c ) , the top part can be in tension , stress - free , or in compression . more specifically , as t2 approaches vertical , its longitudinal stress distribution ( figure 7 ( c ) , left ) looks more - and - more like the ( vertical ) t3 - associated stress ( figure 7 ( d ) ) . as t2 's direction approaches t0 , its stress distribution , figure 7 ( c ) right , starts to resemble the t0 produced stress , figure 7 ( a ) . t 3 ( the lever replica , figures 4 ( d ) and 5 ( d ) ) is vertical , so there is no 3 equivalent stress . its tot / cob stress distribution , figures 1 and 7 ( d ) , is entirely the equivalent of the ccw 3 . andfinally , t4 ( figures 4 ( e ) and 5 ( e ) ) is different from the others , because the 4 equivalent stress is a uniform tension . combined with the ccw 4 's t c gradient , the top portion of the mandible will be in tension , but the bottom portion can be in tension , stress - free , or in compression , figure 7 ( e ) . thus , of the 11 possibilities depicted in figure 7 , only 3 ( left in figure 7 ( c ) , figure 7 ( d ) , and right in figure 7 ( e ) ) are in concert with the lever 's tot / cob longitudinal stress distribution . ( oral surgeons are intimately familiar with the biomechanical principles at work here . during extraction , the tooth can be considered as a vertical analogy to the mandible that is loaded as in figures 5 ( b ) and 5 ( c ) . when the tooth is luxated back and forth , are generated , and to reduce the associated tensile longitudinal stress in the root , a compressive ( intrusive ) force is applied concurrently , thereby reducing or eliminating the tension , analogous to the right sides of figures 7 ( b ) and 7 ( c ) turned 90 degrees . a lever model of extraction would not account for the critical intrusive force component ( ) that prevents tension - induced root fracture . ) for the plated mandible , figure 6 ( b ) , there are an insufficient number of equations to solve for all unknowns . this statically indeterminate problem can be numerically modeled , typically with fea , but whatever the solution may be , it must satisfy ( 2 ) ( 4 ) . thus , as evidenced by the equations , everything is intertwined in a complex manner . furthermore , if the fracture were at an angle , or if the plates were not horizontal or parallel , then ( 2 ) ( 4 ) would be further complicated by trigonometric functions , different values for the upper and lower plates , and so on . this is clearly not a problem that is amenable to commonsensical analysis , especially with intuition that is based on the nonapplicable lever paradigm of the intact mandible . consider plates , ab and cd , secured with single screws at their ends , figure 8 ( a ) . abdc , figure 8 ( b ) , forms a 4 - bar linkage in which b and d are constrained to move along arcs of circles that are centered at a and c , respectively . therefore , if for any reason b moves to b , d must move to d , because the bone dimension , bd ( = bd ) , remains unchanged . thus , with virtually any occlusal force , these plate constraints dictate a downward displacement with a ccw rotation of the anterior segment from bd to bd , hence the inferior border distraction . when the concepts and terminology from the intact mandible are applied to this outcome , it is ascribed to compression on top and tension on the bottom . but , in fact , the top plate , ab , is in tension and cd , the bottom plate , is in compression , and except for the compression at the bone - bone contact on top , there is no tension ( which would be impossible anyway at a fracture ) or compression in bone anywhere along the fracture . thus , contrary to popular notion , the enlarged gap at the inferior border is not caused by tension ; on the contrary , it is caused by compression in cd . there are , of course , many other 4 - bar linkage configurations that would produce different interfragmentary displacements . because plate ab , as the example , is secured by single screws at its ends , it can only transmit pure compression or tension it is a 2 - force member . ( if , in figure 6 , the top plate was affixed with single screws at both ends , then hu 0 , but vu = mu = 0 . ) accounting for friction ( between bone / plate or screw / plate ) , or even just one additional screw , would immensely complicate the problem by necessitating the inclusion of the shear forces ( i.e. , vu 0 in figure 6 ( b ) ) and the bending moments ( i.e. , mu 0 in figure 6 ( b ) ) in the plates . the relative bone movements would then depend mostly on plate deformations caused by those forces and moments . clinically , however , it would be advantageous to conceptualize plate - imposed constraints in terms of linkages rather than the intact mandible paradigm . ( neither is realistic , but in this context , the intact idealization is entirely irrelevant and misleading . ) although the focus is on plates , similar discussions would pertain to other modes of fixation . for example , in a sagittal split osteotomy , the transverse shear stresses within the bicortical screws and bone - bone friction produce the , , and equivalent system . as with plating , a mandible in function , intact or plated , is a complicated 3d statically indeterminate structure that is subjected to the complex interactions of variable anatomy and highly changeable muscle and occlusal forces . and , for many reasons , obvious and subtle , a plated fractured mandible is an entirely different and more complex load bearing structure than an intact mandible . if for no reason other than the impossibility of tensile stresses acting across a break , the tot / cob stress distributions illustrated in figures 1 , 5 , and 7 are not possible at , or near , a fracture . according to saint venant 's principle , these stress distributions can be present only at some distance away from plated areas . nevertheless , the figure 1 tot / cob representations are often invoked explicitly or implicitly in matters of fracture repairs . although the demonstrated analytical method is inadequate for the solution of these problems , it is the best instructional approach , and it is conceptually far more realistic than the ubiquitous lever model . this analysis is appropriate for conceptualizing mandibular biomechanics and for casting doubt on the status quo . in conclusion , ( 1 ) the lever - based tension - on - top / compression - on - bottom ( tot / cob ) stress gradient should not be assumed in the intact mandible . it is only one of several possible stress distributions that depend on the direction of the occlusal force and the relative location of the section in question . ( 2 ) internal forces ( and ) and moment ( ) are necessary for the equilibrium of all mandibles , intact or fixed . beyond sharing , , and , there are no valid comparisons between intact , plated , screwed , and so forth mandibles . ( 3 ) the stress distribution within an intact mandible should not be extrapolated to a plated , or otherwise stabilized , mandible .\noutput:\n" }, { "from": "agent", "value": "objectives . the purpose of this analytical study was to examine and critique the engineering foundations of commonly accepted biomechanical principles of mandible fracture repair . materials and methods . basic principles of static equilibrium were applied to intact and plated mandibles , but instead of the traditional lever forces , the mandibles were subjected to more realistic occlusal forces . results . these loading conditions produced stress distributions within the intact mandible that were very different and more complex than the customary lever - based gradient . the analyses also demonstrated the entirely different mechanical environments within intact and plated mandibles . conclusions . because the loading and geometry of the lever - idealized mandible is incomplete , the associated widely accepted bone stress distribution ( tension on top and compression on the bottom ) should not be assumed . furthermore , the stress gradients within the bone of an intact mandible should not be extrapolated to the mechanical environment within the plated regions of a fractured mandible ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: it is likely that over half of the patients examined each day may have enlarged lymph nodes in the head and neck region . cervical lymphadenopathy may be the only clinical finding or one of the several nonspecific findings , and the discovery of enlarged cervical lymph nodes will often raise the spectrum of serious illness . the common causes of lymphadenitis are malignancies , bacterial , viral , protozoal , fungal infections ; autoimmune disorders ; drugs such as phenytoin and certain vaccines . it is therefore important to differentiate the patients with serious illness from many with benign lymphadenopathy . the advent of ultrasonography ( us ) has revolutionized the field of oral and maxillofacial radiology . us is the name given to high - frequency sound waves over 20,000 hz , inaudible to humans . it is a noninvasive , nonionizing imaging technique which enables to see the anatomical structures with the use of ultrasound waves and provides valuable diagnostic information with a high degree of diagnostic accuracy . the conventional ultrasound uses a gray scale to detect the various anatomical structures of the body and study their morphological characteristics and is capable of detecting vessels as small as those found in lymph nodes . continuous advancement in the field of imaging leads to increase sensitivity of these imaging modalities . cdus is based on the principle of doppler effect which is responsible for the variation in the pitch of sound waves . cdus is used to evaluate and determine the presence of vascularity , direction , and velocity of blood flow within the ultrasound image of the tissue . it may also be used for a variety of conditions such as evaluation of swellings of the neck including lymph node , thyroid and salivary glands , detection of vascular structures and vascularity of masses , and assessment of space infections . the distribution and direction of flowing bloodare shown as a two - dimensional image in which velocities are distinguished with different colors . cdus instrument uses transducer probes consisting of two piezoelectric elements , one to transmit ultrasound by converting the electric signal into ultrasound energy and other to receive returning echoes backscattered from the moving blood cells . vascularity of lymph nodes is directly related to the actual pathology present within the lymph node . blood vessel morphology in malignant or metastatic nodes is usually deranged as internal nodal architecture is destroyed by neoplastic infiltration . inflammatory or benign nodes have dilated intranodal vascular alteration due to local humoral agents . the pattern of vascular flow in the lymph nodes aids in differentiating benign from malignant lymphadenopathy . considering this , one is determined to accept the various advantages of cdus examination and its importance over conventional methods of clinical examination and fine needle aspiration . conducted a study to evaluate the efficacy of cdus in the diagnosis of cervical lymphadenopathy . however , there have been very few studies to determine the efficacy of cdus in the diagnosis of cervical lymphadenopathy . hence , this study was carried out to differentiate benign and malignant cervical lymph nodes using cdus examination . the aims of this study was to differentiate benign / inflammatory / reactive lymph nodes from malignant / metastatic nodes and examine the status of clinically nonsignificant ( deep ) lymph nodes by means of cdus , and also to correlate between cdus findings and cytological or histopathological findings of cervical lymph nodes and determine the value of cdus to minimize the need of fine needle aspiration cytology ( fnac ) . the study was carried out at the department of oral medicine and radiology , institute of dental sciences , bareilly , keshlata hospital , bareilly , india , and sai hospital , bareilly , india . patients with clinically suspected cervical lymphadenopathy were selected in the study after obtaining an informed consent . twenty - five patients were selected from the outpatient department and were divided into two main groups : group i : thirteen patients were clinically suspected to be having malignant cervical lymphadenopathy . group ii : twelve patients who were clinically suspected to be having benign cervical lymphadenopathy . the clinical examination of the lymph nodes was done for their location , number , size , shape , consistency , and fixity to decide whether the palpable node is benign or malignant . in cases of oral cancer , stony hard / indurated lymph nodes were considered malignant , whereas soft or firm nodes were considered benign . if the node was fixed it was considered malignant , implying that the tumor cells have broken through the capsules of the lymph node or that necrosis and inflammation have produced peri - nodular scarring and adhesions , but this feature will usually be absent except with the most aggressive or advanced tumors . all the patients were subjected for cdus and histopathological examination ( by means of fnac ) . for cdus evaluation , sonosite , diagnostic ultrasound system , model micromax , bothell ( usa ) , a high - frequency linear transducer of 6 - 13 mhz was used . settings for cdus were standardized and the wall filters , pulse repetition frequency , color gain , and focusing depth were set upon automatic mode . the technique used was continuous transverse and saggital sweep covering entire neck on both sides . the examination was started with a transverse scan of the submental area , followed with a sequence from the submandibular area to parotid area to upper , middle , and lower cervical area to supraclavicular fossa to the posterior triangle . the minimal and maximal axial diameters of the nodes were measured and their ratios were calculated . the presence or absence of wide echogenic hilum , calcification , and necrosis of the nodethen , the color doppler examination was performed and sonographic features studied were distribution , number , size and shape of nodes , echogenic hilum , internal architecture , ancillary features such as matting of nodes and color doppler flow pattern . the distribution of lymph nodes was classified into eight anatomic areas similar to the ones described by hajek et al . , 1986 . all sonographically detectable lymph nodes were first scanned in the longitudinal plane ( l ) and the transverse plane ( t ) to measure the size of each lymph node l / t ratio is considered . the presence or absence of hilar structurethe vascular pattern and displacement of vascularity of the lymph nodes were assessed by cdus . after the color doppler , flow in the lymph node was stabilized or freezed and the color flow pattern was determined . the vascular pattern of the enlarged lymph nodes with long - axis diameters 10 mm was classified into the following four groups according to cdus findings : central - flow signals branching radially from the center and the signals are not the periphery of the nodesperipheral - flow signals along the periphery of the lymph nodes , with branches perforating the periphery of the node and not arising from the hilar vesselsmixed - presence of central and peripheral flow signalsno flow or apparently avascular - absence of vascular signals within the lymph nodes . central - flow signals branching radially from the center and the signals are not the periphery of the nodes peripheral - flow signals along the periphery of the lymph nodes , with branches perforating the periphery of the node and not arising from the hilar vessels mixed - presence of central and peripheral flow signals no flow or apparently avascular - absence of vascular signals within the lymph nodes . fnac or biopsy and its histopathological appearance were considered for its correlation with cdus features of all lymph nodes of the same group . only cases confirmed with clinically malignant / metastatic nodeswere biopsied whereas clinically confirmed / suspected benign / reactive lymph nodes were confirmed cytologicaly with fine needle aspiration . following this , comparative study was done between clinical features , cdus features , and cytological / histological features of enlarged cervical lymph nodes . data were collected and results were statistically analyzed using student 's t - test test and chi - square test . twenty - five patients with clinically suspected cervical lymphadenopathy were examined , 15 patients were male and 10 patients were female with age range 10 - 60 years . of 25 patients , 13 patients were clinically suspected to have malignant cervical lymphadenopathy whereas remaining 12 patients were suspected to have benign cervical lymphadenopathy ( 3 patients : primary extraoral malignancy , 10 patients : unknown primary malignancy , and 12 patients : lymphadenitis due to chronic specific or nonspecific infection ) . initially , 53 cervical lymph nodes were detected in 25 patients using the clinical criteria , of which 38 were suspected to be clinically benign lymph nodes and 15 were suspected clinically malignant . following this , the same patients were evaluated with cdus and compared with cytological / histological features of enlarged cervical lymph nodes . when the clinical findings of 38 benign lymph nodes were compared with cdus , the result was 33 benign and 5 malignant lymph nodes . of clinically diagnosed 15 malignant lymph nodes , 13 confirmed malignant and 2 were benign . this suggests that the findings of cdus are close to histopathologic findings with 2 false positive results in cdus . while performing cdus of palpable 53 lymph nodes , additional 27 lymph nodes were discovered as they were located in clinically inaccessible region . following cdus evaluation of these lymph nodes , total number of lymph nodes included in the study were 80 ( 53 + 27 ) , all were evaluated by fnac / histopathological examination . spectrum of distribution of cervical lymphadenopathy for total 80 lymph nodes was done and it was found that left and right submandibular nodes were most commonly affected ( 61 of 80 ) . submental lymph nodes involvement was observed in 3 reactive and 1 malignant lymph nodes and supraclavicular group was involved only in benign lymphadenopathy . the smallest lymph node detected by cdus examination measured 7 mm 3 mm , proved benign and the largest lymph node was 46 mm 42 mm , proved malignant . the mean short axis diameters of malignant and benign nodes in centimeters were 1.891.06 and 0.830.54 , respectively , and mean long axis diameters of malignant nodes and benign nodes were 1.630.91 and 1.230.50 , respectively . it was found that the malignant nodes were significantly greater in short axis diameter than other group nodes whereas reactive nodes had the smallest short axis diameter . there was a statistically significant difference between the mean values of the short axis ( p 0.001 ) and statistically significant difference between the long axis ( p 0.01 ) among the benign and malignant cervical lymph nodes [ table 1 ] . comparison of mean values of size , shape , hilum , and color doppler flow in benign and malignant groups of lymph nodes ( 80 nodes ) twenty - six nodes were round in shape and 54 lymph nodes were oval / elliptical in shape . of 54 oval / elliptical nodes , 52 were benign / reactive whereas only 2 elliptical nodes were malignant . among 26 round nodes , 19 were malignant and 7 were found to be benign . the difference in shape was statistically significant with p 0.001 [ figures 1 , 2 and table 1 ] . gray scale color doppler ultrasound image of oval - shaped reactive / benign lymph node . hilum was present in 55 of 80 nodes whereas it was absent in 25 lymph nodes . of these 55 nodes with hilum presence , 54 nodes were histopathologically proven as benign nodes and 1 node as malignant . it had been observed that the presence of echogenic hilum within an enlarged lymph node can be considered a sign of its benign nature . of 25 nodes with absent hilum , 20 were histopathologically proven as malignant whereas 5 as benign nodes . of these 71 nodes , 20 lymph nodes showed central color flow signal and 29 nodes showed hilar signal which are suggestive of benign nature , and all 49 nodes ( 20 + 29 ) were confirmed as benign on histopathologic findings . eighteen lymph nodes showed peripheral flow , of which 16 nodes were malignant and 2 were benign lymph nodes by histopathology . nine lymph nodes showed no flow , of these 8 were ( reactive ) benign and 1 node was malignant by histopathology . in this study , central flow for benign nodes and peripheral flow for malignant nodes were highly significant parameters ( p 0.0001 ) [ figures 3 and 4 , table 1 ] . color doppler ultrasound image of malignant lymph node showing mixed / peripheral vascularity . in this study , clinically suspected benign lymph nodes = 38 ; in cdus examination total benign lymph nodes = 33 + 24 + 2 = 59 ( 33 : of 38 clinically suspected benign lymph nodes ; 24 : of additional 27 nodes ; 2 : clinically malignant were found to be benign ) . histopathological confirmation of 59 cdus confirmed benign nodes revealed 56 lymph nodes to be histopathologically benign and 3 as malignant ( false positive + 3 ) . benign lymph nodes were characterized by the presence of neutrophils and immature lymphocytes within the sinuses and medullary cords whereas malignant nodes showing increased nucleocytoplasmic ratio , hyperchromatism , cellular pleomorphism , and dyskeratosis , thus suggestive of squamous cell carcinoma histologically [ figures 5 and 6 ] . clinically suspected malignant lymph nodes = 15 ; in cdus examination total malignant nodes = 13 + 3 + 5 = 21 ( 13 : of 15 clinically suspected malignant lymph nodes ; 3 : of additional 27 nodes ; 5 : clinically benign were found to be malignant ) . histopathological confirmation of 21 cdus suspected malignant nodes revealed 21 lymph nodes to be malignant and 1 as benign . on clinical examination , the sensitivity and specificity for benign nodes were 94.29 % and 72.22 % , respectively . on cdus examination , the sensitivity and specificity were 98.25 % and 86.96 % , respectively , for benign nodes . the comparison between histopathologically proven benign and malignant lymph nodes with clinically suspected and cdus evaluated lymph nodes revealed that cdus evaluation is highly significant ( p 0.001 by z - test ) . the smallest lymph node detected by cdus examination measured 7 mm 3 mm , proved benign and the largest lymph node was 46 mm 42 mm , proved malignant . the mean short axis diameters of malignant and benign nodes in centimeters were 1.891.06 and 0.830.54 , respectively , and mean long axis diameters of malignant nodes and benign nodes were 1.630.91 and 1.230.50 , respectively . it was found that the malignant nodes were significantly greater in short axis diameter than other group nodes whereas reactive nodes had the smallest short axis diameter . there was a statistically significant difference between the mean values of the short axis ( p 0.001 ) and statistically significant difference between the long axis ( p 0.01 ) among the benign and malignant cervical lymph nodes [ table 1 ] . comparison of mean values of size , shape , hilum , and color doppler flow in benign and malignant groups of lymph nodes ( 80 nodes ) twenty - six nodes were round in shape and 54 lymph nodes were oval / elliptical in shape . of 54 oval / elliptical nodes , 52 were benign / reactive whereas only 2 elliptical nodes were malignant . among 26 round nodes , 19 were malignant and 7 were found to be benign . the difference in shape was statistically significant with p 0.001 [ figures 1 , 2 and table 1 ] . gray scale color doppler ultrasound image of oval - shaped reactive / benign lymph node . hilum was present in 55 of 80 nodes whereas it was absent in 25 lymph nodes . of these 55 nodes with hilum presence , 54 nodes were histopathologically proven as benign nodes and 1 node as malignant . it had been observed that the presence of echogenic hilum within an enlarged lymph node can be considered a sign of its benign nature . of 25 nodes with absent hilum , 20 were histopathologically proven as malignant whereas 5 as benign nodes . cdus detected color flow signals in 71 of 80 lymph nodes . of these 71 nodes , 20 lymph nodes showed central color flow signal and 29 nodes showed hilar signal which are suggestive of benign nature , and all 49 nodes ( 20 + 29 ) were confirmed as benign on histopathologic findings . eighteen lymph nodes showed peripheral flow , of which 16 nodes were malignant and 2 were benign lymph nodes by histopathology . nine lymph nodes showed no flow , of these 8 were ( reactive ) benign and 1 node was malignant by histopathology . in this study , central flow for benign nodes and peripheral flow for malignant nodes were highly significant parameters ( p 0.0001 ) [ figures 3 and 4 , table 1 ] . in this study , a total of 53 lymph nodes were examined by clinical examination . clinically suspected benign lymph nodes = 38 ; in cdus examination total benign lymph nodes = 33 + 24 + 2 = 59 ( 33 : of 38 clinically suspected benign lymph nodes ; 24 : of additional 27 nodes ; 2 : clinically malignant were found to be benign ) . histopathological confirmation of 59 cdus confirmed benign nodes revealed 56 lymph nodes to be histopathologically benign and 3 as malignant ( false positive + 3 ) . benign lymph nodes were characterized by the presence of neutrophils and immature lymphocytes within the sinuses and medullary cords whereas malignant nodes showing increased nucleocytoplasmic ratio , hyperchromatism , cellular pleomorphism , and dyskeratosis , thus suggestive of squamous cell carcinoma histologically [ figures 5 and 6 ] . clinically suspected malignant lymph nodes = 15 ; in cdus examination total malignant nodes = 13 + 3 + 5 = 21 ( 13 : of 15 clinically suspected malignant lymph nodes ; 3 : of additional 27 nodes ; 5 : clinically benign were found to be malignant ) . histopathological confirmation of 21 cdus suspected malignant nodes revealed 21 lymph nodes to be malignant and 1 as benign . on clinical examination , the sensitivity and specificity for benign nodes were 94.29 % and 72.22 % , respectively . the comparison between histopathologically proven benign and malignant lymph nodes with clinically suspected and cdus evaluated lymph nodes revealed that cdus evaluation is highly significant ( p 0.001 by z - test ) . in this study , of total 80 lymph nodes which were evaluated , only 53 lymph nodes could be detected by clinical examination . the results of our study are consistent with bruneton et al . , who demonstrated the unquestionable value of ultrasound in detection of subclinical nodes . in this study , the clinical examination yielded false negative results of 5 , and similar results were found by hain where clinical palpation was found inaccurate with the false negative rates of 5 - 44 % . our study showed statistically significant difference between mean values of short axis diameter and long axis diameter of the malignant and benign nodes . malignant nodes showed greater short axis diameter and long axis diameter than the benign nodes and similar observations were made by yusa et al . overall reliability of shape to differentiate between benign and malignant lymph nodes was statistically significant in our study . hence , the shape appears to be significant in distinguishing between the various abnormal nodes . the diagnostic accuracy of the presence of hilum ( which shows the benign nature of the node ) was highly significant . fifty - five nodes of 80 displayed the presence of hilum whereas 25 nodes displayed its absence . sato et al . stated that rarely metastatic nodes have an intranodalhyperechogenic appearance similar to that of the echogenic / line or hilus as seen in 1 malignant node in our study . the cause of this hyperechogenic appearance in the metastatic nodes is considered ischemic degeneration or extensive keratinization , which occurs within metastatic nodes . the hilum was absent in 25 nodes , of which 20 were histopathologically proven as malignant whereas 5 as benign . this could be due to diffuse adipose infiltration in the node and also seen in the nodes of elderly or immune - compromised patients . the overall reliability of hilum criteria showed sensitivity and specificity of 93.22 % and 100.00 % , respectively , which is comparable to the study by michael ying et al . cdus detected color flow signals in 71 lymph nodes whereas 9 nodes did not show any signals . a total 49 of lymph nodes displayed central / hilar color flow signal , which is suggestive of benign / reactive nature due to increase in vessel diameter and blood flow . eighteen lymph nodes displayed peripheral flow of blood , of which 16 were malignant and 2 were reactive nodes . destruction of hilar vascularity by tumor cells in malignant nodes may be due to induction of vascular supply from the peripheral preexisting vessels or from vessels in the perinodal soft tissue . mixed flow of the metastatic node may be due to the fact that as the tumor replaces the node , the preexisting nodal vessels may be proliferated and transformed into feeding vessels by tumor angiogenesis , resulting in central aberrant nodal vessels . nine lymph nodes did not show any flow , 8 nodes were histopathologically proven to be benign , and 1 as malignant . absent flow signals may be due to the relatively low number of backscattering erythrocytes in the peripheral vessels decreasing the signal intensity . in our study , comparative findings between clinical , cdus , and histopathologic evaluation show that the overall reliability of cdus examination for lymphadenopathy of 80 cervical lymph nodes is highly significant with the sensitivity and specificity of 98.25 % and 86.96 % , respectively , for benign nodes . for malignant nodes , the results of our study are consistent with that of dangore et al . and dangore - khasbage et al . cdus is a reliable and reproducible method which helps in differentiation between reactive and malignant changes of superficial lymph nodes using findings of intranodalangio - architecture . dangore - khasbage et al . recommended the use of cdus in every patient of primary oral cancer before surgical treatment so that reactive and mitotic nodes can be differentiated . in this study , an additional 27 lymph nodes were detected by cdus examination apart from clinically palpable 53 nodes . thus , it can be concluded that cdus evaluation is superior over clinical examination for detection of cervical lymphadenopathy before proceeding for surgeries of primary and secondaries in the neck . within the limitations of this study , it can be concluded that cdus examination is a valuable and a highly specific diagnostic tool in differentiating cervical lymphadenopathy over clinical and histopathological examination . the authors of this manuscript declare that they have no conflicts of interest , real or perceived , financial or non - financial in this article . the authors of this manuscript declare that they have no conflicts of interest , real or perceived , financial or non - financial in this article .\noutput:\n" }, { "from": "agent", "value": "background : to evaluate the efficacy of color doppler ultrasound ( cdus ) in differentiating benign and malignant cervical lymph nodes by detecting differences in blood flow patterns.materials and methods : in this cross - sectional prospective study , 25 untreated patients with clinical evidence of cervical lymphadenopathy were evaluated . cdus was performed for 80 cervical lymph nodes . the gray scale parameters of the lymph node and intranodal perfusion sites were the key cdus features used to differentiate between reactive and metastatic lymph nodes . histopathological confirmations were obtained and compared with the results of cdus.results : initially , 53 cervical lymph nodes were evaluated by clinical examination . twenty - seven additional lymph nodes ( 53 + 27 = 80 ) were discovered by cdus evaluation . gray scale parameters for lymph nodes such as size of lymph node , shape of lymph node , and presence or absence of hilum revealed highly significant results ( p < 0.0001 ) . color doppler flow signals revealed that central / hilar flow was characteristic for benign nodes whereas peripheral / mixed flow was characteristic for malignant nodes , the findings were highly significant ( p < 0.0001 ) . gray scale and color doppler features are used to differentiate benign and malignant nodes.conclusion : within the limitations of this study , cdus evaluation was found to be highly significant with a high sensitivity and specificity over clinical evaluation cdus examination provides a prospect to reduce the need for biopsy / fine needle aspiration cytology in reactive nodes ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: , several research groups studied this subject , and one of the largest studies involved 65 patients . over a four - week period , subjects were administered either a chocolate bar or a placebo bar , and no difference in acne severity was seen . this belief was reflected in textbooks , patient information brochures , and the medical literature . however , later researchers noted methodological flaws in the original study , including the fact that the placebo bar contained a similar total sugar and fat content as the chocolate bar . a randomized controlled trial of australian males demonstrated significant improvement of acne severity after 12 weeks of adherence to a low - glycemic - load diet , compared to the high - glycemic - load diet control group . follow - up studies have noted that switching to a low glycemic diet led to better insulin sensitivity , lower androgen bioavailability , and altered skin sebum production . it is not known , however , what role individual differences , duration of dietary changes , and other factors play in this association . therefore , studies such as di landro et al. s have documented the opposing view that weekly consumption of cakes , sweets , and chocolate foods high in glycemic load was not associated with a higher risk of acne . in addition , researchers examining the link between dairy consumption and acne have noted some association . studies have demonstrated this link in three separate populations , though in each instance the correlation results were considered relatively weak . closer evaluation of this link revealed that only skim milk showed a statistically significant correlation with acne , perhaps due to its increased processing and / or decreased estrogen content in comparison to whole milk . a number of other dietary factors have been studied for their potential role in improving acne . for example , an inverse relationship has been found between acne severity and consumption of omega -3-rich fish with the mechanism of action postulated as omega -3-mediated reduction of inflammatory acne . while some promising results have been noted from in vitro or animal studies , studies in humansare limited , and each of these dietary factors requires further investigation before recommendations may be made to patients . these include foods or supplements containing vitamin a , omega - 3 fatty acids , zinc , antioxidants , and fiber . . given that the scientific literature on this topic is rapidly evolving , it would be expected that patients might receive conflicting advice . patients have long held certain beliefs about diet and acne , including the common perception that fried , greasy foods would lead to oily skin and acne . however , it is not known whether patients are aware of the research findings that support a link between specific dietary factors and acne . patients seek out and receive medical information from multiple sources , and current patient beliefs about diet and acne are not known . this study was designed to be an initial , exploratory survey study of current patient perceptions about the link between diet and acne . the aim was to identify common beliefs , misconceptions , and current information sources regarding the connection between diet and acne . as in other exploratory survey studies , these findings would help indicate directions for future research and would be of benefit to clinicians when counseling patients . patients presenting to an academic dermatology clinic for the treatment of acne or acne scarring were asked if they wished to participate in a survey study about the link between diet and acne . if so , they completed a self - administered questionnaire prior to the physician visit . subjects were asked to classify their acne from mild to severe , based on their personal perception of the disease s impact . demographic data , such as age , gender , weight , height , and education level , was included in the questionnaire . of the 50 questionnaires administered , 49 were completed in full and were included in the analysis . the mean age of patients was 28.5 years ( range , 16 to 45 years ) ; 38 were female and 11 were male . three respondents had an under - weight bmi of less than 18.5 ; 30 respondents had a normal bmi between 18.524.9 ; 13 respondents were overweight with bmi 2529.9 ; and 2 respondents qualified as obese with bmi greater than 30.0 . a majority , 45 of 49 respondents , was educated at the college level ( table ia ) . respondents reported the following acne severity distribution : 13 patients had mild acne , 1 patient had mild - moderate , 29 patients had moderate , 1 had moderate - severe , and 5 had severe acne ( table ib ) . among our populationonly 3 of 38 ( 8 % ) female patients and 1 of 11 ( 9 % ) male patients believed that diet had no effect on acne . of female patients , 30 of 38 ( 81 % ) patients believed that diet affected acne either somewhat , a lot , or was the complete cause of acne . among male patients , a majority , 35 of 49 patients ( 71 % ) , had changed their diets in order to help their acne ( table iia ) . thirteen of the 35 ( 37 % ) tried dietary changes before medications , compared to the 14 patients that first attempted medications . of those 14 , 9 tried over - the - counter medications first ( 25 % ) and 5 tried prescription first ( 14 % ) . four patients tried a combination of dietary changes with prescription medications ( 11 % ) ; 2 combined dietary changes with over - the - counter medications ( 6 % ) ; and the remaining tried a combination of all three or a combination of over - the - counter and prescription medications ( table iib ) . the dietary item most frequently implicated to worsen acne was fried , greasy foods ( 71 % ) . other responses included chocolate ( 53 % ) , followed by dairy products ( 47 % ) . this was followed by soda drinks ( 35 % ) , caffeine ( 27 % ) , and refined carbohydrates ( 27 % ) . amongthe named categories of dietary items believed to aggravate acne , sugar was named by the lowest percentage of respondents ( 16 % ) . the category listed by most respondents as helping acne was that of vitamin a ( 41 % ) , followed by antioxidants ( 33 % ) , fish / omega - 3s ( 29 % ) , and zinc ( 27 % ) ( table iiib ) . twenty percent reported acne improvement with less fried or greasy foods , followed by 14 % reporting improvement with less dairy products and 14 % reporting improvement with less refined carbohydrates ( table iiic ) . the most widely utilized source of information was a google search ( 49 % ) , followed by dermatologist ( 43 % ) and then family members and tv ( tied at 41 % ) . medical websites , specifically sites such as webmd or that of the american academy of dermatology , were used by 31 % , while primary care physician ( pcp ) was used by 18 % ( table iva ) . respondents were split evenly between those satisfied with the information provided on their sources ( 49 % ) and those not satisfied ( 51 % ) ( table ivb ) . this trend was found in almost all categories of sources listed except for : dermatologist , family members , medical websites , and pcp . of the 24 out of 49 satisfied respondents , 18 ( 75 % ) marked dermatologist as one of their sources of diet and acne information . not satisfied with their information , only 3 ( 12 % ) had marked dermatologist as a source of information . similarly , 10 of 24 satisfied respondents ( 42 % ) marked medical websites as one of their sources , whereas 5 of 25 unsatisfied respondents ( 20 % ) reported the use of medical websites . these findings reverse when looking at family members as a source of information . among unsatisfied respondents ,52 % had marked family members as a source of diet and acne education , as compared to 29 % of satisfied respondents ( table ivc ) . in fact , only 5 % of female patients and only 9 % of male patients believed that diet had no effect on acne . a majority of respondents , 71 % , had changed their diet in order to help their acne . of the foods listed , the highest percentage of respondents ( 71 % ) chose a category that patients have historically described as an acne trigger food : that of fried / greasy foods . this is a popular , long - held belief , as anecdotally , patients sometimes make the connection between greasy foods and increased oil production on the face . the strongest research evidence , however , supports a link between a high glycemic index ( gi ) diet and acne . while fried or greasy foods may contribute to a high gi diet , so would sugar , soda drinks , and refined carbohydrates . these categories , however , were listed by much lower percentages of respondents ( 16 % , 35 % , and 27 % , respectively ) . this is an important point to emphasize to our patients . while fried , greasy foods are a concern , so are a number of other foods . as dermatologists , we should be emphasizing that even innocuous foods , such as white bread , pasta , and other refined carbohydrates , when part of an overall high gi diet , may worsen acne . chocolate as a dietary factor triggering acne is also a long - held belief , and studies evaluating its role in acne were performed in the 1960s . at this time , though , there is no evidence that a factor specific to chocolate can trigger acne . rather , research points to its sugar content and contribution to a high gi diet as a possible trigger . ideally , then , chocolate , sugar , and refined carbohydrates would have similar ratings by patients , as they may all contribute to a high gi index diet . in fact , while 53 % reported chocolate as a possible trigger food , only 16 % reported sugar as a potential trigger . while chocolate bars may serve as an acne trigger , sugar and other sugary foods are just as concerning . of note , although some studies have shown a link to dairy , less than half ( 47 % ) of our respondents believed that dairy products could aggravate acne . an interesting finding is that a significant proportion of respondents believed that certain foods or supplements could help acne . this may be due to reports of high - dose vitamin a therapy used in the past as acne therapy , and the fact that acne medications such as tretinoin and isotretinoin are related to vitamin a. our survey did not distinguish between standard vitamin a supplements and high - dose supplementation , and therefore it is not known whether a belief in vitamin a therapy extends to standard supplement dosing . when vitamin a is removed from the analysis , the highest category becomes antioxidants ( 33 % ) , followed by fish or omega - 3s ( 29 % ) , zinc ( 27 % ) , and dietary fiber ( 20 % ) . for each of these nutrients , while some promising results in the treatment of acne have been noted from in vitro or animal studies , studies in humans are limited . at this point , these can not be recommended routinely , but their use by patients can not be dismissed entirely either . in conclusion , while there is limited research performed in the area of foods or supplements that may help in the treatment of acne , many of our respondents believe they may help . in an era of rapid dissemination of information , patients are sometimes made aware of promising findings from small studies . this highlights the need for dermatologists to stay abreast of the latest dietary findings , and in particular not to dismiss these out of hand . in addition , dermatologists must be cognizant of the fact that a significant proportion of patients may believe that certain foods or supplements have the ability to combat acne , and therefore must be able to provide information on the limited evidence that exists to support their use . in order to disseminate accurate , evidence - based informationin our survey study , less than half ( 43 % ) relied on dermatologists for information . the remaining respondents turned to a variety of sources , including the internet ( google search and medical websites ) , mass media ( magazines , television , and newspaper ) , and personal relationships ( mainly family members and friends ) . the sources of information utilized by patients have changed markedly . in a survey study from 1999 , general information on acne was obtained most frequently from family physicians ( 71 % ) . in our surveythe mass media continues to play a role in providing health information . in the 1999 survey study , magazines and television were utilized by 44 % each . in our survey study , magazines were utilized by 27 % , and television was utilized by 41 % of respondents . the most notable change has been the rise of the internet as a tool for health information . our respondents utilized google most frequently ( 49 % ) as a source of information , with medical websites utilized by 31 % . in the 1999 study , it is clear that the internet has had a significant impact on health information - seeking behavior . what is less clear is how physicians should respond to this change when educating our patients . in this study , more patients obtained information from the internet than from their primary care physician or their dermatologist . however , a significant number of those satisfied with their diet and acne education had marked pcp ( 25 % ) or dermatologist ( 75 % ) as one of their sources of information . conversely , the majority of respondents not satisfied with their information source did not mark dermatologist or pcp as a source of information ( 86 % ) . thus , with so many acne patients making dietary changes , and many of them turning to the internet for information to guide them , it becomes even more imperative that physicians be educated on the topic of acne and diet and be able to serve as an authoritative source . for those patients who seek further information , we also need to be able to refer patients to credible sources of online health information , with specific recommendations for high - quality , up - to - date health information websites . our study suggests that education from physicians and medical websites is correlated with higher satisfaction in patients . physicians must also counsel patients on the drawbacks of utilizing search engines for health information , as opposed to utilizing well - regarded medical websites . if relying on a google search , patients may be directed to commercial sites or sites containing inaccurate information . finally , we need to ensure , as a profession , that health education materials are easily available on the internet and that such information is accurate , evidence - based , free from commercial bias , and reflective of the most current research findings . due to the design of this exploratory survey study , patients were recruited from the population of patients seeking treatment for acne at a single academic institution . most , 31 of 49 , were of normal weight ( 63 % ) , with only 15 of 49 ( 31 % ) categorized as overweight or obese . population , in which 69 % are overweight or obese ; 29 % are college educated ; and 51 % are female . another weakness of the study may be the lack of a quantitative definition of acne severity . in the past , multiple quantitative classification systems have been proposed , though these methods have been inconsistently accurate in the clinical setting . given the variable expressions of acne , as well as its psychosocial factors difficult to quantitate , a more important assessment of severity may be the patient s perception of its impact , which we elicited in the study . in fact , only 5 % of female patients and only 9 % of male patients believed that diet had no effect on acne . a majority of respondents , 71 % , had changed their diet in order to help their acne . of the foods listed , the highest percentage of respondents ( 71 % ) chose a category that patients have historically described as an acne trigger food : that of fried / greasy foods . this is a popular , long - held belief , as anecdotally , patients sometimes make the connection between greasy foods and increased oil production on the face . the strongest research evidence , however , supports a link between a high glycemic index ( gi ) diet and acne . while fried or greasy foods may contribute to a high gi diet , so would sugar , soda drinks , and refined carbohydrates . these categories , however , were listed by much lower percentages of respondents ( 16 % , 35 % , and 27 % , respectively ) . this is an important point to emphasize to our patients . while fried , greasy foods are a concern , so are a number of other foods . as dermatologists , we should be emphasizing that even innocuous foods , such as white bread , pasta , and other refined carbohydrates , when part of an overall high gi diet , may worsen acne . chocolate as a dietary factor triggering acne is also a long - held belief , and studies evaluating its role in acne were performed in the 1960s . at this time , though , there is no evidence that a factor specific to chocolate can trigger acne . rather , research points to its sugar content and contribution to a high gi diet as a possible trigger . ideally , then , chocolate , sugar , and refined carbohydrates would have similar ratings by patients , as they may all contribute to a high gi index diet . in fact , while 53 % reported chocolate as a possible trigger food , only 16 % reported sugar as a potential trigger . while chocolate bars may serve as an acne trigger , sugar and other sugary foods are just as concerning . of note , although some studies have shown a link to dairy , less than half ( 47 % ) of our respondents believed that dairy products could aggravate acne . an interesting finding is that a significant proportion of respondents believed that certain foods or supplements could help acne . this may be due to reports of high - dose vitamin a therapy used in the past as acne therapy , and the fact that acne medications such as tretinoin and isotretinoin are related to vitamin a. our survey did not distinguish between standard vitamin a supplements and high - dose supplementation , and therefore it is not known whether a belief in vitamin a therapy extends to standard supplement dosing . when vitamin a is removed from the analysis , the highest category becomes antioxidants ( 33 % ) , followed by fish or omega - 3s ( 29 % ) , zinc ( 27 % ) , and dietary fiber ( 20 % ) . for each of these nutrients , while some promising results in the treatment of acne have been noted from in vitro or animal studies , studies in humans are limited . at this point , these can not be recommended routinely , but their use by patients can not be dismissed entirely either . in conclusion , while there is limited research performed in the area of foods or supplements that may help in the treatment of acne , many of our respondents believe they may help . in an era of rapid dissemination of information , patients are sometimes made aware of promising findings from small studies . this highlights the need for dermatologists to stay abreast of the latest dietary findings , and in particular not to dismiss these out of hand . in addition , dermatologists must be cognizant of the fact that a significant proportion of patients may believe that certain foods or supplements have the ability to combat acne , and therefore must be able to provide information on the limited evidence that exists to support their use . in order to disseminate accurate , evidence - based information , we must understand what sources patients utilize for medical information . in our survey study , the remaining respondents turned to a variety of sources , including the internet ( google search and medical websites ) , mass media ( magazines , television , and newspaper ) , and personal relationships ( mainly family members and friends ) . the sources of information utilized by patients have changed markedly . in a survey study from 1999 , general information on acne was obtained most frequently from family physicians ( 71 % ) . in our surveythe mass media continues to play a role in providing health information . in the 1999 survey study , magazines and television were utilized by 44 % each . in our survey study , magazines were utilized by 27 % , and television was utilized by 41 % of respondents . the most notable change has been the rise of the internet as a tool for health information . our respondents utilized google most frequently ( 49 % ) as a source of information , with medical websites utilized by 31 % . in the 1999 study , it is clear that the internet has had a significant impact on health information - seeking behavior . what is less clear is how physicians should respond to this change when educating our patients . in this study , more patients obtained information from the internet than from their primary care physician or their dermatologist . however , a significant number of those satisfied with their diet and acne education had marked pcp ( 25 % ) or dermatologist ( 75 % ) as one of their sources of information . conversely , the majority of respondents not satisfied with their information source did not mark dermatologist or pcp as a source of information ( 86 % ) . thus , with so many acne patients making dietary changes , and many of them turning to the internet for information to guide them , it becomes even more imperative that physicians be educated on the topic of acne and diet and be able to serve as an authoritative source . for those patients who seek further information , we also need to be able to refer patients to credible sources of online health information , with specific recommendations for high - quality , up - to - date health information websites . our study suggests that education from physicians and medical websites is correlated with higher satisfaction in patients . physicians must also counsel patients on the drawbacks of utilizing search engines for health information , as opposed to utilizing well - regarded medical websites . if relying on a google search , patients may be directed to commercial sites or sites containing inaccurate information . finally , we need to ensure , as a profession , that health education materials are easily available on the internet and that such information is accurate , evidence - based , free from commercial bias , and reflective of the most current research findings . due to the design of this exploratory survey study , patients were recruited from the population of patients seeking treatment for acne at a single academic institution . most , 31 of 49 , were of normal weight ( 63 % ) , with only 15 of 49 ( 31 % ) categorized as overweight or obese . population , in which 69 % are overweight or obese ; 29 % are college educated ; and 51 % are female . another weakness of the study may be the lack of a quantitative definition of acne severity . in the past , multiple quantitative classification systems have been proposed , though these methods have been inconsistently accurate in the clinical setting . given the variable expressions of acne , as well as its psychosocial factors difficult to quantitate , a more important assessment of severity may be the patient s perception of its impact , which we elicited in the study . this survey study was designed to explore patient beliefs regarding the link between diet and acne . in this small sample , this belief impacted behavior , as the majority had changed their diets in order to improve their acne . due to the study design , the results from this patient sample can not be applied to the general population . however , even in this highly educated patient population , there was a persistence of long - held beliefs that certain foods may serve as acne triggers ( i.e. , fried or greasy foods and chocolate ) and less recognition of the foods that research has identified as potential triggers ( i.e. , sugars , refined carbohydrates , and dairy ) . many respondents also reported a belief that certain foods or supplements could help acne , an area with some promising preliminary results but one that requires further investigation before any conclusions may be drawn . especially given the multiplicity of information sources utilized by patients , as well as the ongoing research in this area and subsequent evolving recommendations , dermatologists must serve as an authoritative information source . dermatologists must be able to provide a balanced overview of this topic to their patients and be able to direct patients to credible , balanced sources for additional dietary change recommendations . these findings indicate a need for further study on the best practices in providing health information , especially as medical recommendations are evolving . our population was highly educated , and the majority was of normal weight . further research in this area must target a more diverse population . even within this skewed population , however , we noted widely conflicting beliefs among acne patients . there is a clear need for easily available , evidence - based , and up - to - date information on the link between diet and acne .\noutput:\n" }, { "from": "agent", "value": "background : in the past , medical literature reflected that diet was not a proven cause of acne . however , studies in recent years have substantiated a link between certain dietary factors and acne . it is unclear whether patients are aware of recent research findings.objectives : acne patients were surveyed to explore beliefs regarding the link between diet and acne , to determine whether these beliefs translated into behavior change and to identify health information sources.patients / methods : upon institutional review board ( irb ) approval , surveys were administered to 50 acne patients at an academic dermatology clinic in 2014 , with 49 completed in full and included in this analysis.results : ninety - two percent of respondents believed that diet could affect acne . seventy - one percent attempted to change their diet to improve acne . seventy - one percent believed acne to be caused by fried or greasy foods , although chocolate ( 53 % ) , dairy ( 47 % ) , and soda drinks ( 35 % ) were highly implicated . patients obtained information from google searches ( 49 % ) , dermatologists ( 43 % ) , family members and tv ( 41 % each ) , and medical websites ( 31 % ) . conclusions : in this exploratory study , patients reported utilizing a diversity of information sources , a majority from the internet . in those surveyed , there was a persistence of long - held belief that fried / greasy foods and chocolate may serve as acne triggers , and less belief in trigger foods supported by recent research , including refined carbohydrates and sugar . given the multiplicity of beliefs and utilized sources among acne patients in our survey , there is a need to establish up - to - date and reliable methods to educate patients on diet and acne ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: advances in health care , such as the discovery of diagnostic techniques and therapeutic methods effective in curing or controlling disease , can lead to increasing life expectancy . with these advances , elderly people are expected to maintain their functional capacity so that they remain autonomous and independent as long as possible . for such , it is of great importance to introduce health programs aimed at the prevention , early diagnosis , and treatment of chronic diseases and disabilities that arise over the years .123456 as we age , there is a tendency toward chronic degenerative diseases that compromise the physical and mental functions of the individuals and ultimately lead to difficulties in daily activities or disability of the elderly to perform them .123456 currently it is said that health is measured through the ability of the individual to remain functionally independent and not due to the presence or absence of disease ; the constraints brought by disability can cause more significant problems than the disease itself , as it can make patients dependent on their family and caregivers and can compromise their well - being and quality of life .78910 the concepts for functional capacity are very similar . it is related to the degree of preservation of the individual to perform activities of daily living ( adl ) and instrumental activities of daily living ( iadl ) , so they can live independently .1112 functional capacity is evaluated in two aspects : basic adl ( i.e. , the individual 's ability to feed , bathe , and dress without help ) and iadl , which evaluate more complex tasks , often related to individuals ' social engagement , such as shopping , answering the telephone , and using means of transportation .13 hearing loss is one of the most frequent and disabling sensory changes , not only negatively affecting the elderly socially and emotionally but also affecting their quality of life .14151617 it is believed that hearing loss is strongly associated with loss of functional capacity ,1819 which explains the importance of this study . thus , the present study aimed to examine whether the use of hearing aids improves functional capacity for iadl for hearing - impaired middle - aged and elderly individuals . the population comprised 17 individuals , of both genders , between 58 and 96 years old ( mean 77.110.4 years ) . inclusion criteria were : individuals from 40 years old ( which is considered the beginning of middle age ) ,20 new users of hearing aids with bilateral hearing loss , and participation in all phases of the research . exclusion criteria were : not signing the informed consent form ( icf ) and history of cognitive , neurologic , and / or psychiatric disorders . for participants who met the inclusion criteria , we presented the objectives of the research , and all participants signed icf . first , the individuals were submitted to audiological evaluation , with pure tone audiometry performed in a soundproof booth and with tone thresholds by air ( from 250 to 8,000 hz ) and bone ( 500 to 4,000 hz ) measured using an interacoustics audiometer model ad - 229 , denmark . to classify the degree of hearing loss , we used the average of the hearing thresholds by air at 500 , 1,000 , 2,000 , and 4,000 hz , according to the world health organization .21 mean values between 10 dbhl ( decibel hearing level ) and 25 dbhl indicate that the person has normal hearing thresholds ; between 26 and 40 dbhl , mild hearing loss ; between 41 and 60 dbhl , moderate hearing loss ; between 61 and 80 dbhl , severe hearing loss ; above 81 dbhl , profound hearing loss . for this study we considered the mean of the better ear . in the first stage of evaluation , the procedures were as follows : we applied social history developed ( anamnesis ) especially for this study , containing demographic and hearing history . furthermore , we used a questionnaire created by lawton and brody ( 1969 ) ,22 which measured the ability of the individual to develop iadl . through this , we evaluated the functional capacity ( i.e. , the degree of independence of these individuals in everyday activities , such as using the telephone , preparing meals , managing finances , commuting by means of public transportation , cleaning the house , going shopping , among others ) . these issues were assessed using nine items where the patient had three response options : the maximum achievable score in the evaluation was 27 points , which corresponds to maximum independence , and the minimum achievable score was 9 points , meaning maximum dependency . after completing the questionnaire , hearing aid ( s ) indicated for each subject were selected and tested . all subjects were fitted with hearing aid ( s ) with digital technology , with nonlinear amplification . nine ( 52.9 % ) participants used bilateral hearing aids and 8 ( 47.1 % ) used a single one . the second stage of the research was initiated 3 months after beginning usage of hearing aid ( s ) ; the patient was contacted by telephone and asked to attend a meeting reviewing their hearing aid ( s ) . at the hearing center , the patient answered a questionnaire evaluating functional capacity . in the third stage , which began 6 months after beginning usage of hearing aid ( s ) the project was submitted to and approved by the research and ethics committee of the institution ( no . the rights regarding confidentiality , anonymity , and withdrawal of participation without prejudice to any treatments that were being performed were assured . data were both quantitative and descriptive statistically analyzed . to evaluate the performance of individuals for the task at each stage , the total score was used to assess the overall performance of the individual ( considering performance on all tasks ) . to compare the total score between steps and descriptive statistics , analysis of variance for repeated measuresthe sample consisted of 17 subjects , 13 women ( 76.5 % ) and 4 men ( 23.5 % ) . although the inclusion criteria defined that the minimum age would be 40 years , the sample consisted of subjects aged between 58 and 96 years ( mean 77.110.4 years ) . the other characteristics are shown in table 1 . with regard to education , most individuals had incomplete primary education ( 76.5 % ) . of the population ,76.4 % had moderate hearing loss , 11.8 % presented mild hearing loss , and 11.8 % , severe hearing loss . nine ( 52.9 % ) participants use bilateral hearing aids and 8 ( 47.1 % ) , monoaural aids . data on the ability of the elderly to perform iadl for the three stages of the research are described in table 2 . table 3 shows the total score obtained by participants in the three stages of the research ; a significant increase in the degree of independence of individuals was found comparing the first and third stages ( p = 0.015 ) . note : p = 0.015 from stage 1 to stage 3 . table 4 shows the evolution in the use of the telephone in the three stages of the research . there was a significant difference ( p = 0.011 ) between at least two of the three stages in the degree of independence in using the telephone . although it was not possible to identify the difference in multiple comparison tests , the lowest observed p value ( p = 0.123 ) indicates that this difference is probably between the level of independence of the first and third stage , with the third stage being the higher level of independence . note : p = 0.011 from stage 1 to stage 3 . we observed among the participants of the study a higher ratio of women ( 76.5 % ) , which did not differ from other studies .623 although the scientific literature shows that men are more affected by hearing loss ,24 data show that women seek more health services .25 in addition , data from the 2010 population census in the country and the literature in the field of gerontology show that the majority of brazilian individuals in the age range studied are women .262728 this fact is known asfeminization of aging and is corroborated by previous studies ,623 and it should be taken into consideration for appraisal , diagnosis , and treatment of hearing services , which should be prepared to meet , in most cases , female subjects with specific characteristics , needs , and requirements . a low level of education was expected by the researchers because many participants were elderly . this population , according to the 2010 census , has low levels of education because it had no opportunity to attend school in the life stage considered appropriate .262930 furthermore , it should be stressed again that many of the sample were women . thus , until a few years ago , few women attended schools , and many who abandoned their studies as they finished the initial grades to devote themselves to learning housework . the degree of hearing loss observed in most cases is compatible with that caused by aging . previous studies indicate that the majority of the elderly had mild to moderate hearing loss , which corroborates the results of this research and was expected by researchers due to the age range of the sample components .3132 although all subjects presented bilateral hearing loss , approximately half of the individuals ( 47.1 % ) acquired only one hearing aid . this could be explained by the fact that the purchase was made by the subjects of research , using their own financial resources . thus , in many cases , although there was an indication of binaural fitting of hearing aids , financial issues , aesthetics , manual dexterity , auditory processing , or asymmetrical hearing loss led to monaural fitting .33 this is quite common when analyzing the purchase of hearing aids in private hearing centers , which has been reported in other studies .3435 as previously described , the functional capacity is strongly related to the presence of some diseases and disabilities . studies demonstrate that there is an association between hearing loss and the lack of autonomy of patients .11036 thus , we expected a low autonomy of the individuals to perform iadl in the first stage of the study , an evolution occurring after fitting ( steps 2 and 3 ) . the analysis of data contained in table 2 , however , showed that compared with the ability to carry out iadl between the three stages , the only task in which there was significant change was the ability to use the telephone ( p = 0.011 ) . the change was so evident that it was able to give a significant difference in scores between the three stages of the study ( table 3 ) . most individuals could perform adequately and effectively the investigated iadl , contrary to what was expected by the evaluators because most of the subjects had hearing loss and low levels of education . this finding contradicts other studies , whose results indicated that the low level of education and hearing loss negatively influenced the autonomy of the elderly .161037 most of the subjects had hearing loss from mild to moderate in the better ear , which can make communication difficult through the use of the phone . to carry out the other activities , however , the individual may resort to communication strategies , such as lipreading and requesting repetition of phrases . in addition , some activities investigated by the instrument , such as shopping , ironing , controlling remedies and finance , for example , are more closely related to cognitive and motor activity and may not be influenced by the presence of mild to moderate hearing loss . data in table 4 confirm the change observed between the three evaluations with regard to the use of the phone . the analysis suggests that the change in the behavior of the subjects occurred between steps 1 and 3 of the research . the greater autonomy in the use of the telephone does not confirm previous studies that reported on new hearing aid users whose main complaint was difficulty using the telephone .383940 the studies cited , however , are prior to 2010 , before hearing aid resources facilitating the use of telephone were available . moreover , it should be pointed out that in addition to these resources , all subjects in the research sample received specific guidelines from the pathologist responsible for selecting and fitting hearing aids . in the fitting process , individuals and their families should be targeted , and the use of telephone and other auxiliary equipment should be one of the items addressed .41 thus , considering the test scores ( especially with regard to the use of the telephone ) and the time of use of hearing aids by the subjects , it appears that there was a gradual improvement in auditory skills and speech recognition due to the new use of amplification .42 these findings corroborate other studies describing the acclimatization period starting from week 6 of amplification .4344 in 2002 , 134 elderly in the first year of adjustment of hearing prosthesis showed more significant changes between the first and sixth months of use .44 thus , we can confirm the importance of the intervention with the use of hearing aids in middle - aged adults and seniors . the analysis of the results showed that the use of hearing aid ( s ) improved functional capacity for iadl in the individuals evaluated , especially in using the telephone .\noutput:\n" }, { "from": "agent", "value": "introduction hearing loss is among the sensory changes strongly associated with loss of functional capacity . objective it aims to determine whether the use of hearing aid contributes to the improvement of instrumental activities of daily living ( iadl ) for middle aged and elderly hearing - impaired individuals . methods this is a descriptive , longitudinal , and interventional study . we evaluated 17 subjects , 13 ( 76.5 % ) female , aged between 58 and 96 years old ( mean 77.1 10.4 years ) . all were new users of hearing aids . evaluation included social history , pure tone audiometry , and scale of iadl developed by lawton and brody . the subjects were presented daily life situations and were expected to respond if they could do them without assistance ( 3 points ) , partially assisted ( 2 points ) or if they were unable to perform them ( 1 point ) . iadl was applied before the use of hearing aids adaptation and after a three - and six - month period of use . results data analysis revealed that before the use of hearing aids the average score obtained by the subjects was 22.94 4.04 points . three months after beginning the use the average score was 23.29 4.12 and after six months the average score was 23.71 3.69 points . statistical analysis revealed a significant difference between scores obtained before the use of hearing aids and six months post - fitting ( p = 0.015 * ) conclusion the use of hearing aids among the subjects evaluated promoted positive changes in performing iadl , especially to using the telephone ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: vertebrate vision is initiated by the activation of the phototransduction cascade in rod and cone photoreceptor cells of the retina when photons are absorbed by the ubiquitous chromophore 11 - cis - retinal and converted to its all - trans - isomer . continued function of photoreceptors requires removal of the all - trans - retinal and resupply with chromophore . the classical visual cycle regeneration pathway takes place mostly in the retinal pigment epithelium ( rpe ) and uses a key enzyme , retinoid isomerase , to supply 11 - cis - retinal for both rod and cone photoreceptors using all - trans - retinoid substrates either recycled from photoreceptors as vision byproducts or originating from the choroidal blood supply . the rpe65 protein is the indispensable retinoid isomerase of the canonical rpe visual cycle and it is highly and preferentially expressed in the rpe cells . mutations in the rpe65 gene cause leber 's congenital amaurosis ( lca ) , a hereditary retinal degeneration most often transmitted with an autosomal recessive pattern of inheritance . lca is a blinding disease with an estimated prevalence of about 1 : 80,000 ; mutations in more than a dozen genes can cause lca and rpe65 - lca is thought to represent about 6 % of all lca cases . retinal degeneration 12 ( rd12 ) mouse model is an lca animal model with a nonfunctional rpe65 protein because of a mutation in the rpe65 gene . the absence of a functional rpe65 protein interferes with the visual cycle and leads to substantial reduction in 11 - cis - retinal levels and accumulation of retinyl esters in rpe , which gradually exerts a toxic effect on the retinal photoreceptors and severely affects the visual function . however , histologically rd12 mice show predominantly cone degeneration while rods appear to be intact with normal expression of rhodopsin and rod transducin at early ages , indicating that it might be the lack of the chromophore 11 - cis - retinal that leads to a nonrecordable rod erg response at the early stages of the disease . rpe65 - associated lca recently gained recognition due to the apparent early success achieved in three clinical trials using gene therapy and recombinant adenoassociated virus ( aav ) vectors . nine lca patients received a subretinal injection with an aav vector and demonstrated partially restored local visual function , with local visual sensitivity improved by ~ 50-fold in cones and ~ 63000-fold in rods . however , this reconstituted vision cycle was not completely normal but showed slow rod kinetics , resulting in prolonged course of dark - adaptation and decreased visual ability after photobleaching , indicating that the recycling of the retinal chromophore was still abnormal . currently , most studies are focused on changes in the rpe65 protein , but that may be insufficient to explain this problem . there are several proteins implicated in visual chromophore recycling , but currently there are no reports of changes in these visual cycle - associated proteins as a result of gene therapy . the present study aims to explore the changes in these proteins after rpe65 gene delivery , using rd12 mice , an lca model caused by a mutation in the rpe65 gene . in our previous work , we used the same model to explore the proteomic differences occurring in the retina after gene therapy using two - dimensional electrophoresis ( 2 - de ) and mass spectrometry . in this study , we collected tissue samples containing rpe ( retina - pigment epithelium - choroid - sclera complex , rpe / ch / sc ) in rd12 mice at p42 , 4 weeks after aav subretinal injection . this enabled us to do quantified proteomic study of visual cycle - associated proteins in the rpe , using a more accurate and sensitive technique in protein quantification , the isobaric tagging for relative and absolute protein quantification ( itraq ) . three of them , ralbp - 1 , rbp - 1 , and irbp , were differentially expressed before and after gene therapy . twelve rd12 mice ( rpe65 rd12 or b6 ( a ) - rpe65 rd12 / j ) were purchased from the jackson laboratory ( bar harbor , me ) , and 6 age - matched c57bl / 6j mice were obtained from animal center of wenzhou medical university . they were kept in a 12 - hour light -12-hour dark cycle with an ambient light intensity of 18 lux . all experiments were approved by the wenzhou medical university 's institutional review board and were conducted in accordance with the arvo statement for the use of animals in ophthalmic and vision research . three groups were assigned in the experiment : the treated right eyes of rd12 mice were set as the treated rd12 group , the contralateral untreated left eyes were untreated rd12 group , and both eyes of age - matched wide - type c57bl / 6j mice were the normal control group . the scaav5 - smcba - hrpe65 vector as used in previous studies was used to deliver rpe65 gene in rd12 mice , with the same method of subretinal injections at age p14 . a 30.5 - gauge disposable needle was used to make a small incision in the cornea within the pupil area . then a 33 - gauge , unbeveled , blunt needle mounted on a 5 l syringe ( hamilton co. , reno , nv ) was introduced through the corneal incision to reach the subretinal space in the inferior central region , avoiding touching the lens and penetrating the neuroretina . one microliter of vector suspension ( 110 genome containing particles / ml ) containing 1 % fluorescein was injected slowly in the subretinal space in the right eye of rd12 mice . the injected retinal area was visualized by fluorescein positive subretinal blebs demarking the retinal detachment and more than 95 % retinal detachment indicates successful injection . after injection , 1 % atropine eye drops and 0.3 % tobramycin - dexamethasone eye ointment ( alcon laboratories inc . , animals with any complications , including iris - cornea adhesion , iris or retinal hemorrhage , and lens injury , were excluded from the experiment . full - field ergs were recorded with a custom - built ganzfeld dome connecting to a computer based system ( q450sc uv ; roland consult , wiesbaden , germany ) . six led stimuli intensities of 35 , 25 , 15 , 5 , 5 , and 15 cds / m were applied under scotopic conditions , and 2 white led stimuli intensities ( 1 cds / m , 1.96 cds / m ) with a background of 30 cd / m were used under photopic conditions . after dark adaption overnight , scotopic erg was always recorded between 8 am and 11 am , followed by photopic erg . all testing was performed in a climate - controlled , electrically isolated dark room under dim red light illumination . systemic anesthesia was achieved by the intraperitoneal administration of a mixture of ketamine ( 72 mg / kg ) and xylazine ( 4 mg / kg ) and 0.5 % proparacaine hydrochloride used to ensure full corneal anesthesia . a small amount of 2.5 % methylcellulose gel was applied to the eye , and a special ag / agcl wire loop electrode was placed over the cornea as an active electrode . body temperature was maintained by placing the animals on a 37c warming pad during the experiment . after retinas were dissected from enucleated eyes , the rpe / ch / sc complex was extracted , homogenated , and then mixed with 100 l ice - cold lysis buffer ( 7 m urea , 2 m thiourea , 4 % chaps , 2 m tbp , 20 mm tris - hcl , 1 % ief buffer , 1 mm pmsf , 100 g / ml dnase , and 100 g / ml rnase ) . the supernatant was obtained after centrifugation at 15,000 rpm for 15 minutes at 4c . equal protein amount ( 100 g ) in each group sample was applied to conduct the subsequent itraq . following the itraq protocol ( applied biosystems , foster city , ca ) , each 100 g protein was digested with 0.2 ml of a 50 g / ml trypsin ( promega , madison , wi , usa ) at 37c for 16 h. peptides were labeled with isobaric tags 118 ( normal control group ) , 119 ( untreated rd12 group ) , and 121 ( treated rd12 group ) and incubated at room temperature for 2 h. then the labeled mixtures were dried by vacuum centrifugation , desalted with sep - pak vac c18 cartridge 1 cm / 50 mg ( waters , usa ) , and fractionated using a shimazulc - 20ab hplc pump system ( shimazu , japan ) connected to a strong cation exchange ( scx ) column ( polysulfoethyl column , 2.1 mm 100 mm , 5 m , 200 , the nest group , inc . scx separation was performed using a linear binary gradient of 045 % buffer b ( 350 mm kcl , 10 mm kh2po4 in 25 % acn , ph 2.6 ) in buffer a ( 10 mm kh2po4 in 25 % acn , ph2 .6 ) at a flow rate of 200 l / min for 90 min , and 30 fractions were collected every 3 min . each fraction was dried down and redissolved in buffer c ( 5 % ( v / v ) acetonitrile and 0.1 % formic acid solution ) , and the fractions with high kcl concentration were desalted with pepclean c - 18 spin column ( pierce , usa ) . each fraction was resuspended in buffer a ( 2 % acn , 0.1 % fa ) and centrifuged at 20,000 g for 10 min . in each fraction , the final concentration of peptides was approximately 0.25 g / l . using an autosampler , 20 l of supernatantwas loaded onto a 2 cm c18 trap column ( inner diameter 200 m ) on a shimadzu lc - 20ad nanohplc . peptides were eluted onto a resolving 10 cm analytical c18 column ( inner diameter 75 m ) that was assembled in - house . the samples were loaded at 15 l / min for 4 min and eluted with a 44 min gradient at 400 nl / min from 2 to 35 % b ( 98 % acn , 0.1 % fa ) , followed by a 2 min linear gradient to 80 % b , maintenance at 80 % b for 4 min , and finally a return to 2 % b over 1 min . the peptides were subjected to nanoelectrospray ionization followed by tandem mass spectrometry ( ms / ms ) in an ltq orbitrapvelos ( thermo ) coupled in - line to the hplc . peptides were selected for ms / ms using the high - energy collision dissociation ( hcd ) operating mode with a normalized collision energy setting of 45 % . ion fragments were detected in the ltq . a data - dependent procedure that alternated between one ms scan followed by eight ms / ms scanswas applied for the eight most abundant precursor ions above a threshold ion count of 5,000 in the ms survey scan with the following dynamic exclusion settings : repeat counts : 2 ; repeat duration : 30 s ; and exclusion duration : 120 s. the applied electrospray voltage was 1.5 kv . automatic gain control ( agc ) was used to prevent overfilling of the ion trap ; 110 ions were accumulated in the ion trap to generate hcd spectra . for ms scans , the resulting ms / ms spectra were searched against the international protein index ( ipi ) mouse sequence databases ( version 3.45 ) with mascot software ( matrix science , london , uk ; version 2.2 ) . protein identification and quantification for itraq experiments were carried out using the proteinpilot software v3 .0 ( applied biosystems , usa ) . the paragon algorithm in proteinpilot software was used as the default search program with trypsin as the digestion agent and cysteine modification of methyl methanethiosulfonate . the search also included the possibility of more than 80 biological modifications and amino acid substitutions of up to two substitutions per peptide using the blosum 62 matrix . only proteins identified with at least 95 % confidence , or a protscore of 1.3 , all proteins that showed significantly altered expression levels went through ingenuity pathway analysis software ( ipa ) for pathway and network analysis . every two samples in each group were mixed in one western blot experiment , which was repeated for three times . protein was extracted with lysis buffer and centrifuged to obtain the supernatant and determine the protein content by bca assay . each of the protein samples ( 30 g ) was subjected to sds - page and then transferred to polyvinylidene difluoride ( pvdf ) membranes ( bio - rad , hercules , ca ) . the membranes were blocked for 1 h at room temperature with 5 % nonfat dried milk in tris - buffered saline containing 0.1 % tween 20 ( tbst , applygen gene technology corp ) . then they were probed overnight with primary anti - ralbp - 1 ( ab166655 , abcam , ma , usa , 1 : 1000 ) and anti - rbp - 1 ( ab154881 , abcam , ma , usa , 1 : 2000 ) , followed by incubation with horse radish peroxidase ( hrp ) conjugated goat anti - mouse igg ( santa cruz biotechnology , santa cruz , ca , 1 : 2500 ) . then they were developed with an enhanced chemiluminescence detection kit ( pierce biotechnology , inc . , rockford , il ) . results for continuous variables with normal distributions are presented as means standard deviations ( sd ) . statistical analyses were conducted with spss 18.0 ( spss , chicago , il , usa ) , and a two - tailed p 0.05 was considered significant . the untreated rd12 eyes showed extremely low or even undetectable a - wave and b - wave peaks under scotopic and photopic conditions , indicating severely affected retinal function . four weeks after aav injection , a - wave amplitude of the treated rd12 eyes increased to 210.8326.70 v ( 40-fold of the untreated rd12 level , p 0.001 ) , close to the 284.5018.95 v of the wild - type mice ( 74.11 % , p = 0.001 ) in scotopic erg with normal peak time ; b - wave amplitude increased to 590.0057.59 v ( 48-fold of the untreated rd12 level , p 0.001 ) , also approaching the 797.6789.59 v of the wild - type mice ( 73.97 % , p = 0.002 ) with normal peak time ( figures 1 ( a ) and 1 ( c ) ) . photopic a - wave amplitude of the treated rd12 eyes improved dramatically to 15.322.96 v ( 4-fold of the untreated rd12 level , p 0.001 ) and was not different from the amplitude recorded from wide - type eyes ( 13.383.43 v , p = 0.363 ) ; b - wave amplitude also improved to 84.5011.99 v ( 5-fold of the untreated rd12 level , p 0.001 ) and was similar to the wide - type level ( 91.1210.62 v , p = 0.377 ) ( figure 1 ( d ) ) . this is in accordance with our previous findings and supports the notion that gene therapy could restore retinal function in this animal model . we used itraq proteomics to identify and quantify proteins 4 weeks after rpe65 gene delivery in rd12 mice , compared with the untreated rd12 and normal control c57bl / 6j mice . a total of 14432 unique peptides were identified , corresponding to a set of 610 proteins with more than 95 % confidence ( protscore 1.3 , global false discovery rate ( fdr ) = 0.21 % ) . of these 610 proteins ,536 were identified with relative quantization , in which 7 were identified as visual cycle - associated proteins including retinaldehyde - binding protein 1 ( ralbp - 1 ) , retinol - binding protein 1 ( rbp - 1 ) , interphotoreceptor retinoid - binding protein ( irbp ) , retinal dehydrogenase 2 ( rdh - 2 ) , retinal dehydrogenase 5 ( rdh - 5 ) , lecithin retinol acyltransferase ( lrat ) , and ezrin - radixin - moesin - binding phosphoprotein 50 ( ebp - 50 ) ( table 1 ) . of these proteins , the expressions of ralbp - 1 , rbp - 1 , and irbp were reduced by at least 0.68-fold in the untreated rd12 mice relative to the pooled sample of wild - type tissues , while the other four proteins ( rdh - 2 , rdh - 5 , lrat , and ebp - 50 ) showed normal levels of expression . in the treated rd12 eyes , ralbp - 1 increased about 6-fold compared to the levels of the untreated rd12 samples , although it was still lower ( 66.1 % ) than the one observed in the samples from wild - type mice . the levels of rbp - 1 were also considerably increased in treated rd12 samples , a 2-fold increase compared to the untreated rd12 levels and 1.5-fold increase compared to the levels in wild - type mice . in contrast , the expression of irbp did not increase on p42 , and the level in the treated mice was slightly lower ( 83.2 % ) compared to the untreated mice ( figure 2 ) . in addition , in the 536 relatively quantified proteins , 91 were downregulated and 71 were upregulated by 1.3-fold in untreated rd12 eyes compared to the wide - type levels ( see supplementary tables 1 ( a ) and 1 ( b ) in supplementary material available online at http://dx.doi.org/10.1155/2015/918473 ) . western blot analysis was performed to validate the changes observed in the differentially expressed visual cycle - related proteins before and after gene therapy . the results confirmed that the expression of ralbp - 1 and rbp - 1 was much weaker in the untreated rd12 eyes and that gene therapy increased their level similar to that in the normal c57bl / 6j mice ( figure 3 ) . gene therapy by subretinal administration of scaav5 - smcba - hrpe65 vector is a safe and effective treatment to rescue rod and cone photoreceptor function in rd12 mice , as demonstrated previously . the current investigation focuses on the changes of the visual cycle - associated proteins in rd12 eyes before and after gene therapy , using the technique of itraq - based 2d lc - ms / ms . three of the seven proteins , ralbp - 1 , rbp - 1 , and irbp , were found to be downregulated in the rpe of rd12 eyes . subretinal delivery of rpe65 by gene therapy demonstrated normalization of the levels of ralbp - 1 and rbp - 1 , while no positive effect was observed on the levels of irbp . visual cycle ( or retinoid cycle ) is the process by which 11 - cis - retinal is regenerated from all - trans - retinal after photoisomerization , and it mainly takes place in the rpe layer . after conversion from all - trans - retinyl ester to 11 - cis - retinol by isomerase , ralbp - 1 acts as an acceptor of 11 - cis - retinol to produce 11 - cis - retinal and fulfill the visual cycle . ralbp - 1 is another essential protein in the isomerization reaction of the visual cycle , and it plays a critical role to sustain normal retinal function and dark adaptation . our results demonstrated that the levels of ralbp - 1 were dramatically reduced in rd12 mice , and rpe65 gene delivery not only regenerated the isomerase rpe65 but also increased the production of ralbp - 1 , leading to visual cycle restoration and normalization of the visual function . the incomplete recovery of ralbp - 1 expression in treated rd12 eyes may help to explain why the dark adaption was still delayed after similar therapy in lca patients . thus , a supplementation of ralbp - 1 protein by certain treatment might be a strategy to solve this problem . irbp is a large glycoprotein synthesized in the photoreceptors and situated in the interphotoreceptor matrix . it functions as a retinoid - transport vehicle to facilitate the exchange of 11 - cis - retinal , 11 - cis - retinol , and all - trans - retinol between the rpe , photoreceptors , and mller cells . despite some histological and electrophysiological changes because of cytotoxic effects of large amounts of free retinoids , the absence of irbp in irbp mice did not cause gross abnormalities in the visual cycle . in this study , the expression of irbp in rd12 mice was decreased , which might be attributed to the negatively affected function of the photoreceptors . rpe65 gene delivery can restore rod and cone function ; however , the production of irbp was not increased and even slightly lower levels were detected compared to pretreatment . one possible explanation for this finding might be that the distribution of irbp could be influenced by the retinal reattachment after temporary detachment caused by subretinal injection . rbp - 1 is localized in the rpe and serves as a chaperone of all - trans - retinol to lrat in the visual cycle . rbp - 1 has been recognized as a pigment epithelium derived factor which supports photoreceptor health and structural integrity . in our results , the production of rbp - 1 was reduced in rd12 mice , suggesting that the rpe function might also be influenced by photoreceptor integrity . gene therapy could increase the expression of rbp - 1 in the rpe substantially , indicating that rbp - 1 could resume its function to transport all - trans - retinol once the process of retinol recycling is recovered . the other four visual circle - associated proteins including lrat , rdh - 2 , rdh - 5 , and ebp - 50 were found to remain at relatively normal expression levels in the rpe of rd12 mice , demonstrating that not all proteins implicated in vision cycle were affected by the lack of rpe65 function . the fate of the visual cycle proteins in lca animal models deserves further investigation since it may reveal unrecognized aspects of the disease process and provide important indications to further improve the visual function in lca patients after gene therapy . one limitation in this study is that only one time point ( p42 ) after gene therapy was tested . the results could be more informative if earlier ( p21 ) and longer time point ( p98 ) analyses were included . besides , the dark - adapted erg seems normal in treated rd12 eyes , so the erg after photobleaching could also be tested to illustrate whether the dark adaption course was delayed only after photobleaching , as happened in lca patients after gene therapy . in conclusion , our study identified and quantified the rpe levels of visual cycle - associated proteins in rd12 mice before and after gene therapy . rpe65 gene delivery restored rpe65 expression and modified the levels of other functional proteins implicated in visual cycle . gene therapy resulted in incomplete recovery of the levels of ralbp - 1 in the rpe of rd12 mice , indicating that this may also occur in lca patients undergoing gene therapy and be one of the main causes of observed delayed dark adaption .\noutput:\n" }, { "from": "agent", "value": "purpose . to investigate the itraq - based proteomic changes of visual cycle - associated proteins in rpe of rd12 mice before and after rpe65 gene delivery . mehtods . the right eyes of rd12 mice underwent rpe65 gene delivery by subretinal injection at p14 , leaving the left eyes as control . c57bl / 6j mice were served as a wide - type control group . ergs were recorded at p42 , and rpe - choroid - sclera complex was collected to evaluate the proteomic changes in visual cycle - associated proteins by itraq - based analysis . western blot was used to confirm the changes in the differentially expressed proteins of interest . results . erg parameters improved dramatically at p42 after rpe65 delivery . the proteomics analysis identified a total 536 proteins with a global false discovery rate of 0.21 % , out of which 7 were visual cycle - associated proteins . ralbp - 1 , rbp - 1 , and irbp were reduced in the untreated rd12 eyes and the former two were improved after gene therapy , confirmed by western blot analysis . conclusions . rpe65 gene delivery restored retinal function at p42 and modified the expression of other functional proteins implicated in the visual cycle . the level of ralbp - 1 was still below the normal level after gene therapy in rd12 mice , which may explain the delayed dark adaption in lca patients undergoing similar therapy ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: ir means that circulating insulin does not do its function in insulin sensitive tissues such as skeletal muscle , adipose tissue , liver , and endothelium . ir is related with central obesity , low high - density lipoprotein cholesterol , high triglycerides , raised blood pressure , and hemostatic defects . diet , body composition , and usual physical activity ( pa ) levels are known factors . diet management is a key component in the long - term health and quality of life of people with ir , and many features of the diet composition have been considered to be critical in the alteration of ir . one of these diets is the dietary approaches to stop hypertension ( dash ) , which encourages the eating of vegetables , fruits , and low - fat dairy products with sodium restriction . this diet is high in unsaturated fatty acids , fiber , antioxidant constituents , and low - fat dairy , which may be beneficial for decreasing ir . the metabolic efficiency of the dash diet , including its impact on insulin sensitivity is less known . genetic variations with affecting on insulin signaling , as well as environmental factors such as diet and pa , plays an important role in insulin sensitivity . candidate genes for insulin sensitivity either directly or indirectly encode the proteins , which are participated in glucose metabolism . insulin receptor substrate ( irs ) type 1 which is a main substrate for the insulin receptor , controls insulin signaling in skeletal muscle , adipose tissue , and the vascular , so it is an important candidate gene for ir . it is determined that decreased tyrosine phosphorylation of the irs1 proteins and dysregulation of the insulin receptor participates in peripheral ir and b - cell malfunction . the gene - environmental interaction may effect on insulin sensitivity , clarify the fundamental mechanisms of type 2 diabetes , and provide effective prevention strategies . dietary factors and nutrient intake are the main environmental factors in the incident and expansion of the typical polygenic , diet - related diseases such as ir . to date , no intervention studies in humans have thoroughly explored the effects of dash diet on gene expression . the purpose of this study , therefore , was to evaluate whether dash diet effects on irs1 gene expression and ir . fifty - one healthy , overweight , or obese ( body mass index 25 kg / m ) female volunteers aged 20 - 50 years that were referred by the general health center were recruited . subjects were not included by nutritionist if they were pregnant or lactating women or they had history of incidence of cardiovascular , gastrointestinal , hepatic , renal , thyroid , diabetes , rheumatoid arthritis , lupus , severe infection , trauma , allergy , and if they consumed of multivitamin and mineral or omega - 3 fatty acids supplements , antacid drugs that containing magnesium and calcium , aspirin and nonsteroidal anti - inflammatory drugs , anti - inflammatory and anti - depressant , and hormone drugs . they were excluded if they had changed their normal pa or they had not complete compliance . the nature of the trial was explained to the individuals , and all subjects provided written informed consent . after a 2 - week run - in period with the usual dietary advices ( uda ) diet participants were randomly assigned to 12 weeks to a uda diet or the dash diet . we conducted a run - in to homogenize in the consumption of macronutrients and base of diets . in this periodgroup assignments were made by statistic using random sequencing created in spss ( spss inc . , the nutritionist that prescribed the diets had to be aware of the group assignment , but laboratory staff members were not aware of that . participants were controlled every 2 weeks , and measurements were taken . during the study period , patients were prescribed the diet and prepared their own meals while living independently . they were demanded to record their pa for 3 days every month and not to change and it was assessed by using compendium of pa . participants were randomly assigned to one of two diets : a uda diet and the dash diet . the uda group was not given a diet and simply recommended to eat as regular and the intervention group was prescribed dash diet that was rich in fruits , vegetables , whole grains , and low - fat dairy products , and low in saturated fat , total fat , cholesterol , refined grains , sweets , and red meat . furthermore , it contained 2400 mg sodium per day [ table 1 ] . to calculate the energy requirement for each participantthe diets were individually prescribed using a calorie count system , and an exchange list was given to each patient for changing food items and counting the calories . every participant had to bring her 3 - day dietary records every month , and trained nutritionist reviewed the diaries . in these sessions , they were questioned about their diets and the food items that they should be eaten and their compliance was assessed by analyzing the three food record diaries by the nutritionist iv software ( version 7.0 ; n - squared computing , salem , or , usa ) that was modified for iranian food items . dietary goals of the dash intervention versus usual dietary advice participants were weighed wearing minimal clothing and without shoes , using digital scales ( seca , germany ) and recorded to the nearest 0.1 kg . height was measured without shoes in a standing position while the shoulders were in a normal state . waist circumference was measured where the waist was narrowest and the hip at the maximum level over light clothing , using an outstretched tape , without any pressure to the body surface and measurements were recorded to the nearest 0.1 cm . blood samples ( 5cc ) were collected at baseline and at 12 weeks , and human peripheral blood mononuclear cells ( pbmc ) was isolated by centrifugation on a ficoll - paque plus ( amersham biosciences ) density gradient . total rna was isolated from the pbmc using trizol reagent ( invitrogen ) according to the manufacturer 's instructions . briefly , 1.0 ml trizol reagent and 200 l chloroform were added to the sample , and the admixture was vortexed for 15 s and stood at 25c for 3 min . the supernatant was transferred to a fresh tube after centrifugation at 12,000 g for 15 min at 4c , and then 500 l isopropanol was added . the mixture was centrifuged at 12,000 g for 10 min at 4c after incubation at 20c for 20 min , to remove the supernatant and the rna pellet was washed with 75 % ethanol . ethanol was removed by centrifugation at 7500 g for 5 min at 4c , and rna was air - dried for 5 min and then dissolved in 25 l rnase - free water . the purity of isolated rna was ascertained by od260 / 280 using a nanodrop nd - 1000 ( thermo scientific , worcester , ma ) . isolated rna was dissolved in rnase - free water , and the amount of rna was determined by measuring absorbance at 260 nm with a spectrophotometer . the rna samples were treated with dnase i ( thermo scientific ) in order to avoid potential contamination with genomic dna . two micrograms of total rna were used to synthesize double - stranded cdna by revert aid first strand cdna synthesis kit ( thermo scientific ) and oligo dt primers . the primers for all assayed genes were designed using the allele i d 7 software ( premier biosoft international , palo alto , usa ) [ table 2 ] . the real - time polymerase chain reaction ( pcr ) was performed using sybr green pcr master mix ( thermo scientific ) and the step one plus real time pcr detection system ( applied bio systems ) . the expression level of each target gene was calculated as 2 , as previously described . primers used in real - time pcr the normality of continuous variables was assessed by normal probability plots and by one - sample kolmogorov - smirnov test . paired - samples t - test and tests were used to determine the significance of any baseline differences between diet groups . energy - adjusted dietary intake of nutrients was computed using the residual method and compared using analysis of covariance . we used independent sample t - test and paired - samples t - test to compare means of all variables within and between two groups , respectively . statistical analyses were performed by using the spss - software package 16.0 ( spss inc . , chicago , il ) , statistical power was 90 % , and a priori defined value of p 0.05 was considered statistically significant . this study was a randomized , parallel clinical trial . after a 2 - week run - in period with the usual dietary advices ( uda ) diet participantswe conducted a run - in to homogenize in the consumption of macronutrients and base of diets . in this period , patients consumed a uda diet . group assignments were made by statistic using random sequencing created in spss ( spss inc . , the nutritionist that prescribed the diets had to be aware of the group assignment , but laboratory staff members were not aware of that . participants were controlled every 2 weeks , and measurements were taken . during the study period , patients were prescribed the diet and prepared their own meals while living independently . they were demanded to record their pa for 3 days every month and not to change and it was assessed by using compendium of pa . participants were randomly assigned to one of two diets : a uda diet and the dash diet . the uda group was not given a diet and simply recommended to eat as regular and the intervention group was prescribed dash diet that was rich in fruits , vegetables , whole grains , and low - fat dairy products , and low in saturated fat , total fat , cholesterol , refined grains , sweets , and red meat . furthermore , it contained 2400 mg sodium per day [ table 1 ] . to calculate the energy requirement for each participantthe diets were individually prescribed using a calorie count system , and an exchange list was given to each patient for changing food items and counting the calories . every participant had to bring her 3 - day dietary records every month , and trained nutritionist reviewed the diaries . in these sessions , they were questioned about their diets and the food items that they should be eaten and their compliance was assessed by analyzing the three food record diaries by the nutritionist iv software ( version 7.0 ; n - squared computing , salem , or , usa ) that was modified for iranian food items . participants were weighed wearing minimal clothing and without shoes , using digital scales ( seca , germany ) and recorded to the nearest 0.1 kg . height was measured without shoes in a standing position while the shoulders were in a normal state . waist circumference was measured where the waist was narrowest and the hip at the maximum level over light clothing , using an outstretched tape , without any pressure to the body surface and measurements were recorded to the nearest 0.1 cm . blood samples ( 5cc ) were collected at baseline and at 12 weeks , and human peripheral blood mononuclear cells ( pbmc ) was isolated by centrifugation on a ficoll - paque plus ( amersham biosciences ) density gradient . total rna was isolated from the pbmc using trizol reagent ( invitrogen ) according to the manufacturer 's instructions . briefly , 1.0 ml trizol reagent and 200 l chloroform were added to the sample , and the admixture was vortexed for 15 s and stood at 25c for 3 min . the supernatant was transferred to a fresh tube after centrifugation at 12,000 g for 15 min at 4c , and then 500 l isopropanol was added . the mixture was centrifuged at 12,000 g for 10 min at 4c after incubation at 20c for 20 min , to remove the supernatant and the rna pellet was washed with 75 % ethanol . ethanol was removed by centrifugation at 7500 g for 5 min at 4c , and rna was air - dried for 5 min and then dissolved in 25 l rnase - free water . the purity of isolated rna was ascertained by od260 / 280 using a nanodrop nd - 1000 ( thermo scientific , worcester , ma ) . isolated rna was dissolved in rnase - free water , and the amount of rna was determined by measuring absorbance at 260 nm with a spectrophotometer . the rna samples were treated with dnase i ( thermo scientific ) in order to avoid potential contamination with genomic dna . two micrograms of total rna were used to synthesize double - stranded cdna by revert aid first strand cdna synthesis kit ( thermo scientific ) and oligo dt primers . the primers for all assayed genes were designed using the allele i d 7 software ( premier biosoft international , palo alto , usa ) [ table 2 ] . the real - time polymerase chain reaction ( pcr ) was performed using sybr green pcr master mix ( thermo scientific ) and the step one plus real time pcr detection system ( applied bio systems ) . the expression level of each target gene was calculated as 2 , as previously described . the normality of continuous variables was assessed by normal probability plots and by one - sample kolmogorov - smirnov test . paired - samples t - test and tests were used to determine the significance of any baseline differences between diet groups . energy - adjusted dietary intake of nutrients was computed using the residual method and compared using analysis of covariance . we used independent sample t - test and paired - samples t - test to compare means of all variables within and between two groups , respectively . statistical analyses were performed by using the spss - software package 16.0 ( spss inc . , chicago , il ) , statistical power was 90 % , and a priori defined value of p 0.05 was considered statistically significant . one patient was diagnosed with polycystic syndrome and another with high weight change , so these two patients had to be excluded from the analyses . five patients deviated from the study protocol and therefore , their data were not available . differences in distribution of several characteristics among 22 individuals in dash group and 22 subjects within the uda group are shown in table 3 . the mean patient age was 388 years in uda group and 379 years in the intervention group . there was no difference between groups regarding age , socioeconomic status , weight , pa , and gene expression at the baseline . consort diagram template effects of recommendations to follow the dash diet and uda diet on anthropometric , gene expression ( mean values with their sd ) analysis of diet showed that calorie and protein intake of two groups was not significantly different between groups , but these two diets were different in total fat and fat composition intake , as well as the percentage of the carbohydrate intake . these two diets were different in sodium content although these differences were not statistically significant but nutritionally are important . the dash diet had a higher amount of calcium , potassium , and fiber [ table 4 ] . daily energy and nutrient intakes in dash group and uda group at baseline an at end of the study the result of reverse transcription - pcr showed that dash diet significantly increased the expression of irs1 compared to uda group ( p = 0.000 ) and after adjusting for weight change , the results did not appreciably alter . this suggests that dash diet may increase the expression of irs1 [ table 3 ] . the finding of this study indicated that the dash diet could induce the expression of irs1 , which is an early substrate for the insulin receptor and plays a key role in mediating some of the insulin 's actions . however , to the best of our knowledge , effect of the dash diet on gene expression has not been reported previously , but a number of studies show the dash diet is high in fiber , unsaturated fatty acids , antioxidant components , and low - fat dairies improve ir . the mechanism behind this effect is not clear , but it may be due to the increased expression of some genes such as irs1 whose activation leads to translocation of glut4 - containing vesicles and subsequent increase in glucose uptake . because irs1 is a membrane - bound protein and its function is membrane - dependent , it is logical to hypothesize that alteration in membrane lipid induced by dietary fat may impression on the function of the plasma membrane insulin receptor . as it can be seen from the table 4 , fat intake is significantly less in dash group , and its composition is different between two groups such as polyunsaturated fat ( pufa ) , saturated fatty acid ( sfa ) and monounsaturated fatty acids ( p 0.05 ) . these findings further support the idea of previous studies have shown that long - term high - fat diets and increased plasma free fatty acid levels impair insulin signaling by alteration in irs1 expression and tyrosine / serine phosphorylation of irs1 , leading to decreased irs1 - associated pi3k activity . in fact , the insulin - stimulated uptake of glucose in visceral fat deposits and muscle were damaged by the high fat diet ( hfd ) as corn oil - based hfd intervention causes the expansion of ir concurrently in the liver , adipose tissue , and skeletal muscle in young adult c57bl / 6 mice . furthermore , the evidence shows that the diet composition , such as quality and quantity of fat , plays a notable role in glucose homeostasis and insulin sensitivity . it is commonly approved that saturated fats have a negative effect on insulin sensitivity , whereas unsaturated fats have a positive effect . it has been established that a high - pufa diet can increase receptor tyrosine kinase activity and a high pufa : sfa diet also improved insulin receptor function , glucose oxidation , and glucose transport in rats . some studiesestablished that dietary supplementation with calcium and magnesium reduce ir and low amount of potassium , magnesium , calcium , and fiber in the diet are correlated with diminished insulin sensitivity , so fruits and vegetables ; rich sources of magnesium , potassium , and fibers may improve ir . thus , as regard to a transactional study that shown the fruit and vegetable consumption was inversely associated with mrna expression of some pro inflammatory indicators in healthy young adults a possible explanation for our results may be higher fruit and vegetable consumption in dash diet that may similarly effects on ir related genes . in the same way , epidemiologic research data show a useful effect of raised whole grain , nuts , and dairy on diabetes risk and insulin sensitivity . thus , other possible explanations for irs1 up - regulation are consumption more dairy product , and so more ca intake that may be supported by study which show high - calcium whey , causes smaller adipocyte size , can also partly explain the clustering of up - regulated genes in the insulin signaling pathway . another important finding was that weight for the dash diet group significantly has reduced in spite of fixing calorie intake and no change in pa during the study . as regards to the dairy product were higher in the dash diet than the uda diet , this finding are consistent throughout the study which has indicated the macronutrient variability of the dash diet might be related to weight reduction . although the study has successfully demonstrated that dash diet induces irs1 expression , it has certain limitations in terms of dietary intake in this study was self - reported , and patients were advised to follow a special diet rather than getting prepared foods , thus possibly lead to incomplete adherence to the diets . dash diet increased irs1 gene expression and it may be one of the mechanisms , which diets influence on ir . food security research center , isfahan university of medical sciences . mk involved in conception , design , data collection , statistical analysis , and data interpretation .\noutput:\n" }, { "from": "agent", "value": "background : insulin receptor substrate ( irs ) type 1 is a main substrate for the insulin receptor , controls insulin signaling in skeletal muscle , adipose tissue , and the vascular , so it is an important candidate gene for insulin resistance ( ir ) . we aimed to compare the effects of the dietary approaches to stop hypertension ( dash ) and usual dietary advices ( uda ) on irs1 gene expression in women at risk for cardiovascular disease.materials and methods : a randomized controlled clinical trial was performed in 44 women at risk for cardiovascular disease . participants were randomly assigned to a uda diet or the dash diet . the dash diet was rich in fruits , vegetables , whole grains , and low - fat dairy products and low in saturated fat , total fat , cholesterol , refined grains , and sweets , with a total of 2400 mg / day sodium . the uda diet was a regular diet with healthy dietary advice . gene expression was assessed by the real - time polymerase chain reaction at the first of study and after 12 weeks . independent sample t - test and paired - samples t - test were used to compare means of all variables within and between two groups respectively.results : irs1 gene expression was increased in dash group compared with uda diet ( p = 0.00 ) . weight and waist circumference decreased in dash group significantly compared to the uda group ( p < 0.05 ) but the results between the two groups showed no significant difference.conclusion : dash diet increased irs1 gene expression and probably has beneficial effects on ir risks ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the role of endoscopic injection of dextranomer / hyaluronic acid copolymer ( dx / ha ) has expanded , as an alternative to open surgery , to a treatment option for observation protocols using prophylactic antibiotics . deflux has been fda approved since 2001 as a treatment option for grade 24 vesicoureteral reflux ( vur ) in single systems with no accompanying urological malformations in children above one year of age . the operative ease of technique , short procedure , and recovery time as well as repeatability of injections have popularized the technique with surgeons and parents alike . reports of expanded use to patients of all ages and grades of vur even in the presence of duplication , ureterocele , or other lower tract anomalies are published worldwide . in a statement of the aua board of directors from october 2007 , it was determined that : it is the current position of the american urological association that endoscopic injection of the dextranomer / hyaluronic compound deflux is an option in the management of pediatric vesicoureteral reflux ( vur ) . the initial success rate was quoted as 68 % and is still mentioned on the current website of the manufacturing company ( q - med , scandinavia inc ) . in the meantime , the original subureteric injection technique ( sting ) has evolved to the intraureteric injection technique introduced by the atlanta group . using this hydrodistention - implantation technique ( hit ) , the authors reported success rates of 89 % . however , the reported worldwide success rates differ considerably ( 55 % 89 % ) . unpublished data from our institution show an overall radiographic success rate of 75 % for patients and 84 % for renal units after the first injection . although the success rates continuously improve , the numbers of most institutions still differ significantly from the traditional 98 % for open reimplants . since up to 25 % of patients will have remaining vur after dx / ha injection , we still perform voiding cystograms 2 months after surgery . positional instillation of contrast ( pic ) cystography was developed to detect occult vur in patients with recurrent urinary tract infections ( uti ) after a negative standard voiding cystogram . it has a higher sensitivity than standard voiding cystogram ( vcug ) and can detect occult vur . parents can be advised that in case of a positive pic , dx / ha injection can be performed during the same anesthesia . in the current study , we compared two different pic techniques and evaluated two different scenarios : first , whether pic cystography or high - pressure cystograms were useful to detect de novo contralateral vur in the case of preoperative unilateral vur and second , whether pic cystography , when performed intraoperatively immediately after dx / ha injection , can predict a successful surgical outcome by correlating the results with a standard 2 - month postprocedure vcug . a retrospective chart review was performed on all intraoperative cystograms performed at the time of dx / ha injections at our institution from 20052007 . dx / ha injections were performed for all grades of vur and included complex cases such as duplicated systems . in case of preoperative unilateral reflux , a pic cystogram was performed on the contralateral unaffected side before dx / ha injection . if positive , bilateral injection took place . the injections were done using the hit technique as described by kirsch et al . . dx / ha was injected until a sufficient mound and good ureteral coaptation was observed . at this pointthe outflow portion of the 10 french off set cystoscope ( wolf , germany ) was placed at the bladder neck filling the bladder with contrast material ( cystografin ) to 100 cm water pressure until voiding occurred around the cystoscope ensuring complete bladder filling . the second group underwent standard pic cystography with the outflow portion of the cystoscope directed at the ureteral orifice at a 100 cm water pressure for 5 seconds ( figure 2 ) . radiographic views for both tests were performed in anterior - posterior and lateral as well as upper tract views . the intraoperative cystogram was noted to be positive if any grade of vur was present ( figure 3 ) . in cases of a positive study on the contralateral side or for remaining vur after injection , the patients were left on prophylactic antibiotics and followed up at 4 weeks postoperatively with an ultrasound and 2 months postoperatively with a vcug . the correlations of the intra - and postoperative study as well as the detection of de novo vur were noted . altogether 116 patients and 177 renal units ( ru ) were treated and available for evaluation . out of the 116 patients , new contralateral vur ( de novo ) for the 34 preoperative unilateral refluxing patients was found intraoperatively in 27 ru ( figure 4 ( c ) ) . the high - pressure intraoperative cystogram ( group 1 ) was performed in 86 rus and the standard pic ( group 2 ) in 91 rus . there was no statistically significant difference between groups 1 and 2 for the detection of de novo vur ( figure 4 ( b ) ) . for both groups , only 5 ru were found to have remaining vur intraoperatively after dx / ha injection ( 2 in group 1 and 3 in group 2 ) . postoperative pain management , if necessary , consisted of ibuprofen or acetaminophen according to parental preference . in all patients , the postoperative us at four weeks were negative for hydronephrosis or any other new abnormality . the dx / ha deposits were seen in the bladder in all cases . at 2 monthspostoperative standard vcug detected 20 ru ( 23 % ) to be positive for vur in group 1 and 16 ru ( 18 % ) positive for vur in group 2 . altogether 36 ru were positive , for an allover success rate of 80 % for ru and 75 % for patients ( figure 4 ( a ) ) . the grade of vur , age and gender of patient as well as amount of deflux injected did not influence the result . vesicoureteral reflux remains a common disease , and especially for lower grades the prospect of spontaneous resolution is good . but , the data on the value of daily prophylactic antibiotics remain controversial , and most parents are concerned about their long - term use . the discussion becomes evident by the current multi - institutional nih - funded rivur study , which aims to evaluate the role of prophylactic antibiotic in vur . in addition to prolonged antibiotic use , parents and patients alike dread the yearly necessary voiding cystogram to check for resolution . therefore , to avoid the daily antibiotics and the yearly vcug , many parents consider surgical treatment options . the endoscopic injection of dx / ha is an attractive management alternative for parents . when presenting the surgical options , all parents are enthusiastic about the minimal invasive nature of the procedure with low complication possibilities and fast recovery times . however , the 20 % 25 % lower success rate of the endoscopic procedure in comparison to the open surgery is a concern . although dx / ha can be reinjected , it requires further testing , anesthesia , and time spent away from school or work . therefore , it would be highly desirable to develop a method to check the success of the deflux injection intraoperatively . pic cystography is used to detect occult vur in patients with a negative standard voiding study who suffer from recurrent utis . according to rubenstein , the procedure is a 100 % sensitive and 91 % specific in identifying vur and can , therefore , detect occult vur . recently confirmed the findings in 5 patients . in a study on 39 patients with febrile utis and negative voiding studies from 4 different institutions , pic cystograms were performed and vur identified in 82 % of these patients . additionally , the authors noted that orifices that were patulous , laterally displaced , or positive for hydrodistention were much more likely to be positive for vur than normal orifices . also performed intraoperative pic cystograms and found that 23 % of patients had a positive , postoperative vcug despite a negative intraoperative pic study , and palmer confirmed these results . the authors concluded that pic cystography was not useful to raise the success rate of deflux injection . in the current study , we used two different cystogram techniques : the standard pic study and a high - pressure cystogram , filling the bladder until irrigation fluid leaked around the cystoscope . even with this aggressive cystogram technique only an 80 % correlation between a negative intraoperative cystogram and postoperative cystogram was achieved . the success rate of 75 % for patients and 80 % for ru could not be improved . a relative wound edema might increase the coaptation of the ureteral orifice , temporarily giving a negative intraoperative study result . other possibilities include decrease in the size of the injected dx / ha deposit over time , also thought to be responsible for long - term failure after dx / ha injection . this phenomenon has been noted during cystoscopy at the time of the planned second injection of deflux after initial failure . the dx / ha deposits tend to migrate medially and toward the bladder neck causing long - term failure of injection . elmore et al . reported the onset of new contralateral vur after dx / ha implantation in approximately 13 % of 126 patients with preoperatively unilateral vur . in the current study , twenty seven of these 34 patients demonstrated a positive pic cystography intraoperatively and were successfully injected with dx / ha . none of these de novo detected refluxing units were positive for vur in the postoperative cystograms . a negative intraoperative cystogram correlates with the postoperative vcug in only 80 % . considering that the success rates of dx / ha injections are commonly between 7580 % , the addition of intraoperative cystograms can not replace postoperative studies . in patients treated with unilateral vur , pic cystography can detect occult reflux and prevent postoperative contralateral new onset of vur .\noutput:\n" }, { "from": "agent", "value": "the endoscopic injection of dx / ha in the management of vesicoureteral reflux ( vur ) has become an accepted alternative to open surgery . in the current study we evaluated the value of cystography to detect de novo contralateral vur in unilateral cases of vur at the time of dx / ha injection and correlated the findings of immediate post - dx / ha injection cystography during the same anesthesia to 2 - month postoperative vcug to evaluate its ability to predict successful surgical outcomes . the current study aimed to evaluate whether an intraoperatively performed cystogram could replace postoperative studies . but a negative intraoperative cystogram correlates with the postoperative study in only 80 % . considering the 7580 % success rate of dx / ha implantation , the addition of intraoperative cystograms can not replace postoperative studies . in patients treated with unilateral vur , pic cystography can detect occult vur and prevent postoperative contralateral new onset of vur ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the symptoms of malaria include fever and anemia , and most of the deaths are caused by the parasite plasmodium falciparum . the merozoite form of the parasite invades red cells , grows to form ring - , trophozoite - and schizont stages , and after rupture of the infected red cell new merozoites are released that are ready to enter uninfected red cells . merozoite invasion is a process that takes only a few minutes , but it involves several complex receptor - ligand interactions . initial attachment of the merozoite is mediated by merozoite surface proteins such as msp1 and msp2 , and is followed by reorientation of the merozoite where apical membrane antigen 1 ( ama1 ) is of importance . other ligands such as erythrocyte - binding antigens ( ebas ) , for example , eba140 , eba175 , and eba181 and p. falciparum reticulocyte - binding homologues ( pfrhs ) , including pfrh1 , pfrh2 , pfrh4 , and pfrh5 have also shown to be involved in the invasion process , even though the exact function of each antigen is not known . genetic polymorphisms exist for many of the above - mentioned ligands , and based on some genes like msp2 , parasites can be grouped into two major allelic types : 3d7 and fc27 . serine repeat antigens ( seras ) are proteases that take part in forming a protein complex that is associated with the merozoite surface , and entry into the red blood cell is finally completed by an actin - myosin motor movement . individuals who live in malaria endemic areas eventually develop immunity , but only slowly and after repeated exposure . women have a greater risk of succumbing to malaria , and the fetus is also at risk . it is known that antibodies are important in the defence against malaria , and it has been shown that passive transfer of antibodies from immune donors to individuals with p. falciparum infection reduces parasitemia and clears clinical symptoms . however , exactly which specific antibodies are protective against future disease are not yet defined , and how they should be measured is even less clear . this information is urgently needed to be able to develop a functioning vaccine , something that has so far failed . we will here discuss the pros and cons for different methods available such as elisa , invasion inhibition assays ( iias ) , antibody - dependent cellular inhibition ( adci ) , and affinity , and we compare it to measurements of antibodies in other diseases and how the overall evaluation of immunity or vaccine status of malaria could possibly be improved . when antibodies directed against different p. falciparum antigens have been measured , elisa has usually been the method of choice . in this static method , proteins are coated to a plate and levels of antibodies in plasma from patients with ( or without ) malaria can be estimated . when recombinant proteins are used , only antibodies directed against specific antigens are analyzed . in real life , the antigen of choice is located together with several other antigens , for example , on the merozoite surface , and there might be interaction or competition between binding of different antibodies , something that is not accounted for in an elisa . it has , for example , been shown for msp1 that there are blocking antibodies that can compete with the binding of cleavage - inhibiting antibodies for epitopes on the merozoite , and there are also other studies that have demonstrated that mixing of different antibodies can influence the outcome of the assay . this kind of studies indicates that we should more look at using assays where the function of antibodies is studied , but the reason for why elisas are continued to be used to such a major extent is probably that they are very easy , fast , and robust to perform compared to functional assays . when recombinant proteins are applied in elisas , the result might depend on which part of an antigen that is selected for use in the assay . for msp1 , it has been shown that antibodies against msp1 - 19 were associated with some protection , while antibodies against msp1 block - 1 were not . however , even when the same subdomain has been used such as in studies of eba175 , contradictory results have been achieved for whether there was a protective effect of antibodies or not . when red cells burst due to egress of merozoites , a lot of debris will be left in the blood stream that needs to be removed , and many of the antibodies might help in doing this but this does not mean that the antibodies will protect from future disease . if only elisas are used , it is difficult to discern which antibodies are functionally important . in general , higher levels of antibodies are found in elisas in older individuals in endemic areas , while lower levels of antibodies are seen in younger individuals in the same areas . this was recently shown for the ebas for example and it has been shown earlier for other antigens as well . however , even though an individual has high levels of antibodies , they can still develop malaria , and an individual with relatively low levels of antibodies can be fully protected from clinical and severe malaria . in vaccine trials , antibodies measured by elisahave been shown to often be short - lived , and most patients will still get malaria in spite of presence of antigen - specific antibodies . from a population perspective , elisas can be used to make an overall estimation of how much exposure there has been to malaria , but for each individual it is not possible to make an exact determination of the immune status . the only thing that can for sure be concluded from a positive response in elisa is that the individual has at some stage during his / her lifetime been exposed to malaria . when elisas against different antigensare combined , more information can possibly be acquired about the level of immunity in investigations of the breadth of antibodies , but the question of whether it is just a measure of exposure will still remain . a way of improving the elisas would be to more often use standardized controls , allowing for the measurement of exact amounts of specific antibodies instead of titers . in conclusion , elisas are easy and robust to perform , and they can clearly give us information about whether or not an individual has ever been exposed to malaria . with combinations of different antigens and standardization of the assays , more information can possibly be provided . however , elisas do not tell us anything about the function of the antibodies , and on an individual level , elisas will not give us complete information about immunity . one assay that has been used to try and better determine the function of antibodies in plasma is growth inhibition assay or invasion inhibition assay ( iia ) . antibodies directed against merozoite antigens are thought to function by directly inhibiting invasion of new red cells , which will then stop further multiplication of parasites , or through adci . by adding immune plasma , which contains antibodies to growing parasites , the inhibitory function of the antibodies can be evaluated in comparison to parasites where no plasma has been added . the downside of iias compared to elisas is that they are much more labor intensive , but on the other hand all proteins are expressed in their native environment and many both known and unknown potential interacting factors are included in the assay . there have been several studies that have shown invasion inhibitory activity of antibodies from human plasma , both when total igg has been used and when malaria - antigen - specific fractions have been used . some studieshave shown increasing invasion inhibition with age while others have shown more invasion inhibition in children . this kind of contradictory results might be explained by different functions in the antibodies repertoire being important during development of immunity , compared to when immunity is already established , but it might also mean that the assay is not yet fully optimized to show who is immune or not . one attempt to improve the iia is by adding monocytes ( adci ) . when adci has been employed , some antigens like msp3 and glurp have shown an inhibitory effect only when monocytes were included in the iia . however , with adci there seems to be a major variability in the assay that can be seen from day to day even using the same donor of monocytes , making it difficult to standardize the assay . if this assay could be improved and standardized , it might add very valuable information about different antibodies . another attempt to try and improve iia is to use knockout lines of parasites . here , a single antigen can be studied in its natural environment and with the correctly folded protein , and a comparison can be made between the wild - type and the knockout parasites . this has been used , for example , for the ebas , where it was shown that antibodies against eba175 was responsible for a major part of the inhibitory activity in some individual plasma samples , while other samples seemed not to have any functional antibodies against this protein at all . this kind of results is important for selection of potential vaccine candidates , especially for ruling out those antibodies that have no effect . some antigens have been difficult to knock out , in which case other reagents might have to be added to the assay such as blocking agents , to find out which antibodies are causing the inhibitory effect . in conclusion , iias are labor intensive but can provide important information especially for comparisons between knockout and wild - type parasites , where the function of a single potential vaccine candidate antigen can be evaluated . another way of looking at antibodies against merozoite antigens is to study the affinity / avidity of antibodies . some studies have tried to use elisa with added nh4scn to evaluate affinity , but the results for this have been inconsistent . a new way of investigating affinity for vaccine trials has opened up with methods like surface plasmon resonance ( spr ) , where affinity of antibodies can be estimated under flow , something that ought to be more similar to the physiological situation compared to static assays . with this method , association and dissociation of antibodies binding to their target antigensthis method has before mainly been used with monoclonal antibodies in malaria research , but it has recently been applied also to polyclonal antibodies . it has , for example , been shown that affinity of antibodies against ama1 increased with age , and the presence of high affinity antibodies in plasma against msp2 - 3d7 was associated with protection against malaria . in this study , most plasma samples showed a relatively rapid on - rate , indicating that whether the concentration of antibodies in the samples is high or low , the antibodies will still bind quite fast to their antigens . this is important for considering whether an antibody will function in inhibiting merozoite invasion or not , since invasion is a process that takes only a couple of minutes . the dissociation rate ( which is concentration independent ) might therefore be more important for whether an antibody will function or not . in the referred study , monoclonal antibodies were also used and it could be seen that some bound with so low dissociation rates , that a value for the dissociation rate could not be obtained . however , investigations of affinity of antibodies in malaria are yet a very new field which needs a lot more studies to be able to make firm conclusions , and standardized protocols needs to be in place to facilitate interpretation of the results . in other infectious diseases , such as bacterial diseases , toxoplasma , or hiv , studies of affinity of polyclonal antibodies in malaria is a new field that could add a lot of information both about how immunity is formed and for vaccine trials , and more work in this area is needed . when different assays are used to evaluate antibodies against malaria , the methods often show results that do not correlate with each other . for example , spr has been shown to correlate with elisa for ama1 , which binds with relatively high affinity , but not for msp2 , which binds with lower affinity . when iia has been compared to elisa , some people have shown correlations while others have not seen any correlations . this is probably because iia is a functional assay , while elisa only estimates the levels of antibodies . an example of the lack of major correlations between methods ( iia and elisa ) is shown in figure 1 . this illustrates the difficulties in estimating immunity against malaria . for vaccine trials , one has to be careful with interpretation of results , as the results could vary a lot depending on which method is used . in other fields such as hiv , international consortia have established common standards to be used in immunological assays , and this might be applicable for elisas , but more challenging for the functional methods yet available in malaria . none of the methods described here are good enough on their own to give a complete picture of an individual 's immune status . elisas are good at giving us information about whether any immune response at all is mounted against a potential vaccine candidate , and from a population perspective when many samples need to be analyzed , elisas are easy to perform . however , if we want to know something about the function of a specific antibody , iia with the usage of knockout and wild - type parasites should be the way forward . even though these assays are more cumbersome to perform , they will add valuable information . affinity of antibodies has so far been very scarcely studied in malaria research compared to many other diseases , and expansion of this field should add important information both for knowledge about immunity and for vaccine trials . more studies are needed that employ different methods together in the same patient cohorts to get a more full picture of which functions of antibodies are important during different stages of development of immunity against malaria . in conclusion , which method should be used depends on what we want to know about the antibodies . if we only want to know whether antibodies are formed or not , elisas can be used , but if we want to know something about the function of the antibodies , more elaborate assays such as iia have to be applied . to get the full picture about immunity status in an individual , the methods available have to be developedmore and probably combined to a bigger extent , but with new methods such as those available for affinity measurements there is hope that this situation can be improved .\noutput:\n" }, { "from": "agent", "value": "immunity against malaria develops slowly and only after repeated exposure to the parasite . many of those that die of the disease are children under five years of age . antibodies are an important part of immunity , but which antibodies that are protective and how these should be measured are still unclear . we discuss the pros and cons of elisa , invasion inhibition assays / adci , and measurement of affinity of antibodies and what can be done to improve these assays , thereby increasing the knowledge about the immune status of an individual , and to perform better evaluation of vaccine trials ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the estrogen receptor ( er ) is a ligand - inducible intracellular transcription factor that mediates most of the biological effects of estrogens at the level of gene regulation . estrogen biology is exceedingly complex and important in the development and function of numerous tissues and physiological phenomena . in the nucleus , the er up - or downregulates the expression of target genes by interacting through its site - specific dna and with other coregulatory proteins that include coactivators and corepressors . the ligand - bound er binds as homodimer to specific dna sequences termed estrogen response elements ( eres ) and regulates transcription through interaction with transcription modulators and recruitment of the general transcription machinery . in recent years , new information regarding the er structures , intra - and intermolecular interactions , posttranslational modifications , and several other factors pertaining to the er actions has emerged . like other members of the nuclear hormone receptor ( nhr ) family , the er is composed of several functional domains that serve specific roles . starting from nh2 - to coo - terminus , the principal domains are ( 1 ) the n - terminal domain ( ntd ) ; ( 2 ) dna - binding domain ( dbd ) ; ( 3 ) ligand - binding domain ( lbd ) . two activation function ( af ) domains , af1 and af2 , located within the ntd and lbd , respectively , are responsible for regulating the transcriptional activity of er ( figure 1 ( a ) ) . full transcription activity of the er is thought to be achieved by synergism between the two afs , and their activities are promoter and cell specific . af1 functions as hormone independent , whereas af2 function requires the presence of hormone / steroid . in this paper , we focus on the two isoforms of human er ( er ( nr3a1 ) and er ( nr3a2 ) ) , encoded by two different genes . both have been cloned and characterized . the physiological effects of estrogen are manifested through both er and er . the er and er receptor isoforms display distinct tissue distributions and signaling response . er and er have also been shown to form hetero dimers on eres . in terms of sequence homology , the er shows a high homology to er in the dbd ( more than 95 % amino acid identity ) and in the lbd ( ~ 55 % amino acid identity ) . however , the ntd of er is shorter than that of er with a very poor sequence homology of only 15 % compared to that of er . the three - dimensional structures of the independently expressed dbd and lbd have been solved and show overall folds that represent globular proteins with natively ordered conformations . to date , no three - dimensional natively folded structure for the ntd is available not only for the er but for the entire nuclear hormone receptor ( nhr ) superfamily . even though the full length structure of the peroxisome proliferator - activated receptor - ( ppar - ) has been solved , it failed to show any signature of structure formation in its ntd . warnmark et al . have previously provided insights about the structural and functional correlations regarding the er ntd . in this paper , we discuss the knowledge about the structural characteristics of the er and its role in gene regulation . the d domain which follows dbd is known as a hinge region ( figure 1 ( a ) ) . it contains nuclear localization signal which gets unmasked upon ligand binding and serves as a flexible region connecting dbd and lbd . its action was first characterized by montano et al . by single - point mutations in the domain as well as by whole domain deletion . f domain was found to modulate gene transcription in a ligand - specific manner . the ligand , promoter , and tissue - specific modulation capabilities of the f domain were recently studied in detail by koide et al . . like other nhrs , the e domain of er contains lbd ( figure 1 ( a ) ) . it consists of 12 helices , contains hormone binding pocket , and is responsible for the most part of functions activated by ligand binding , such as coregulator binding to af2 and dimerization interface . while er and er have both overlapping and unique functions , the overall homology between the er protein lbd and er protein lbd does not exceed 55 % . however , the two proteins ( er and er ) display distinct regions of sequence homology . the amino acid residues 223343 and 404457 in er and er show a significantly higher homology than that of the sequence encompassing 223457 and 344403 , respectively . interestingly , the stretch of the er lbd amino acid residues 465468 , with lowest homology to er , has been found to be most solvent accessible . on the other hand , the conserved regions with greater homology are protected against degradation and are in direct contact with the ligand . despite low sequence homology in lbds within the nhr superfamily , both isoforms of er - lbds have been shown to form dimers with agonist and antagonist ligands . the dimer interface is primarily encompassed by helices 10 and 11 . as a member of the nhr superfamily of transcription factors , er contains a globular lbd structure that harbors a hormone - binding site , a homo - or heterodimerization interface , and coregulator ( activator and repressor ) interaction sites . the er lbd structure contains 11 - helices ( h1h12 ) ( figure 1 ( c ) ) . the first crystal structure of an er lbd bound to its natural ligand 17 - estradiol ( e2 ) showed that in a compact ellipsoid cavity , e2 is buried in a highly hydrophobic environment . within this pocket ( formed by 22 residues ) , hydroxyl groups in estradiol at positions 3 and 17 play a crucial role in orienting the steroid / hormone ligand . these hydroxyl groups of the a and d rings are hydrogen bonded to glu353 from h3 , arg394 from h5 , and a water molecule and his524 from h11 . in an agonist - bound form , er is spatially organized in a three - layered structure with helices 4 , 5 , 6 , 8 , and 9 lining up on one side by h1 and h3 , and on the other side are helices 7 , 10 , and 11 . due to the central role of estrogen signaling in diverse diseases ranging from cancer to aging , the crystal structure of the complex of er lbd bound to the nonsteroidal ligand , diethylstilbestrol , also shows that the hydrophobic interactions primarily govern the accommodation of distinct lbd structures . the crystal structures of the human er bound to genistein , estradiol ( figure 1 ( c ) ) , and rat er to raloxifene assert the importance of hydrogen bond network on the opposite sides of the respective ligands . the bicyclic moiety of genistein orients in a position similar to the c - and d - ring of e2 , facilitating the formation of hydrogen bonds of hydroxyl moieties with histidine groups of the receptor . the specificity of the ligand association between the er and er may stem from the distinction in the residues lining the binding pocket . quite diverse family of compounds ( estrogens , some androgens , phytoestrogens , antiestrogens , and environmental estrogens ) have been shown in the past to have estrogenizing activity , and to interact with the er from rat uterus and human breast tumor cells . interactions of these structurally diverse ligands highlight the intrinsic er and er lbd plasticity . adjacent to the n - terminal transactivation region ( a / b domain ) , a conserved c domain encompasses the dna - binding sequence . this dna - binding domain associates with the response elements which can either reside proximally to the promoter regions or enhancer regions located distant from the transcription initiation site . er dna binding domain usually binds to the estrogen response element ( ere ) composed of a palindromic hexanucleotide 5aggtcannntgacct3 . the ere sequences play an important regulatory role . not only does it dictate the binding affinity of the er , but also it has been shown to modulate the recruitment of coactivators . the er dbd : ere structures have been studied extensively by several biophysical techniques . three - dimensional structure of the er has been solved using nuclear magnetic resonance as well as x - ray crystallographic techniques both alone and in complex with dna ( figure 1 ( b ) ) . the dbd : ere interactions and ere - facilitated dimerization are in part mediated through the p box and d box sequences in the zinc finger domains . these zn finger subdomains are comprised of 8 cysteine residues that coordinate with the two zn ions . while p box actively interacts with the ere nucleotides , the d box is present at the dimerization interface . the specificity of er recognition by ere is exemplified by interesting studies describing its association with glucocorticoid response element ( gre ) . three amino acids in the first zn finger region or er dictate its interaction with ere and gre . substitution of these three amino acids with the corresponding amino acids from the glucocorticoid receptor 's dbd completely changes er dbd 's specificity for an ere , and it strongly binds to a gre sequence to initiate gre - mediated transcriptional activity . transcriptional regulation at the ere can be mediated via two separate mechanisms of er action . liganded er can directly associate with specific response element sequences . in the other mode of action , the er may participate in a multiprotein , preinitiation complex and regulate gene transcription without a direct interaction with any dna sequence . together , these mechanisms highlight the complex role of coactivators and response elements in eliciting specificity in transcriptional output . to date relatively little information has been available on the structure of the n - terminal regions of the nhrs . even though the full - length structure of the peroxisome proliferator - activated receptor - ( ppar - ) has been solved it failed to show any signature of structure formation in its very short ntd . we and others have shown that the glucocorticoid receptor 's n - terminal transactivation af1 region and a shorter core fragment of af1 , the af1 core , are unstructured in aqueous solution . in other words , the ntd amino acid sequences possess an intrinsically disordered ( i d ) conformation , a feature of activation domains of many transcription factors . similar results have been reported for the er and er , androgen - , and progesterone receptor . thus , activation domains of many signaling proteins including the er 's ntd / af1 are known to exist in an i d state . one of the reasons for their existence as an i d region seems to be to help them in promoting molecular recognition by providing surfaces capable of binding specific target molecules . the computational analyses have established that under physiological conditions , the combination of low mean hydrophobicity and relatively high net charge represent an important prerequisite for the lack of well - defined compact structure in proteins or protein regions / domains . the i d nature of the er ntd / af1 has been confirmed by circular dichroism method . we performed secondary structural analyses of the er and er ntd using network protein sequence analysis . the analytical results show that more than 67 % of er ntd contains random coli conformation , whereas in case of er , the amount of random coil is found to be more than 80 % with only a small proportion as helix and sheet in both the cases ( figure 2 ) . it has been proposed that the i d nature of an activation domain allows it to rapidly sampleits environment until appropriate concentration and affinity of the binding partner proteins are found , meaning that they may not be structured until they have recruited and bound their proper interaction partners . then , either by induced - fit or selective binding of a particular conformer , a high - affinity activation domain : binding partner protein interaction occurs . in case of nhrs ' i d ntd / af1 domains , it has been shown that they undergo a transition to a folded state upon interaction with either components of the general transcription machinery or with other comodulators . several coregulatory proteins are involved in the effect of the er on target gene transcription . the tata box - binding protein ( tbp ) has a central role in the basal transcription machinery and can directly bind to the ntd of the er but fails to bind to er ntd and to potentiate er - activated transcription . this difference in tbp binding could imply differential recruitment of target proteins by the ntds of er and er . the affinity of the er ntd : tbp interaction was determined to be in the micromolar range , as assessed by surface plasmon resonance spectroscopy . based on these results , it has been proposed that the interaction between er ntd and tbp may proceed in a two - step manner with initial very fast , low - affinity association , followed by a slow , folding event and tighter association . the initial association may be occurring by electrostatic interactions between the acidic residues of highly negatively charged er ntd and the positively charged tbp . however , this initial unstable protein complex subsequently may convert into a more stable form by the folding of the i d er ntd and the formation of specific contacts between the two proteins . in this study , the secondary structures of the independently expressed ntds of the er and er were analyzed using nmr and circular dichroism spectroscopy . further , when er ntd was bound to tbp , structural changes were induced in er ntd . these results support models of tbp as a target - protein for the n - terminal activation domain of er . further , the dissociation of this binding suggests a complex behavior , with a rapid dissociation for er ntd molecules that did not undergo proper folding and a slower dissociation for those molecules that did fold successfully upon physical interaction with the tbp . such a two - step binding mechanism is consistent with the change in protein conformation that accompanies the er ntd : tbp interaction . observed differences in binding of tbp to er ntd and er ntd supports a model where the two receptors may be utilizing different sets of target binding proteins . this is consistent with the reports of functional differences between er ntd and er ntd where it has been shown that the er af1 domain can function in an autonomous manner , whereas the af1 function of er can not . it has also been reported that under most conditions er possesses a weaker transactivational potency compared to er , and these differences appear to be cell and promoter specific . we have earlier shown that tbp binding induces secondary / tertiary structure formation in the i d af1 domain of the glucocorticoid receptor such that af1 's interaction with specific coregulatory proteins and subsequent af1 - mediated transcriptional activity is significantly enhanced . based on the binding of tbp and consequent folding of these i d activation domains , it can be hypothesized that the interaction between nhrs ' ntd / af1 and tbp may be a unified mechanism , through which these i d af1 / ntd acquire a functionally active conformation under physiological conditions . in this conformation , the ntd / af1 may be able to create favorable protein interaction surfaces for its interaction with specific coregulatory proteins . of course , the exclusion of certain other binding partners can not be ruled out . it could thus be hypothesized that a complex and dynamic binding pattern for the n - terminal activation domains of the nhrs occurs to achieve transcriptional activation , where the ntd / af1 region must be able to obtain different conformations dependent on the binding partner ( s ) . however , a clear picture will emerge only when the functionally folded three - dimensional structure of the ntd / af1 is solved . at least for now , the differential effects observed in case of two er isoforms ( er ntd and er ntd ) suggests that tbp may not be a common coregulator that must bind / fold all the nhrs ' ntd / af1 . thus , it is quite possible that other protein components from the basal transcription machinery may provide such interactions . in fact , we and others have observed that at least in case of the androgen receptor , its i d ntd / af1 undergoes disorder / order transition through its interaction with rap74 , a subunit of tfiif , an important component of basal transcription machinery . recent observations have led to the conclusion that in cells , er and several other nhrs behave very dynamically such that their kinetic behavior in cells allows them to rapidly interact with various coregulatory proteins , and with chromatin and dna . further , the er moves to various sites in cells to function , and the local concentrations and various other constellations of potential coregulatory proteins are required to associate with the er to activate or repress the expression of target genes . the lbd crystal structures have clearly demonstrated that differing sets of coactivators / corepressors come together in response to agonist or antagonist ligand binding , such that agonist in one cell type can be an antagonist in another cell type . the overall picture is one of a complex , dynamic network controlled by the er . it is not yet clear whether unique tissue / cell - specific coregulatory protein interactions can fully explain the tissue / cell - specific actions of the er and other nhrs . when the clear picture will emerge , it is certain that other dynamic considerations will prove to be the dominant underlying mechanism .\noutput:\n" }, { "from": "agent", "value": "the estrogen receptor ( er ) mediates most of the biological effects of estrogens at the level of gene regulation by interacting through its site - specific dna and with other coregulatory proteins . in recent years , new information regarding the dynamic structural nature of er has emerged . the physiological effects of estrogen are manifested through er 's two isoforms , er and er . these two isoforms ( er and er ) display distinct regions of sequence homology . the three - dimensional structures of the dna - binding domain ( dbd ) and ligand - binding domain ( lbd ) have been solved , whereas no three - dimensional natively folded structure for the er n - terminal domain ( ntd ) is available to date . however , insights about the structural and functional correlations regarding the er ntd have recently emerged . in this paper , we discuss the knowledge about the structural characteristics of the er in general and how the structural features of the two isoforms differ , and its subsequent role in gene regulation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: medullary thyroid cancer ( mtc ) is a malignant tumour originating from the calcitonin producing parafollicular ( c ) cells of the thyroid . among well - differentiated thyroid carcinomas , it is the most aggressive , with survival rates of 40 - 50 % at 10 years . early diagnosis and radical surgical treatment are key to improving morbidity and mortality amongst patients with mtcs . fine needle aspiration cytology ( fnac ) is a very sensitive and specific procedure for the diagnosis of malignant thyroid nodules , but cytological typing of mtc may be difficult with routine staining . serum calcitonin ( ct ) measurement in patients with thyroid nodules is the most specific and sensitive marker of mtc , having even better accuracy than fnac in diagnosing unsuspected mtc [ 2 - 3 ] . an elevated level of serum ct , confirmed by an exaggerated response to pentagastrin stimulation , is almost invariantly associated with mtc . hereditary mtc accounts for 25 % of cases and is transmitted with an autosomal dominant pattern caused by germline mutation of the ret proto - oncongene , coding for a transmembrane tyrosine kinase ( tk ) receptor mapped to chromosome 10q11 .2 [ 4 - 6 ] . the hereditary form of mtc may be associated with other endocrine neoplasias such as pheochromocytoma and parathyroid adenomas ( multiple endocrine neoplasia type 2a , or men 2a ) , or pheochromocytoma and mucosal neurinomas ( multiple endocrine neoplasia type 2b , or men 2b ) . alternatively , the hereditary form may be the only manifestation of the disease ( familial mtc , or fmtc ) . in 1987 , the men2a gene was assigned by linkage analysis to the pericentromeric region of chromosome 10 . in 1993 , men 2a and fmtc were shown to be associated with mutations in exon 10 or 11 of the ret proto - oncogene , and specific ret mutations were detected in affected families . subsequently , ret proto - oncogene mutation was also found to be involved in men 2b . the proto - oncogene ret comprises 21 exons and encodes a receptor tk that has a large extracellular domain , a single transmembrane region , and two cytoplasmic tk domains . approximately 95 % of men2a families have mutations involving exons 10 ( codons 609 , 611 , 618 , and 620 ) and 11 ( codon 634 ) of the ret proto - oncogene , which encode the cysteine - rich domain of the ret receptor . ret mutations that affect the intracellular tk domain , however , are rare . mutations that involve the cysteine - rich extracellular domain of the ret receptor are thought to cause disease through constitutive dimerization and activation of the receptor . the fmtc phenotype is associated with mutations involving both the extracellular cysteine - rich and intracellular tk domains of the ret receptor . these mutations are located in exons 10 ( codons 618 and 620 ) , 11 ( codons 630 , 631 , and 634 ) , 13 ( codons 768 , 790 , and 791 ) , 14 ( codons 804 and 844 ) , and 15 ( codon 891 ) .95 % of cases of men 2b are associated with a point mutation in the methionine residue in exon 16 ( codon 918 ) in the intracellular tk domain of ret ; this is thought to induce tumour formation by altering the substrate specificity of the kinase domain , thereby activating growth - stimulating pathways . recently , the european thyroid association ( eta ) has included routine measurement of serum ct in the diagnostic evaluation of thyroid nodules . in contrast with eta recommendations , the american thyroid association ( ata ) guidelines are neither in favor nor against routine measurement of serum ct in patients with thyroid nodules , although a recent american study demonstrated that it has a cost effectiveness comparable to thyroid stimulating hormone ( tsh ) measurement , mammography and colonoscopy screening . this study is the first effort to measure the cost effectiveness of ct screening in the usa . evidence such as this is essential and should prompt physicians to screen thyroid nodules by serum ct measurement in their clinic , and should contribute to the improvement of practice guidelines . another recent study suggests extending the screening for the ret proto - oncogene to every patient with mtc . since 1993 , screening for the germline ret mutation has been introduced to define the hereditary nature of an mtc tumour in the first affected family member that seeks medical attention ( the proband ) and , where positive , to search for additional family members carrying the mutation ( 50 % risk of carrying the mutation ) . if the screening is performed early in life , it can identify the member at risk even before development of the disease , or at least at an earlier stage . the practical consequence is the possibility of performing prophylactic total thyroidectomy or beginning early treatment of the limited disease . . demonstrated that germline ret mutations are present in 7.3 % of patients erroneously diagnosed with sporadic mtc . reclassifying this form as hereditary has a great clinical impact on the discovery of new mtc families . although the entire spectrum of genetic alterations causing sporadic mtc has not yet been defined , nearly 50 % of sporadic mtcs harbour a somatic point mutation of the ret proto - oncogene . it is reported that patients with sporadic mtcs carrying a somatic ret mutation have a worse outcome compared with patients who have ret negative tumours [ 15 - 17 ] . the identification of the ret mutation in the dna extracted from fnac could help in planning a more aggressive surgical strategy in ret - positive cases , hopefully improving the long - term survival . in conclusion , early diagnosis is mandatory for effective treatment of mtc . in sporadic cases this can be achieved through routine screening of thyroid nodules by serum ct and in familial cases by genetic ret screening of family members of a proband with hereditary mtc . in addition , the screening of tumour dna from all mtc patients for ret somatic mutations may not only help to distinguish sporadic mtcs from familial forms ( with important clinical and predictive consequences ) , but will also be useful in the prediction of clinical outcomes and designing therapy for patients with certain sporadic tumours carrying a ret somatic mutation .\noutput:\n" }, { "from": "agent", "value": "medullary thyroid cancer ( mtc ) accounts for 5 - 10 % of all thyroid cancers . the majority of medullary thyroid cancers are sporadic , but 25 % of cases are inherited as a result of germline mutations in the ret proto - oncogene . in sporadic cases mtc presents as a thyroid nodule discovered at palpation or at thyroid ultrasonography , and is indistinguishable from thyroid nodules of different histology . since effective treatment of mtc is only possible when the tumour is limited to the thyroid gland , early discovery has a decisive impact on how radical initial surgical treatment needs to be . recent data suggest that in sporadic cases , early discovery of thyroid nodular disease is possible when screening serum calcitonin measurement , while screening for germline ret proto - oncogene mutations is fundamental in first degree relatives of patients with hereditary mtc ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: epilepsy is considered by some authors as a symptom that responds to different neurological disorders . these disorders may be strokes , head traumas , brain malformations , and the effect of neurotoxic substances among others . all of them are discontinuities that affect normal brain activity , enabling the creation of conditions for the occurrence of the attack . the mechanism of the attack is not clear yet , although there are several hypotheses based on the incorrect communication between neurons . for some reason , this results in synchronizing the activation of a mass of neurons which generates the crisis . according to the more accepted postulates , the problem of the epilepsy occurs when an error in the communication between neurons is not blocked by the inhibition system that controls them . in this caseone neuron excites another neuron causing a cascade of stimulation that grows and propagates recruiting other neurons . if during that propagation neither factor inhibits the recruitment of neurons , that small initial failure takes a critical mass of neurons and ends in an epileptic seizure . under the hypothesis that the uncontrolled neuronal synchronization propagates and recruits more neurons each time , we are going to try to detect it as early as possible by signal analysis . this synchronization is not evident just by looking at the eeg , so we need mathematical tools to identify it . to deal with this problem , we propose to study the entropy of the signal , using it as a numerical method to evaluate the degree of freedom or dispersion of the spectral energy of the signal . this variation has the particularity to show , in a single number , the uniformity of the spectrum distribution . low entropy shows a greater concentration of energy in a group of band frequencies . the latter concept would permit to identify an eventual neuronal synchronization by modifying the spectrumthis study aims to evaluate which of the bands is more sensitive to changes in the entropy of the signal before the attack occurs . it is assumed that , in brief periods before the attack , the entropy varies linearly . to evaluate the variation of entropy , we are going to obtain regression lines for each of the three bands . also the correlation coefficient foreach line is going to be calculated in order to observe the spread of values . concerning the regression line we are going to consider its slope . the band of higher rate is going to be the most sensitive . the one with less dispersion means greater certainty in the measurement . we analyze the data of patient records from the epilepsy center of the university hospital of freiburg in germany , used for freiburg seizure prediction project , which were shared for experimental use . the database contains records of eeg of 20 patients who suffer from focal epilepsy , pharmacologically intractable . data were recorded during a presurgical invasive monitoring of epilepsy in the epilepsy center of the university hospital of freiburg in germany . in order to obtain a high - ratio signalnoise , less artifacts and register directly from focal areas , grids , strips , subdural , and depth electrodes were used . eeg data were acquired using a digital eeg video system neurofile nt with 128 channels , 256 hz sampling frequency , and analog - digital conversion of 16 bits . exists a set of data called ictal which contains files with the seizure register at least 50 minutes before it happens . the patients present different types of seizures ( simple partial , complex , and generalized tonic - clonic ) , with different origin locations ( frontal , temporal , occipital temporal , and parietal ) and affection of different structures ( hippocampus or neocortical ) . to do the calculation , we used the spectral entropy ( sen ) , which is the shannon entropy properly normalized and applied to the power spectrum density of the eeg signal . that is , ( 1 ) sen = pklogpklog ( n ) , where pk are the spectral powers of normalized frequency , such that pk = 1 and n = number of frequencies ( bin ) . first the signals were filtered with a notch at 50 hz ( line filter in germany ) and then arbitrarily divided into bands , generating three vectors per patient . the following are the frequencies for each band : low band of frequencies : 0.1 to 12 hz , mid band of frequencies : 12 to 32 hz , high band of frequencies : 32 to 128 hz . low band of frequencies : 0.1 to 12 hz , mid band of frequencies : 12 to 32 hz , high band of frequencies : 32 to 128 hz . each vector was analyzed with a time window for the application of the fft of 16 s ( 4096 samples ) , without overlapping the windows . once assumed the linear variation , we are going to obtain the regression lines and the correlation of the points representing each variation of the entropy . to improve the visualization and comprehension of the entropy variation , we are going to draw the movable mean with an averaging interval of 4 minutes . figures 1 and 2 show the electroencephalographic signals and their respective entropy analyses for two patients with their regression lines in each band during the 30 minutes prior to the attack . these figures provide data to identify the entropy variation in function of time for each frequency band analyzed in the patient . the regression line and the correlations were calculated considering an interval of 32 to 4 minutes before the seizure . during the period between the previous 4 minutes and the seizure , the entropy can increase considerably , so we did not take it into account for the calculation . graphics show the entropy of this period very close to the attack , for illustrative purposes only . the graph corresponding to the moving average across the time of the entropy considers the whole period , from the previous 32 minutes to the time of the seizure . table 1 shows the slopes of the regression line and the correlation for each frequency band and each patient . from the results we can identify that the highest band of frequencies shows a rate of entropy increase prior to the seizure that on the average for all the attacks is of p = 5.41110 , with a mean correlation coefficient r = 0.07 . in all cases , the slopes are positive . in the lowest band of frequencies , the mean rate of growth of the entropyis p = 1.7710 , with a correlation coefficient r = 0.2 in absolute value . slopes are mostly positive , except in one sample that was negative . in the band of the mid frequenciesthe rate of growth was p = 1.8810 , with a correlation coefficient r = 0.15 in absolute value . the ability of mathematical methods of signal analysis in the recognition of nonevident changes for the visual detection becomes important for the observation of gamma activity . this activity has been observed in preictal animal records in eeg registers with implanted and external electrodes . a recent observation points out the importance of the detection of these rhythms in scalp registers for the detection of the focal crisis onset . however the use of signal from scalp electrodes presents a disadvantage regarding the implanted electrodes . this fact would produce an increase in the power of the fast frequencies , which is not observed in our analysis . from the table of resultswe can see that the highest band of frequencies undergoes a more pronounced change of entropy as we approach the attack , evidenced by the slopes which are notoriously larger than in the other two bands . instead , the correlation of values obtained with this line is very low , which shows us the dispersion of the entropy values when calculated for this band of frequencies . it is noteworthy that , in all the analyzed patients , the entropy increases in this band , meaning that its slope is positive . in the opposite case , we have the lowest band of frequencies where there is a variation of entropy almost null and with a very superior correlation regarding the rest of the bands . the band of mid frequencies does not follow any fixed trend , changing both between positive and negative slopes and having low correlation . the increase of the entropy evidences that a signal with energy concentrated in a band of frequencies tends to distribute that energy to the rest of the bands . the maximum entropy is achieved when all the bands have equal energy . in the band of the high frequencies , it could have a transference of energy from the low frequencies to the highest . a possible explanation would be to associate this redistribution of energy with communication faults between neurons , which occur at much higher frequencies than what is considered physiologically normal and which could trigger off the crisis process ending in the epileptic attack . there exists an uncertainty factor due to the great variability of instantaneous entropy , which leads us to have a low correlation . this behavior could be associated with the communication errors , or on the contrary , to the action of some system of control which tries to inhibit the propagation of the error . recent findings perhaps could give us an alternative explanation because they show that , prior to the crisis , there exists desynchronization rather than synchronization , and the presence of gamma activity may then become an expression of columnar cortical fast spiking . the spikes in the plot are another factor which contributes to the uncertainty of the entropy value . these spikes mostly stand out in the highest frequency band . as a conclusion we can say that the entropy in high frequencies has great potential as a predictor because it reveals changes in the previous moments to the attack . its main problem is the variability , which makes it difficult to setting the threshold that ensures an accurate prediction . this variability may be due to the presence of ubiquitous spikes in the electroencephalographic records of epileptic patients , that although they affect the whole spectrum , they are prevalent in the band of high frequencies . it could be a good criterion for future works to filter spikes and repeat the entropy measurement for the band of high frequencies .\noutput:\n" }, { "from": "agent", "value": "introduction . under the hypothesis that the uncontrolled neuronal synchronization propagates recruiting more and more neurons , the aim is to detect its onset as early as possible by signal analysis . this synchronization is not noticeable just by looking at the eeg , so mathematical tools are needed for its identification . objective . the aim of this study is to compare the results of spectral entropies calculated in different frequency bands of the eeg signals to decide which band may be a better tool to predict an epileptic seizure . materials and methods . invasive ictal records were used . we measured the fourier spectrum entropy of the electroencephalographic signals 4 to 32 minutes before the attack in low , medium and high frequencies . results . the high - frequency band shows a markedly rate of increase of the entropy , with positive slopes and low correlation coefficient . the entropy rate of growth in the low - frequency band is practically zero , with a correlation around 0.2 and mostly positive slopes . the mid - frequency band showed both positive and negative slopes with low correlation . conclusions . the entropy in the high frequencies could be predictor , because it shows changes in the previous moments of the attack . its main problem is the variability , which makes it difficult to set the threshold that ensures an adequate prediction ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: glass ionomer cement introduced by wilson and kent in 1972 was initially used as a substitute for silicate cement , for anterior esthetics .1 zinc phosphate cement has long been the material of choice for luting permanent cast restoration because of its good manipulative properties and relatively high strength . however , this material relies on mechanical interlocking for its retentive effects .2 the quest for improved alternative cementing material that can form a physiochemical bond to the tooth structure led to the development of glass ionomer luting cement in 1977.3 it has showed considerable promise as a means of reducing secondary caries by its fluoride release . other favorable traits include significantly less disintegration in vivo , a film thickness comparable to that of zinc phosphate and biocompatibility .4 the conventional glass ionomer cement , however , is susceptible to moisture contamination and dehydration in the early stages . resin modified glass ionomer cement shows less early water sensitivity and their tensile strength and flexural strength exceeds the conventional glass ionomer .5,6 however , they remain susceptible to water loss and exhibit crack formation when subjected to dehydration stress .7 the glass ionomer is also highly sensitive to power / liquid ratio and the material can not be under proportioned or over proportioned . premeasured glass ionomer in the form of capsule was introduced to obtain a correct ratio of powder and liquid , but it also could not solve the problem of wastage . a later introduced , paste to paste system was provided with a dispenser to ensure dispensing the required amount of material without altering the proportion . the low film thickness of 3 also permits stress - free seating of restoration and reduce the chances of high occlusion . confocal laser scanning microscope ( clsm ) enables to view subsurface features of tooth / cement interface under normal environmental conditions without disrupting the interface morphology .8 this is especially useful to study the interaction of glass ionomer cement with the tooth surface , which is very sensitive to dehydration .9 this study compared the effect of dehydration in a conventional glass ionomer luting cement , resin reinforced powder / liquid system , and resin reinforced paste / paste system after 0 min , 15 min , 30 min , 60 min by examining the cement / dentin interface in a clsm . freshly extracted non - carious 50 human maxillary premolars that were extracted for orthodontic treatment in the age group 10 - 18 years were selected as samples . the superficial occlusal dentin was exposed by using a slow speed diamond disc under the water spray . the surface was prepared flat and polished with 600 grit silicon carbide paper for placement of glass ionomer cement . conditioner ) for a period of 20 s and rinsed with distilled water for 20 s. the samples were divided into three groups based on the type of glass ionomer cement used and in group iii there were three subgroups based on the amount of material dispensed from the cartridge ( table 1 ) . three groups based on the type of glass ionomer cement used and three subgroups in group iii based on the amount of material dispensed from the cartridge . in group i and group ii the cements were mixed as per the manufactures instructions . in groupiii a , group iii b , group iii c , the material was dispensed from the cartridge with a dispenser . three lines were marked on the lever for the 3 subgroups , one in the most forward position , one in the middle , and one in the rear position to obtain least , moderate , and large quantity of material , respectively . rhodamine b that has an excitation wavelength for 514 nm was used in the study to visualize the cement matrix . the cement was placed on the dentin surface in the respective groups to a dimension of 4 mm diameter and 2 mm height using a mold . a single coat of fuji coat lc was applied and light cured for 10 s for all 50 samples . the cement was allowed to mature in distilled water for a period of 24 h and the samples were later sectioned longitudinally to examine the cement / dentin interface under clsm after 0 min , 15 min , 30 min , 60 min of dehydration in all the groups . the width of the crack after dehydration near the dentinal interface at 0 min , 15 min , 30 min and 60 min were measured in microns . in group i , group iii a , group iii b , and group iii c changes were visible ( tables 2 and 3 ) . an independent student s t - test was done to test the mean values between the groups and also within each group at various time duration ( table 4 ) . when p 0.05 the , difference between the groups was considered significant . graphical illustration of the width of the crack is tabulated in graphs 1 and 2 . width of the crack in microns ( ) in group i. width of the crack in microns ( ) in subgroups of group iii . comparison of the width of the crack in each group at different time intervals . from the above results following have been concluded : no specimens showed crack formation at the beginning of the experiment.group ii specimens did not show any crack formation even at the end of 60 min.group i specimens showed the maximum width of the crack at the end of 60 min.the width of the crack increased gradually starting from the beginning of the experiment up to 60 min in group i , group iii a , group iii b , and group iii c and there was statistical significant difference in all the groups.at 15 min and 30 min , group i specimens showed the maximum width of crack , followed by group iii a , group iii b , and iii c. group 1 iii a iii b iii c.at 60 min group i specimens showed the maximum width of the crack followed by group iii b. there was statistical significance among all the groups except between group iii a and group iii c. group i iii b iii a = iii c. no specimens showed crack formation at the beginning of the experiment . group ii specimens did not show any crack formation even at the end of 60 min . group i specimens showed the maximum width of the crack at the end of 60 min . the width of the crack increased gradually starting from the beginning of the experiment up to 60 min in group i , group iii a , group iii b , and group iii c and there was statistical significant difference in all the groups . at 15 min and 30 min , group i specimens showed the maximum width of crack , followed by group iii a , group iii b , and iii c. group 1 iii a iii b iii c. at 60 min group i specimens showed the maximum width of the crack followed by group iii b. there was statistical significance among all the groups except between group iii a and group iii c. group i iii b iii a = iii c.glass ionomer cement is a water based cement and the acid - base reaction between aluminosilicate glass powder and polyacrylic acid occurs only in the presence of water .10 the water formed as a result of the acid base reaction , initially lies free in the matrix , and the cement remain susceptible to water loss at this stage . later this loosely bound water becomes tightly bound water by incorporating water molecules into the aluminum ion to form stable aluminum polyacrylate salt .11 when glass ionomer cement was allowed to dehydrate the silaceous hydrogel around the glass core was subjected to shear stress and crack tend to occur cohesively in the cement .12 the thickness of the silaceous hydrogel ranges from 150 to 300 m for conventional glass ionomer cement and resin - modified glass ionomer cement showed thinner hydrogel ranging between 100 and 150 m. 13 the presence of thicker hydrogel widened the crack in conventional glass ionomer cement compared to resin - modified glass ionomer cement . complete maturing and resistance to water loss is not available for at least 2 weeks for fast setting cements and up to 6 months for slow setting conventional cements .14 the group i specimens ( conventional glass ionomer ) showed the maximum width of the crack , when it was subjected to dehydration under the microscope throughout the 60 min dehydration period ( figures 1 and 2 ) . the crack was cohesive and occurred close to the interface leaving a thin layer of glass ionomer cement attached to the dentin . the crack was also not uniform throughout and was interrupted in between by the glass particles . when the cement was dehydrated , it is the unbound water that is readily lost by evaporation . the ratio of bound to unbound water in conventional glass ionomer has been found to increase with time .15,16 group i sample at 0 min ( cement / dentin interface under confocal laser scanning microscope ) . group 1 sample at 60 min ( cement / dentin interface under confocal laser scanning microscope ) . the group ii specimens ( resin reinforced powder / liquid system ) did not show any crack formation throughout the dehydration procedure under the microscope ( figure 3 ) . in this hybrid material part of the water content of the glass , polyalkenoate system is replaced by water soluble polymer or polymerizable resin .17 the addition of hema into the liquid along with the catalyst permitted initial polymerization of resin to occur along with shower acid - base reaction . the polymerization of hema also offered protection to the calcium polyacrylate chains against dissolution in water .18 the addition of resin caused on the overall increase in fracture toughness of the material . group ii sample at 60 min ( cement / dentin interface under confocal laser scanning microscope ) . the group iii specimens ( resin reinforced paste to paste system ) developed a cohesive crack close to the interface upon dehydration of the specimen . the crack was observed at 15 min and gradually widened at 30 min and 60 min ( figures 4 and 5 ) . however , the width of the crack was significantly less than that of the group i specimens . statistical significance was found at different quantities of mixing ( group iii a , group iii b , group iii c ) , but they are not important because no single quantity was able to completely eliminate crack formation . group iii c sample at 0 min ( cement / dentin interface under confocal laser scanning microscope ) . group iii c sample at 60 min ( cement / dentin interface under confocal laser scanning microscope ) . in this study , it had been shown that cohesive failure of the cement in the form of crack was associated with the dentin interface , which might be due to localized increase in strength of the glass ionomer close to the dentin by the strong ion - exchange layer .18 during cementation of crowns , some amount of cement gets exposed at the margins to the oral environment . extended operative procedures and also in mouth breathers , the exposed margin of the cement will remain continuously in a state of dehydration .7 as a result , cracks can develop and marginal leakage can occur at the crown margins . dehydration of a specimen under the microscope is an effective means of applying stress and indicates some of the stresses that can be placed on the system during the extended operative procedure . monitoring the interface for the crack at 0 min , 15 min , 30 min , and 60 min , permitted to observe whether there is widening of the crack over time . the range and particle size distribution will have a bearing on the physical properties of each material .14 finer the particle size , the lesser will be the film thickness of the cement . conventional glass ionomer cement ( group i ) and resin - modified glass ionomer powder / liquid system ( group ii ) has an average filler particle size of 3.8 m and a maximum of 15 m . in case of resin - modified glass ionomer paste to paste system ( group iii ) , the filler particle size is 1.8 m and a maximum of 4 m , which is significantly less than that of the group i and group ii materials . in resinreinforced paste to paste system , the fine particle size has got a bearing on the development of crack . the lesser the particle size , more will be the acid - base reaction , and the amount of glass core filler in the cement will be less . this would have resulted in the crack formation , which was otherwise absent in powder / liquid system . in this study , the use of unfilled resin did not provide protection to both water loss and water gain in all the groups . further studies are required to examine the cohesive failure in other areas of the cement . the use of bioactive materials like ceramir , which is a calcium aluminate luting cement , a luting cement that incorporates the principle of two cements , calcium aluminate , and glass ionomer cement will to a certain extent mitigate the deficiencies of conventional glass ionomer cement . within the limitations of the study , the following conclusions were drawn : conventional glass ionomer luting cement ( fuji 1 ) is more susceptible to cohesive failure when subjected to dehydration compared to resin - modified glass ionomer paste / paste luting cement ( fuji cem ) . among the luting cements , resin - modified glass ionomer powder / liquid system ( fuji plus ) showed the best results when subjected to dehydration . conventional glass ionomer luting cement ( fuji 1 ) is more susceptible to cohesive failure when subjected to dehydration compared to resin - modified glass ionomer paste / paste luting cement ( fuji cem ) . among the luting cements , resin - modified glass ionomer powder / liquid system ( fuji plus ) showed the best results when subjected to dehydration .\noutput:\n" }, { "from": "agent", "value": "background : the purpose of this study was to evaluate the effect of dehydration of resin - modified glass ionomer powder / liquid system , resin - modified glass ionomer paste / paste luting cements in three different quantities and to compare them with a conventional glass ionomer luting cement using confocal laser scanning microscope.materials and methods : a conventional glass ionomer ( group i ) , a resin modified powder / liquid system ( group ii ) , and a resin - modified paste / paste system ( group iii ) were selected for the study . in group iii , there were three subgroups based on the quantity of material dispensed . 50 premolar teeth were selected and randomly divided among the groups with 10 samples in each . the teeth were ground flat to expose a flat occlusal dentin . a device was made to standardize the thickness of cement placed on the teeth . the teeth were stored in distilled water for 24 h and then longitudinally sectioned to examine the tooth dentin interface under a confocal microscope . the specimens were allowed to dehydrate under the microscope for different time intervals . the width of the crack after dehydration near the dentinal interface was measured at definite intervals in all the groups and analyzed statistically using student s t - test.results : conventional glass ionomer cement showed the maximum width of the crack followed by resin modified paste / paste system during the dehydration period . resin modified powder / liquid system did not show cohesive failure.conclusions : conventional glass ionomer luting cement is more susceptible to cohesive failure when subjected to dehydration compared to resin - modified glass ionomer paste / paste luting cement . among the luting cements , resin - modified glass ionomer powder / liquid system showed the best results when subjected to dehydration ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: malignant small round cell tumor ( msrct ) of temporal bone is very rare , with rapid aggressive patterns . differential diagnosis of small round cell tumors is particularly difficult due to their undifferentiated or primitive character .1 ) many tumors belong to the category of \" small , round , blue cell tumor \" . rhabdomycosarcoma , lymphoma , lymphoblastic leukemia , small cell carcinoma , neuroblastoma and ewing 's sarcoma all have a similar histologic appearance .2 ) for exact categorization of these tumors , immunohistochemistry and chromosomal study is essential . the authors will describe a case of msrct of the temporal bone which showed negative results in all immunohistochemical studies . a 5 - year old boy visited outpatient clinics for left idiopathic acute facial paralysis ( house - brackmann grade iv ) . oral steroid medication was prescribed for 10 days as scheduled during admission . on imaging study , temporal magnetic resonance imaging showed a partial fluid signal at the left mastoid air cells and abnormal enhancement at the left facial nerve around the genu area ( fig . he showed marked improvement without any treatment and there were no sequelae ( house - brackmann grade i ) . he had a medication history of local clinics for the last month . on physical examination , the left tympanic membrane could not be observed due to severe narrowing of left external auditory canal ( fig . temporal bone computed tomography revealed expansile soft tissue densities and diffuse erosive destruction on left temporal bone ( fig . we performed an emergency modified radical mastoidectomy under general anesthesia . during the operation , we found a pale , grayish tumor occupying the mastoid and middle ear cavity ( fig . pathologic examination of the resected tumor showed an infiltrating tumor consisting of small round cells ( fig . the results of immunohistochemical stainings for vimentin , neuron specific enolase ( nse ) , s - 100 protein , pancytokeratin , synaptophysin , chromogranin a , smooth muscle actin , sarcomeric actin , glial fibrillary acidic protein ( gfap ) , leuko - cyte common antigen were all negative , so we could n't categorize the tumor . after the pathologic confirmation , the patient transferred to hematooncologic department for chemotherapy and radiotherapy . temporal bone and facial nerve involvement by a malignant tumor is not common ; it comprises about 5 % of peripheral paralysis causes , and malignant tumors are even rare .3 ) msrct is a term used for tumors composed of malignant round cells that are slightly larger up to double the size of red blood cells in air - dried smears . they generally include ewing 's sarcoma , primitive neuroectodermal tumor ( pnet ) , rhabdomyosarcoma , synovial sarcoma , non - hodgkin 's lymphoma , retinoblastoma , neuroblastoma , hepatoblastoma and nephroblastoma . differential diagnosis of small round cell tumors is particularly difficult due to their undifferentiated or primitive character .1 ) for exact categorization of these tumors , immunohistochemistry and chromosomal study is useful . recently nse , s - 100 protein , gfap , synaptophysin , neural cell adhesion molecule and protein gene product 9.5 have been clinically tested as neural antibodies for establishing a diagnosis for pnet .4 ) in chromosomal study , ewing sarcoma / pnet typically shows a recurrent chromosomal translocation , most commonly involving chromosomes 11 and 22 resulting in the fusion of the genes ews and fli .5 ) in the present case , staining with all markers was negative . jones and mcgill7 ) reported 11 cases in the head and neck region out of 26 patients with pnet . combined treatment ( surgery , chemotherapy and radiotherapy ) is currently applied depending on the tumor size and location although the prognosis remains poor . eralp , et al. 8 ) reported a 30.5 % 3 - year disease free and overall survival rate .\noutput:\n" }, { "from": "agent", "value": "malignant small round cell tumor is very rare , especially in the head and neck area . it is also difficult to make a differential diagnosis due to their undifferentiated or primitive character . immunohistochemical staining and chromosomal study is useful to categorize these tumors . since these are rare tumors , treatment protocols are is not well established . while combined treatments ( surgery , chemotherapy , radiotherapy ) is currently being applied , the tumor still has a poor prognosis . we present a rare case of a rapidly growing temporal bone malignant small round cell tumor which initially showed facial paralysis ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: asian indians appear to have a higher propensity toward developing type 2 diabetes than other race / ethnic groups . india is home to the second - largest population of individuals with type 2 diabetes worldwide ( 1 ) . furthermore , immigration to developed countries is traditionally associated with higher type 2 diabetes risk ( 24 ) , and asian indian immigrants have a higher prevalence of type 2 diabetes than the general u.s . population ( 46 ) . however , given that india has recently undergone rapid economic and nutrition transitions ( 7,8 ) , it is unclear whether diabetes risk among asian indians immigrants in the u.s . such a comparison of two genetically similar populations living in different environmental settings could shed light on the behavioral and environmental factors associated with increased diabetes risk in this ethnic group . we therefore compared the age - specific prevalence of type 2 diabetes and prediabetes in two current population - based studies of urban asian indians aged 40 years : n = 2,305 residents of chennai , india , using data from the centre for cardiometabolic risk reduction in south - asia study ( carrs ) ( 20102011 ) ( 9 ) , and n = 757 from the u.s . - based mediators of atherosclerosis in south asians living in america ( masala ) study ( 20102013 ) ( 10 ) . we also analyzed the relative associations of demographic and anthropometric characteristics on prevalent glycemic status in urban asian indians in both india and the u.s . the design , sampling strategy , recruitment , enrollment , and questionnaire and examination components of the masala and carrs studies have previously been described in detail ( 9,10 ) . in brief , carrs is a multisite cohort study that recruited participant populations from three urban megacities in india and pakistan ( delhi , chennai , and karachi ) . the baseline examination for this cohort included a representative cross - sectional survey conducted in each city between 2010 and 2011 . for the purposes of this study , data were analyzed from the chennai study site only , as this site was the only one to perform an oral glucose tolerance test ( ogtt ) in order to identify diabetes accurately . households were selected for participation using multistage random sampling technique in order to be representative of the city of chennai ( 9 ) . a total of 6,920 individuals were screened for participation , of whom 6,906 ( 99 % ) provided questionnaire data . fasting plasma glucose was obtained from 5,952 participants ( 86 % ) and 2 - h post glucose challenge on 4,051 participants . for this study , we limited our population to the 4,865 ( 70 % ) participants who were previously diagnosed with diabetes as determined by questionnaire data or who provided fasting and 2 - h postchallenge glucose measurements . participants with existing cardiovascular disease as ascertained through self - report ( n = 283 ) and those of age 40 years ( n = 2,277 ) were excluded from the carrs study for valid comparisons with masala . masala is based on a community - based sample of south asians living in the greater chicago and san francisco bay areas . the masala study was modeled to be similar to the multi - ethnic study of atherosclerosis ( mesa ) cohort study ( 11 ) , and only individuals without a known history of cardiovascular disease were eligible . recruitment was conducted using telephone - based recruitment methods , similar to the mesa study ( 11 ) . sampling frames were created by clinical site ( either the university of california , san francisco , or northwestern university ) and included all nine counties of the san francisco bay area and the seven census tracts closest to the northwestern university medical center , as well as suburban locations around chicago where census data revealed high proportions of asian indian residents . name , address , and telephone number were obtained for 10,000 households in the targeted census tracts from commercial mailing list companies ( infousa , omaha , ne , and marketing systems group , horsham , pa ) . random samples of south asian surnames from the desired geographic locations were created using a specific cultural coding algorithm to identify 162 ethnicities , 16 ethnic groups , 80 language preferences , 21 countries of origin , and 12 religions using a five - step matching process to classify a person 's first and last name , thereby reducing selection bias among participants with uncommon south asian surnames ( 10 ) . all participants were screened by telephone and were invited to either the university of california , san francisco , or the northwestern university clinical field center for a 6 - h baseline clinical examination . in total , 9,097 households were attempted to be reached . within these households , 3,053 individuals were reached and 1,801 ( 59 % ) were eligible for participation ( 10 ) . of all those eligible , a total of 906 individuals participated in the study . however , for the purposes of our analysis , data were analyzed only for individuals who identified as being born in india ( n = 757 ) . details regarding the eligibility criteria , questionnaire , and examination components in carrs and masala are shown in table 1 . eligibility , questionnaire , and exam components in carrs and masala in both studies , after at least a 9 - h overnight fast , a 75 - g ogtt was administered to participants without previously diagnosed diabetes who were willing and able to participate in the glucose challenge . blood samples were obtained from a peripheral vein just before glucose ingestion ( time 0 ) and at 30 and 120 min post glucose challenge for plasma glucose measurements . type 2 diabetes was defined similarly as self - reported use of glucose - lowering medication ( either an oral agent or insulin ) , fasting glucose 126 mg / dl , or 2 - h postchallenge glucose 200 mg / dl ; prediabetes was defined as fasting glucose 100125 mg / dl and / or a 2 - h postchallenge glucose 140199 mg / dl ( 12 ) . normal weight was classified as bmi 18.524.99 kg / m , overweight was classified as bmi 2529.99 kg / m , and obese was classified as bmi 30 kg / m . asian - specific cut points for bmi classification were also used for sensitivity analyses ( 14 ) . prevalence values and 95 % cis were estimated by study site , sex , age - group , and bmi category . participant characteristics were stratified by sex and were compared by study using test or anova as appropriate . the non normally distributed variables of fasting and 2 - h plasma glucose were log transformed . the effect of location of residence ( india or the u.s . ) on the odds of prediabetes and type 2 diabetes compared with normal glucose tolerance was assessed using standardized polytomous regression . initially , an unadjusted regression model was created to compare the individual association between study location and prevalent glycemic status . subsequent multivariable models were then created to adjust for covariates including age , sex , blood pressure , waist circumference , educational status , and years since migration to the u.s . all analyses were performed using sas , version 9.4 ( sas institute , cary , nc ) . prevalence values and 95 % cis were estimated by study site , sex , age - group , and bmi category . participant characteristics were stratified by sex and were compared by study using test or anova as appropriate . the non normally distributed variables of fasting and 2 - h plasma glucose were log transformed . the effect of location of residence ( india or the u.s . ) on the odds of prediabetes and type 2 diabetes compared with normal glucose tolerance was assessed using standardized polytomous regression . initially , an unadjusted regression model was created to compare the individual association between study location and prevalent glycemic status . subsequent multivariable models were then created to adjust for covariates including age , sex , blood pressure , waist circumference , educational status , and years since migration to the u.s . all analyses were performed using sas , version 9.4 ( sas institute , cary , nc ) . table 2 displays participant characteristics by sex and study . of the 2,305 participants from carrs - chennai , the mean duration of residence in the u.s . for masala study participants was 27.810.8 years for men and 26.510.8 years for women . participants in the masala study were on average older than those in carrs - chennai and had higher educational attainment . on average , for both sexes , participants in masala were taller and had greater weight and waist circumference measurements than those in carrs - chennai . additionally , men in the masala study had a higher mean bmi than men in carrs - chennai ; however , this was reversed among women . in both studies , fasting glucose was obtained from all participants who were willing to provide a sample ; however , a 75 - g ogtt was only administered to participants without a prior diagnosis of type 2 diabetes ( masala n = 617 , carrs n = 1,674 ) . participants in the masala study had lower log fasting glucose values than participants in carrs - chennai but higher log fasting 2 - h glucose values . those in masala also had lower systolic and diastolic blood pressure levels and took more blood pressure lowering medications than participants in carrs - chennai . of those with a prior diagnosis of type 2 diabetes , participants in masala had on average a longer duration since diagnosis . baseline participant characteristics by study center * data are mean ( sd ) or % unless otherwise indicated . log fasting glucose : men , carrs - chennai ( n = 1,027 ) , masala ( n = 402 ) ; women , carrs - chennai ( n = 1,215 ) , masala ( n = 345 ) . log 2 - h glucose : men , carrs - chennai ( n = 780 ) , masala ( n = 323 ) ; women , carrs - chennai ( n = 894 ) , masala ( n = 294 ) . age - adjusted type 2 diabetes prevalence was higher among indians in carrs - chennai than those in the masala study both overall ( 38 % [ 95 % ci 3640 ] vs. 24 % [ 95 % ci 2127 ] ) and by sex ( men 36 % [ 95 % ci 3339 ] vs. 27 % [ 95 % ci 2331 ] ; women 42 % [ 95 % ci 3945 ] vs. 23 % [ 95 % ci 1928 ] ) . of participants with type 2 diabetes , 65 % of asian indians living in the u.s . age - adjusted prediabetes prevalence was lower in asian indians in chennai than in the u.s . ( overall 24 % [ 95 % ci 2226 ] vs. 33 % [ 95 % ci 3036 ] , men 21 % [ 95 % ci 1924 ) vs. 35 % [ 95 % ci 3140 ] , and women 25 % [ 95 % ci 2328 ] vs. 29 % [ 95 % ci 2434 ] ) . these patterns were consistent across age - and sex groups , but differences in type 2 diabetes prevalence by age were more significant in women ( fig . the prevalence of diabetes was higher in asian indians living in india than in asian indians living in the u.s . differences in diabetes prevalence between the groups were significant in normal and overweight participants but were not significant in participants who were obese . in all categories of bmi , the prevalence of prediabetes was lower in native asian indians than those in the u.s . and was significantly different in participants with normal bmi . the pattern of higher diabetes prevalence and lower prediabetes prevalence in asian indians living in india than asian indians in the u.s . in all bmi categories was consistent using the asian bmi cut points . however , when using the asian specific cut points , the prevalence of diabetes and prediabetes was most significantly different in participants who were overweight . prevalence of diabetes and prediabetes by study and bmi category . * p 0.05 . of the 757 participants from masala ,189 ( 25 % ) had origins from one of four of the south indian states of tamil nadu , karnataka , andhra pradesh , or kerala . after restriction of participants from masala to only those with origins from south india , age - adjusted type 2 diabetes prevalence was again higher among indians in carrs - chennai than those in the masala study both overall ( 38 % [ 95 % ci 3640 ] vs. 25 % [ 95 % ci 2032 ] ) and by sex ( men 36 % [ 95 % ci 3339 ] vs. 27 % [ 95 % ci : 1935 ] ; women 42 % [ 95 % ci 3945 ] vs. 25 % [ 95 % ci 1534 ] ) . age - adjusted prediabetes prevalence was again lower in asian indians in chennai than in those in the u.s . with origins from south indiaspecifically ( overall 24 % [ 95 % ci 2226 ] vs. 33 % [ 95 % ci 2639 ] , men 21 % [ 95 % ci 1924 ) vs. 36 % [ 95 % ci 2745 ] , and women 25 % [ 95 % ci 2328 ] vs. 27 % [ 95 % ci 1938 ] ) . these patterns were again consistent in all age - and sex groups , but differences in diabetes prevalence between asian indians in chennai compared with asian indians in the u.s . with origins in south india were more significant than differences in prediabetes prevalence between these groups . table 3 shows the association of place of residence ( either india [ chennai ] or the u.s . [ greater san francisco and chicago areas ] ) with glycemic status . after adjustment for age , sex , waist circumference , and systolic blood pressure , asian indians in the masala study had a 50 % ( 95 % ci 0.40.6 ) decreased odds of type 2 diabetes but a 20 % ( 95 % ci 0.91.5 ) increased odds of prediabetes than those in carrs - chennai . the inclusion of education and years since migration in multivariable models somewhat attenuated the effect of place of residence on the odds of having diabetes compared with normal glucose tolerance . income could not be assessed in the models , as it was found to be collinear with place of residence . the inclusion of height in multivariable models as a proxy for socioeconomic status prior to migration did not alter the effect of place of residence on the odds of having diabetes or prediabetes compared with normal glucose tolerance between the groups . however , the inclusion of height and education together in multivariable models significantly attenuated the effect of place of residence on the odds of having diabetes . risk factors associated with prediabetes and type 2 diabetes ai , asian indian ; sbp , systolic blood pressure . * asian indians living in india ( carrs - chennai study ) were used as the referent group . * few studies have compared asian indians in india to those who have immigrated to the u.s . in this study comparing middle - to older - aged urban asian indians , we found that a community - based sample of asian indians in the u.s . had a lower prevalence of type 2 diabetes but a higher prevalence of prediabetes than asian indians living in urban south india . asian indians in the u.s . also had better blood pressure levels than those in india , possibly explained by their higher usage of blood pressure lowering medications . however , the adjustment for age , sex , waist circumference , and systolic blood pressure did not fully explain the increased odds of type 2 diabetes in asian indians in the carrs - chennai study . it is possible that india is in an early stage of the type 2 diabetes epidemic wherein those who are most susceptible to the disease develop it the earliest ( 15 ) . have adopted more positive dietary and exercise habits , thereby lowering their risk for progression from prediabetes to overt type 2 diabetes ( 16 ) . have poorer metabolic profiles than their counterparts in india ( 17,18 ) , our results indicate that while asian indians in india had lower bmi and waist circumference measurements than those living in the u.s . , they still had a higher prevalence of type 2 diabetes even at normal levels of bmi and in both sexes , thereby suggesting a shift in the association between migration and type 2 diabetes risk in this population . paradoxically , both the overall and the age - specific prevalence of prediabetes were lower in asian indians living in india than in the u.s . , which may be due to a more rapid conversion through the natural history of disease in asian indians living in india . our results also add strength to the notion that factors besides age and central adiposity play a large role in type 2 diabetes development in asian indians ( 7 ) in both developed and developing country settings , since the adjustment for age , sex , waist circumference , and systolic blood pressure did not explain differences in the odds of prediabetes or type 2 diabetes between the two groups . furthermore , while the prevalence of type 2 diabetes was lower in asian indians living in the u.s . than in india , it was still considerably higher than the general u.s . risk factors for type 2 diabetes development such as high - carbohydrate and / or - fat diets and sedentary lifestyles were once considered to influence those who had migrated to developed countries leading to an increased prevalence of diabetes in migrants than in those who remained in developing country settings ( 17,18 ) . the results of our study are among the first to highlight a higher prevalence of diabetes in individuals living in india than their counterparts who have immigrated to the u.s . it is therefore possible that , given the rapid economic and nutritional transitions currently taking place in india ( 7,8 ) , these factors now exacerbate risks in asian indians both in india and abroad . it is also possible that with more increased knowledge of beneficial diet and lifestyle choices , migrant asian indians may be shifting toward more health - promoting dietary patterns . a more thorough understanding of the dietary transitions taking place in india and in diaspora indians could provide important insights into the development of type 2 diabetes in nonobese phenotypes . it is possible that asian indians in the u.s . may also have increased knowledge regarding diabetes prevention and greater access to health care ( 16,22 ) than asian indians in india . such factors may serve to protect immigrant populations against type 2 diabetes risk ; however , further research is needed in this area . our study directly compared the age - specific prevalence of prediabetes , type 2 diabetes , and the associated risk factors between asian indians living in the u.s . and india . while there were differences in the sampling frames and sociodemographic characteristics between the two studies , both are large population - based samples with similar anthropometric and laboratory measures that are representative of asian indians in large urban centers either in india or in the u.s . additionally , while participants from carrs are primarily of south indian origin and participants from masala migrated from all parts of india , it is possible that the differences in type 2 diabetes prevalence between the groups could be attributed to differences in regional origins . however , when we restricted our analyses to participants from masala with origins in south india only , the finding of a high prevalence of diabetes and a relatively lower prevalence of prediabetes in asian indians from carrs compared with asian indians from masala remained virtually unchanged . these results suggest that the differences in type 2 diabetes prevalence between the groups are likely not attributable to region of origin . furthermore , while there were large differences in education status as well as height between asian indians living in india and the u.s . , adjustment for education and height in multivariable models as proxy measures for socioeconomic status prior to migration attenuated the effect of migration on the odds of diabetes between the two groups . these results suggest a possible healthy migrant effect , whereby individuals with greater access to education as well as early maternal and childhood nutrition were more likely to have the means for migration . however , while participants from the masala study had high levels of educational attainment , diabetes prevalence in this group was still considerably higher than that in the general u.s . population ( 20,21 ) , thereby suggesting that factors besides education attainment play a large role in diabetes risk in asian indians . being that our study directly compares two distinct asian indian populations from differing geographic regions ( chennai , india , and the greater san francisco and chicago areas of the u.s . ) the results can not be generalized to asian indians living in other parts of india or the u.s . however , several studies have noted an increasingly high prevalence of diabetes in urban india ( 2325 ) with recent evidence indicating a rise of diabetes in rural areas of india as well ( 26 ) . therefore , the high prevalence of diabetes in one urban indian city as reported in this study may be indicative of an even larger burden of disease in india yet to come . furthermore , the diabetes prevalence in masala study participants was similar to what was found in a recently published study of asian indians in michigan ( 27 ) . however , additional national level data are needed to assess the prevalence of diabetes among asian indians living in the u.s . our findings point to a high prevalence of type 2 diabetes in urban india with a paradoxically low prevalence of prediabetes compared with urban asian indians in the u.s . furthermore , the increased type 2 diabetes prevalence in asian indians in india is evident in both sexes , in all age - groups , and at all levels of bmi and therefore can not be explained by differences in anthropometry or age alone . these findings suggest the need for collaborative longitudinal research efforts between india and the u.s . such collaborations could help identify the gene - environment - lifestyle exposures that underlie the elevated risk for type 2 diabetes development in asian indians .\noutput:\n" }, { "from": "agent", "value": "objectiveto assess the prevalence of diabetes and prediabetes and the associated risk factors in two asian indian populations living in different environments.research design and methodswe performed cross - sectional analyses , using representative samples of 2,305 asian indians aged 4084 years living in chennai , india , from the centre for cardiometabolic risk reduction in south - asia study ( carrs ) ( 20102011 ) , and 757 asian indians aged 4084 years living in the greater san francisco and chicago areas from the u.s . mediators of atherosclerosis in south asians living in america ( masala ) study ( 20102013 ) . diabetes was defined as self - reported use of glucose - lowering medication , fasting glucose 126 mg / dl , or 2 - h glucose 200 mg / dl . prediabetes was defined as fasting glucose 100125 mg / dl and / or 2 - h glucose 140199 mg / dl.resultsage - adjusted diabetes prevalence was higher in india ( 38 % [ 95 % ci 3640 ] ) than in the u.s . ( 24 % [ 95 % ci 2127 ] ) . age - adjusted prediabetes prevalence was lower in india ( 24 % [ 95 % ci 2226 ] ) than in the u.s . ( 33 % [ 95 % ci 3036 ] ) . after adjustment for age , sex , waist circumference , and systolic blood pressure , living in the u.s . was associated with an increased odds for prediabetes ( odds ratio 1.2 [ 95 % ci 0.91.5 ] ) and a decreased odds for diabetes ( odds ratio 0.5 [ 95 % ci 0.40.6 ] ) . conclusionsthese findings indicate possible changes in the relationship between migration and diabetes risk and highlight the growing burden of disease in urban india . additionally , these results call for longitudinal studies to better identify the gene - environment - lifestyle exposures that underlie the elevated risk for type 2 diabetes development in asian indians ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the singapore chinese health study is a population - based cohort of 63,257 chinese women and men , aged 4574 years and enrolled between april 1993 and december 1998 from government housing estates , where 86 % of the entire singapore population resided ( 4 ) . our cohort subjects were drawn from the two major dialect groups of chinese in singapore , the hokkiens and the cantonese , who originated from two contiguous prefectures in southern china . the institutional review boards at the national university of singapore and the university of minnesota approved this study . at recruitment , subjects were interviewed in person using a structured questionnaire that asked for information including demographics , use of tobacco , menstrual ( including menopausal status ) and reproductive ( including use of hormone replacement therapy ) histories ( women only ) , medical history , as well as a dietary component assessing current intake patterns ( 4 ) . the subjects were asked if they had a history of physician - diagnosed diabetes , and positive subjects were also asked for their ages at the time of diagnosis to compute duration of disease as the difference between age of diagnosis and age at recruitment . identification of hip fracture cases among cohort members was accomplished through record linkage of cohort files with databases of the mediclaim system , which has captured inpatient discharge information from all private and public hospitals in singapore since 1990 ( 5 ) . all cases identified via linkage were verified by records of the appropriate surgical procedures or manual review of medical records . records of death were captured through linkage with the singapore registry of births and deaths . as of 31 december 2008we excluded from statistical analysis 103 prevalent cases of hip fracture that occurred before subjects ' recruitment to the cohort . thus , 1,213 subjects with hip fractures and 61,941 subjects without hip fractures were included in the final analysis . for each studysubject , person - years were counted from the date of baseline interview to the date of hip fracture diagnosis , date of death , or 31 december 2008whichever occurred first . we used the test ( for categorical variables ) or the student 's t test ( for continuous variables ) to examine the difference in distributions of baseline characteristics between case subjects and non case subjects . hip fracture associations in men and women separately and both sexes combined , with adjustment for sex . to adjust for the potential confounding effects of other demographic and exposure characteristics on the diabeteship fracture association , the following variables were included in all regression models : age at recruitment ( years ) , year of recruitment , dialect group ( hokkien , cantonese ) , level of education ( no formal education , primary , secondary or higher ) , weekly vigorous work or strenuous sports ( yes , no ) , bmi ( kg / m ) , number of cigarettes smoked per day ( never smoker , 112 , 1322 , or 23 ) , number of years of smoking ( never - smoker , 119 , 2039 , or 40 ) , number of years since quitting smoking ( continuous smoker , 1 , 14 , 519 , 20 , or never smoker ) , total calcium intake from food and supplement ( mg / 1,000 kcal / day ) , total soy isoflavone intake ( mg / 1,000 kcal / day ) , and history of physician - diagnosed stroke . linear trend tests for exposure - disease associations were based on the ordinal values of the quartiles . statistical computing was conducted using sas version 9.1 ( sas institute , cary , nc ) . all cited p values were two - sided . after excluding the 103 subjects with hip fractures before recruitment , among the 63,154 subjects included in this analysis , 5,668 ( 9.0 % ) reported a history of physician - diagnosed diabetes . the age at diagnosis of diabetes was 51.89.5 years ( mean sd ) , with a range of 3074 years . people with diabetes were older , were less educated , had higher bmi , were more likely to have smoked cigarettes over their lifetime , were more likely to have a history of stroke , and consumed greater amount of dietary calcium ( table 1 ) . as of 31 december 2008 , after a mean duration of 12.23.3 years in follow - up , 1,213 incident cases ( 342 men and 871 women ) of hip fracture had occurred in this cohort . case subjects were less educated , more likely to have a history of stroke , and possessed a lower bmi . patients with hip fracture smoked for a greater number of years , if they ever smoked , than subjects without hip fracture . hip fracture patients had lower intake of soy isoflavones but higher intake of calcium than individuals without hip fracture ( table 1 ) . baseline characteristics of cohort members by history of diabetes and incident hip fracture status : the singapore chinese health study ( 19932008 ) data are means sd or percent . * among ever - smokers only . the risk of hip fracture among people with diabetes was twice that among individuals without diabetes ( rr 1.98 , 95 % ci 1.712.29 ) after adjustment for other risk factors , including bmi , physical activity , smoking , calcium and soy consumption , and self - reported history of stroke . the risk estimate in the model that did not include bmi as a covariate was essentially unchanged ( rr 1.94 , 95 % ci 1.682.25 ) . this risk elevation was present in both sexes regardless of levels of bmi ( table 2 ) . after excluding 10 % of subjects with diabetes whose age at diagnosis was 40 years , the results remained essentially the same ( rr 1.83 , 95 % ci 1.572.13 ) . risk of hip fracture and history of diabetes in the singapore chinese health study ( 19932008 ) * adjusted for age at recruitment , sex ( for all ) , year of recruitment , dialect group ( hokkien , cantonese ) , level of education ( no formal education , primary , secondary or higher ) . further adjusted for weekly vigorous work or strenuous sports ( yes , no ) , bmi ( kg / m ) , number of cigarettes smoked per day ( never - smoker , 112 , 1322 , or 23 ) , number of years of smoking ( never - smoker , 119 , 2039 , or 40 ) , number of years since quitting smoking ( continuous smoker , 1 , 14 , 519 , 20 , or never smoker ) , total calcium intake from food and supplement ( mg / 1,000 kcal / day ) , total soy isoflavone intake ( mg / 1,000 kcal / day ) , and self - reported stroke . hip fracture association according to the duration of physician - diagnosed diabetes at the time of the baseline interview . because most subjects with longer duration of disease might be older than subjects with shorter disease duration , we adjusted for age at recruitment in these analyses . while the relative risk ( 95 % ci ) for hip fracture among patients with diabetes diagnosed 5 years before baseline interview was 1.40 ( 1.081.82 ) compared with subjects without a history of diabetes , the risk increased to 2.66 ( 2.043.47 ) for patients with diabetes whose initial diagnosis was 15 years before the recruitment ( table 3 ) . risk of hip fracture and duration of diabetes in the singapore chinese health study ( 19932008 ) * adjusted for age at recruitment , sex , year of recruitment , dialect group ( hokkien , cantonese ) , level of education ( no formal education , primary , secondary or higher ) . further adjusted for weekly vigorous work or strenuous sports ( yes , no ) , bmi ( kg / m ) , number of cigarettes smoked per day ( never - smoker , 112 , 1322 , or 23 ) , number of years of smoking ( never - smoker , 119 , 2039 , or 40 ) , number of years since quitting smoking ( continuous smoker , 1 , 14 , 519 , 20 , or never - smoker ) , total calcium intake from food and supplement ( mg / 1,000 kcal / day ) , total soy isoflavone intake ( mg / 1,000 kcal / day ) , and self - reported stroke . our results are consistent with the body of epidemiologic evidence from western populations that links a history of diabetes with risk of osteoporotic hip fractures . to our knowledge , this is the first prospective cohort study that examines such an association in a nonwhite population living in asia . our results show that the risk of hip fracture is higher among people with diabetes than among individuals without diabetes ; this risk increases with duration of diabetes , and the risk estimates are similar between men and women , as well as between lean and obese individuals . the results in this study are compatible with the results of a meta - analysis involving 11 cohort studies from western populations that documented a risk elevation of 1.8 ( 95 % ci - 1.32.4 ) among people with diabetes relative to individuals without a history of diabetes . although we did not differentiate between the two types of diabetes in this study , it can be assumed from the age of onset that the majority in this middle - aged and elderly cohort had type 2 diabetes . consequently , our results are similar to the risk documented for type 2 diabetes in this meta - analysis , which was lower than that for type 1 diabetes ( 3 ) . while the earlier world health organization hip fracture risk prediction tool ( frax ) did not include diabetes as a clinical risk factor ( 6 ) , a more recently developed hip fracture assessment algorithm derived from a cohort in the u.k . , the qfracturescore , included type 2 diabetes as a significant clinical factor and documented that men with diabetes had a 38 % increased risk , whereas women with diabetes had a 67 % increased risk compared with their counterparts without diabetes , respectively , in a multivariate model . this elevation in risk was comparable to other well - established risk factors such as moderate smoking and current use of corticosteroids ( 7 ) . several mechanisms have been proposed to explain the increased fracture risk associated with diabetes ( 8 ) . although bone mineral density is decreased in type 1 diabetes but increased in type 2 diabetes ( 9 ) , both types of diabetes may be linked to inhibited bone formation from hyperglycemia ( 10,11 ) . human studies also concur with experimental animal models that suggested that bone samples from animals with diabetes were weaker than those from animals without diabetes , possibly due to mechanical deterioration and decrease in bone strength ( 12,13 ) . while osteoporosis is often defined in terms of bone mineral density according to world health organization guidelines , in light of recent advances on the structural basis of skeletal fragility , it became clear that bone density represents only one of the contributors to bone strength . even if bone mineral density is within the acceptable range , disruption of bone microarchitecture or alteration in the amount and variety of proteins in bone can still increase the risk of fractures ( 14 ) . patients with diabetes also experience accelerated bone loss from hypercalciuria , impaired renal function , endogenous insulin deficiency , and microvascular complications . other complications of diabetes , including retinopathy , peripheral neuropathy , and vasculopathy , can also potentially increase the risk of falls in elderly patients with diabetes ( 8 ) . high bmi or obesity , which is common among people with diabetes , is a known protective factor for hip fracture ( 15 ) . consistent with published literature , we have earlier reported results from this cohort that showed an inverse dose - dependent relation between bmi and hip fracture risk ( 16 ) . in the present study , we show that higher bmi does not provide any significant protection for individuals with diabetes , since the risk estimates with and without adjustment for bmi were essentially the same . these results are consistent with published data from cohort studies that adjusted for bmi ( 1719 ) . a study of u.s . women in the nurses ' health study divided the women into two groups using a cutoff of 30 kg / m and showed that the association between diabetes and hip fracture risk was similar in obese and nonobese women ( 20 ) . our results support this earlier finding in showing that the impact of diabetes on hip fracture risk is consistent across four strata of bmi . thus , our results do not support the notion that increased bmi in people with diabetes may ameliorate the increased hip fracture risk associated with diabetes ( 9 ) . although a meta - regression analysis did not show any significant association between duration of diabetes and bone mineral density ( 9 ) , the meta - analysis of 10 cohort studies in western populations showed that the risk of hip fracture among patients with diabetes was higher in studies with 10 years of follow - up compared with patients with shorter durations of follow - up ( 3 ) . a study among elderly australians from the blue mountains eye study showed significant association between duration of diabetes and risk of fracture of proximal humerus but not the hip ( 21 ) , while another prospective study on elderly women from the iowa women 's health study failed to show significant associations with duration of diabetes 12 years at baseline ( 22 ) . we hypothesized that if diabetes played an etiologic role in hip fracture , the impact of diabetes on the risk of developing hip fracture would be stronger in patients with diabetes who had longer duration than patients who had shorter duration of the disease . in this study , we had a sufficient number of patients with diabetes to allow us to conduct analysis across four different time intervals between the diagnosis of diabetes and the interview at baseline . these results showed a compelling dose - dependent association with diabetes duration as well as a significant 40 % increase in risk , even in patients with diabetes 5 years from baseline , which concurred with findings from the nurses ' health study ( 20 ) . because the information about the diagnosis and duration of diabetes , as well as other lifestyle and dietary factors , was obtained before the occurrence of hip fracture , the exposure data can be considered free of recall bias and allow us to establish the temporal sequence in this diabeteship fractures have the most devastating consequence in morbidity and mortality among all osteoporotic fractures , and the incidence of hip fracture is commonly used to indicate the prevalence of osteoporosis ( 23 ) . hence , the examination of hip fracture risk has direct and important public health implication on prevention of osteoporosis in any population . singapore is a small city - state with a system for easy access to specialized medical care . because practically all hip fracture case subjects will seek medical attention immediately and the majority of case subjects are hospitalized for surgical intervention , our capture of hip fracture incidence in this cohort can be considered complete by using linkage with this comprehensive nationwide hospital database that was established 3 years before the initiation of the cohort study . unlike other western studies with few subjects in the low bmi categories , this singapore chinese cohort had enough subjects in the low range of bmi to examine if bmi had a modifying effect on diabetes hip fracture association . although the diagnosis of diabetes was obtained through self - report , in another study conducted on a subset of 1,651 subjects who had a self - reported history of physician - diagnosed diabetes in this cohort , 98.8 % had their diabetes status verified either by their hospital records of diabetes in the mediclaim system or through a second interview specific to the diagnosis , treatment , or complications of diabetes ( 24 ) . on the other hand , undiagnosed diabetes among the 57,486 subjects who did not report a history of diabetes is a real possibility . however , since diabetes status was ascertained before the hip fracture outcome , any misclassification of diabetes would probably not differ by fracture status , and such nondifferential misclassification of exposure would only lead to an attenuation of the real risk estimate . a limitation of the current study is its lack of information on potential confounders such as previous history of falls , use of corticosteroids , and serum vitamin d status . we also did not have information on treatment or control of diabetes , or information on other complications related to diabetes that may increase the risk of falls , such as hypoglycemia , retinopathy , and neuropathy . when this cohort was established between 1993 and 1998 , only individuals between 45 and 74 years of age ( a mean age of 58 years ) were eligible for the cohort study . hence , the average age of hip fracture among our cohort was younger ( 72.8 years ) than that observed in a general population . a previous report showed that the incidence of hip fracture increased markedly with age after the age of 64 years in singapore , which is similar to the trend in western populations such as the u.s . our results fill the existing void in population - based prospective data derived from nonwhite populations . this study strengthens the epidemiologic evidence of an association between diabetes and hip fracture risk . however , because of the dire consequences of hip fracture , we propose that active management of osteoporosis through early and regular assessment of bone mineral density , regular exercise to improve muscle strength and balance , and specific measures for preventing falls should be included in the management of elderly individuals with longstanding diabetes . because the information about the diagnosis and duration of diabetes , as well as other lifestyle and dietary factors , was obtained before the occurrence of hip fracture , the exposure data can be considered free of recall bias and allow us to establish the temporal sequence in this diabetes hip fracture risk association . hip fractures have the most devastating consequence in morbidity and mortality among all osteoporotic fractures , and the incidence of hip fracture is commonly used to indicate the prevalence of osteoporosis ( 23 ) . hence , the examination of hip fracture risk has direct and important public health implication on prevention of osteoporosis in any population . singapore is a small city - state with a system for easy access to specialized medical care . because practically all hip fracture case subjects will seek medical attention immediately and the majority of case subjects are hospitalized for surgical intervention , our capture of hip fracture incidence in this cohort can be considered complete by using linkage with this comprehensive nationwide hospital database that was established 3 years before the initiation of the cohort study . unlike other western studies with few subjects in the low bmi categories , this singapore chinese cohort had enough subjects in the low range of bmi to examine if bmi had a modifying effect on diabetes hip fracture association . although the diagnosis of diabetes was obtained through self - report , in another study conducted on a subset of 1,651 subjects who had a self - reported history of physician - diagnosed diabetes in this cohort , 98.8 % had their diabetes status verified either by their hospital records of diabetes in the mediclaim system or through a second interview specific to the diagnosis , treatment , or complications of diabetes ( 24 ) . on the other hand , undiagnosed diabetes among the 57,486 subjects who did not report a history of diabetes is a real possibility . however , since diabetes status was ascertained before the hip fracture outcome , any misclassification of diabetes would probably not differ by fracture status , and such nondifferential misclassification of exposure would only lead to an attenuation of the real risk estimate . a limitation of the current study is its lack of information on potential confounders such as previous history of falls , use of corticosteroids , and serum vitamin d status . we also did not have information on treatment or control of diabetes , or information on other complications related to diabetes that may increase the risk of falls , such as hypoglycemia , retinopathy , and neuropathy . when this cohort was established between 1993 and 1998 , only individuals between 45 and 74 years of age ( a mean age of 58 years ) were eligible for the cohort study . hence , the average age of hip fracture among our cohort was younger ( 72.8 years ) than that observed in a general population . a previous report showed that the incidence of hip fracture increased markedly with age after the age of 64 years in singapore , which is similar to the trend in western populations such as the u.s . our results fill the existing void in population - based prospective data derived from nonwhite populations . this study strengthens the epidemiologic evidence of an association between diabetes and hip fracture risk . however , because of the dire consequences of hip fracture , we propose that active management of osteoporosis through early and regular assessment of bone mineral density , regular exercise to improve muscle strength and balance , and specific measures for preventing falls should be included in the management of elderly individuals with longstanding diabetes .\noutput:\n" }, { "from": "agent", "value": "objectiveasian populations are documenting rapid increases in the rates of diabetes and hip fracture , but there are no prospective data linking both diseases in asian studies . we investigated this association among a cohort of chinese in singapore.research design and methodsa prospective cohort of 63,257 chinese in the singapore chinese health study , established between 1993 and 1998 , was followed up for a mean duration of 12 years . diabetes status was ascertained by baseline interviews , and incidence of hip fracture post - enrollment was identified through a nationwide hospital discharge database.resultsthe risk of hip fracture , after adjustment for other risk factors , was almost double among people with diabetes compared with people without diabetes ( relative risk 1.98 , 95 % ci 1.712.29 ) . when stratified by bmi , the increase in risk of hip fracture among people with diabetes relative to people without diabetes was similar in all four strata . there was a very strong dose - dependent relationship between duration of diabetes and risk of hip fracture ( p for trend < 0.0001 ) . compared with people without diabetes , the relative risk ( 95 % ci ) among subjects with diabetes for < 5 years at recruitment was 1.40 ( 1.081.82 ) , and this risk increased to 2.66 ( 2.043.47 ) among individuals with diabetes for 15 years.conclusionsasians with diabetes , like their western counterparts , experience an increased risk of hip fracture . early assessment for osteoporosis and increased fracture risk , as well as prevention of falls , should be part of the management of diabetes ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: hepatitis c virus ( hcv ) is a ribonucleic acid ( rna ) virus that causes chronic hepatitis and liver failure , worldwide .1,2 it consists of six different genotypes that are differentially distributed geographically .3,4 success of treatment varies greatly depending on the genotype .4,5 the genome contains cis - acting replication elements ( cres ) that are critical for hcv rna replication and translation .6,7 rna structural elements present in 5 - and 3 - untranslated regions ( 3utr ) of the hcv genome interact with viral and cellular proteins to initiate and facilitate the replication and translation processes .811 in our previous studies , we showed that rna secondary structure of the nonstructural ( ns ) 5b coding region of the hcv genome was required for hcv rna replication , and hence viral particle production .1215 it has been shown that the x region in the 3 - utr of the hcv rna genome contains a highly conserved sequence .16 the latter have also been found to form stable secondary stem - loop structures that require physical contact between its rna - dependent rna polymerase for hcv replication .1719 we hypothesized that rna structural analogs resembling secondary stem - loop structure of the x region could be created that can compete with natural hcv genomic structure for binding to proteins and inhibit hcv replication . the aim of this study was to introduce rna structural analogs resembling these cres into human liver cells and to identify secondary structural elements of the hcv x - region involved in hcv replication and infection . in order to identify important secondary structural elements , the effects of hcv structural analogs on hcv replication in two model cell lines were studied : a constitutive replication model and an infection model . in addition , to evaluate whether differences in viral genotype could affect the possible interactions of structural analogs , viruses representing two different genotypes 1 and 2 , were studied . replicon cells , bb7 , a cell culture system containing the hcv genotype 1b genome , were obtained from apath ( st . louis , usa ) .20,21 cells were maintained in dulbecco 's modified eagle medium ( dmem ) supplemented with antibiotic / antimycotic solution ( invitrogen , usa ) , 10 % fetal bovine serum ( fbs ) and 0.5 mg / ml g418 . for jfh - 1 hcv genotype 2a studies , huh7 .5 cells ( human hepatoma cell line ) ( obtained from dr . charles rice , rockefeller university , ny , usa ) were maintained in dmem supplemented with antibiotic / antimycotic solution and 10 % fbs . jfh - 1 complementary deoxyribonucleic acid ( cdna ) , an hcv genotype 2a strain , from dr . takaji wakita ( national institute of infectious diseases , tokyo , japan ) 2224 was used to produce infectious hcv viral particles in huh7 .5.25,26 to make jfh - 1 hcv stocks for infection , huh 7.5 cells were infected with jfh - 1 hcv . media were collected 5 days post - infection and centrifuged at 1000g for 20 min to remove debris . jfh - 1 hcv in media was concentrated with a centrifugal device ( 100k nmwl , amicon ultra , millipore , usa ) . infectivity levels of viral stocks were checked by quantitation of jfh - 1 hcv rna in media 48 h post - infection of huh7 .5 cells with hcv genotype 2a specific primers ( table 1 ) using real time reverse transcriptase polymerase chain reaction ( rt - pcr ) . the pcr conditions were : one cycle of 2 min at 50 c and 10 min at 95 c followed by 40 cycles of 15 sec at 95 c and 1 min at 60 c . specificity of all designed primers was determined with pcr amplification and sequencing of amplified product ( data not shown ) . melt curve analysis was performed following each rt - pcr to identify the presence of primer dimers and analyze the specificity of the reaction . cmv , cytomegalovirus ; fw , forward ; hcv , hepatitis c virus ; jfh - 1 , japanese fulminant hepatitis virus - 1 ; ldha , lactate dehydrogenase a ; rv , reverse . rna structural analog x-94 was designed to be 100 % identical to the ( + ) strand of x - region ( 9508 - 9605 nucleotides ( nt ) ) on the 3 - end of the hcv genotype 1b ( 94 % identical to genotype 2a ) genome ( fig .1 a ) . to determine whether stem - loop structures versus specific sequences of hcv of rna were most important in hcv replication , base pair changes , described below , were made in stems ( analog x-12 ) and loops ( analog x-12c ) of analog x-94 ( fig . 1b and 1d ) . several software products are available for prediction of secondary structures of rna based on thermodynamic parameters . because of its high reliability and reproducibility , mfold ver3 .2 was used in the current study .2729 rna structural analogs x-12 and x-12c were predicted to adopt stem - loop structure identical to analog x-94 ( fig . table 3 shows the percent identity of the various rna structural analogs with hcv genotypes 1b and 2a . to determine the minimal structure of the x - region that could inhibit hcv rna replication , shorter rna structural analogs x-12a and x-12b ( fig .1 c ) were designed that were predicted to retain individual stem - loop structures of analog x - 94.2729 all analogs were named based on hcv genome region studied and sequence homology of the analogues relative to the jfh - 1 hcv genotype 2a genome . for expression studies , the x-94 sequence was subcloned into a psilencer 4.1 cytomegalovirus ( cmv ) puro plasmid ( ambion , usa ) , as previously described .12 psilencer 4.1 cmv puro plasmid enables high level expression of cloned hairpin short rna templates . expression vectors for rna structural analogs x-12 and x-12c were constructed from a plasmid expressing the rna analog x-94 using a quikchange ii site - directed mutagenesis kit ( agilent technologies , inc .1 b shows nucleotide replacements made in stems of analog x-94 resulting in analog x-12 , and fig .1 d illustrates nucleotide replacements made in loops of analog x-12 to construct analog x-12c . shorter rna structural analogs x-12a and x-12b ( fig .1 c ) were constructed from a plasmid expressing rna analog x-12 using a quikchange ii site - directed mutagenesis kit . these sequences were selected as non - overlapping fragments of x-12 that were individually predicted by mfold to retain all the structural elements present in the parent x-12 analog .5 b - 74 rna analog , which was previously shown to inhibit viral genome replication12 was used as a positive control for inhibition of viral replication , and a plasmid expressing an unrelated sequence , hb , from hepatitis b virus was used as negative control . an rna structural analog 5b - 46 was predicted to adopt stem - loop structures identical to analog 5b - 74 as determined by mfold , and was constructed using a plasmid expressing rna analog 5b - 74 with quikchange ii site - directed mutagenesis kit . sequences of each analog in psilencer 4.1 cmv puro plasmid ( ambion ) were verified with cmv puro primers ( table 1 ) as recommended by the manufacturer . for bb7hcv genotype 1b replicon studies , cells were plated in 6 - well plates 2 days before transfection . seventy - five percent confluent cells were transfected with various amounts of each plasmid to generate rna structural analogs individually or in combinations using lipofectamine ( life technologies ) according to manufacturer 's instructions . in brief , lipofectamine and plasmid dna were separately diluted in opti - mem i medium ( invitrogen ) without serum . after 15 min incubation , they were combined , incubated for 20 min at room temperature , and added to cells in varying concentrations . cells were harvested 48 h post - transfection with trizol ( invitrogen ) , and hcv rna levels quantitated in the cell lysates . for hcv genotype2a infection studies , two models were used : transfection into cells with a pre - existing infection and transfection into cells before infection . for pre - existing jfh - 1hcv infection studies , 75 % confluent huh7 .5 cells were infected with jfh - 1 hcv for 8 h and then transfected with plasmids expressing rna structural analogs with lipofectamine , as described above . in brief , cells were washed with phosphate buffered saline ( pbs ) . lipofectamine and plasmid dna were separately diluted in opti - mem i medium without serum . after a 15 min incubation , they were combined , and incubated for 20 min at room temperature before being added to cells . culture medium , 200 l , was collected for quantification of jfh - 1 hcv levels , and replaced with fresh 200 l of cell culture medium at 0 , 4 , 8 , 12 , 24 , 36 , 48 , and 72 h of transfection . for before infection studies , 75 % confluent huh7 .5 cells in 6 - well plates were transfected with 16 g of each plasmid expressing rna structural analogs , as described above . after 8 h of infection , cells were washed twice with pbs to remove input jfh - 1 hcv . culture medium , 200 l , was collected for quantification of jfh - 1 hcv levels and replaced with fresh 200 l of cell culture medium at 0 , 4 , 8 , 12 , 24 , 36 , 48 , and 72 h of infection . for bb7 hcv genotype 1b studies , whole cell rna was isolated from replicon cell lysates with an rneasy kit ( qiagen , germany ) according to manufacturer 's instructions and treated with rnase free dnase ( invitrogen ) . cdna was synthesized using 4 g dnase treated rna with superscript iii first - strand kit ( invitrogen ) and quantified by real time rt - pcr with power sybr green pcr master mix ( applied biosystems , usa ) using hcv genotype 1b specific primers ( table 1 ) according to manufacturer 's instructions . human lactate dehydrogenase a ( ldha ) mrna levels were quantified in each sample to normalize hcv rna levels using human ldha specific primers ( table 1 ) . assays were done in quadruplicate , and results expressed as mean standard error of hcv rna levels in cells transfected with analogs compared to untreated controls . for jfh - 1 hcv infection studies , viral rna was extracted from 200 l media collected from infected cells with a qiaamp viral rna kit ( qiagen , germany ) according to manufacturer 's instructions . cdna was synthesized using 4 g rna with superscript iii first - strand kit ( invitrogen ) , and quantified by real - time rt - pcr with power sybr green pcr master mix ( applied biosystems ) using jfh - 1 hcv rna specific primers ( table 1 ) according to manufacturer 's instructions . assays were repeated with three independent replicates , and results are expressed as means standard error of jfh - 1 hcv rna levels in media from infected cells transfected with analogs before or after infection compared to untreated controls . in order to identify important secondary structural elements , the effects of hcv structural analogs on hcv replication in two model cell lines were studied : a constitutive replication model and an infection model . in addition , to evaluate whether differences in viral genotype could affect the possible interactions of structural analogs , viruses representing two different genotypes 1 and 2 , were studied . replicon cells , bb7 , a cell culture system containing the hcv genotype 1b genome , were obtained from apath ( st . louis , usa ) .20,21 cells were maintained in dulbecco 's modified eagle medium ( dmem ) supplemented with antibiotic / antimycotic solution ( invitrogen , usa ) , 10 % fetal bovine serum ( fbs ) and 0.5 mg / ml g418 . for jfh - 1 hcv genotype 2a studies , huh7 .5 cells ( human hepatoma cell line ) ( obtained from dr . charles rice , rockefeller university , ny , usa ) jfh - 1 complementary deoxyribonucleic acid ( cdna ) , an hcv genotype 2a strain , from dr . takaji wakita ( national institute of infectious diseases , tokyo , japan ) 2224 was used to produce infectious hcv viral particles in huh7 .5.25,26 to make jfh - 1 hcv stocks for infection , huh 7.5 cells were infected with jfh - 1 hcv . media were collected 5 days post - infection and centrifuged at 1000g for 20 min to remove debris . jfh - 1 hcv in media was concentrated with a centrifugal device ( 100k nmwl , amicon ultra , millipore , usa ) . infectivity levels of viral stocks were checked by quantitation of jfh - 1 hcv rna in media 48 h post - infection of huh7 .5 cells with hcv genotype 2a specific primers ( table 1 ) using real time reverse transcriptase polymerase chain reaction ( rt - pcr ) . the pcr conditions were : one cycle of 2 min at 50 c and 10 min at 95 c followed by 40 cycles of 15 sec at 95 c and 1 min at 60 c . specificity of all designed primers was determined with pcr amplification and sequencing of amplified product ( data not shown ) . melt curve analysis was performed following each rt - pcr to identify the presence of primer dimers and analyze the specificity of the reaction . cmv , cytomegalovirus ; fw , forward ; hcv , hepatitis c virus ; jfh - 1 , japanese fulminant hepatitis virus - 1 ; ldha , lactate dehydrogenase a ; rv , reverse . rna structural analog x-94 was designed to be 100 % identical to the ( + ) strand of x - region ( 9508 - 9605 nucleotides ( nt ) ) on the 3 - end of the hcv genotype 1b ( 94 % identical to genotype 2a ) genome ( fig .1 a ) . to determine whether stem - loop structures versus specific sequences of hcv of rna were most important in hcv replication , base pair changes , described below , were made in stems ( analog x-12 ) and loops ( analog x-12c ) of analog x-94 ( fig . 1b and 1d ) . several software products are available for prediction of secondary structures of rna based on thermodynamic parameters . because ofits high reliability and reproducibility , mfold ver 3.2 was used in the current study .2729 rna structural analogs x-12 and x-12c were predicted to adopt stem - loop structure identical to analog x-94 ( fig . 1b and 1d ) . table 3 shows the percent identity of the various rna structural analogs with hcv genotypes 1b and 2a . to determine the minimal structure of the x - region that could inhibit hcv rna replication , shorter rna structural analogs x-12a and x-12b ( fig .1 c ) were designed that were predicted to retain individual stem - loop structures of analog x - 94.2729 all analogs were named based on hcv genome region studied and sequence homology of the analogues relative to the jfh - 1 hcv genotype 2a genome . for expression studies , the x-94 sequence was subcloned into a psilencer 4.1 cytomegalovirus ( cmv ) puro plasmid ( ambion , usa ) , as previously described .12 psilencer 4.1 cmv puro plasmid enables high level expression of cloned hairpin short rna templates . expression vectors for rna structural analogs x-12 and x-12c were constructed from a plasmid expressing the rna analog x-94 using a quikchange ii site - directed mutagenesis kit ( agilent technologies , inc .1 b shows nucleotide replacements made in stems of analog x-94 resulting in analog x-12 , and fig .1 d illustrates nucleotide replacements made in loops of analog x-12 to construct analog x-12c . shorter rna structural analogs x-12a and x-12b ( fig .1 c ) were constructed from a plasmid expressing rna analog x-12 using a quikchange ii site - directed mutagenesis kit . these sequences were selected as non - overlapping fragments of x-12 that were individually predicted by mfold to retain all the structural elements present in the parent x-12 analog .5 b - 74 rna analog , which was previously shown to inhibit viral genome replication12 was used as a positive control for inhibition of viral replication , and a plasmid expressing an unrelated sequence , hb , from hepatitis b virus was used as negative control . an rna structural analog 5b - 46 was predicted to adopt stem - loop structures identical to analog 5b - 74 as determined by mfold , and was constructed using a plasmid expressing rna analog 5b - 74 with quikchange ii site - directed mutagenesis kit . sequences of each analog in psilencer 4.1 cmv puro plasmid ( ambion ) were verified with cmv puro primers ( table 1 ) as recommended by the manufacturer . for bb7hcv genotype 1b replicon studies , cells were plated in 6 - well plates 2 days before transfection . seventy - five percent confluent cells were transfected with various amounts of each plasmid to generate rna structural analogs individually or in combinations using lipofectamine ( life technologies ) according to manufacturer 's instructions . in brief , lipofectamine and plasmid dna were separately diluted in opti - mem i medium ( invitrogen ) without serum . after 15 min incubation , they were combined , incubated for 20 min at room temperature , and added to cells in varying concentrations . cells were harvested 48 h post - transfection with trizol ( invitrogen ) , and hcv rna levels quantitated in the cell lysates . for hcv genotype2a infection studies , two models were used : transfection into cells with a pre - existing infection and transfection into cells before infection . for pre - existing jfh - 1 hcv infection studies , 75 % confluent huh7 .5 cells were infected with jfh - 1 hcv for 8 h and then transfected with plasmids expressing rna structural analogs with lipofectamine , as described above . in brief , cells were washed with phosphate buffered saline ( pbs ) . lipofectamine and plasmid dna were separately diluted in opti - mem i medium without serum . after a 15 min incubation , they were combined , and incubated for 20 min at room temperature before being added to cells . culture medium , 200 l , was collected for quantification of jfh - 1 hcv levels , and replaced with fresh 200 l of cell culture medium at 0 , 4 , 8 , 12 , 24 , 36 , 48 , and 72 h of transfection . for before infection studies , 75 % confluent huh7 .5 cells in 6 - well plates were transfected with 16 g of each plasmid expressing rna structural analogs , as described above . cells were then infected with jfh - 1 hcv 48 h post - transfection . after 8 h of infection , cells were washed twice with pbs to remove input jfh - 1 hcv . culture medium , 200 l , was collected for quantification of jfh - 1 hcv levels and replaced with fresh 200 l of cell culture medium at 0 , 4 , 8 , 12 , 24 , 36 , 48 , and 72 h of infection . for bb7 hcv genotype 1b studies , whole cell rna was isolated from replicon cell lysates with an rneasy kit ( qiagen , germany ) according to manufacturer 's instructions and treated with rnase free dnase ( invitrogen ) . cdna was synthesized using 4 g dnase treated rna with superscript iii first - strand kit ( invitrogen ) and quantified by real time rt - pcr with power sybr green pcr master mix ( applied biosystems , usa ) using hcv genotype 1b specific primers ( table 1 ) according to manufacturer 's instructions . human lactate dehydrogenase a ( ldha ) mrna levels were quantified in each sample to normalize hcv rna levels using human ldha specific primers ( table 1 ) . assays were done in quadruplicate , and results expressed as mean standard error of hcv rna levels in cells transfected with analogs compared to untreated controls . for jfh - 1 hcvinfection studies , viral rna was extracted from 200 l media collected from infected cells with a qiaamp viral rna kit ( qiagen , germany ) according to manufacturer 's instructions . cdna was synthesized using 4 g rna with superscript iii first - strand kit ( invitrogen ) , and quantified by real - time rt - pcr with power sybr green pcr master mix ( applied biosystems ) using jfh - 1 hcv rna specific primers ( table 1 ) according to manufacturer 's instructions . assays were repeated with three independent replicates , and results are expressed as means standard error of jfh - 1 hcv rna levels in media from infected cells transfected with analogs before or after infection compared to untreated controls . analogs x-94 and x-12 were 100 % and 59 % identical to hcv genotype 1b , respectively , but were only 94 % and 12 % identical to the jfh - 1 hcv genome , respectively . analog x-12c was 50 % identical to hcv genotype 1b , and 0 % identical to the jfh - 1 hcv genome . to determine whether short rna sequences predicted to fold into secondary structural analogs of the x region of hcv rna genome could inhibit hcv replication , plasmids expressing rna analogs x-94 , x-12 , and x-12c were transfected in replicon cells .2 shows that the effects of transfection of plasmids expressing rna structural analogs were dose - dependent and most effective at 16 g of plasmid . higher doses did not increase effects beyond those at 16 g , and based on this information , 16 g of each plasmid was used for transfection for subsequent experiments .3 - ( 4,5 - dimethylthiazol -2-yl ) -2,5-diphenyltetrazolium bromide ( mtt ) assays showed no significant toxic effects due to dna transfection ( data not shown ) . replicon cells were transfected with various concentrations of plasmids expressing hb , 5b - 74 , x-94 , and x-12 . hcv rna levels were quantified in cell lysates by qrt - pcr 48 h post - transfection . the values represent hcv1b rna levels in transfected cells compared to untreated controls ( n = 4 ) , * p 0.001 .3 shows that transfection of plasmids generating rna analogs affected hcv rna levels in replicon cells . after transfection of 5b - 74 , 5b - 46 , x-94 , x-12 , and x-12c at 16 g , hcv rna levels were decreased to 42 % , 55 % , 52 % , 53 % , and 54 % , respectively , compared to levels of untreated controls . these differences were significant ( p 0.001 for all ) . an unrelated control plasmid ( hb ) generating an hbv sequence had no significant effect under identical conditions . furthermore , combinations of 5b - 74 plus x-94 and 5b - 46 plus x-12 administered at the same total dose , and under identical conditions , decreased hcv rna levels to 21 % and 30 % , ( p 0.001 ) , respectively , compared to untreated controls ( fig . these levels of inhibition for the combinations were greater than that for any individual analog alone . replicon cells were transfected with hb , 5b - 74 , x-94 , x-12 , x-12c , 5b - 74 plus x-94 , and 5b - 46 plus x-12 , and hcv rna levels were quantified in cell lysates by qrt - pcr 48 h post - transfection . the figure represents hcv 1b rna levels in transfected cells compared to untreated controls ( n = 4 ) , * p 0.001 . we wondered whether smaller structural elements could be produced that retained inhibitory effects . to test this hypothesis , two smaller analogs , x-12a and x-12b , were created that corresponded to nt 1 - 55 and nt 56 - 95 regions , respectively , of analog x-12 ( fig . transfection with x-12a decreased hcv rna to 58 % , about the same as intact x-12 ( p 0.001 ) . however , the other fragment , x-12b , was much less effective , resulting in a level of only 78 % and not significantly different from untreated control . a combination of x-12a plus x-12b inhibited levels to 60 % of untreated controls , which was similar to the effects of x-12a alone ( fig . the data suggested that the x-12a region was the portion of the x analog that was responsible for the majority of the inhibitory activity . replicon cells were transfected with hb , 5b - 74 , x-12a , x-12b , and x-12a plus x-12b , and hcv rna levels were quantified in cell lysates by qrt - pcr 48 h post - transfection . the figure represents hcv 1b rna levels in transfected cells compared to untreated controls ( n = 4 ) , * p 0.001 . to determine whether rna structural analogs were also effective in an infection model and against a different hcv genotype ,5 shows that the levels in untreated controls increased progressively , and by 12 h , exceeded the level of input hcv rna levels by 6-fold ( extreme left bars ) at 72 h. in contrast , huh7 .5 cells transfected with analogs 5b - 74 , 5b - 46 , x-94 , and x-12 and infected with jfh - 148 h later , inhibited hcv rna levels to 5.9 % , 6.2 % , 6.6 % , and 1.8 % , respectively , compared to untreated controls ( p 0.001 ) . even after 72 h , no cells treated with analogs had hcv rna levels that exceeded more than 30 % of input levels . huh7 .5 cells were transfected with analogs hb , 5b - 74 , 5b - 46 , x-94 , and x-12 and then infected with jfh - 1 hcv 48 h post - transfection . hcv rna levels in media were quantified by qrt - pcr at various time points post - infection . the values represent jfh - 1 hcv rna levels in media from cells transfected with analogs 48 h before infection compared to untreated controls at various time points ( n = 3 ) , * p 0.001 . to determine whether rna structural analogs could inhibit a pre - existing hcv infection , cells were infected with jfh - 1 hcv for 8 h and then transfected with analogs hb , 5b - 74 , 5b - 46 , x-94 , and x-12 .6 shows that there was a progressive increase in jfh - 1 hcv rna levels with time in the media compared to uninfected controls . rna levels exceeded those of input virus at 12 h post - transfection and were four - fold higher by 72 h. however , 72 h after transfection with analogs 5b - 74 , 5b - 46 , x-94 , and x-12 ; hcv rna levels were 8.8 % , 10.5 % , 9.0 % , and 11.6 % , respectively , compared to untreated controls . huh7 .5 cells infected with jfh - 1 hcv , and then transfected with analogs hb , 5b - 74 , 5b - 46 , x-94 and x-128 h post - infection . hcv rna levels in media from infected cells were quantified by qrt - pcr at various time points post - transfection . the figure represents jfh - 1 hcv rna levels in media from infected cells transfected with analogs 8 h post - infection compared to untreated controls at various time points ( n = 3 ) , * p 0.001 . many previous studies , including our own , have shown that specific domains of the genomes of some rna viruses are critical for viral translation and replication .3032 the ns5b coding region of the hcv genome adopts a stem - loop structure that is involved in the replication of hcv . expression of rna structural analogs predicted to mimic the stem - loop structure identical to the ns5b region of the hcv genome was able to inhibit replication of hcv genotype 2a .12 the current study confirms previous reports that rna secondary structure is important for hcv rna replication .16,33 conserved genomic rna sequences have been shown to fold to adopt stem - loop motifs that interact with other rna motifs and / or proteins required for translation and replication .10,31,3437 identification of such rna sequences and determination of secondary structure formed by these sequences are challenging because structural motifs depend on various parameters , including host cellular microenvironments and the presence of other host and viral interacting molecules .29,3840 several types of software have been developed to predict the stable structures formed by rna sequences based on thermodynamic parameters . the current data generated by mfold software confirm our previous findings that structures predicted using these two - dimensional models do have substantial inhibitory activity against hcv replication . it is also clear that the actual molecules exist not in a two - dimensional but a three - dimensional state , and it is the latter that causes the inhibitory activity . nevertheless , the data support the notion that two - dimensional structures are related to and can predict the activity of analogs in three - dimensions . the structural analogs were effective in models of both genotype 1 and 2 viruses , suggesting that because the design of the molecules was based on secondary rather than primary structure , the effects are more likely to be multigenotypic . this may be clinically relevant as it has already been demonstrated that some current direct acting antiviral agents vary in efficacy against hcv genotypes41 ,42 and even subtypes .43 design of novel anti - hcv agents based on secondary structural considerations may offer a strategy to develop new agents that are independent of viral genotype or subtype . for hcv genotype 1b studies , a replicon cell model with an integrated hcv genome was used to constitutively generate subgenomic hcv1b replicons in huh7 .5 cells .20 this system has been used extensively to determine the effects of various drugs and proteins on viral replication and infection .44,45 however , because hcv rna replication in this model is constitutive , it is not a simulation of hcv infection . for this reason , we examined here the effects of structural analogs on jfh1 , to provide a more realistic hcv infection model system .24,46,47 the results from the jfh - 1 infection model systems offered insight into the differences in efficacy among structural analogs depending on whether they were introduced before or after viral infection . the jfh - 1 hcv infection system has been used to determine the anti - hcv activity of several proteins and inhibitors ( example : raloxifene , nsc compounds ) before or after infection of hepatic cells .48,49 introduction of rna structural analogs after viral infection resembles treatment strategies for hepatocytes already infected with hcv , while exposure of cells before viral infection represents a potential prophylactic approach . expression of the stem - loop structure of x - region in the 3 - utr of hcv genome ( using rna analogs x-94 , x-12 , and x-12c ) was found to be effective against hcv replication , regardless of the sequence of rna . furthermore , we have identified a small portion , one of the stem - loop structures of the x - region , x-12a , as the smallest identified portion of the x - region analog that retains inhibitory activity . the other stem - loop structure , x-12b of approximately the same length ; which also possesses natural hcv sequences , was virtually ineffective . these data confirmed that a specific structure , the stem - loop conformation , was involved , and that the observed inhibitory effects were not due a nonspecific interaction of hcv sequences . the studies on nucleotide base substitution in the x - region showing reduction in the identity to the natural hcv sequence to less than 50 % , while retaining secondary structure , indicated that the observed inhibitory effects did not likely involve anti - sense mechanisms . the data indicate that conformation of secondary structures in 3 - utr of hcv rna genome is required for hcv replication . stable expression of rna analogs predicted to have identical stem - loop structures , but sequences vastly different from hcv genomic rna , might inhibit hcv infection of hepatocytes in liver , and may represent a novel approach to design anti - hcv agents .\noutput:\n" }, { "from": "agent", "value": "background and aimsthe noncoding regions in the 3 - untranslated region ( utr ) of the hepatitis c virus ( hcv ) genome contain secondary structures that are important for replication . the aim of this study was to identify detailed conformational elements of the x - region involved in hcv replication.methodsribonucleic acid ( rna ) structural analogs x94 , x12 , and x12c were constructed to have identical conformation but 94 % , 12 % , and 0 % sequence identity , respectively , to the x region of hcv genotype 2a . effects of structural analogs on replication of hcv genotypes 1b and 2a hcv rna were studied by quantitative reverse transcriptase polymerase chain reaction.resultsin replicon bb7 cells , a constitutive replication model , hcv rna levels decreased to 55 % , 52 % , 53 % , and 54 % after transfection with expression plasmids generating rna structural analogs 5b - 46 , x-94 , x-12 , and x-12c , respectively ( p < 0.001 for all ) . in an hcv genotype 2a infection model , rna analogs 5b - 46 , x-94 , and x-12 in hepatic cells inhibited replication to 11 % , 9 % , and 12 % , respectively . because the x-12 analog was only 12 % identical to the corresponding sequence of hcv genotype 2a , the sequence per se , or antisense effects were unlikely to be involved.conclusionsthe data suggest that conformation of secondary structures in 3 - utr of hcv rna genome is required for hcv replication . stable expression of rna analogs predicted to have identical stem - loop structures might inhibit hcv infection of hepatocytes in liver and may represent a novel approach to design anti - hcv agents ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: fluoride penetration in the enamel occurs through the replacement of the relatively weak hydroxyl ions in the enamel mineral structure by the much more active fluoride ions , thereby improving the chemical stability of the enamel structure and making it more resistant to acids .14 the presence of fluoride in the oral cavity , especially in the saliva , has also been shown to have beneficial effects .58 for these reasons , a number of fluoride products with different contents and uptake levels have been developed to provide supplemental fluoride in various forms . after dentifrices , fluoride mouthrinses represent one of the most useful fluoride products .1,2,812 the fluoride mouthrinses commonly used today are neutral ph , 0.05 % naf , stable chemical compounds13 that act topically to decrease enamel decalcification and increase remineralization .14,15 the most important function of fluoridated agents is to increase the enamel resistance to acid by decreasing solubility through the incorporation of fluoride into the enamel apatite structure . fluorapatite formation is based on a chemical equilibrium that allows the penetration of fluoride into the enamel . as with all chemical reactions , this process is strongly influenced by concentration and temperature .16 in a study examining the effects of heat on tin and fluoride uptake from topical snf2 solutions by enamel samples prepared from extracted bovine teeth , putt et al17 noted an increase in both tin and fluoride uptake with increase in temperature . barrancos18 also found that higher temperatures enhanced fluoride uptake by the enamel from topical acidulated phosphate fluoride ( apf ) solutions . in study conducted using powdered enamel over a wide temperature range , stearn and berndt19 found apf solutions to be correlated with an increase in fluoride content and caf2 formation . stookey and stahlman20 suggested that thermal changes resulting from friction were responsible for the enhanced fluoride uptake provided by fluoride - impregnated prophylactic cups . in order to better understand the effects of temperature on fluoride uptake , this study compared the rates and amounts of fluoride uptake by the enamel from a fluoridated mouthrinse at 3 different temperatures . the chemical substances and equipment used in this study are listed in tables 1 and 2 , respectively . all the teeth were visually examined to ensure that they were free from apparent caries , macroscopic cracks , abrasion , and excessive staining on the lingual and buccal surfaces . prior to use , the teeth were cleaned by gentle brushing with a fluoride - free toothpaste and stored in distilled water containing 0.1 % thymol at 4c . the crowns were separated from the roots 2 mm above the cemento - enamel junction and sectioned mesiodistally ; then , the labial surfaces were sectioned into 3 slabs by using a diamond saw ( isomet ; buehler , lake bluff , il , usa ) . the inner surfaces of each section were abraded using wet 360 - and 600 - grit silicon carbide paper to remove any remaining dentin , and the slabs were examined under a stereomicroscope ( leica mz12 ; leica ag , ch - 9435 heerbrugg , switzerland ) to confirm that they consisted of enamel alone . specimens were randomly divided into 3 groups ( n = 30 ) for treatment at different temperatures , namely , room temperature , 25c ; human body temperature , 37c ; and hyper - fever temperature , 43c . each group was further divided into 3 subgroups ( n = 10 ) to demonstrate the reproducibility of the measurements in each temperature group , and the average mass of each subgroup was calibrated ( 0.74120.0043 g ) using an analytical balance to ensure standardization ( table 3 ) . the slabs were stored in distilled water in polyethylene tubes that had been previously washed with distilled water , rinsed with bidistilled water , and dried in a sterilizer oven on blotting paper . a fluoride - specific ion electrode ( orion model 96 - 09 ; orion research , boston , ma , usa ) the total ion strength adjustment buffer ( tisab ) was used as a stabilizer .7,20 a standard 100 ppm fluoride solution ( orion research 940907 , boston , ma . , usa ) was used to prepare the calibration solutions .7,21 in order to establish calibration graphs , 50 ml of the calibration solutions were prepared using 25 ml of tisab solution and 25 ml of 2 , 4 , 6 , and 8 ppm fluoride solutions prepared from a standard fluoride solution of 100 ppm fluoride and distilled water . the actual fluoride content of the mouthrinse was determined using the calibration graph constructed from the calibration solutions ( figure 1 ) . calibration of the mouthrinse fluoride solution using the standard solution calibration graph ( r = 0.9924 ) , the fluoride concentration of the mouthrinse was determined to be 235 ppm , which is similar to the measurement reported by the manufacturer ( 230 ppm ) . on the basis of this calibration graph , the rinse volumes were calculated for solutions of 0.5 , 1.0 , 1.5 , 2.0 , and 2.5 ppm fluoride . calibration graphs for all the temperatures were constructed for determining the fluoride uptake by the enamel from the mouthrinse solution . table 4 shows the fluoride ppm and the corresponding mouthrinse volumes for 50 ml of the calibration solutions . calibration graphs for 25c , 37c , and 43c are shown in figures 2 , 3 , and 4 , respectively . test solutions of 0.426 ml of the fluoride mouthrinse were freshly prepared for each subgroup . magnetic stirrers and small magnets were used to maintain the stability and integrity of the solutions . all experiments were performed using freshly prepared solutions .22 temperature sensors , thermometers , and fluoride - specific electrodes were held in place in the solutions by using fixed holders . the surfaces of the electrodes and the temperature equipment were washed with distilled water and dried between groups . the fluoride content of each solution was measured using a potentiometer and recorded prior to the addition of the enamel specimens at 15 - s intervals up to 1 min , 1 - min intervals from 1 to 10 min , 5 - min intervals from 10 to 50 min , and 10 - min intervals from 50 to 120 min . the fluoride uptake by the enamel specimens was calculated in mv by subtracting the measured concentration from the previously measured concentration before the addition of the specimens . the calibration graphs were constructed with mv values on the y - axis and the ppm f values on the x - axis ; the ppm f values were calculated using the equation y = mx + n. the uptake of fluoride by the enamel specimens from the mouthrinse was measured and recorded from 15 s to 120 min . graphs of the fluoride uptake for each temperature group were drawn , and intragroup and intergroup comparisons were assessed using one - way analysis of variance and the least significant difference , with the level of significance set at p .05 . all the teeth were visually examined to ensure that they were free from apparent caries , macroscopic cracks , abrasion , and excessive staining on the lingual and buccal surfaces . prior to use , the teeth were cleaned by gentle brushing with a fluoride - free toothpaste and stored in distilled water containing 0.1 % thymol at 4c . the crowns were separated from the roots 2 mm above the cemento - enamel junction and sectioned mesiodistally ; then , the labial surfaces were sectioned into 3 slabs by using a diamond saw ( isomet ; buehler , lake bluff , il , usa ) . the inner surfaces of each section were abraded using wet 360 - and 600 - grit silicon carbide paper to remove any remaining dentin , and the slabs were examined under a stereomicroscope ( leica mz12 ; leica ag , ch - 9435 heerbrugg , switzerland ) to confirm that they consisted of enamel alone . specimens were randomly divided into 3 groups ( n = 30 ) for treatment at different temperatures , namely , room temperature , 25c ; human body temperature , 37c ; and hyper - fever temperature , 43c . each group was further divided into 3 subgroups ( n = 10 ) to demonstrate the reproducibility of the measurements in each temperature group , and the average mass of each subgroup was calibrated ( 0.74120.0043 g ) using an analytical balance to ensure standardization ( table 3 ) . the slabs were stored in distilled water in polyethylene tubes that had been previously washed with distilled water , rinsed with bidistilled water , and dried in a sterilizer oven on blotting paper . a fluoride - specific ion electrode ( orion model 96 - 09 ; orion research , boston , ma , usa ) was used to measure the fluoride concentrations . a standard 100 ppm fluoride solution ( orion research 940907 , boston , ma . , usa ) was used to prepare the calibration solutions .7,21 in order to establish calibration graphs , 50 ml of the calibration solutions were prepared using 25 ml of tisab solution and 25 ml of 2 , 4 , 6 , and 8 ppm fluoride solutions prepared from a standard fluoride solution of 100 ppm fluoride and distilled water . the actual fluoride content of the mouthrinse was determined using the calibration graph constructed from the calibration solutions ( figure 1 ) . calibration of the mouthrinse fluoride solution using the standard solution calibration graph ( r = 0.9924 ) , the fluoride concentration of the mouthrinse was determined to be 235 ppm , which is similar to the measurement reported by the manufacturer ( 230 ppm ) . on the basis of this calibration graph , the rinse volumes were calculated for solutions of 0.5 , 1.0 , 1.5 , 2.0 , and 2.5 ppm fluoride . calibration graphs for all the temperatures were constructed for determining the fluoride uptake by the enamel from the mouthrinse solution . table 4 shows the fluoride ppm and the corresponding mouthrinse volumes for 50 ml of the calibration solutions . separate solutions were prepared for each temperature at all ppm values . the mv values were recorded from the potentiometer screen after the readings stabilized . calibration graphs for 25c , 37c , and 43c are shown in figures 2 , 3 , and 4 , respectively . test solutions of 0.426 ml of the fluoride mouthrinse were freshly prepared for each subgroup . magnetic stirrers and small magnets were used to maintain the stability and integrity of the solutions . all experiments were performed using freshly prepared solutions .22 temperature sensors , thermometers , and fluoride - specific electrodes were held in place in the solutions by using fixed holders . the surfaces of the electrodes and the temperature equipment were washed with distilled water and dried between groups . the fluoride content of each solution was measured using a potentiometer and recorded prior to the addition of the enamel specimens at 15 - s intervals up to 1 min , 1 - min intervals from 1 to 10 min , 5 - min intervals from 10 to 50 min , and 10 - min intervals from 50 to 120 min . the fluoride uptake by the enamel specimens was calculated in mv by subtracting the measured concentration from the previously measured concentration before the addition of the specimens . the calibration graphs were constructed with mv values on the y - axis and the ppm f values on the x - axis ; the ppm f values were calculated using the equation y = mx + n.the uptake of fluoride by the enamel specimens from the mouthrinse was measured and recorded from 15 s to 120 min . graphs of the fluoride uptake for each temperature group were drawn , and intragroup and intergroup comparisons were assessed using one - way analysis of variance and the least significant difference , with the level of significance set at p .05 . the fluoride absorption by the enamel specimens from the mouthrinse was found to increase with increase in temperature ( table 5 ) . the changes in the mv and ppm values of the fluoride solution at 25c are shown in figures 5 and 6 , respectively . at 25c , most of the reduction in the solution s fluoride concentration occurred in the first 16 min , during which the concentration decreased at a rate of approximately 20 % to 1.60 ppm . at 50 min , the mean fluoride concentration had decreased to 1.56 ppm ( 23 % ) and at 120 min , the mean fluoride concentration had decreased to 1.52 ppm ( 25 % ) . differences in the rate of change in fluoride concentrations were significant up 70 min ( p .05 ) but they were not significant from 70 min to 120 min ( p .05 ) . changes in the mv and ppm values of the fluoride solution at 37c are shown in figures 7 and 8 , respectively . at 37c , most of the reduction in the solution s fluoride concentration occurred in the first 12 min , during which the fluoride concentration of the solution decreased at a rate of approximately 30 % to 1.4 ppm . at 50 min , the mean fluoride concentration had decreased to 1.00 ppm ( 50 % ) and at 120 min , the mean fluoride concentration had decreased to 0.7 ppm ( 65 % ) . differences in the rate of change in fluoride concentrations were significant up to 60 min ( p .05 ) but they were not significant from 60 min to 120 min ( p .05 ) . changes in the mv and ppm values of the fluoride solution at 43c are shown in figures 9 and 10 , respectively . at 43c , most of the reduction in the solution s fluoride concentration occurred in the first 5 min , during which the fluoride concentration of the solution decreased at a rate of approximately 65 % to 0.7 ppm . at 50 min , the mean fluoride concentration had decreased to 0.60 ppm ( 70 % ) , and no further changes in concentration were observed . differences in the rate of change in fluoride concentrations were significant up 50 min ( p .05 ) but they were not significant from 50 min to 120 min ( p .05 ) . regardless of temperature , fluoride uptake occurred most rapidly during the first few minutes , after which it decreased until the enamel reached saturation . moreover , the speed and amount of fluoride uptake increased with temperature , with majority of the fluoride uptake at 25c occurring during the first 16 min , compared to the first 12 min at 37c and the first 5 min at 43c . significant increase occurred in the rate of uptake until 70 min at 25c , 60 min at 37c , and 50 min at 43c ( p .05 ) , after which the changes were not statistically significant . the changes in the mv and ppm values of the fluoride solution at 25c are shown in figures 5 and 6 , respectively . at 25c , most of the reduction in the solution s fluoride concentration occurred in the first 16 min , during which the concentration decreased at a rate of approximately 20 % to 1.60 ppm . at 50 min , the mean fluoride concentration had decreased to 1.56 ppm ( 23 % ) and at 120 min , the mean fluoride concentration had decreased to 1.52 ppm ( 25 % ) . differences in the rate of change in fluoride concentrations were significant up 70 min ( p .05 ) but they were not significant from 70 min to 120 min ( p .05 ) . changes in the mv and ppm values of the fluoride solution at 37c are shown in figures 7 and 8 , respectively . at 37c , most of the reduction in the solution s fluoride concentration occurred in the first 12 min , during which the fluoride concentration of the solution decreased at a rate of approximately 30 % to 1.4 ppm . at 50 min , the mean fluoride concentration had decreased to 1.00 ppm ( 50 % ) and at 120 min , the mean fluoride concentration had decreased to 0.7 ppm ( 65 % ) . differences in the rate of change in fluoride concentrations were significant up to 60 min ( p .05 ) but they were not significant from 60 min to 120 min ( p .05 ) . changes in the mv and ppm values of the fluoride solution at 43c are shown in figures 9 and 10 , respectively . at 43c , most of the reduction in the solution s fluoride concentration occurred in the first 5 min , during which the fluoride concentration of the solution decreased at a rate of approximately 65 % to 0.7 ppm . at 50 min , the mean fluoride concentration had decreased to 0.60 ppm ( 70 % ) , and no further changes in concentration were observed . differences in the rate of change in fluoride concentrations were significant up 50 min ( p .05 ) but they were not significant from 50 min to 120 min ( p .05 ) . regardless of temperature , fluoride uptake occurred most rapidly during the first few minutes , after which it decreased until the enamel reached saturation . moreover , the speed and amount of fluoride uptake increased with temperature , with majority of the fluoride uptake at 25c occurring during the first 16 min , compared to the first 12 min at 37c and the first 5 min at 43c . significant increase occurred in the rate of uptake until 70 min at 25c , 60 min at 37c , and 50 min at 43c ( p .05 ) , after which the changes were not statistically significant . the present study examined the effect of temperature on fluoride uptake by enamel specimens from a mouthrinse . in order to ensure comparability between groups , utmost care was taken in the preparation of the samples to provide standardization of volume and mass . numerous studies have relied on fluoride - specific ion electrodes for measuring the fluoride uptake .1,7,2328 our study also utilized a fluoride - specific ion electrode as a practical , economical , and accurate measuring tool . fluoride mouthrinses may be categorized by naf concentrations as either low concentration ( 230 ppm , 0.05 % ) or high concentration ( 900 ppm , 0.2 % ) .29 in addition to naf formulations , snf2 , amine fluoride , and ammonium fluoride mouth - rinses are also available .5,3032 mouthrinses routinely available on the market tend to be low - concentration , neutral - ph , 0.05 % naf solutions .12,33,34 in this study , a 0.05 % naf mouthrinse solution was chosen because it possessed a stable structure , almost neutral ph , and high solubility ; did not cause enamel discoloration ( as with snf2 ) ; and was readily available on the market . in line with many earlier studies , our study found that majority of the fluoride uptake by the enamel specimens occurred during the first minutes following application and continued over time . moreover , our study showed that increasing the temperature of the fluoride solution resulted in an increase in the fluoride uptake by the enamel specimens as well as a decrease in the time needed to reach saturation . fluoride absorption was found to cease at around 60 min ; however , measurements continued until 120 min to control for additional changes / recycling . mouthrinse has been reported to be one of the most effective methods of providing low but consistent fluoride levels in the oral cavity .6,32,35,36 as with other fluoride preparations , fluoridated mouthwashes are designed to increase the level of fluoride released in the saliva and maintain it at a certain level .37 most importantly , fluoridated agents are able to increase the resistance and decrease the solubility of the enamel to acids through the incorporation of fluoride ions into the enamel apatite structure . as with all chemical reactions , the degree and speed of penetration of fluoride into the enamel and the formation of fluorapatite are strongly dependent upon concentration and temperature .16 however , very few studies have examined the effect of temperature on fluoride uptake by the enamel from a mouthrinse . barrancos18 reported that fluoride absorption increases with increase in room temperature , and stookey and stahlman20 showed that uptake from a fluoride solution could be increased by raising the temperature of the storage container by scrubbing . moreover , in a study examining the effects of heat ( 25c , 45c , 65c , and 85c ) on tin and fluoride uptake from a topical snf2 ( 8 % ) solution by enamel samples prepared from extracted bovine teeth , putt et al17 reported increase in both fluoride and tin uptake in line with increase in temperature , with the most significant increase in fluoride content observed at 65c and 85c . our study used a 0.05 % naf solution and examined temperatures up to only 43c , the body s hyper - fever limit . nevertheless , in line with these previous studies , significant increase in fluoride uptake was observed with increase in temperature . our study found that the amount and rate of fluoride uptake by tooth enamel increased with increase in temperature . the temperature of naf mouthrinse may easily and safely be increased beyond room temperature by placing a container of naf mouthrinse in a bowl of hot water , allowing greater fluoride penetration into the enamel when the mouthrinse is used at home as a routine prophylactic agent . it should be noted that fluoride absorption and release may change depending upon an individual s dental structure and eating habits . other studies are required to examine the effects of temperature on fluoride uptake in the enamels of different populations from other mouthrinse derivatives and at different temperatures and application times .\noutput:\n" }, { "from": "agent", "value": "objective : the aim of this study was to examine the effect of temperature on fluoride uptake by enamel specimens from a 0.05 % naf - fluoridated mouthrinse ( oral - b advantage ; oral - b laboratories , newbridge , uk ) . methods : enamel specimens were prepared from extracted human maxillary central incisors . a fluoride - specific ion electrode was used to measure the uptake from a 2 ppm fluoride solution containing 50.0 ml of distilled water , total ion strength adjustment buffer , and fluoridated rinse at 3 different temperatures ( room temperature , 25c ; human body temperature , 37c ; hyper - fever temperature , 43c ) . one - way analysis of variance and least significant difference were used to assess intragroup and intergroup differences ( p < .05 ) . results : the study found that both the amount and the rate of fluoride uptake increased significantly with increase in temperature . this effect was particularly noticeable at 43c . conclusions : the temperature of the naf mouthrinse may easily and safely be increased beyond room temperature by placing a container of the naf mouthrinse in a bowl of hot water , allowing greater fluoride penetration into the enamel from the mouthrinse when used at home as a routine prophylactic agent ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: it is generally accepted that genomic instability , whether inherent or induced by external agents , is a primary event leading to neoplastic transformation in the multistep path of carcinogenesis . genomic instability in women with cervical carcinoma has been demonstrated using chromosomal abnormalities , sister chromatid exchange , micronuclei , single - cell gel electrophoresis assays , also known as the comet assay . studies relying on the comet assay are of particular interest , because this method is simple and has been used extensively to detect dna damage at the single - cell level in genotoxic testing and biomonitoring under various circumstances . the comet assay in combination with fluorescence in situ hybridization is a tool for assessing the distribution of region - or locus - specific dna damage in the whole genome . although software - based analysis is the recommended method for the assessment of dna damage , visual scoring is also acceptable , as significant correlations have been detected between visual scoring and computer - based image analysis . moreover , visual scoring continues to be the method of choice for laboratories involved in the analysis of large numbers of samples , for example , biomonitoring studies . the principle of the comet assay is based on alterations found in dna such as strand breaks resulting in the extension of dna loops from lysed and salt - extracted nuclei , which , in turn , form a comet - like tail after either alkaline electrophoresis , indicating global dna damage ( ssb + dsb ) , or neutral electrophoresis , indicating dsb . the procedure for detecting ssb has been improved by performing a strong alkaline incubation during lysis and / or before and during the electrophoresis step . the original comet assay was carried out under neutral conditions but using relatively low doses , so the comet images were dependent on the relaxation of dna supercoiling by ssb . since dsb are 2540 times less frequently induced than ssb , much higher doses and strong lysis are employed for their detection by the neutral comet assay . it is known that ssb can be induced by a number of agents , such as ultraviolet light , reactive oxygen species , and many mutagens , and that they can be easily and rapidly repaired , but do not pose a major threat to genomic integrity . by contrast , dsb represent the most dangerous damage inflicted by mutagens , because they are potent inducers of mutations and chromosomal abnormalities . this type of dna damage has not been studied comprehensively in women with cervical neoplasia . the aim of this hospital - based unmatched case - control study was to evaluate the global dna damage ( ssb + dsb ) and dna dsb in cervical epithelial cells in mexican women with low - grade squamous intraepithelial lesions ( lg - sil ) and with high - grade squamous intraepithelial lesions ( hg - sil ) using alkaline and neutral comet assays . this information helps build a better picture of the degree and type of dna damage present in these patients . the data analyzed in this study were collected during 2010 from unidad mdica de alta especialidad ( umae ) no .23 of the instituto mexicano del seguro social ( imss ) in monterrey , mexico . written informed consent was obtained from all subjects and approval was given by the local centro de investigacin biomdica del noreste ( cibin ) , imss ethical committee . the study included 20 women diagnosed with different stages of cervical neoplasia and 10 control women . the average age of the patients was 3911 years ( range , 2459 years ) , and that of the controls was 4310 years ( range , 2957 years ) ; no significant age difference was found ( p 0.05 ) . all women received a gynecological examination , at which time a papanicolaou ( pap ) smear was obtained using a cytobrush . a biopsy was taken if the examination revealed the presence of a macroscopic cancer lesion . all women who did not have macroscopic cancer lesions were examined using a colposcope and a biopsy was performed if indicated during the examination . pap smears were read and interpreted by a single pathologist according to the bethesda system of pap smear classification . another pathologist examined the biopsy according to the criteria of the international federation of gynecology and obstetrics ( figo ) . based on the results of the pap smears and colposcopy / biopsy , the women were classified into the following categories : 10 had lg - sil , 10 had hg - sil , and 10 were controls . none had a clinical history of chronic disease , such as diabetes mellitus , arterial hypertension , or another type of cancer . women with chronic infection , drug use ( including contraceptives ) , cigarette smoking , antioxidant intake , or radiation exposure ( within the preceding month ) were excluded from the study . hpv was detected and genotyped using the innolipa hpv genotyping kit ( microgen bioproducts ltd , surrey , uk ) . this kit detect all currently known high - risk hpv genotypes and probable high - risk hpv genotypes ( 16 , 18 , 26 , 31 , 33 , 35 , 39 , 45 , 51 , 52 , 53 , 56 , 58 , 59 , 66 , 68 , 73 , 82 ) as well as a number of low - risk hpv genotypes ( 6 , 11 , 40 , 43 , 44 , 54 , 70 ) and some additional types ( 69 , 71 , 74 ) . cytological specimens were collected from colposcopically abnormal areas ( patients ) and normal areas ( controls ) using a cytobrush . the samples were brought to the laboratory under cold conditions and were processed within 1 h of sampling to avoid artifact damage to dna . to perform the comet assay , the cell suspension of cervical epithelial cells was mixed with low melting - point agarose at 37c , to a final concentration of 0.7 % . the mixture ( 15 l ) was pipetted onto slides pretreated with 0.5 % normal - melting - point agarose , to retain the agarose cell suspension . the drop containing the cells was covered with a glass cover slip ( 24 mm 24 mm ) and left at 4c for 5 min . the slides were treated with a lysis solution containing 2 m nacl , 0.4 m tris - base , 1 % sodium dodecyl sulfate , and 0.05 m edta , at room temperature for 30 min . after protein removal , the resultant nucleoids were washed in tbe buffer ( 89 mm tris , 89 mm boric acid , 2.5 mm edta , ph 8.3 ) for 10 min . the slides were treated with fresh alkaline solution ( 0.03 m naoh and 1 m nacl 0.9 % ) for 2.5 min , to cleave the alkali - labile sites . the slides were placed horizontally on an electrophoresis tray that was filled with fresh alkaline electrophoresis solution ( 0.03 m naoh , ph 13 ) . electrophoresis was then performed on ice using an electric field of 23 v / cm for 12.5 min . after electrophoresis , the slides were gently removed from the tray and washed with neutralizing buffer ( 0.4 m tris - hcl , ph 7.5 ) for 5 min , and in tbe for 2 min . to detect dsb , the comet assay was adapted to neutral electrophoresis in tbe buffer at 23 v / cm for 2 min . all steps described previously were carried out in a dark room , to prevent the interference of additional dna damage . the slides were dehydrated in sequential baths of 70 % , 90 % , and 100 % ethanol ( 2 min each ) and were then air dried . finally , the slides were stained with propidium iodide ( 1 g / ml ) in vectashield ( vector laboratories , burlingame , ca , usa ) . comets in the alkali assay revealed dna ssb + dsb and those in the neutral nondenaturing assay exhibited dna dsb . each experiment included two positive controls of sample from one woman without cancer ; cells treated with hydrogen peroxide at 20 m as dna ssb control and cells treated with the alui restriction enzyme as dna dsb control . hydrogen peroxide and alui produced pronounced dna ssb and dsb damage ( 92 % and 84 % of comet resp . ) , which confirmed the accessibility of the cells to the tested chemicals . the slides were examined at 400x magnification using an inverted fluorescence microscope ( ix70 ; olympus , tokyo , japan ) equipped with an excitation filter at 549 nm and a barrier filter at 590 nm and attached to a video camera ( olympus , tokyo , japan ) . the arbitrary units were obtained by one hundred comets scored , and for each comet was assigned a value of 0 to 3 according to its class ; 0 representing undamaged cells ( comets with no or barely detectable tails ) and 13 representing increasing relative tail intensities ( figure 1 ) . summing the scores ( 03 ) of 100 comets gives an overall score of between 0 and 300 arbitrary units . dna dsb were confirmed by dna breakage detection - fish ( dbd - fish ) on neutral comets . in this technique , cells are embedded in agarose microgels , lysed , and subjected to electrophoresis under nondenaturing conditions . subsequently , the neutral comets produced are exposed to a controlled denaturation step that transforms dna breaks into single - stranded dna regions , which are detected via hybridization with whole - genome fluorescent probes dna . for ssdna production , protein - depleted slides were incubated in an alkaline unwinding solution ( 0.03 m naoh , 1 m nacl ) for 2.5 min at room temperature . after neutralizing with 0.4 m tris - hcl , ph 7.5 , for 5 min , nucleoids were washed in tbe ( 89 mm tris , 89 mm boric acid , 2.5 mm edta , ph = 8.3 ) buffer for 2 min . for ssdna stabilization , slides were dehydrated in sequential 70 % , 90 % , and 100 % ethanol baths for 2 min each , and then air - dried . whole - genome dna probes were obtained from lymphocyte pellets of women without cancer used a dna isolation kit for mammalian blood ( roche diagnostics corporation , indianapolis , in , usa ) . one microgram from dna sample was labeled with biotin - 14 - 2 - deoxyuridine 5 - triphosphate ( dutp ) employing a commercial nick - translation kit ( roche diagnostics corporation , indianapolis , in , usa ) . after overnight incubation at room temperature , slides were washed twice at room temperature in each of 50 % formamide / 2 ssc , ph 7 , for 5 min , and then in 2 ssc , ph 7 , for 3 min . the hybridized dna probe was detected using 30 min incubation with rhodamine - labeled antidigoxigenin antibody ( roche diagnostics corporation , indianapolis , in , usa ) . the slides were counterstained with dapi ( 1 g / ml ) in vectashield ( vector laboratories , burlingame , ca ) . the fluorescence intensity and migration length values were calculated using image j version 1.4.3.67 image analysis software . the migration length of the dbd - fish signal is proportional to the number of dsb , whereas its fluorescence intensity depends on the number of ssb ( figure 2 ) . first , data were analyzed using levene 's test for variance , and one - way anova with the student - newmank - keuls test for multiple comparisons at the interpopulation level was used to investigate any possible differences between global dna damage and dsb damage in the three groups of women ( lg - sil , hg - sil , and control ) . second , a pearson correlation coefficient was using to determine the grade of relation between global dna damage and dsb damage levels and progression of cervical neoplasia . the sample size used for anova comparison of meanswas estimated using the minitab software ( version 15 ) for dna ssb damage ( = 0.05 , 1 = 0.80 , corrected sum of the squares of means = 371.85 , and sigma = 17.11 ) and dna dsb damage ( = 0.05 , 1 = 0.80 , = 3.43 , corrected sum of the squares of means = 171.17 , and sigma = 11.77 ) . the comet assay allowed the clear visualization of cervical epithelial cells with dna damage and of cells with no dna damage . the alkaline denaturing comet assay allowed migration of global dna damage ( ssb + dsb ) , whereas the neutral nondenaturing method permits the preferential migration of dna dsb . the morphology , percentage , and length of the tails of comets showed marked differences between the two methods used . tails were longer with the neutral method , and the percentage of cells showing comet formation was higher in the alkaline assay . the global dna damage ( ssd + dsb ) and dna dsb in the cervical epithelial cells of lg - sil , hg - sil , and controls , as assessed using alkaline and neutral comet assays , are presented in table 1 . anova one - way test revealed a significant increase in global dna damage and dna dsb was observed in patients with hg - sil compared with lg - sil and controls . the dna damage observed in controls was considered as normal - level or constitutive damage . pearson correlation coefficient revealed a strong relation between the levels of ssb and dsb ( r = 0.99 , p = 0.03 , and r = 0.94 , p = 0.16 resp . ) and progression of neoplasia ( tables 2 and 3 ) . dbd - fish signal on neutral comet is proportional to the number of dsb , whereas it depends on the number of ssb ( table 4 ) . all patients presented a high risk for hpv , with hpv - 16 , hpv - 52 , and hpv - 51 being the more frequent . genetic instability in women with cervical cancer has been demonstrated previously based on chromosomal abnormalities , sister chromatid exchange , micronuclei , and single - cell gel electrophoresis assays . evaluate the relationship between instability genetic and susceptibitly towards in cervical neoplasia patients with the alkaline comet assay . a significant increased was founded in the mean tail length in peripheral blood leukocytes and cervical epithelial cells of patients with dysplasia and cervical cancer respect to control group . recently we studied the association between the progressive stages of neoplasia cervical and dna damage by alkaline comet assay using visual scorning . an increase of high dna damage in cervical epithelial cells was found according to neoplasia development . the present study confirmed these observations , as it revealed significantly higher level of dna damage compared with control . in addition , we demonstrated a similar elevation in dna dsb in women with cervical neoplasia than was confirmed by dbd - fish . dbd - fish had a much higher resolution , showing a hybridization signal at the end of the tail that was not detected by dapi staining ( comet ) . thus , dbd - fish on neutral comets allows the easy and simultaneous estimation of both dna break types in the same nucleus . in fact , the present study was performed , analyzing the overall genome , using a whole genome probe . however , many different specific probes could be hybridized , with the possibility of simultaneous analysis of ssb and dsb induction . dna ssb are considered an indicator of early damage . moreover , dna ssb are intermediate processing products of dna damage , which , if left unrepaired , may develop into mutagenic and lethal dsb . by contrast , dna dsb are a more disruptive form of strand break , as , if left unrepaired , they can lead to either cell death or loss of genetic information , or , if the repair process is compromised , they may cause neoplastic progression . it is well established that inaccurate repair or lack of repair of dsb can lead to mutations or to larger - scale genomic instability via the generation of dicentric or acentric chromosomal fragments . furthermore , the loss and / or amplification of chromosomal material that is characteristic of many cancer cells is explained most easily as having arisen via inappropriate dsb repair events . defects in cellular responses to dsb may be a frequent initiating event of carcinogenesis . in view of these facts , our results confirmed other observations of a higher number of deletions , breaks , and gaps in these patients . one previous study suggests that inflammation may be involved in directing the course of disease progression by accumulating higher levels of dna lesions . the p - 1 , pl - 1 , pl - 2 and l - 1 ( p , polarity ; l , lipophilicity ; pl , adducts that are neither very polar nor lipophilic ; number , descending order of polarities ) adducts were elevated 3 - to 13-fold in inflammation compared with normal cervix , and were also higher in dysplasia and cancer . perhaps , the association of hpv in dna breaks in patients with neoplasia , with and without hpv infection was not possible determinate . however in one previous study we demonstrated this association evaluated by micronuclei test . in this context , the possible mechanisms that could explain the progressive increase in genetic instability in these patients are related directly to hpv - 16 infection . the hpv - 16 e7 oncoprotein induces centrosome abnormalities , thereby disrupting mitotic fidelity and increasing the risk for chromosome missegregation and aneuploidy . in addition , expression of the high - risk hpv e7 oncoprotein stimulates dna replication stress , which is a potential source of dna breakage and structural chromosomal instability . an increase in the number of dsb , mediated by ku70 depletion , is associated with hpv - 16 episomal loss in cervical keratinocytes and with a new integration event . normal levels of host dna repair proteins , including ku70 , may protect against such events by preventing the generation of host dsb and linearized virus . interestingly , the hpv - 16 e7 protein may play a direct role in inducing integration by interference with the nonhomologous end joining ( nhej ) pathway . expression of hpv - 16 e7 in the hpv - negative cervical keratinocyte cell line c33a resulted in the upregulation of the ku70 - binding protein , which may interfere with normal nhej and increase the frequency of dsb . , 2009 reported that cigarette smoke condensate - mediated dna strand breaks are highly persistent , and suggest that persistence of cigarette smoke - associated dna damage in the presence of hpv infection may lead to increased mutations in cervical cells and ultimately higher cancer risk , however , in our study the status of smoking was not ascertained . from a clinical perspective , the presence of dna dsb , as assessed using the comet assay in neutral conditions , may differentiate patients with clinically significant cervical lesions from those with insignificant lesions , thus discriminating lesions with a high risk of progression from those with a low risk of progression . in conclusion , our results argue in favor of the presence of a real genomic instability in women with cervical neoplasia , which was strengthened by our finding of a higher proportion of dsb . this information should provide additional data to determine whether the comet assay is a useful early diagnostic and prognostic biomarker for cervical cancer .\noutput:\n" }, { "from": "agent", "value": "a hospital - based unmatched case - control study was performed in order to determine the relation of dna single ( ssb ) and double ( dsb ) strand breaks in women with and without cervical neoplasia . cervical epithelial cells of 30 women : 10 with low grade squamous intraepithelial lesions ( lg - sil ) , 10 with high - grade sil ( hg - sil ) , and 10 without cervical lesions were evaluated using alkaline and neutral comet assays . a significant increase in global dna damage ( ssb + dsb ) and dsb was observed in patients with hg - sil ( 48.90 12.87 and 23.50 13.91 ) , patients with lg - sil ( 33.60 14.96 and 11.20 5.71 ) , and controls ( 21.70 11.87 and 5.30 5.38 ; resp . ) . pearson correlation coefficient reveled a strong relation between the levels ssb and dsb ( r2 = 0.99 , p = 0.03 , and r2 = 0.94 , p = 0.16 , resp . ) and progression of neoplasia . the increase of dsb damage in patients with hg - sil was confirmed by dna breakage detection - fish ( dbd - fish ) on neutral comets . our results argue in favor of a real genomic instability in women with cervical neoplasia , which was strengthened by our finding of a higher proportion of dna dsb ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: periodontal disease , including gingivitis and periodontitis , is considered to be one of the most common diseases among population and , if left untreated , can lead to tooth loss . the main cause of periodontal disease is bacterial plaque although many other factors such as hormonal changes , diabetes , poor nutrition , smoking , and stress may affect the initiation and progression of gingival and periodontal diseases . the development of the common periodontal diseases depends mainly on human behavior , and the control of these diseases is greatly supported by the fact that the etiological factors are well documented . many studies showed that effective plaque control for each person can not be achieved without interactive motivation that includes educational and informative knowledge for the patient about periodontal diseases , their initiating factors , and the major role of dental plaque as the initiating cause for inflammatory periodontal changes . nettleton emphasized the need for offering patients accurate information so that they can make an educated decision about their own behavior and actions . in arab world , although studies were carried - out regarding the prevalence of gingival and periodontal diseases , as well as periodontal disease knowledge and awareness among adults and children , none were carried out among university students to assess their knowledge towards gingival and periodontal health , except for three studies which assessed the dental and oral health attitudes and behaviors among dental - field - related university students . quteish taani showed that 25 % of adults suffered bleeding gums on brushing and around the same percentage suffered bad breath . these data indicate that development and implementation of well - structured dental health education programs are needed to improve and maintain suitable oral health standards among the population . in saudi , the oral health system is in a transitional developmental stage , and systemic data collection is needed to plan oral health care for the public . comprehensive preventive programs for oral health care are still lacking in saudi , and more dental health education is needed to improve oral health standards among saudi population . by reviewing the available literature , it appeared that we lack data concerning the effect of the student 's level of studies and study discipline ( i.e. , humanities or scientific faculties ) on oral health knowledge . these factors might have a great influence on student 's knowledge through the types of courses they submit , and the effects of these courses on the information which could be delivered to them , or from their colleagues in different faculties at the university . little is known about the oral health knowledge among university students from developing countries such as saudi in comparison with those from developed countries although such knowledge is an indication of the efficacy of applied dental health education programs . oral health knowledge related to periodontal diseases has a major role in the treatment and prevention of the disease among children , adolescents , and adults including university students . consequently , the purpose of this study was to investigate the knowledge about periodontal oral health and the knowledge of the causes of inflammatory periodontal diseases among university students . this study provides data for future research and allows comparisons with university students ' oral health knowledge in other nations . two hundred and fifty nondental students were recruited into this cross - sectional study after being randomly selected from the university students who attended the university campus during the second semester of the academic year 2011/2012 . the study was approved by university of al - jouf , and participants consent was obtained before being recruited into the study . a previously prepared structured questionnaire was distributed to the participants through personal interview by the researcher . medical and dental terms of the questionnaire related to causes , signs , and symptoms of periodontal diseases were also explained to them during the study . once completed , each questionnaire was double - checked to make sure that all the items were answered and participants were requested to complete any missing data . the data were processed by the computer after auditing , reviewing , and coding the completed questionnaires for data processing and analysis . the questionnaire included items regarding causes , signs , symptoms , and preventive measures of periodontal disease . each question was given one correct statement and the other statements were wrong , and the participant responded to the statement by selecting one of three responses , namely , yes , no , or i do not know . to test its validity the questionnairewas presented to three arbitrators from the teaching staff of the faculty of dentistry , the university of al - jouf ; accordingly , reformulation of some of the terminology was carried out and some of the answers that are common errors were added . the final form of the questionnaire ( table 1 ) included data relevant to the characteristics of the participants , that is , gender , year of study , and study discipline . it also consisted of seven items to assess the students ' knowledge regarding the periodontal disease causes , signs , symptoms , preventive measures , and relations to general heath . to test its reliability , the students completed the test twice on two occasions separated by 5 days , and the reproducibility of the answers ranged between 90 and 100 % which indicated adequate reliability and stability of the questionnaire . chi - squared test was used to identify significant relations and differences between oral health knowledge and gender , level of study , and discipline of study . statistical significance was based on probability values of less than 0.05 ( p 0.05 ) . the final study sample consisted of 250 male nondental university students ( mean age 21 years 2 ) . table 2 presents the distribution of the study sample according level of study and the study discipline ( humanities or scientific studies ) . more than half of the sample were first year students ( 54.8 % ) and 40 % of the participants were studying in scientific faculties of the university of al - jouf . table 3 summarizes the distribution of participants ' knowledge of causes , signs , and preventive measures of periodontal disease according the level of the study . similar levels of knowledge regarding the cause of periodontal disease ( bacterial plaque ) were reported by students from both study levels ( p = 0.9 ) . however , final year students were more knowledgeable than first year students regarding gingival bleeding being the most important sign of periodontal disease ( p = 0.0004 ) . also , final year students had better knowledge of the preventive measures for periodontal disease than first year students ( p = 0.0012 ) . table 4 demonstrates the distribution of the participants ' knowledge of causes , signs , and preventive measures of periodontal disease according the discipline of the study . students from scientific faculties had better knowledge of the causes and preventive measures of periodontal disease than those from humanities faculties ( p = 0.0001 ) . although students from scientific faculties had slightly better knowledge of the signs of periodontal disease , the difference was not significant ( p = 0.1 ) . final year students had better knowledge of the relationship between periodontal disease , and general health than first year students ( p 0.05 ) ( table 5 ) . students from higher study levels had better knowledge of the relationship between periodontal disease on one hand and each of smoking , heart disease , and diabetes on the other hand ( p = 0.0001 ) . also , final year students had better knowledge of the effect of mouth wash in reducing bad breath than first year students ( p = 0.0001 ) ( table 5 ) . students of scientific faculties had better knowledge of the relationship between smoking and diabetes on one hand and periodontal disease on the other hand ( p = 0.02 and 0.0001 resp . ) than students of humanities faculties ( table 6 ) . also , students of scientific faculties had better knowledge of the effect of mouth wash in reducing bad breath as well as better knowledge of the relationship between heart disease and periodontal disease ( p = 0.0001 ) than students of humanities faculties . the aim of this study was to compare the oral health knowledge of nondental students of different disciplines and study levels . the literature lacks studies about oral health knowledge regarding periodontal disease among nondental saudi university students . this study is of prime importance in this field as it is the first one to explore this area among nondental students and among saudi university students . university students are a good representative sample for the population since they reflect education , socioeconomic conditions , acculturation , psychological stress , and culture , which can affect their oral health behavior and status . higher levels of studies had better knowledge of periodontal disease signs , preventive measures , and relations to general health , and this might be due to receiving more dental health care and thus know more about periodontal disease . periodontal disease . other studies proved that within the same specialty the dental health knowledge and attitudes became more positive with the increase of level of education . the finding that students from scientific faculties had better knowledge of periodontal disease causes , signs , preventive measures , and relations to general health than students from humanity disciplines might be explained by those students from scientific disciplines might be more interested with health related - issues and thus get some kind of general health education that could involve some oral health issues and their relations to general health . so , the variations in favorability of oral health knowledge in the study sample reflect the students ' interests , education , and their curriculum . it does worth comparing the oral health knowledge between different specialties from different countries , and this might cast the light on the weaknesses in the oral health education programs and allow improving such programs . when the results of this study were compared to european populations , european adults demonstrated better dental knowledge than their saudi peers . we believe that oral care educational needs to improve oral health knowledge do exist in many developing countries especially in the third world . the results of this study might help to evaluate the efficacy of public education programs in future . the results also indicate that potential parents ' ( university students ) education must be included in any national program that promotes preventive oral care in schools as well as in other oral health educational program aimed at the general public . due to political and economical changes in baltic and eastern european countries , dental health care has been given greater weight , and a decrease in caries prevalence was recorded . comprehensive oral health educational programs were directed toward the professionals and the public and aimed at adults and young people . meanwhile , the governmental legislations and financial support assisted the implication of such programs and thus maximized the gains . political as well as economic reforms led to the participation of the un and international organizations in the process of reforming the health sector and thus boosted the standards of oral health care . the experience of eastern european countries might be relevant to saudi and implemented by the dental health authorities here because saudi is witnessing very promising economic and social reforms . lack of both parents and children oral health education might also explain the findings of this study . poor oral health knowledge among the participants in this study coincided with findings from the previous studies that reported lack of acceptable levels of knowledge and awareness of periodontal problems among saudi adults . during the last decade extensive efforts have been made by the dental schools in saudi in an attempt to improve the periodontal knowledge and practice of the dental personnel , but still these efforts are not enough to raise the standards of professional periodontal practice among dentists which directly affects the public . consequently , dental health education programs that aim to improve oral health knowledge and practice among the public are very important . improving public awareness of periodontal healthin many developing countries , there is no emphasis on dental health care during primary , secondary , and high school teaching . knowledge and awareness concerning some oral health subjects ( such as periodontal disease ) are still poor , and more dental health education is needed to improve oral health . quteish taani showed that high percentage of adults reported gum bleeding on brushing , bad breath , and being irregular attendees to the dentist . in another study , he showed that around 80 % of the subjects attended the dentist only in an emergency . furthermore , nondental university students receive no oral health education at all during their university study , and their curriculums contain no information regarding oral health education . the abovementioned findings in the literature might explain why many participants demonstrated poor knowledge of periodontal disease signs , causes , preventive measures , and relations to general health , systemic disease , and smoking . these findings make it necessary to carry out more research on saudi oral health knowledge and behavior as well as to improve their oral health care education systems . further studies are required to assess oral health knowledge and behavior among saudi female university students . this study was only carried out on males since the tested disciplines does not include females . emphasis on dental health care and education should be developed and maintained during early school education in order to improve the oral health knowledge of adults later on . oral health education should also be included and emphasized in university curriculums for nondental students during their university study . it is well known that the oral health of parents reflects on their children and that their attitudes and knowledge affect their children . hence , educating adults and university students seems among the means to improve the oral health knowledge and behavior of the nation in future . therefore , preuniversity and university curriculum and education about dental health care might be an important factor that can influence the oral health knowledge and attitudes of students not related to dental field . this study demonstrated that there were significant differences in oral health knowledge among students from different levels of studies and different disciplines . the findings might reflect the difference in students ' experience , attitudes , behavior , and education . students from scientific faculties had better knowledge of periodontal disease causes , signs , preventive measures , and relations to general health than students from humanity disciplines . students from higher levels of studies had better knowledge of periodontal disease signs , preventive measures , and relations to general health than those from lower levels of study . finally , oral health education should be included and emphasized in university curriculums for nondental students during their university study .\noutput:\n" }, { "from": "agent", "value": "objectives . the aim of this study was to evaluate levels of oral health knowledge of periodontal disease among nondental university students . materials and methods . two hundred and fifty university students ( mean age 20.1 years 2.5 ) were recruited into this study . the participants completed a structured questionnaire during a personal interview . the questionnaire consisted of items to assess participants ' personal data ( age , gender , level of study , and specialty ) and oral heath knowledge related to periodontal disease . statistical significance was based on probability values of less than 0.05 . results . participants showed poor knowledge of causes , signs , symptoms , and preventive measures of gum disease . the level of study had no relationship with students ' knowledge of the initiating factors of periodontal disease ( p < 0.05 ) , but had a significant relationship with the knowledge of periodontal disease 's signs , preventive measures , and relations to general health and systemic disease ( p < 0.05 ) . students from scientific disciplines had more knowledge of periodontal disease 's causes , preventive measures , and relations to general health and systemic disease ( p < 0.05 ) than those from humanity disciplines . conclusions . there were significant differences in oral health knowledge regarding periodontal disease between students from different levels of studies and different disciplines ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: we began this exploration of pawhuskin opioid activity by probing the selectivity of pawhuskin a for human ( kop ) , ( mop ) , and ( dop ) receptors . even at a 10 m concentration , pawhuskina was found to have no intrinsic agonist activity at these receptors . however , further testing showed antagonist activity at all three of the opioid receptor subtypes . furthermore , pawhuskin a caused a rightward shift in the agonist concentration response curve , and its antagonism was surmountable , suggesting a competitive mode of antagonism ( figure 2 ) . pawhuskin a is modestly selective for the receptor , with a ke of 203 nm ( / = 14.5 , / = 2.9 ) . pawhuskin c ( 2 ) also displayed some antagonist activity at the kop receptor , but was much less potent than compound 1 . representative graph of the antagonist activity of pawhuskin a in the kop receptor affinity assay . each data point represents the mean and sem of duplicate samples . while the natural product salvinorin a and many of its analogues are kop receptor agonists , there are only limited examples of non - nitrogenous kop receptor antagonists including some flavanoids . pawhuskin a rivals the potency of the flavonoids , although catechin ( 5 ) displayed higher selectivity versus the other opioid receptors ( / 31 ) . however improved kop receptor selectivity might be uncovered by a synthetic exploration involving the pawhuskin s stilbene scaffold . synthetic efforts along these lines are encouraged by the recent interest in kop receptor antagonists as potential treatments for stimulant abuse . while there has been some interest in using kop agonists for treatment of substance abuse , compounds such as salvinorin a have been accompanied by serious side effects including potent hallucinogen activity . indeed encounters with stressors , and even images that induce stress , have been shown to induce craving in stimulant abusers . the potent kop receptor antagonist jdtic has been shown to block stress - induced cocaine seeking behavior and also has demonstrated antidepressant - like activity . this result was confirmed and expanded to show that pretreatment with the - opioid antagonist arodyn prevented stress - related induction of cocaine - conditioned place preference , which further heightens interest in - selective antagonists . our approach to exploration of the structure activity relationships of pawhuskin a analogues took advantage of a core strategy used in the synthesis of other natural stilbenes ( figure 3 ) . a disconnection of the central olefinic moiety ( 9 ) through a horner wadsworthemmons transform allows choice of phosphonate coupling partners such as 10 and aldehydes such as 11 , although the reversed pairing is also viable . this permits maximum convergence and provides for divergence through condensations of one aldehyde with several phosphonates or one phosphonate with several aldehydes . to begin exploration of the pharmacophore of pawhuskin a and the essential binding motifs for - selective antagonist activity , we undertook syntheses aimed at preparation of a small set of analogues through this strategy . phenolic h - bonding is important to the kop receptor selectivity of the antagonist jdtic and other members of the phenylpiperidine class of opioid receptor modulators . furthermore , as in past studies of salvinorin a , the lack of a readily ionizable group that would form salt bridges with an opioid receptor suggested that attention should be directed at the h - bonding groups of pawhuskin a. thus , we chose to prepare various methylated analogues to assess the importance of h - bond donation from the various hydroxy groups without a significant change in electron donation . synthetic strategy for pawhuskin analogues . to allow efficient preparation of several analogues , as well as synthesis of regiospecifically methylated materials , the permethylatedpawhuskin a analogue was pursued through preparation of both coupling partners aldehyde 14 ( scheme 1 ) and phosphonate 19 ( scheme 2 ) rather than methylation of the natural product . to access compound 14 , halogen metal exchange was carried out on the known bromide 12 . hydrolysis of the acetal protecting group and oxidation of the resulting benzylic alcohol with mno2 gave aldehyde 14 in satisfactory yield . the alcohol 15 is known from our synthesis of pawhuskin a , and oxidation of that benzylic alcohol gave the methoxymethyl ( mom ) - protected aldehyde 16 . to prepare the complementary phosphonate 19 , the known aldehyde 17 ( 46 ) was reduced to the corresponding alcohol , and the alcohol was treated with mesyl chloride and et3n , then libr , and finally allowed to react with triethyl phosphite to obtain the phosphonate 18 . after hydrolysis of the mom protecting group , standard reaction with mei and base afforded the dimethylated phosphonate 19 . emmons condensation afforded the fully methylated pawhuskin a analogue 20 in good yield ( scheme 3 ) . with this compound in hand , we employed our small library of readily available phosphonates of type 10 to synthesize additional pawhuskin analogues . thus , coupling of aldehyde 14 with known phosphonate 21 ( 47 ) afforded the stilbene 22 , which upon deprotection gave stilbene 23 . condensation of compound 16 with phosphonate 21 , followed by hydrolysis of the protecting groups in the resulting stilbene , gave the free phenolic pawhuskin a analogue 26 . to reposition the prenyl group so that it is isomeric to pawhuskin a ( 1 ) that prenylated benzylic alcohol could be prepared from bromovanillin through reactions parallel to those reported in a schweinfurthin synthesis . condensation of phosphonate 27 with aldehyde 14 gave stilbene 28 , and hydrolysis of the mom groups gave the dimethylated analogue 29 . finally , condensation of aldehyde 14 with phosphonate 18 gave the selectively trimethylated pawhuskin a derivative 30 . this compound was methylated to provide permethylated pawhuskin a ( 20 ) via a different route . because pawhuskin c ( 2 ) showed activity , this set includes the natural product schweinfurthin j ( 32 , scheme 4 ) , which was isolated from the african plant macaranga schweinfurthii ( 48,49 ) and can be viewed as lacking one phenolic hydroxy group and bearing a farnesyl side chain in relation to pawhuskin c. we then used the known phosphonate 33 ( 50,51 ) to access the prenylated pawhuskin c analogue 37 and the natural product trans - arachidin - 2 ( 39 ) . condensation of phosphonate 33 with the known aldehydes 34 and 35 ( 52 ) gave the protected stilbenes 36 and 38 , respectively . use of the mom protecting group for all the hydroxy groups of compound 38 allows for deprotection to stilbene 39 in a single step , which is more efficient than the previous synthesis . of the various analoguesstudied for binding to opioid receptors , only the pawhuskin a analogue 29 and schweinfurthin j ( 32 ) demonstrated appreciable activity ( table 1 ) . schweinfurthin j with a 3 m ke for the mop receptor and limited selectivity ( / = 0.67 , / = 0.33 ) is the only stilbene we have studied that shows selectivity for the - opioid receptor . interestingly , schweinfurthin j is also closely related to chlorophorin ( 8 ) , which was shown by sobolev and co - workers to lower agonist binding to the and receptors to an equal extent but to have no substantial effect on the binding of agonists to the - opioid receptor . of greater interestis analogue 29 , which showed better binding affinity to the receptor than pawhuskin a and also demonstrated dramatically improved selectivity ( / at least 4-fold larger and / at least 20-fold larger for compound 29 than for pawhuskin a ) . indeed we could not find antagonist activity at the or receptors for compound 29 up to the highest concentrations typically tested ( 10 m ) . this compound demonstrates that methylation of the malonate - derived hydroxy groups on the pawhuskin a scaffold does not abrogate the kop receptor antagonist activity on this stilbene scaffold . comparisons to compounds 20 , 23 , and 24 indicate that the presence and position of the prenyl substituent are important factors in binding to the kop receptor . these results point to the importance of the shikimate - derived substructure and should allow further design with the aim of introducing more drug - like characteristics . representative graph of the antagonist activity of compound 29 in the kop receptor affinity assay . this study has shown that the natural stilbene pawhuskin a is a competitive antagonist with selectivity for the kop receptor . we also have shown that improved selectivity for the kop versus the dop and mop receptors is possible within the constraints of the stilbene structure , which encourages further efforts to improve these molecules via synthesis . the isomeric pawhuskin a analogue 29 exhibited greater affinity and selectivity for the kop receptor than pawhuskin a itself , indicating that the shikimate - derived ring is a key for - opioid receptor binding . compound 29 shows significantly greater selectivity for the kop than pf - 04455242 , which was advanced to phase 1 clinical trials for alcohol dependency , albeit with significantly lower potency ( 150 nm vs 3 nm ) . thus far , none of the new compounds reported here have shown any agonist activity . while the study of kop agonists for treatment of pain and addiction has been moving forward , their potential may be limited by side effects such as hallucinations and dysphoria . therefore , this stilbene scaffold may present new opportunities for the discovery of compounds with utility in the treatment of addiction and depression . solutions of n - buli were purchased from a commercial source and titrated with diphenylacetic acid prior to use . all other reagents and solventsall reactions in nonaqueous solvents were conducted in flame - dried glassware under a positive pressure of ar and with magnetic stirring . nmr spectra were obtained at 300500 mhz for h and 75125 mhz for c with cdcl3 or cd3od as solvent and ( ch3 ) 4si ( h , 0.00 ppm ) or cdcl3 ( c , 77.0 ppm or 49.0 ppm ) as internal standards unless otherwise noted . the p chemical shifts were reported in ppm relative to 85 % h3po4 ( external standard ) . high - resolution mass spectra were obtained at the university of iowa mass spectrometry facility . silica gel ( 60 , 0.0400.063 mm ) was used for flash chromatography . to a stirred solution of tmeda ( 0.58 ml , 3.9 mmol ) and n - buli ( 2.47 m solution in hexanes ,1.5 ml , 3.6 mmol ) in et2o ( 20 ml ) at 10 c was added the bromide 12 ( 979 mg , 3.0 mmol ) dissolved in et2o ( 4 ml ) . after 45 min of stirring , cui ( 742 mg , 3.9 mmol ) was added and then geranyl bromide ( 840 mg , 3.9 mmol ) was added slowly over 8 min to the reaction . after the mixture was stirred overnight , the reaction was quenched by addition of saturated aqueous nh4cl . the resulting mixture was extracted with etoac , and the combined organic extracts were washed with brine , dried ( mgso4 ) , filtered , and concentrated in vacuo . final purification by flash column chromatography ( 4 % etoac in hexanes ) afforded compound 13 ( 364 mg , 32 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 6.61 ( d , j = 2.4 hz , 1h ) , 6.42 ( d , j = 2.5 hz , 1h ) , 5.075.04 ( m , 2h ) , 4.74 ( d , j = 12.2 hz , 1h ) , 4.70 ( t , j = 3.7 hz , 1h ) , 4.48 ( d , j = 12.1 hz , 1h ) , 3.943.90 ( m , 1h ) , 3.80 ( s , 3h ) , 3.79 ( s , 3h ) , 3.373.29 ( m , 2h ) , 2.061.80 ( m , 5h ) , 1.801.54 ( m , 5h ) , 1.75 ( s , 3h ) , 1.65 ( s , 3h ) , 1.57 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 158.6 , 158.4 , 138.0 , 134.5 , 131.2 , 124.4 , 123.3 , 121.3 , 105.0 , 98.0 ( 2c ) , 66.9 , 62.2 , 55.7 , 55.3 , 39.8 , 30.7 , 26.8 , 25.7 , 25.5 , 24.1 , 19.5 , 17.7 , 16.1 ; hrms ( esi ) m / z calcd for c24h36o4na ( m + na ) 411.2511 , found 411.2495 . to a solution of the thp acetal 13 ( 364 mg , 0.9 mmol ) in meoh ( 8 ml ) at room temperature was added tsoh ( 356 mg , 1.9 mmol ) . the mixture was extracted with etoac , and the combined organic extracts were dried ( mgso4 ) , filtered , and concentrated in vacuo to afford the benzylic alcohol as a yellow oil . this material was used in further reactions without additional purification : h nmr ( 300 mhz , cdcl3 ) 6.59 ( d , j = 2.4 hz , 1h ) , 6.43 ( d , j = 2.2 hz , 1h ) , 5.095.02 ( m , 2h ) 4.64 ( d , j = 3.9 hz , 2h ) , 3.81 ( s , 3h ) , 3.80 ( s , 3h ) , 3.35 ( d , j = 6.8 hz , 2h ) , 2.101.94 ( m , 4h ) , 1.76 ( s , 3h ) , 1.65 ( s , 3h ) , 1.57 ( s , 3h ) ; cnmr ( 75 mhz , cdcl3 ) 158.7 , 158.3 , 140.6 , 135.0 , 131.4 , 124.1 , 123.5 , 120.3 , 104.0 , 97.9 , 63.3 , 55.6 , 55.3 , 39.6 , 26.6 , 25.6 , 23.7 , 17.6 , 16.1 ; hrms ( ei ) m / z calcd for c19h28o3 ( m ) 304.2038 , found 304.2044 . to a stirred solution of the benzylic alcohol ( 285 mg , 0.9 mmol , assuming 100 % conversion in the previous step ) in ch2cl2 ( 15 ml ) was added activated mno2 ( 815 mg , 9.4 mmol ) . final purification by flash column chromatography ( 12 % etoac in hexanes ) afforded aldehyde 14 ( 146 mg , 52 % from 13 ) as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 10.3 ( s , 1h ) , 6.98 ( d , j = 2.2 hz , 1h ) , 6.68 ( d , j = 1.9 hz , 1h ) , 5.135.07 ( m , 1h ) , 5.055.00 ( m , 1h ) , 3.82 ( s , 6h ) , 3.70 ( d , j = 6.5 hz , 2h ) , 2.241.90 ( m , 4h ) , 1.76 ( s , 3h ) , 1.64 ( s , 3h ) , 1.56 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 191.8 , 158.8 , 158.6 , 135.2 , 134.9 , 131.4 , 127.3 , 124.0 , 123.4 , 104.8 , 101.9 , 55.8 , 55.5 , 39.5 , 26.5 , 25.6 , 22.5 , 17.6 , 16.2 ; hrms ( esi ) m / z calcd for c19h26o3na ( m + na ) 325.1780 , found 325.1783 . activated mno2 ( 644 mg , 7.1 equiv ) was added to a solution of alcohol 15 ( 5 ) ( 267 mg , 0.7 mmol ) in ch2cl2 ( 15 ml ) at room temperature , and the mixture was stirred overnight . final purification by flash column chromatography ( 50 % etoac in hexanes ) afforded aldehyde 16 ( 256 mg , 96 % ) as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 10.26 ( s , 1h ) , 7.21 ( d , j = 2.7 hz , 1h ) , 7.04 ( d , j = 2.2 hz , 1h ) , 5.21 ( s , 2h ) , 5.19 ( s , 2h ) , 5.145.10 ( m , 1h ) , 5.055.00 ( m , 1h ) , 3.73 ( d , j = 6.5 hz , 2h ) , 3.48 ( s , 6h ) , 2.081.93 ( m , 4h ) , 1.86 ( s , 3h ) , 1.73 ( s , 3h ) , 1.65 ( s , 3h ) ; cnmr ( 125 mhz , cdcl3 ) 191.6 , 156.3 , 156.2 , 135.3 ( 2c ) , 131.5 , 128.1 , 124.1 , 123.2 , 109.3 , 108.7 , 94.7 , 94.5 , 56.2 , 56.1 , 39.6 , 26.6 , 25.6 , 22.9 , 17.6 , 16.3 ; hrms ( esi ) m / z calcd for c21h30o5na ( m + na ) 385.1991 , found 385.1983 . to a stirred solution of aldehyde 17 ( 1.16 g , 4.5 mmol ) in meoh ( 10 ml ) at 0 c was added nabh4 ( 282 mg , 7.5 mmol ) as a single aliquot . this solution was stirred for 30 min , and then h2o ( 50 ml ) was added and the resulting solution was extracted with etoac . after concentration in vacuo , the resulting alcohol ( 1.07 g , 90 % ) was dissolved in thf ( 10 ml ) and treated with et3n ( 0.80 ml , 5.7 mmol ) followed by methanesulfonyl chloride ( 0.31 ml , 4.01 mmol ) . after 15 min , libr ( 391 mg , 0.45 mmol ) was added in thf ( 15 ml ) . the resulting solution was stirred for an additional 45 min and quenched by addition of h2o . this mixture was extracted with etoac , and then the combined organic extracts were washed with brine , dried ( mgso4 ) , filtered , and concentrated in vacuo . the resulting yellow oil was dissolved in triethyl phosphite ( 5 ml ) and heated at reflux for 5 days . purification by flash column chromatography ( 100 % etoac ) afforded phosphonate 18 ( 622 mg , 40 % ) as a clear oil : h nmr ( 300 mhz , cdcl3 ) 6.976.93 ( m , 1h ) , 6.676.63 ( m , 1h ) , 4.95 ( br s , 3h ) , 3.923.86 ( m , 4h ) , 3.70 ( s , 5h ) , 3.56 ( s , 3h ) , 3.01 ( d , jhp = 21 hz , 2h ) , 1.70 ( s , 3h ) , 1.58 ( s , 3h ) , 1.161.10 ( m , 6h ) ; c nmr ( 75 mhz , cdcl3 ) 150.8 ( d , jcp = 3.6 hz ) , 143.7 ( d , jcp = 3.7 hz ) , 134.8 ( d , jcp = 6.7 hz ) , 131.3 , 126.3 ( d , jcp = 5.2 hz ) , 122.7 ( d , jcp = 9.3 hz ) , 122.5 , 109.4 ( d , jcp = 3.9 hz ) , 98.6 , 61.6 ( d , jcp = 7.1 hz , 2c ) , 57.1 , 55.2 , 29.5 ( d , jcp = 139 hz ) , 25.3 , 25.2 , 17.6 , 16.0 ( d , jcp = 5.8 hz , 2c ) ; p nmr ( 122 mhz , cdcl3 ) 27.2 ; hrms ( ei ) m / z calcd for c19h31o6p ( m ) 386.1858 , found 386.1857 . to a stirred solution of mom ether 18 ( 103 mg , 0.3 mmol ) in etoh ( 2.5 ml ) was added tsoh ( 152 mg , 0.8 mmol ) . the solution was stirred overnight , quenched by addition of saturated aqueous nh4cl , and extracted with etoac . the combined organic extracts were washed with brine , dried ( mgso4 ) , and concentrated in vacuo to afford the phenol as a yellow oil . to a stirred solution of the phenol ( 88 mg , 0.3 mmol ) in acetone ( 6 ml ) were added k2co3 ( 242 mg , 1.8 mmol ) and mei ( 0.1 ml , 1.6 mmol ) . after the mixture was heated to reflux and stirred overnight , it was quenched by addition of h2o , and the mixture was extracted with etoac . the organic extracts were washed with 2 m naoh , dried ( mgso4 ) , and concentrated in vacuo . without additional purification , methyl ether 19 ( 56 mg , 59 % , 2 steps ) was obtained as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 6.96 ( dd , j = 8.7 hz , jhp = 3.2 hz , 1h ) , 6.68 ( d , j = 8.8 hz , 1h ) , 4.96 ( t , j = 6.5 hz , 1h ) , 3.993.86 ( m , 4h ) , 3.79 ( s , 3h ) , 3.70 ( s , 3h ) , 3.42 ( d , j = 6.5 hz , 2h ) , 3.04 ( d , jhp = 21 hz , 2h ) , 1.72 ( s , 3h ) , 1.61 ( s , 3h ) , 1.18 ( td , j = 7.5 hz , jhp = 3.7 hz , 6h ) . to a stirred suspension of nah ( 60 % dispersion in mineral oil , washed with hexanes , 33 mg , 0.8 mmol ) in thf ( 2.5 ml ) were added phosphonate 19 ( 56 mg , 0.2 mmol ) , aldehyde 14 ( 39 mg , 0.1 mmol ) , and 15 - crown - 5 ( 3 drops ) . the mixture was stirred for 2 h and quenched by addition of saturated aqueous nh4cl . the resulting mixture was extracted with etoac , and the combined organic extracts were washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification by flash column chromatography ( 10 % etoac in hexanes ) afforded stilbene 20 ( 20 mg , 31 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.32 ( d , j = 8.7 hz , 1h ) , 7.12 ( s , 2h ) , 6.80 ( d , j = 8.8 hz , 1h ) , 6.71 ( d , j = 2.5 hz , 1h ) , 6.21 ( d , j = 2.5 hz , 1h ) , 5.165.11 ( m , 2h ) , 5.075.04 ( m , 1h ) , 3.88 ( s , 3h ) , 3.84 ( s , 3h ) , 3.81 ( s , 3h ) , 3.81 ( s , 3h ) , 3.523.50 ( m , 2h ) , 3.42 ( d , j = 6.7 hz , 2h ) , 2.072.03 ( m , 2h ) , 1.981.92 ( m , 2h ) , 1.81 ( s , 3h ) , 1.78 ( s , 3h ) , 1.67 ( s , 3h ) , 1.62 ( s , 3h ) , 1.55 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 158.5 , 158.4 , 152.3 , 146.9 , 138.4 , 134.4 , 134.0 , 131.4 , 131.2 , 130.4 , 128.0 , 127.0 , 124.4 , 123.5 , 123.3 , 121.6 , 121.1 , 110.2 , 101.6 , 97.9 , 60.7 , 55.7 ( 2c ) , 55.3 , 39.7 , 26.8 , 25.7 , 25.6 , 25.5 , 24.3 , 18.1 , 17.6 , 16.3 ; hrms ( ei ) m / z calcd for c33h44o4 ( m ) 504.3240 , found 504.3237 . to a stirred suspension of nah ( 60 % dispersion in mineral oil , washed with hexanes , 28 mg , 0.7 mmol ) in thf ( 2.5 ml ) were added aldehyde 14 ( 35 mg , 0.1 mmol ) , phosphonate 21 ( 38 ) ( 49 mg , 0.1 mmol ) , and 15 - crown - 5 ( 3 drops ) . the resultant mixture was extracted with etoac , and the combined organic extracts were washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification of the residue by flash column chromatography ( 10 % etoac in hexanes ) gave stilbene 22 ( 38 mg , 67 % ) as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 7.32 ( d , j = 1.6 hz , 1h ) , 7.21 ( d , j = 16.1 hz , 1h ) , 7.15 ( d , j = 8.4 hz , 1h ) , 7.10 ( dd , j = 8.5 hz , 1.7 hz , 1h ) , 6.89 ( d , j = 16.2 hz , 1h ) , 6.72 ( d , j = 2.2 hz , 1h ) , 6.42 ( d , j = 2.1 hz , 1h ) , 5.28 ( s , 2h ) , 5.26 ( s , 2h ) , 5.145.03 ( m , 2h ) , 3.85 ( s , 3h ) , 3.81 ( s , 3h ) , 3.54 ( s , 3h ) , 3.53 ( s , 3h ) , 3.43 ( d , j = 6.7 hz , 2h ) , 2.081.95 ( m , 4h ) , 1.81 ( s , 3h ) , 1.61 ( s , 3h ) , 1.54 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 158.5 , 158.3 , 147.3 , 146.8137.8 , 134.3 , 132.4 , 131.2 , 129.7 , 125.8 , 124.3 , 123.5 , 121.1 , 120.8 , 116.5 , 114.6 , 101.2 , 98.0 , 95.4 , 95.3 , 56.2 ( 2c ) , 55.6 , 55.3 , 39.7 , 26.7 , 25.6 , 24.3 , 17.6 , 16.2 ; hrms ( esi ) m / z calcd for c30h41o6 ( m + h ) 497.2903 , found 497.2918 . to a solution of bis ( methoxymethyl ) ether 22 ( 18 mg , 0.04 mmol ) in meoh ( 2 ml ) was added tsoh ( 29 mg , 0.15 mmol ) . after the solution was stirred overnight , the reaction was quenched by addition of saturated aqueous nahco3 . the resultant mixture was extracted with etoac , and the combined organic extracts were dried ( mgso4 ) , filtered , and concentrated in vacuo . final purification of a portion ( 25 % ) of the residual oil by preparative tlc ( 25 % etoac in hexanes ) afforded the stilbene 23 ( 5 mg , 100 % by nmr ) as a yellow oil ; the remaining material ( 75 % ) was moved forward without additional purification . for compound 23 : h nmr ( 300 mhz , cdcl3 ) 7.206.82 ( m , 5h ) , 6.71 ( m , 1h ) , 6.42 ( m , 1h ) , 5.194.98 ( m , 2h ) , 3.86 ( s , 3h ) , 3.81 ( s , 3h ) , 3.42 ( d , j = 5.9 hz , 2h ) , 2.071.97 ( m , 4h ) , 1.80 ( s , 3h ) , 1.62 ( s , 3h ) , 1.55 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 158.5 , 158.4 , 143.8 , 143.5 , 137.9 , 134.5 , 131.3 , 129.9 , 125.1 , 124.3 , 123.5 , 121.1 , 119.9 , 115.5 , 113.1 , 110.9 , 101.4 , 97.9 , 55.7 , 55.4 , 39.7 , 26.7 , 25.6 , 24.3 , 17.7 , 16.3 ; hrms ( esi ) m / z calcd for c26h33o4 ( m + h ) 409.2379 , found 409.2374 . to a stirred solution of stilbene 23 in acetone ( 3 ml ) was added k2co3 ( 35 mg , 0.25 mmol ) followed by mei ( 38 l , 0.61 mmol ) . the mixture was stirred for 2 days , and the reaction was quenched with h2o . the resulting mixture was extracted with etoac , and the combined organic extracts were washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification by flash column chromatography ( gradient of hexanes to 40 % etoac in hexanes ) provided stilbene 24 ( 4 mg , 27 % ) as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 7.277.18 ( m , 1h ) , 7.067.04 ( m , 2h ) , 6.946.85 ( m , 2h ) , 6.75 ( d , j = 2.7 hz , 1h ) , 6.43 ( d , j = 2.4 hz , 1h ) , 5.14 ( t , j = 7.5 hz , 1h ) , 5.06 ( t , j = 7.5 hz , 1h ) , 3.94 ( s , 3h ) , 3.91 ( s , 3h ) , 3.86 ( s , 3h ) , 3.83 ( s , 3h ) , 3.463.44 ( m , 2h ) , 2.051.95 ( m , 4h ) , 1.82 ( s , 3h ) , 1.62 ( s , 3h ) , 1.55 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 158.9 , 149.1 , 138.0 , 134.2 , 131.3 , 130.8 , 130.1 , 125.2 , 124.2 , 123.4 , 121.1 , 119.9 , 111 . . 3 , 108.8 , 107.1 , 105.8 , 101.4 , 97.9 , 56.0 , 55.8 , 55.7 , 55.4 , 39.7 , 26.8 , 25.6 , 24.4 , 17.6 , 16.3 ; hrms ( ei ) m / z calcd for c28h36o4 ( m ) 436.2614 , found 436.2606 . to a solution of potassium hexamethyldisilazane ( khmds ) ( 0.5 m solution in toluene , 2.3 ml , 1.16 mmol ) in thf ( 1.5 ml ) were added phosphonate 21 ( 46 mg , 0.13 mmol ) and aldehyde 16 ( 35 mg , 0.10 mmol ) . after the solution was stirred for 4 h , the reaction was quenched by addition of nh4cl . the resulting mixture was extracted with etoac , washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification by flash column chromatography ( 7 % etoac in hexanes ) provided stilbene 25 ( 46 mg , 86 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.317.11 ( m , 4h ) , 6.96 ( s , 1h ) , 6.88 ( d , j = 15.7 hz , 1h ) , 6.74 ( s , 1h ) , 5.275.05 ( m , 10h ) , 3.543.48 ( m , 14h ) , 2.041.97 ( m , 4h ) , 1.82 ( s , 3h ) , 1.61 ( s , 3h ) , 1.54 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 156.1 , 155.8 , 147.4 , 146.9 , 138.2 , 134.5 , 132.4 , 131.3 , 130.1 , 125.5 , 124.2 , 123.3 , 122.8 , 120.9 , 116.7 , 114.8 , 106.2 , 102.9 , 95.5 , 95.4 , 94.6 ( 2c ) , 56.2 ( 2c ) , 56.0 ( 2c ) , 39.7 , 26.7 , 25.6 , 24.7 , 17.6 , 16.2 ; hrms ( ei ) m / z calcd for c32h44o8 ( m ) 556.3036 , found 556.3056 . to a solution of stilbene 25 ( 23 mg , 0.04 mmol ) in meoh ( 4 ml ) was added tsoh ( 63 mg , 0.33 mmol ) . the solution was stirred for 24 h , and the reaction was quenched by addition of nahco3 . the resulting mixture was extracted with etoac , dried ( mgso4 ) , and concentrated in vacuo . final purification by preparative tlc ( 30 % etoac in hexanes ) afforded stilbene 26 ( 6 mg , 38 % ) as a yellow oil : h nmr ( 500 mhz , cd3od ) 6.96 ( d , j = 16 hz , 1h ) , 6.85 ( d , j = 2.3 hz , 1h ) , 6.71 ( d , j = 2 hz , 1h ) , 6.70 ( d , j = 1.7 hz , 1h ) , 6.65 ( d , j = 15.8 hz , 1h ) , 6.63 ( d , j = 8.3 hz , 1h ) , 6.44 ( d , j = 2.1 hz , 1h ) , 6.13 ( d , j = 2.3 hz , 1h ) , 5.015.00 ( m , 1h ) , 4.954.92 ( m , 1h ) , 3.27 ( d , j = 6.6 hz , 2h ) , 1.971.92 ( m , 2h ) , 1.881.85 ( m , 2h ) , 1.70 ( s , 3h ) , 1.47 ( s , 3h ) , 1.42 ( s , 3h ) ; c nmr ( 125 mhz , cd3od ) 157.0 , 156.7 , 146.5 , 146.4 , 139.8 , 134.5 , 132.1 , 131.6 , 130.7 , 125.8 , 125.4 ( 2c ) , 120.0 , 119.1 , 116.4 , 114.0 , 104.3 , 102.6 , 40.8 , 27.8 , 25.8 , 25.1 , 17.7 , 16.5 ; hrms ( ei ) m / z calcd for c24h28o4 ( m ) 380.1988 , found 380.2014 . to a stirred solution of aldehyde 14 ( 21 mg , 0.07 mmol ) and phosphonate 27 ( 51 mg , 0.12 mmol ) in thf ( 1.4 ml ) at 0 c was added khmds ( 0.5 m in toluene , 0.69 ml , 0.35 mmol ) . the solution was stirred for 22 h at rt , and the reaction was quenched with nh4cl . the resultant mixture was extracted with etoac , and the combined organic extracts were washed with brine , dried ( mgso4 ) , filtered , and concentrated in vacuo . final purification by preparative tlc ( 30 % etoac in hexanes ) gave stilbene 28 ( 36 mg , 92 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.20 ( d , j = 16.0 hz , 1h ) , 7.14 ( d , j = 1.8 hz , 1h ) , 6.98 ( d , j = 2.1 hz , 1h ) , 6.87 ( d , j = 15.7 hz , 1h ) , 6.72 ( d , j = 2.4 hz , 1h ) , 6.41 ( d , j = 2.6 hz , 1h ) , 5.345.31 ( m , 1h ) , 5.22 ( s , 2h ) , 5.12 ( s , 2h ) , 5.065.03 ( m , 1h ) , 3.85 ( s , 3h ) , 3.81 ( s , 3h ) , 3.61 ( s , 3h ) , 3.52 ( s , 3h ) , 3.443.41 ( m , 4h ) , 2.062.02 ( m , 2h ) , 1.981.95 ( m , 2h ) , 1.81 ( s , 3h ) , 1.76 ( s , 3h ) , 1.74 ( s , 3h ) , 1.60 ( s , 3h ) , 1.53 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 158.5 , 158.4 , 150.0 , 144.4 , 137.9 , 136.1 , 134.2 , 133.9 , 132.7 , 131.2 , 130.1 , 126.3 , 124.3 , 123.5 , 122.6 , 121.5 , 121.2 , 112.1 , 101.4 , 99.1 , 98.1 , 95.2 , 57.5 , 56.2 , 55.7 , 55.4 , 39.7 , 28.6 , 26.7 , 25.8 , 25.6 , 24.4 , 17.9 , 17.6 , 16.2 ; hrms ( esi ) m / z calcd for c35h49o6 ( m + h ) 565.3529 , found 565.3524 . to a solution of bis - mom acetal 28 ( 36 mg , 0.06 mmol ) in meoh ( 6.4 ml ) was added tsoh ( 49 mg , 0.26 mmol ) . after the solution was stirred for 19.5 h at rt , additional tsoh ( 25 mg , 0.13 mmol ) was added due to incomplete conversion to product . after the solution was stirred for an additional 22.5 h , the reaction was quenched by addition of nahco3 . the resultant mixture was extracted with etoac , and the combined organic extracts were dried ( mgso4 ) , filtered , and concentrated in vacuo . final purification by preparative tlc ( 35 % etoac in hexanes ) provided stilbene 29 ( 14 mg , 47 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.37 ( d , j = 15.6 hz , 1h ) , 6.94 ( s , 1h ) , 6.846.80 ( m , 2h ) , 6.71 ( d , j = 2.1 hz , 1h ) , 6.40 ( d , j = 2.0 hz , 1h ) , 5.45 ( br s , 1h ) , 5.34 ( t , j = 6.1 hz , 1h ) , 5.11 ( t , j = 6.7 hz , 1h ) , 5.065.04 ( m , 1h ) , 3.84 ( s , 3h ) , 3.80 ( s , 3h ) , 3.42 ( d , j = 6.5 hz , 2h ) , 3.37 ( d , j = 7.1 hz , 2h ) , 2.072.03 ( m , 2h ) , 1.981.95 ( m , 2h ) , 1.811.79 ( m , 9h ) , 1.61 ( s , 3h ) , 1.54 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 158.5 , 158.4 , 144.2 , 141.9 , 138.0 , 135.3 , 134.4 , 131.3 , 130.6 , 130.1 , 127.3 , 125.2 , 124.3 , 123.6 , 121.6 , 121.1 , 120.5 , 110.9 , 101.5 , 97.9 , 55.7 , 55.4 , 39.7 , 29.9 , 26.8 , 25.8 , 25.6 , 24.4 , 17.9 , 17.6 , 16.3 ; hrms ( esi ) m / z calcd for c31h41o4 ( m ) 477.3005 , found 477.2994 . to a stirred solution of aldehyde 14 ( 27 mg , 0.1 mmol ) and 18 ( 51 mg , 0.1 mmol ) in thf ( 1.5 ml ) at room temperature were added nah ( 60 % dispersion in mineral oil , 22 mg , 0.6 mmol ) and 15 - crown - 5 ( 2 drops ) . after the mixture was stirred overnight , the reaction was quenched by addition of nh4cl . the resulting mixture was extracted with etoac , and then the combined organic extracts were dried ( mgso4 ) , filtered , and concentrated in vacuo . final purification by flash column chromatography ( 10 % etoac in hexanes ) provided 30 ( 18 mg ) in 38 % yield as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 7.33 ( d , j = 8.7 hz , 1h ) , 7.11 ( m , 2h ) , 6.80 ( d , j = 8.6 hz , 1h ) , 6.70 ( d , j = 2.3 hz , 1h ) , 6.41 ( d , j = 2.5 hz , 1h ) , 5.165.03 ( m , 3h ) , 5.09 ( s , 2h ) , 3.86 ( s , 3h ) , 3.83 ( s , 3h ) , 3.81 ( s , 3h ) , 3.60 ( s , 3h ) , 3.57 ( d , j = 6.6 hz , 2h ) , 3.42 ( d , j = 6.7 hz , 2h ) , 2.051.96 ( m , 4h ) , 1.80 ( s , 3h ) , 1.78 ( s , 3h ) , 1.68 ( s , 3h ) , 1.62 ( s , 3h ) , 1.55 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 158.8 , 158.7 , 152.1 , 144.1 , 138.7 , 134.8 , 134.5 , 131.6 ( 2c ) , 130.9 , 128.4 , 127.3 , 124.7 , 123.8 , 123.6 , 122.2 , 121.4 , 110.4 , 101.8 , 99.4 , 98.2 , 58.0 , 56.1 , 56.0 , 55.6 , 40.1 , 30.0 , 27.1 , 26.1 , 26.0 ( 2c ) , 24.7 , 18.5 , 18.0 , 16.6 ; hrms ( ei ) m / z calcd for c34h46o5 ( m ) 534.3345 , found 534.3330 . to a stirred solution of mom ether 30 ( 27 mg , 0.1 mmol ) in meoh ( 2.5 ml ) was added tsoh ( 40 mg , 0.2 mmol ) . the solution was stirred overnight , and the reaction was quenched by addition of saturated aqueous nahco3 . the resulting mixture was extracted with etoac , and the organic extracts were dried ( mgso4 ) , filtered , and concentrated in vacuo . stilbene 31 ( 22 mg , 88 % ) was obtained as a yellow oil : h nmr ( 300 mhz , cdcl3 ) 7.14 ( m , 2h ) , 7.10 ( m , 1h ) , 6.76 ( m , 1h ) , 6.73 ( d , j = 2.4 hz , 1h ) , 6.42 ( d , j = 2.2 hz , 1h ) , 5.215.04 ( m , 3h ) , 3.90 ( s , 3h ) , 3.84 ( s , 3h ) , 3.81 ( s , 3h ) , 3.52 ( d , j = 6.5 hz , 2h ) , 3.43 ( d , j = 6.4 hz , 2h ) , 2.091.96 ( m , 4h ) , 1.82 ( s , 3h ) , 1.78 ( s , 3h ) , 1.68 ( s , 3h ) , 1.62 ( s , 3h ) , 1.55 ( s , 3h ) ; c nmr ( 75 mhz , cdcl3 ) 158.9 , 158.1 , 146.2 , 143.6 , 138.7 , 134.7 , 131.9 , 131.5 , 131.0 , 128.5 , 127.5 , 126.1 , 124.7 , 123.9 , 123.0 , 121.5 , 117.5 , 108.8 , 101.9 , 98.3 , 56.0 , 55.7 , 55.3 , 39.8 , 26.8 , 25.7 , 25.6 , 25.1 , 24.4 , 18.1 , 17.6 , 16.3 ; hrms ( ei ) m / z calcd for c32h42o4 ( m + h ) 490.3083 , found 490.3087 . to a solution of stilbene 31 ( 11 mg , 0.02 mmol ) in thf ( 3 ml ) were added nah ( 60 % dispersion in mineral oil , 6 mg , 0.2 mmol ) and mei ( 2 drops ) . the mixture was stirred for 5 h , and the reaction was quenched by addition of h2o . the resultant mixture was extracted with etoac , and the combined organic extracts were washed with 2 m naoh , dried ( mgso4 ) , and concentrated in vacuo . stilbene 20 ( 6 mg , 55 % ) was obtained as a yellow oil , with h nmr data that were identical to the data given above . to a solution of khmds ( 0.5 m solution in toluene , 2.12 ml , 1.06 mmol ) in thf ( 1.5 ml ) were added phosphonate 23 ( 51 ) ( 46 mg , 0.11 mmol ) and aldehyde 34 ( 52 ) ( 20 mg , 0.09 mmol ) . after the solution was stirred for 2 h , the reaction was quenched by addition of nh4cl . the resulting mixture was extracted with etoac , washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification by flash column chromatography provided stilbene 36 ( 25 mg , 58 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.32 ( d , j = 1.9 hz , 1h ) , 7.147.09 ( m , 2h ) , 6.986.89 ( m , 4h ) , 5.29 ( s , 2h ) , 5.255.21 ( m , 7h ) , 3.56 ( s , 3h ) , 3.53 ( s , 3h ) , 3.50 ( s , 6h ) , 3.39 ( d , j = 7.2 hz , 2h ) , 1.79 ( s , 3h ) , 1.66 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 155.8 ( 2c ) , 147.4 , 146.8 , 136.4 , 132.1 , 131.0 , 127.7 ( 2c ) , 122.7 , 121.0 , 119.7 , 116.6 , 114.3 , 106.0 ( 2c ) , 95.4 ( 2c ) , 94.5 ( 2c ) , 56.2 ( 2c ) , 56.0 ( 2c ) , 25.7 , 22.7 , 17.7 ; hrms ( ei ) m / z calcd for c27h36o8 ( m ) 488.2410 , found 488.2416 . after tsoh ( 40 mg , 0.21 mmol ) was added to a solution of stilbene 36 ( 13 mg , 0.03 mmol ) in meoh ( 2.5 ml ) , the solution was stirred for 24 h. the reaction was quenched by addition of nahco3 , and the resulting mixture was extracted with etoac , dried ( mgso4 ) , and concentrated in vacuo . final purification by preparative tlc ( 30 % etoac in hexanes ) gave stilbene 37 ( 4 mg , 50 % ) as a yellow oil . the h and c nmr spectra matched published data . to a solution of khmds ( 0.5 m solution in toluene , 4.62 ml , 2.31 mmol ) in thf ( 1.5 ml ) were added phosphonate 33 ( 99 mg , 0.24 mmol ) and aldehyde 35 ( 52 ) ( 32 mg , 0.19 mmol ) . after the solution was stirred for 3 h , the reaction was quenched by addition of nh4cl . the resulting mixture was extracted with etoac , washed with brine , dried ( mgso4 ) , and concentrated in vacuo . final purification of the residue by flash column chromatography ( 4 % etoac in hexanes ) provided stilbene 38 ( 33 mg , 40 % ) as a yellow oil : h nmr ( 500 mhz , cdcl3 ) 7.44 ( t , j = 2.7 hz , 1h ) , 7.42 ( t , j = 1.9 hz , 1h ) , 7.037.01 ( m , 2h ) , 6.986.95 ( m , 1h ) , 6.926.90 ( m , 1h ) , 6.92 ( s , 2h ) , 5.245.19 ( m , 5h ) , 5.19 ( s , 2h ) , 3.50 ( s , 6h ) , 3.49 ( s , 3h ) , 3.39 ( d , j = 7.2 hz , 2h ) , 1.79 ( s , 3h ) , 1.66 ( s , 3h ) ; c nmr ( 125 mhz , cdcl3 ) 156.8 , 155.8 ( 2c ) , 136.6 , 131.3 , 131.0 , 127.7 , 127.6 ( 2c ) , 127.2 , 122.7 , 119.6 , 116.4 ( 2c ) , 106.0 ( 2c ) , 94.5 ( 2c ) , 94.4 , 56.0 ( 3c ) , 25.8 , 22.8 , 17.8 ; hrms ( ei ) m / z calcd for c25h32o6 ( m ) 428.2199 , found 428.2191 . to a solution of compound 38 ( 17 mg , 0.04 mmol ) in meoh ( 5 ml ) was added tsoh ( 46 mg , 0.24 mmol ) . after the solution was stirred for 24 h , the reaction was quenched with nahco3 . the resulting mixture was extracted with etoac , dried ( mgso4 ) , and concentrated in vacuo . final purification by flash column chromatography ( 12 % etoac in hexanes ) provided stilbene 39 ( 12 mg , 100 % ) as a yellow oil . all compounds were initially screened for intrinsic and antagonist activity at 10 m in the [ s ] gtp -- s binding assay at the human and the and opioid receptors overexpressed in cho cells . larry toll ( sri international , and ) . compounds were identified as antagonist characterized for functional antagonism ( ke ) and selectivity by measuring the ability of the test compounds to inhibit stimulated [ s ] gtp -- s binding produced by one of the selective agonists damgo ( ) , dpdpe ( ) , or u69 ,593 ( ) . response curves were run in the presence or absence of a single concentration of test compound . briefly , the test compounds were assayed in duplicate in 1.4 ml polypropylene tubes in a 96 - well format . cho membrane homogenates ( 2040 g protein ) were incubated with a positive control or the test compound , 0.1 nm [ s ] gtp -- s , and 1 m gdp in 50 mm hepes buffer ( ph 7.4 ) at room temperature for 1 h , after which bound radioligand was separated from free radioligand via rapid vacuum filtration over gf - b filters with a brandel scientific ( gaithersburg , md , usa ) 96 - well harvester . bound radioactivity is determined using a topcount 12 - detector instrument ( packard instruments ) using standard scintillation counting techniques . bounda four - parameter logistic function was fit to these data to calculate the ec50 and emax values using prism ( v. 6 ; graph pad software , san diego , ca , usa ) . the ke values were calculated using the formula ke = [ l ] / dr 1 , where [ l ] is the concentration of test compound , and dr is the ratio of agonist ec50 value in the presence or absence of test compound .\noutput:\n" }, { "from": "agent", "value": "the natural stilbene pawhuskin a has been shown to function as an opioid receptor antagonist , with preferential binding to the receptor . this finding encouraged assembly of a set of analogues to probe the importance of key structural features . assays on these compounds determined that one ( compound 29 ) shows potent opioid receptor binding activity and significantly improved selectivity for the receptor . these studies begin to illuminate the structural features of these non - nitrogenous opioid receptor antagonists that are required for activity ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: with increasing oil prices and forecasts of a future lack of availability , renewable non - petrochemical - based alternatives to materials synthesis could become more important . polysaccharides are the products of a natural carbon - capture process , photosynthesis , followed by further biosynthetic modifications . some are produced on a very large scale in nature , and some have industrial relevance with , for example , materials and food applications , either in their native or chemically modified forms . the topic of general modification of polysaccharides has been reviewed previously , and several more specific reviews are referenced later . in this review , i have limited myself to discussing the synthesis of modifications whereby the polymeric chain remains intact or at least while degradation may take place to some extent , the products are still polysaccharides . the conversion of polysaccharides into small molecules has been reviewed elsewhere and is not covered here . chemical modification can change the character of the polysaccharides , for example , rendering them hydrophobic . some such processes , such as the formation of cellulose esters ( including nitrocellulose , celluloid , cellulose acetate ) , are very well known and have been carried out at an industrial level for more than a hundred years . the object of this review is not to cover such well - known processes in detail but rather to describe published results of current research and the state - of - the - art in polysaccharide derivatisation . neither have i gone into details about the possible applications of the products but have focussed on aspects related to reactivity and chemical structure . the structures of the natural ( native ) polysaccharides whose chemical modification is described in this review are shown in figure 1 . structurally , the simplest molecules consist of a monosaccharide repeating unit with hydroxyl groups as the only functional groups . examples of this type of structure include the very common polysaccharides , cellulose and amylose . other related structures such as curdlan , a ( 13 ) - linked glucan , and inulin , the only polysaccharide based on furanosides considered here , also have simple structures . amylopectin has a structure similar to amylose ( these to polysaccharides are the components of starch ) , but it is a branched structure , with many amylose - like chains linked together by ( 16 ) - branching points . dextran is basically an ( 16 ) - linked glucan , but it may have a little or a lot of branching at the secondary hydroxyl groups . for example , in so - called regular comb dextran , every residue in the backbone is substituted by an ( 13 ) - linked glucose unit . xylans , a component of hemicelluloses , are made up of a ( 14 ) - linked xylopyranose backbone , but it also may be branched , for example , by 4 - o - methylglucuronic acid , or acetylated to a greater or lesser degree . xylose is a pentose , so the pyranose units in xylan do not have a primary hydroxyl group . guar gum and locust bean gum both consist of ( 14 ) - linked mannan backbones substituted by gal ( 16 ) units to some extent . in guar gum , approximately every other mannose residue is substituted with galactose , whereas in locust bean gum , long unsubstituted regions alternate with regions of heavy galactose branching . pullulan , alternan , and lichenan are glucans with more than one type of glycosidic linkage in the polysaccharide backbone . pullulan is an unbranched polysaccharide with three monosaccharides in the repeating unit , [ glc ( 14 ) glc ( 14 ) glc ( 16 ) ] . alternan has two monosaccharides in its repeating unit , [ glc ( 13 ) glc ( 16 ) ] , but it can also contain some glc ( 13 ) branching . lichenan is an unbranched polysaccharide based on glucose with mixed ( 13 ) and ( 14 ) linkages . alginates and pectins are based on uronic acids ; their monosaccharide constituents are all oxidised at c - 6 to the carboxylic acid level . alginates consist of domains of ( 14 ) - linked l - guluronic acid interspersed with domains of ( 14 ) - linked mannuronic acid . pectins are polysaccharides rich in galacturonic acid , although this acid commonly will be found as its methyl ester . a simple backbone of ( 14 ) - linked galacturonic acid methyl ester may also be substituted by other monosaccharide branches . a very common polysaccharide based on aminosugars is chitin / chitosan . the chitin / chitosan relationship can be regarded as a continuum , with polysaccharides containing more of the free base being called chitosan and those mostly n - acetylated being called chitin . the extent of derivatisation reactions is given in terms of the degree of substitution ( ds ) . for example , cellulose has three hydroxyl groups per monomer , so in an acetylation of cellulose , all three may be acetylated , and the maximum ds would be 3 . but only one of the alcohols is primary , so in an oxidation reaction that only acted on primary alcohols , the maximum ds would be 1 . the degree of polymerisation ( dp ) is another important factor , giving an average length ( expressed in number of monomer units ) of the polysaccharide . a loss in dp during a reaction indicates that degradation of the polysaccharide backbone has occurred . it has been pointed out that many reports use cellulose with low dp ( which is more soluble ) and also that many do not comment on whether there is any decrease in dp during derivatisation reactions . order of magnitude values of the dp of cellulose samples could be ca 280 for avicel and ca 2000 for cotton linters . if uniform partial derivatisation is to be achieved , it can be important that the reaction is conducted in homogeneous solution . running a reaction under homogeneous conditions may also lead to a cleaner product , due to fewer side reactions , as less forcing conditions ( lower reaction temperature and lower excesses of reagents ) may be necessary than in heterogeneous reactions ; hence , the choice of an appropriate solvent for a polysaccharide substrate is important . swelling of solid material by a solvent will not dissolve the solid to give a homogeneous solution , but it will nevertheless increase the accessibility of the reactive groups of the polymer to reagents in solution . polysaccharides are often insoluble in water or organic solvents , so solvent mixtures can be used . non - aqueous solvent mixtures that dissolve cellulose often consist of an organic liquid and an inorganic salt . examples include dma ( dimethylacetamide ) / licl ; dmf / licl ; dmi ( 1,3 - dimethyl -2-imidazolinone ) / licl ; and dmso / tbaf ( tetrabutylammonium fluoride ) . the dmso / et3n / so2 mixture is a salt - free solvent for cellulose . it will sometimes be necessary to heat to high temperature ( 150c ) before cellulose will dissolve in these solvents , but it will then remain in solution on cooling . inorganic salts are often formed as by - products in derivatisation reactions ( e.g. , stoichiometric nacl would be formed in a benzylation reaction using naoh / bncl ) , so when they are added at the start of a reaction to aid solubility , this is unlikely to cause problems in itself . similar solvents or solvent mixtures to those used for cellulose are often used for other neutral polysaccharides , but many are more soluble and some are water - soluble . solvents for chitin include licl ( 5 % ) / dma , licl / n - methyl -2-pyrrolidone , cacl2 / meoh , and hexafluoroisopropyl alcohol . charged polysaccharides such as chitosan ( which may be protonated on nitrogen ) or polyuronates such as alginates ( which can form carboxylate salts ) will have very different solubility properties . hence , chitosan is soluble in aqueous organic or mineral acids below ph 6.5 and also in dmso . ionic liquids ( room - temperature ionic liquids ) are relatively new solvents that have found use in polysaccharide chemistry . they can dissolve polysaccharides , including cellulose , hemicellulose , and wood , allowing derivatisation reactions to take place under homogeneous conditions . cellulose dissolves in ionic liquids , aided by conventional heating , microwave irradiation , or sonication , with up to 25 % ( w / w ) being obtained in [ bmim ] cl . the properties of ionic liquids can be fine - tuned by structural modification of one or other of the two ionic components . increasingthe length of the alkyl chains in the cation component resulted in a less efficient dissolution of cellulose . amylose was shown to have a very high solubility in ether - derived ionic liquids . ionic liquids have been called green solvents due to their recyclability and low vapour pressures ( low volatility ) , but a low vapour pressure can limit the recyclability of a solvent , as it can make its purification difficult after it has been used in chemical reactions . as a result , volatile and distillable ionic liquids have been designed for polysaccharide derivatisation . this section covers the formation of ethers and esters , in which the saccharide oxygen acts as a nucleophile in the reaction and is retained in the product . different degrees of reaction can be considered . as well as very low ds , where only a few hydroxyl groups per polysaccharide chain are derivatised , and maximum ds , where all the hydroxyl groups are derivatised , and points in between these extremes , we can consider regioselective reactions in which a single hydroxyl group on each monosaccharide residue reacts preferentially to ( say ) near completion . but more than this , if a regioselective reaction goes to completion , reaching ds = 1 , then it can be followed in principle by further derivatisations that do not have to be selective , but that can nevertheless introduce further functionality at specific positions in a polysaccharide structure . there is a significant disadvantage of working with polysaccharides when it comes to matters of regioselectivity . in monomeric molecules , when a reaction gives incomplete regioselectivity ( resulting in the formation of regioisomers , disubstituted or trisubstituted products , etc . ) the desired product may be purified from the other components of the product mixture by crystallisation or chromatography . in polysaccharides , any such purification is impossible , as correctly modified monosaccharide residues of the polysaccharide will be covalently linked to incorrectly modified monosaccharide residues . this means that only the most regioselective modifying reactions may be used for polysaccharide modification if a homogeneous polysaccharide structure is required . etherification involves the reaction of an alcohol ( here a saccharide alcohol ) with an alkylating agent in the presence of a base ( ( 1 ) ; figure 2 ) typical alkylating agents include alkyl halides ( chlorides , bromides , iodides ) or , less commonly , alkyl sulfonates . normally , a strong base will be used to deprotonate the alcohol to give the alkoxide . alkylation reactions generally have a poor water - compatibility , as water can hydrolyse the alkylating agent . the formation of cellulose ethers under homogeneous conditions in typical nonderivatising solvents is possible , but it is more problematic than ester formation ( see below ) . the solvent of choice for cellulose etherification appears to be dmi ( 1,3 - dimethyl -2-imidazolidinone ) / licl . in thistreatment with naoh and mei for 5 h at 70c gave 2,3,6 - tri - o - methylcellulose with a ds of 3 . it should be pointed out that when the naoh was added , the cellulose crashed out of solution to some extent , and so the reaction was in fact not entirely homogeneous . complete etherification ( i.e. , tri - o - alkylation ) of cellulose was also investigated in other solvents for etherification with various alkyl groups . different solvents and bases were evaluated in the benzylation reaction , and the best conditions of those tested were found to be powdered naoh and bncl ( both in an excess of 10 equiv . / hydroxyl ) , in a solvent of dmso / so2 / et2nh , heating at ca 80c for 3 - 4 h . subsequent papers covered the formation of substituted benzyl ethers and allyl ethers and of simple alkyl ethers of cellulose , all under essentially the same reaction conditions . purification was achieved by extraction into chloroform , precipitation after the addition of etoh , and then washing with water , etoh and hexane . in dma / licl , methyl , hydroxyethyl , and hydroxypropyl ethers of cellulose could be formed under homogeneous conditions , using iodomethane or the epoxides as alkylating agents . but high excesses of reagents were required , slow reactions were seen , and only products with low ds values ( 1.11.7 ) were accessible . a dmso / licl solvent was used for the homogeneous etherification ( methyl , ethyl , propyl , and butyl peretherification ) of cellulose , using dimsyl sodium ( from nah and dmso ) as base . ionic liquids have been tested as solvents for the etherification of polysaccharides ( cellulose and starch ) under basic conditions but with little success to date , in contrast to esterification reactions ( see below ) . xylan was benzylated using bnbr , naoh , and 18 - crown - 6 in dmso , and amylose was converted into its tri - o - benzyl derivative by treatment with naoh and bncl in dmso . a detailed investigation into the benzylation of starch in water ( naoh , bncl ) was reported . as expected , widespread hydrolysis of the bncl occurred under these conditions . - chitin was suspended in dmso , and sodium hydride ( 5 equiv . ) and benzyl chloride ( 10 equiv . ) were added . after heating at 60c for 24 h , was used , a product with ds = 2 was obtained , but n - alkylation is likely to occur as well as o - alkylation under such reaction conditions . alternatively , chitin was suspended in dmso and treated with koh ; this insoluble deprotonated chitin was then filtered and washed to remove water , then it was resuspended in dmso and bncl was added . considering other alkyl ethers , amylose and starch were treated with propyl bromide and naoh in dmso to give propyl ethers with ds of up to 3.0 . the purification of polysaccharides with high ds was achieved by precipitation from water , but those with low ds were more difficult to purify . pullulan was converted into its propyl and butyl ethers with ds between 1 and 2.6 by treatment with the alkyl bromides and naoh in h2o / dmso . carboxymethyl cellulose is an industrially important ionic cellulose ether , and the synthesis of this type of derivative based on some hemicellulose polysaccharides has been investigated to some extent . the synthesis of carboxymethyl ethers of xylan was investigated under homogeneous conditions ( in water ) or slurry conditions ( in i - proh or etoh / toluene ) using naoh as base and clch2coona as alkylating agent . guar gum was derivatised with carboxymethyl ethers in water or in etoh / toluene ( as for xylan , above ) to give a product with a ds of 0.8 . repeating the procedure gave further substitution and a product with a higher ds . konjac glucomannan was derivatised with carboxymethyl ethers in methanol to give a product with a ds of 0.3 . other than cellulose derivatives , which are produced industrially by epoxide - ring opening , guar gum and xylan were etherified ( up to ds = 2 ) by treatment with ethylene oxide or propylene oxide and sodium hydroxide . esterification in general will involve the reaction of an alcohol ( here a saccharide alcohol ) with an acylating agent ( ( 2 ) , figure 3 ) carboxylate esters can be formed using carboxylic acids as acylating agents under strong - acid catalysis ( fischer esterification ) or by using an activated derivative such as an acid chloride or anhydride , either with base or with a lewis acid . the strong - acid catalysis method is used to produce cellulose acetate , an important industrial product . but this method does not produce the triacetate , due to partial transient sulfation during the reaction . cellulose triacetate can be prepared in a similar way using an acid catalyst that does not covalently attach to the cellulose , such as hclo4 . when an activated carboxylic acid derivative ( e.g. , acid anhydride , acid chloride ) reacts with an alcohol under basic conditions , the base should be present in a stoichiometric amount ( it will be protonated by the acid by - product of the reaction ) , but it can be a weak base , such as pyridine or triethylamine . ( ds of up to 2.42.8 ) were prepared by the reaction of cellulose under homogeneous conditions in dma / licl solution with acid chlorides and triethylamine or with acid anhydrides and sulfuric acid . the cellulose carboxylate products were purified by precipitation into water followed by soxhlet extraction into methanol . similarly , starch was esterified with acyl chlorides and pyridine in dma / licl solution at 100c for 6 h , followed by purification by precipitation . with long - chain fatty acid chlorides , ds values of up to 3 were seen . xylan acetates with ds of up to 2 ( i.e. , complete acetylation ) could be prepared either with ac2o / pyridine in dmf / licl or under acid catalysis in acoh . alternatively , a xylan acetate with high ds ( 1.9 ) and clean h nmr spectra was prepared using ac2o and pyridine in dmf . with longer - chain acyl chlorides , xylan reacted under homogeneous conditions in dmf / licl to give polysaccharides with lower ds values ( 0.31.5 ) . vinyl carboxylates have also been used as acyl donors , reacting spontaneously with cellulose in dmso / tbaf to give polysaccharides with ds values of up to 2.6 . the acetylation of cellulose in an ionic liquid solvent , [ amim ] cl ( 1 - allyl -3-methylimidazolium chloride ) , was achieved in 2004 using acetic anhydride to give products with ds of ca 2.52.7 . several ionic liquids gave similarly good results , with [ bmim ] cl ( 1 - butyl -3-methylimidazolium chloride ) being the best . acetic anhydride or acetyl chloride reacted with cellulose without any added base within 2 h at 80c to give cellulose acetates with ds of up to 3 . however , only lower ds values ( e.g. , 1.6 for lauryl chloride ) were obtainable with fatty acid chlorides in ionic liquids , presumably because the partially acylated polysaccharide becomes more and more nonpolar until it precipitates out of the polar ionic solvent , stopping the reaction . the use of carboxylic acids themselves as acylating agents rather than derivatives such as acid anhydrides or acyl chlorides could be attractive , as the acids may have a wider availability and be more soluble in polar solvents . the fischer esterification using the carboxylic acid as solvent and with strong - acid catalysis has already been mentioned , but in situ activation of carboxylic acids under mild conditions can also be used for polysaccharide acylation . when tosyl chloride was used as an activating agent for with various long - chain carboxylic acids in a dmso / tbaf solvent , acylated celluloses with ds of up to 2.62.9 could be formed . cellulose reacted with carboxylic acids using classic peptide coupling reagent , dcc , in nonaqueous solvents ( e.g. , dma / licl ) to give derivatised polysaccharides with low ds values . starch was acylated under similar conditions by the in situ activation of carboxylic acids with tscl or cdi ( carbonyldiimidazole ) . the solubility of alginates can be changed by changing the ionisation state ( i.e. , acid versus salt ) and ( for the salt form ) the counterion [ e.g. , sodium versus tetrabutylammonium ( tba ) ] . tba - alginates were soluble in dmso / tbaf , but dma / licl did not dissolve either the acid or salt ( na or tba ) forms . when the alginate solution was treated with ac2o and pyridine , only low ds of up to ca 1 were obtained . it is worth mentioning here that dmso can react with acylating agents to generate a swern - type oxidant that can destructively oxidise polysaccharide hydroxyl groups . in a method for the selective o - acylation of chitosan , the polysaccharide was suspended in water , and a carboxylic acid ( c2c9 as well as some halogenated or unsaturated acids ) and h2so4 ( 2 m ) were added at room temperature . the mixture was then stirred at 80c for 4 h , and the products ( with low ds values of 0.020.2 ) were purified by ph adjustment , precipitation from acetone , and soxhlet extraction . under these conditions , but then dissolution may or may not occur during the course of the reaction ; only surface groups may be acylated , or alternatively bulk hydroxyls may also react ( due to solvent swelling of the material ) ; the macroscopic structure of the material may be retained after derivatisation ( fibre , paper , cloth , or nanofibrils , etc . ) . heating a suspension of insoluble cellulose in a mixture of pyridine and acylating agent ( 5 equiv . / glc = 1.3 equiv . / oh ) can give acylated celluloses with some acylating agents after purification by precipitation from water . polysaccharides with ds values of 2.62.9 were obtained with acetyl chloride and with long - chain acyl chlorides ( c10 ) after 3 h. with pivaloyl chloride , a much longer reaction time was required to obtain a product with ds = 2.5 in low yield , and with shorter chain acyl chorides ( c6 ) , decomposition was seen . a similar synthesis of cellulose esters was reported from a suspension of the polysaccharide in pyridine and the acid chloride , while initially heterogeneous cellulose reacted with acetyl chloride without added base to give cellulose acetates with ds values of up to 2.96 . konjac glucomannan was acylated with palmitoyl chloride and pyridine in benzene in a heterogeneous reaction in which the polysaccharide dissolved during the course of the reaction to give a product with ds up to 2.7 . arabinoxylan was fully esterified under fischer conditions by suspending the polysaccharide in a carboxylic acid anhydride ( acetic , propionic , butyric ) and treating with catalytic methanesulfonic acid . also here , the polysaccharide dissolved during the course of the reaction . mixed anhydrides generated from a carboxylic acid and other more reactive acids ( e.g. , trifluoroacetyl ) have also been used as acylating agents with polysaccharides under heterogeneous conditions . sulfonate esters can act as leaving groups in sn2 reactions ( see below ) , and many of their applications derive from this aspect of their reactivity . they may be introduced with reasonably good regioselectivity for the primary hydroxyl groups , and regioselective sulfonate syntheses are described in the section on regioselective reactions ( see below ) . but polysaccharide sulfonates with ds 2 are also accessible . the most commonly seen sulfonates in polysaccharides are toluenesulfonates ( tosylates , ts ) and methanesulfonates ( mesylates , ms ) . the classic reaction conditions for tosylate formation involve heating the ( initially heterogeneous ) polysaccharide with tosyl chloride in pyridine . three possible side reactions that may occur during sulfonate ester formation , all arising from nucleophilic displacement of the formed sulfonate ester are as follows : ( i ) cyclisation by attack of one of the secondary hydroxyl groups ( e.g. , o - 3 ) ; ( ii ) attack by pyridine to form a c - 6 pyridinium salt ; ( iii ) attack by chloride to form a c - 6 chloride . these side reactions are a result of the long reaction times and high temperatures required for the heterogeneous reaction . tosylation and mesylation reactions of cellulose in solution in dma / licl gave uniform and well - defined products with ds values between 0.4 and 2.3 . the tosylation of cellulose underhomogeneous conditions in the ionic liquid [ amim ] cl was also recently achieved . chitin was tosylated under homogeneous conditions in dma / licl , dextran tosylates were prepared in organic solvent without any added salt , and konjac glucomannan was tosylated to give products with ds of up to 2.3 . the primary alcohol of a saccharide will , with very few exceptions , always be more nucleophilic than the secondary alcohols . the difference in reactivity between the primary and secondary alcohols can vary , though , and complete regioselective distinction between primary and secondary alcohols ( i.e. , normally c - 6 versus all of c - 2 , c - 3 , and c - 4 ) will often not be seen . the respective rate constants for the substitution of primary and secondary alcohols do not change during a reaction , and if a primary alcohol reacts more quickly than a secondary alcohol , its concentration will decrease more rapidly as the reaction progresses . therefore , as the reaction progresses , the rates of reaction of the primary and secondary alcohols will become similar and regioselectivity will decrease . differentiation between the nucleophilicity of the different secondary hydroxyl groups in a polysaccharide will often be difficult or impossible , and polysaccharides containing different substitution patterns may often be formed . having said that , there are a few examples of regioselectivity between the secondary positions of polysaccharides that can be exploited synthetically . the regioselective protection of cellulose , focussing on ether and ester protecting groups has been reviewed and covered to some extent in other reviews . the hydroxyl groups of cellulose are much more reactive in solution than they are in the solid phase , because when cellulose dissolves , the extensive hydrogen - bonding network is broken up . as a result , reactions in solution can be carried out under milder conditions than in the solid phase , and this allows a higher degree of selectivity . thus , regioselective derivatisations of cellulose and other polysaccharides are generally carried out under homogeneous reaction conditions , and the solvent system dma / libr ( or licl ) is often used . only a rather limited number of groups / transformations live up to the very high regioselectivity criteria that are necessary for the modification of polysaccharides . these include the installation of trityl ethers ( at o - 6 ) and of bulky silyl ethers ( at o - 6 or at both o - 2 and o - 6 ) . the installation of carboxylate esters ( at o - 6 , but not normally selective enough ) and tosylate esters ( at o - 6 , but not normally completely selective , or at o - 2 ) are also considered here . the installation of halides at c - 6 in a phosphane - mediated reaction is also often a regioselective process , but this in this reaction , the polysaccharide behaves as an electrophile , so it is considered in a later section of this review . the trityl group reacts with cellulose preferentially at the primary hydroxyl , o - 6 , on steric grounds ( scheme 1 ) . trityl ethers may be installed by heating cellulose ( rayon ) with pyridine and trityl chloride ( i.e. , under initially heterogeneous conditions with dissolution occurring as the reaction proceeds ) , and ds values close to 1 with little substitution of the secondary positions are obtainable . cellulose has also been tritylated under homogeneous conditions to give products with ds values of 1.0 . the solvents used were dmso / n2o4 ; dma / licl ; or dmso / so2 / dea .6 - o - trityl derivatives of some other polysaccharides have been prepared , directly or indirectly . - chitin was suspended in pyridine and heated at 90c for 72 h with trityl chloride ( 10 equiv . ) and dmap ( 36 equiv . ) . a 6 - o - trityl derivative of chitosan was prepared by a three - step sequence . first , the nitrogen was protected as a phthalimide derivative , then o - 6 was tritylated , and finally n - deprotection gave the 6 - o - tritylchitosan with ds = 1 . thexyldimethylsilyl chloride ( tmdscl ) has been shown to react with cellulose with very good regioselectivity , and different regioselectivities , o - 6 only or for both o - 2 and o - 6 , are seen under different reaction conditions ( scheme 2 ) . treatment of cellulose ( undissolved , i.e. , under initially heterogeneous conditions ) with tmdsc1 in dmf saturated with ammonia at 15c resulted in the introduction of tmds groups at c - 6 only , with a ds of 0.99 . when the reaction was carried out under homogeneous conditions in dma / licl and with imidazole as base , 2,6 - di - o - thexyldimethylsilylcellulose was formed with a ds of 2.0 . moreover , this 2,6 - protected derivative can be used for the regiospecific introduction of substituents at o - 3 of cellulose . liquid ammonia has also been used as an effective solvent for silylation reactions of cellulose . regioselectivities ( for o - 6 ) are generally lower for carboxylate esterification reactions of cellulose than those seen for the formation of trityl ethers or silyl ethers . an investigation of various sterically hindered acylating agents , including pivaloyl chloride , adamantoyl chloride , and 2,4,6 - trimethylbenzyl chloride , in solvents including dma / licl , dmso / tbaf , and the ionic liquid [ amim ] cl , failed to give satisfactory regioselectivity . but having said that , in a different study , excellent regioselectivity for o - 6 of cellulose was observed in an esterification reaction using benzyl chloride in [ amim ] cl without any added base . it is relevant in this context to note that silyl ether protection may be regiospecifically replaced by carboxylate protection . when a cellulose derivative bearing trimethylsilyl ethers is treated with an acyl chloride in the absence of a base , the silyl ethers are regiospecifically replaced by acyl groups ( in the presence of a base , the silyl ethers remain , and the free hydroxyl groups are acylated ) . but while this process is well known for trimethylsilyl ethers , it has apparently not yet been investigated for thexyldimethylsilylethers , which ( as described above ) can be introduced into cellulose with excellent regioselectivity . cellulose reacts preferentially at o - 6 in tosylation reactions ( see above ) , but the regioselectivity is not perfect . the esterification of cellulose with various sulfonic acid chlorides , including the 2,4,6 - trimethylbenzenesulfonyl group , under homogeneous conditions ( in dma / licl ) , was investigated in an attempt to improve the regioselectivity for substitution at o - 6 , but in general , the products contained mixtures of 2 - and 6 - tosylation . a very interesting result has been obtained concerning the regioselectivity of the tosylation of starch . when starch ( 70 % amylose ) was tosylated in solution in dma / licl , o - 2 reacted preferentially , with very good regioselectivity ( over o - 3 and o - 6 ) , to give a product with a ds 1 , with the tosyl groups essentially exclusively at c - 2 . this regioselectivity is counterintuitive , and apparently , it is also solvent - dependent : horton had previously reported that when the tosylation of amylose was carried out in pyridine , the more expected product , 6 - o - tosyl - amylose , was formed with ds 0.6 ( scheme 3 ) . inulin was tosylated by treatment with tscl and et3n , in dmf / licl at 0c . purification by precipitation then dialysis gave a polysaccharide product derivatised at o - 6 and with some partial derivatisation at o - 4 . in general , regioselectivity in chemical reactions is controlled by a combination of steric , electronic , and stereoelectronic factors . in enzymatic reactions in contrast , the reaction will occur at the position that is held close to the relevant catalytic amino acid side chains when the substrate is bound in the active site of the enzyme . that is true at least when the substrate of the reaction is the same as , or close in structure to , the natural structure that the enzyme has evolved to modify , for example , for galactose -6-oxidase and galactose ( see below ) . some enzymes , though , have broad substrate tolerance and catalyse reactions on rather generic structures . when esterases , lipases , and proteases are used to catalyse the formation and hydrolysis of esters on polysaccharides in the laboratory , this is not the natural function of the enzyme , so they have not evolved to differentiate the different hydroxyl groups . rather , in these enzyme - catalysed reactions , the enzyme will tend to act on the hydroxyl group ( for esterification ) or ester ( for hydrolysis ) that is most sterically accessible , i.e. , those at the primary positions . hence in principle , 6 - monoesters may be accessible by enzyme - catalysed regioselective acylation of an unprotected polysaccharide , and in principle , 6 - mono - unprotected polysaccharides may be accessible by peracylation followed by regioselective hydrolysis of the primary esters . the considerations regarding solvents for enzyme - catalysed reactions can be summarised briefly as follows . enzymes normally require at least a trace of water to function properly , and they may also be structurally unstable in nonaqueous media . however , water is not a good solvent for acylation reactions , as the enzyme - catalysed reactions are reversible . when water is present in excess ( i.e. , as solvent ) , the equilibrium would lie towards hydrolysis , so the ds values of the products would be very low . polar solvents ( e.g. , dmf , dmso , etc . ) can strip the essential catalytic water from the surface of enzymes , rendering them inactive . solvents with lower hydrogen - bonding ability will thus be more likely to lead to higher enzyme activity , but those with a better hydrogen - bonding ability would better dissolve the polysaccharide substrates . thus , in choosing a solvent , a balance must be struck between dissolving the substrate and maintaining the activity of the enzyme . nonpolar solvents are not ideal , as the enzyme and the substrate are insoluble , and insoluble enzymes can not catalyse reactions on insoluble substrates . butenzymes can be made soluble in nonpolar solvents by micelle formation , or they can be made accessible by immobilisation in the pores of a solid surface ( as in novozyme , i.e. , immobilised candida antarctica lipase b ) . in a pioneering approach to the enzymatic modification of solvent - insoluble polysaccharides in organic solvents , a method was developed to use surfactants to solubilise enzymes in organic solvents . in this way , insoluble amylose could be acylated with a protease from bacillus subtilis ( subtilisin carlsberg ) using vinyl caprate as acyl donor in isooctane as solvent . as the starting polysaccharide is completely insoluble in the very nonpolar solvent , only surface - accessible hydroxyls could be acylated , and the authors estimated that 90 % of the surface - accessible primary hydroxyls were esterified . this corresponded to ds values of ca 0.15 and 0.30 , respectively , for a thin amylose film and a milled amylose powder . subsequently , the enzymatic esterification of various solid celluloses was addressed , including cloth , thread , paper , and milled particles . the cellulose samples failed to react in isooctane , but esterification did occur in pyridine when the subtilisin carlsberg ( protease ) was transferred into that more polar solvent , presumably due to better preswelling of the cellulose . in a related approach , the enzymatic acylation of starch in toluene was achieved by coating polysaccharide nanoparticles in surfactant . reverse - micelles were formed with the starch particles and the surfactant in octane , and then the octane was removed . these surfactant - coated particles then underwent acylation in toluene at 60c with immobilised c. antarctica lipase b ( i.e. , novozyme 435 ) , using vinyl esters or acid anhydrides as acyl donors . a ds of up to 0.9 was obtained with acylation occurring regioselectively at o - 6 . nanoparticles have a high surface area / volume ratio , which allows efficient derivatisation of a heterogeneous system . enzyme - catalysed esterification reactions are reversible , so in water , the ds values of the products will tend to be very low . the esterification of starch in water using decanoic acid as acyl donor , catalysed by a lipase from thermomyces lanuginosus , was reported . the authors compared different methods of measuring the ds , including the classic titrimetric method ( saponification followed by back titration ) and nmr and ft - ir based methods , and proposed a new method based on ester hydrolysis followed by gc analysis . the acetylation of ( insoluble ) cellulose in water using vinyl acetate as the acyl donor , catalysed by a lipase from aspergillus niger , was reported . but here again , only very low ds values were seen ( quoted as 0.16 % by weight ) . a series of papers describe the lipase - catalysed esterification of starch with fatty acids , either in polar aprotic solvents ( dmso or dmf ) or under solvent - free conditions with microwave heating . the esterification of starch was investigated using lipases from thermomyces lanuginosus , burkholderia cepacia , and candida rugosa . both neat ( ds = 1.01.5 ) and solution ( ds = 1.01.45 ) methods resulted in significant esterifcation of the starch , except for when t. lanuginosus was used in solution in dmso , when only a low ds ( 0.08 ) was obtained . the free hydroxyl groups of cellulose acetate were acylated using novozyme ( immobilised candida anctarctica lipase b ) in acetonitrile . ionic liquids might seem to be a promising candidate for this transformation , as they can dissolve polysaccharides , and they are good solvents for the regioselective enzymatic acylation of unprotected monosaccharides . when conventional organic solvents are used for the enzymatic acylation of unprotected monosaccharides , the initial reaction products ( typically 6 - o - acyl derivatives ) will tend to be more soluble than the starting material in the reaction solvent and so are more available for further reaction . this can result in overacylation ( to give , e.g. , 3,6 - di - o - acyl derivatives ) and mixtures of products . but ionic liquids dissolve the starting monosaccharides , so the reaction mixtures are homogeneous and good regioselectivity results . however , the regioselective enzymatic acylation of polysaccharides in ionic liquids does not appear to have been investigated . an example of the cleavage of esters from 6 - o - acyl - cellulose ( i.e. , only o - 6 acylated ) using a protease is reported in the literature . partial hydrolysis occurred in water , and the authors concluded that the more accessible surface esters were cleaved from the heterogeneous ( insoluble solid ) substrate . a very interesting development concerns esterases that have naturally evolved to hydrolyse the esters of polysaccharides . acetyl xylan esterases are enzymes that hydrolyse these acetates at the 2 - and 3 - positions of xylopyranose in xylan . several of these enzymes were screened for cleavage activity of ester groups in partially acetylated celluloses ( ds = 0.7 or 1.4 ) , and some of the enzymes showed regioselective behaviour , as shown by c nmr spectroscopy . the xylan esterase from aspergillus oryzae cleanly cleaved the o - 2 and o - 3 acetates , leaving the o - 6 acetate . other xylan esterases ( e.g. , from schizophyllum commune or aspergillus niger ) cleaved the o - 2 acetate , leaving the o - 3 and o - 6 acetates ( albeit less cleanly ) . the replacement of a saccharide oxygen by a heteroatomic nucleophile in a nucleophilic substitution ( sn ) reaction typically requires at least two steps . first , a saccharide hydroxyl group must be transformed into a good leaving group , which results in the attached carbon becoming susceptible to nucleophilic attack . second , treatment with a nucleophile results in attack at the electrophilic carbon of the polysaccharide and displacement of the leaving group . saccharide electrophiles are much less reactive towards nucleophilic displacement than their more typical hydrocarbon - derived counterparts . in considering the reactions of polysaccharides , we consider nucleophilic substitution reactions at the primary and secondary positions ( but not the anomeric position ) of the constituent monosaccharides . in contrast to typical hydrocarbon substrates , saccharides will almost certainly never undergo nucleophilic substitution by an sn1 mechanism at the secondary positions nor at the primary positions . this is because an intermediate carbocation would be strongly destabilised by the multiple electron - withdrawing hydroxyl groups . hence all nucleophilic substitution at the primary and secondary positions in a polysaccharide will occur by sn2 processes . even sn2 reactions are disfavoured in saccharides , at the primary positions , and very much so at the secondary positions . the empirical effect , sometimes called the - oxygen effect or oldham and rutherford 's rule , has electronic and steric explanations , which i summarise very briefly here . in an sn2 reaction , electrons must be relocalised onto the departing leaving group , and this aspect of the mechanism is disfavoured by having electron - withdrawing groups in the vicinal positions . also , the bulk of neighbouring alkoxy or acyloxy groups makes saccharide - derived electrophiles less reactive in sn2 reactions ( cf the neopentyl effect in sn2 reactions of hydrocarbons ) . a further factor that disfavours sn2 reactions at the secondary positions of pyranoses ( but not furanoses ) derives from the well - known high stability of a six - membered ring in the chair conformation , especially one bearing multiple equatorial substituents . at the sn2 transition state , a ring - conformational change occurs to accommodate the nucleophile and leaving group in the coordination sphere of the central carbon . this ring - conformational change is less favourable in a six - membered ring due to the loss in the stability of the molecule in moving away from a very stable to a less stable ring - conformation . thus , sn2 reactions at the secondary positions of polysaccharides are almost unknown , but the fact that they can be achieved in high yields in monosaccharide systems , using good nucleophiles and good leaving groups , means that this could be a possible avenue for future exploration in the synthesis of polysaccharide derivatives . the derivatisation of cellulose by nucleophilic substitution ( saccharide electrophile ) has been reviewed . leaving groups that are useful at the primary positions include bromide , iodide , less reactive sulfonates , or phosphonium leaving groups generated in situ ( in mitsunobu and related reactions ) . leaving groups that are useful at the secondary positions of monosaccharides are triflates and epoxides , but nucleophilic displacement at the secondary positions has hardly been exploited in the polysaccharide series , with only a rare example of a well - defined epoxide - opening reaction by an oxygen nucleophile ( see below ) . thus , almost all of the nucleophilic substitution chemistry of polysaccharide electrophiles that has been reported to date has taken place at the primary positions . . it may be possible to activate the primary alcohol ( oh - 6 ) regioselectively , but for more details on this process , see the section above on nucleophilic reactions of polysaccharide hydroxyl groups . the sulfonate group has a general structure rs ( o ) 2o , and the r group can be varied to tune the electronic properties and thus the reactivity of the sulfonate ester . despite the almost unlimited possibilities for structural variation here , only a few sulfonates have been in common usage in the nucleophilic displacement reactions of polysaccharides . mesylate ( methanesulfonate , r = me ) and tosylate ( p - tolunesulfonate , r = p - mec6h4 ) have broadly similar reactivities and will normally undergo nucleophilic displacement at the primary positions but not at the secondary positions of pyranosides . when there are free hydroxyl groups at the vicinal positions to tosylates or mesylates at the secondary positions of partially protected monosaccharides or polysaccharides , nucleophilic substitution may take place . presumably , though , this process goes via epoxide intermediates , as when there is no vicinal alcohol group , there is no substitution reaction . triflate ( trifluoromethanesulfonate , r = cf3 ) has a strongly electron - withdrawing r group . consequently , it is a better leaving group , and it can be used in nucleophilic substitution reactions at the secondary positions of monosaccharides , but examples on polysaccharide substrates do not appear to be known . halides are the classic leaving groups in nucleophilic substitution reactions , and the displacement of halides from the primary positions ( e.g. , c - 6 of cellulose , amylose , etc . ) of polysaccharides has been used to introduce nucleophilic groups ( scheme 4 ) . one method that has been used for the introduction of the halide leaving groups at c - 6 of polysaccharides is the treatment of c - 6 sulfonates ( including tosylates and mesylates ) with halide salts using acetone as solvent ( i.e. , finkelstein conditions ) . an obvious disadvantage of this approach , though , is that if the halide is to be used as a leaving group in a nucleophilic substitution reaction , it can seem pointless to add an extra step to a reaction sequence when the c - 6 sulfonate in the starting material can itself act as a leaving group in substitution reactions with the same nucleophiles . thus , methods for the preparation of polysaccharide halides directly in one step from the native polysaccharides would appear to be advantageous . in the monosaccharide series , several sets of mild reaction conditions based on treatment with pph3 together with a halide source that can be reduced ( e.g. , cbr4 in the appel reaction , i2 in the garegg reaction , etc . ) have been developed for the regioselective preparation of bromides or iodides from the unprotected glycosides . under these mild reaction conditions , polysaccharides may also be halogenated directly and regioselectively under related phosphane - based conditions , or using classical halogenating agents such as socl2 , without initial protecting - group manipulations . in cellulose , c - 6 is halogenated first , and c - 3 may also be halogenated under certain conditions , while c - 2 does not normally react . in chitin , thus , chitin may be transformed into a polysaccharide containing three different functional groups , halogen , alcohol , and amide , in a single step . cellulose could be chlorinated with the classical chlorinating agents , thionyl chloride and mesyl chloride ( mscl ) , to give polysaccharides with ds values of up to 2.8 , meaning that almost complete chlorination had occurred at both primary and secondary positions . the reagent system of n - chlorosuccinimide ( ncs ) / pph3 / licl in dma was more regioselective for the chlorination of cellulose . several other polysaccharides were chlorinated with good regioselectivity for the primary positions using mscl , including amylose ( in dmf / licl ) , inulin ( in dmf , 70c , 16reagent , reaction at c - 6 was seen at low temperatures , and at higher temperatures , c - 3 was also chlorinated . chitin could be chlorinated regioselectively at c - 6 using ncs / pph3 in dma / licl to give a product with a ds of 1.0 , but some depolymerisation was seen under these conditions . the bromination of cellulose could be carried out with the tribromoimidazole / pph3 / imidazole reagent system in dma / libr to give bromocelluloses with ds values of up to 1.6 . here , bromination had occurred at c - 6 and c - 3 , and the brominated c - 3 carbons were found to have a mixture of gluco and allo configurations . an essentially completely regioselective bromination of cellulose ( at c - 6 ) was achieved using n - bromosuccinimide ( nbs ) / pph3 in dma / libr , giving a 6 - bromo -6-deoxycellulose with ds = 0.9 . the regioselectivity of this bromination reaction can be better than that of a tosylation reaction . this makes phosphane - mediated bromination an attractive method for the very regioselective modification of cellulose ( at c - 6 ) ; the analogous direct iodination of unprotected polysaccharides does not appear to be known , however . similar bromination reactions of other polysaccharides with the nbs / pph3 reagent system gave similarly excellent regioselectivity and high degrees of substitution . when amylose was treated with nbs / pph3 in dmf , only derivatisation of the primary positions was observed , and it was possible to monitor the progress of this reaction by following the development of the nmr spectra . the analogous bromination of chitin was achieved with nbs / pph3 in dma / libr to give a product with a ds of 0.94 , but here some loss in dp was seen . it is possibly relevant that while chitin is soluble in dma / licl , it is not soluble in dma / libr , so this reaction was heterogeneous . the bromination of curdlan was achieved with a different phosphane - based reagent system , cbr4 / pph3 in dmf / licl . the reaction proceeded essentially to completion and with complete selectivity for the primary position ( c - 6 ) . to date , polysaccharide epoxides do not appear to have been widely investigated , but the synthesis of a 2,3 - anhydro derivative of cellulose ( i.e. , a 2,3 - epoxide ) has been reported ( scheme 5 ) . first , o - 6 was protected as a trityl ether , then o - 2 was converted regioselectively into a tosylate . treatment of this compound with base resulted in attack of o - 3 onto c - 2 , displacement of the tosylate , and closure of the epoxide ring to give a 2,3 - anhydro -6-o - tritylcellulose . the ds of this polysaccharide was ca 0.3 , as determined from the incorporation of methyl groups after ring - opening by methoxide . cyclodextrin ( per ) epoxides are also known , and they have been synthesised by a similar but possibly more regioselective sequence of 6 - o - silylation , 2 - o - sulfonation , and base treatment for epoxide closure . normally , esters or ethers of polysaccharides ( or indeed of monosaccharides ) would be prepared by the reaction of a saccharide oxygen nucleophile with an alkylating agent or acylating agent ( see above ) . the complementary approach , where the saccharide acts as an electrophile and is attacked by an alcohol ( for ether formation ) or a carboxylate ( for ester formation ) , is much less common , but examples of this type of derivatisation do exist for polysaccharide substrates . a situation where the more usual approach of nucleophilic attack by a saccharide oxygen nucleophile would be impossible would be in the synthesis of phenyl ethers . and indeed , a 6 - o - phenyl ether derivative of cellulose was synthesised by displacement of a 6 - tosylate by phenoxide . nucleophilic substitution reactions at the secondary positions of polysaccharides are extremely rare , but a 2,3 - epoxide derivative of cellulose underwent ring - opening by methoxide in a reaction that was assumed to be quantitative . for example , starch was converted into a 3,6 - anhydro derivative with a ds of 0.85 using the following sequence : tritylation of o - 6 , acetylation of o - 2 and o - 3 , detritylation of o - 6 , tosylation of o - 6 , and finally deacetylation of o - 2 and o - 3 , which also resulted in intramolecular nucleophilic attack of o - 3 onto c - 6 , displacing the tosylate and cyclisation to form the 3,6 - anhydrosugar . carboxylate salts have been used in nucleophilic displacement reactions with primary amylose halides to give c - 6 esters . finally , esterification is possible under the conditions of the mitsunobu reaction , an overall formal condensation reaction between an ( unactivated ) alcohol and a carboxylic acid nucleophile . the basis of the mitsunobu reaction is a redox reaction between stoichiometric amounts of an oxidising agent [ normally dead ( diethyl azodicarboxylate ; which is reduced to dead - h2 ) ] and a reducing agent [ normally pph3 ( which is oxidised to ph3p = o ) ] that require a mole equivalent of water to allow their reaction . the mechanism involves the in situ activation of an alcohol by the generation of a phosphonium leaving group and its subsequent displacement by a nucleophile to give the product . the reactions are normally high - yielding and regioselective , so it is often possible to refunctionalise the primary position of an unprotected monosaccharide . however , the reactivity of amylose under the conditions of mitsunobu esterification has been investigated . initially esterification occurred regioselectively at c - 6 , but as the reaction proceeded above ds = 0.5 , some esterification of the secondary positions started to be observed . the introduction of different types of nitrogen - containing groups at the primary positions of polysaccharides by nucleophilic displacement has been fairly extensively investigated . amines will be neutral nucleophiles and will carry one or more alkyl chains that will be retained in the final product . alternatively , a negatively charged nucleophile such as azide could be used . the azide in the polysaccharide product could then be reduced to reveal an amine that could be further functionalised if desired . the monovalent nature of an azide nucleophile can have the advantage of avoiding possible multiple substitution of amine nucleophiles that would lead to cross - linking and complex product mixtures . a synthesis of 6 - amino -6-deoxycellulose ( ds = 1.0 ) by the essentially uniform introduction of nitrogen at c - 6 of cellulose has been described . tosylation of cellulose resulted in complete derivatisation of o - 6 , but the reaction was not completely regioselective , and significant tosylation of o - 2 and o - 3 also occurred . treatment with lialh4 reduced the c - 6 azides to give c - 6 amines and , at the same time , reductively cleaved the 2 - and 3 - tosylates to give the final product . the displacement of the c - 6 tosylate by azide was carried out in dmso at 50c . when higher temperatures ( 100c ) or an acetone / water solvent were used , some introduction of azide at c - 2 or c - 3 was also seen ( possibly via epoxide intermediates , see above ) . an alternative approach to 6 - amino -6-deoxycellulose going via the c - 6 bromide , which can be formed from cellulose more regioselectively than the c - 6 tosylate , has been published . thus , bromination of cellulose followed by azide displacement and reduction gave 6 - amino -6-deoxycellulose with very clean c nmr spectra ( ds = 0.96 ) in only three steps . however , some depolymerisation occurred ( the avicel microcrystalline cellulose starting material had dp = 114 ; product dp = 66 ) . but when microwave irradiation was used for heating , the reaction times could be shortened , and the degradation minimised ( starting dp = 114 ; product dp = 106 ) . primary halides or tosylates of several other polysaccharides have been shown to undergo nucleophilic displacement by azide .6 - azido -6-deoxyamylose was prepared from the corresponding amylose bromide ( sodium azide , dmso , 50c , 6h ) or chloride ( sodium azide , dmso , 70c , 65 h ) . as expected , the bromide was much more reactive than the chloride . similarly , a starch tosylate reacted with sodium azide ( dmf , 100c , 24 h ) to give a starch azide with a ds of 0.96 . treatment of 6 - bromo -6-deoxycurdlan ( ds 1 ) with azide gave complete substitution , as judged by the very clean c nmr spectrum of the product . the introduction of azide into phthalimide - protected chitosan was achieved by displacement of both tosylate and bromide leaving groups . the reaction of tosylates of lichenan , pullulan , and dextran with an azide nucleophile was investigated . heating with sodium azide in dmf ( 24 h , 100c ) resulted in higher degrees of substitution of tosylate by azide ( 6775 % ) for the tosylates of lichenan and pullulan than for the tosylate of dextran ( 45 % ) , probably because the number of primary tosylates in dextran [ predominantly a ( 16 ) - linked polymer ] is lower . azide substitution of a 6 - chloro -6-deoxypullulan ( nan3 , water , 100c ) and of tosyl or chloride derivatives of inulin ( nan3 in dmso ) has also been reported . the direct introduction of azide into unprotected polysaccharides in a phosphane - based process related to the appel , garegg , and mitsunobu reactions discussed above offers an advantageous straightforward one - step route to 6 - azido -6-deoxy derivatives of some polysaccharides ( scheme 7 ) . amylose or pullulan could be treated with pph3 / cbr4 in dmf / lin3 under homogeneous conditions at room temperature to readily give the c - 6 azides regioselectively . this procedure was extended to starches , replacing lin3 by the more easily available nan3 , and using either dmf or dma as solvent . native starches failed to react unless their granular structures were disrupted , in which case full conversion was seen . with amylose or amylopectin starches , when nan3 ( 2 equiv . ) was used and the reaction was run at 100c for 1 h , essentially homogeneous incorporation of azide at c - 6 ( ds = 1 ) was observed ; no evidence of substitution at c - 2 or c - 3 could be seen . the functionalisation of cellulose derivatives ( but not other polysaccharides ) using amine nucleophiles has also been investigated . the reaction of tosylated cellulose with methylamine was studied in detail [ typical conditions : dma , menh2 ( aq . , ca 40 equiv . ) , 60c , 48 h ; purification by precipitation ] . the nucleophilic substitution reaction occurred only at c - 6 , and conditions were found that allowed the preparation of a polysaccharide with dsn of ca 1 , but presumably some unreacted tosylate groups remained at the secondary positions of this product . similarly , the reaction of tosylated cellulose ( dstotal 2 ; dsc - 6 = 1.0 ) with butylamine was studied under different conditions . the reaction proceeded much more quickly ( and regioselectively for c - 6 ) in neat butylamine ( neat bunh2 , 50c , 24 h ) than it did in dmso solution ( dmso , bunh2 ( ca 5 equiv . ) , 75c , 24 h ) . it has also been shown that bromide can be an effective leaving group in such reactions , as 6 - bromo -6-deoxycellulose ( ds = 0.92 ) reacts with amines in dmso at 90c to give , after purification by precipitation and dialysis , polysaccharide amine products with dsn 0.9 . finally , tertiary amines have been shown to react with tosylated cellulose to give ammonium salts . the introduction of sulfur nucleophiles into polysaccharides ( cellulose and starch ) has been the subject of some research ( scheme 8 ) , albeit to a much lesser extent than for nitrogen nucleophiles . thiols were used as nucleophiles in nucleophilic substitution reactions with 6 - bromo -6-deoxycellulose ( rsh ; r = me , ph , ch2ch2oh , ch2ch2nh2 , etc . ) under heterogeneous conditions in aqueous sodium hydroxide , giving a maximum conversion of 65 % . when the ph was too basic , 5,6 - elimination and 3,6 - cyclisation competed with the sn reaction . a similar reaction between a 6 - bromo -6-deoxycellulose and thiolswas also carried out under homogeneous conditions in dma / libr , using triethylamine as base , followed by purification by precipitation or dialysis .6 - o - tosyl - cellulose has also been used as an electrophile in a thioether - forming reaction with sodium methanethiolate ( dmf , 0c , 8 h ) . other sulfur nucleophiles have been used in reactions with polysaccharide electrophiles for the indirect synthesis of polysaccharide thiols .6 - bromo -6-deoxycellulose ( ds = 0.85 ) was converted into the thiol in a two - step process . first , sulfur was introduced using a thiourea nucleophile ( dmso , 70c , 48 h ) . the initial product , a ( poly ) thiouronium salt , then underwent hydrolysis to give the polysaccharide thiol . alternatively , 6 - bromo -6-deoxycellulose ( ds = 0.92 ) underwent substitution with potassium thiocyanate ( dmf , 150c , 2 h ) . purification by precipitation and dialysis gave a product with dsscn = 0.88 and residual dsbr = 0.02 . thus , 6 - o - tosyl - amylose ( or alternatively 2,3 - di - o - phenylcarbamoyl -6-o - tosyl - amylose ) underwent a nucleophilic substitution reaction with kscn , and then the thiocyanate product was reduced ( and the 2,3 - protection cleaved ) by treatment with lialh4 . xanthates were used as nucelophiles in reactions with tosylates of starch ( ds 0.2 ) , and the products were reduced to give the polysaccharide thiols . here , though , the conversion of the tosylates in the nucleophilic substitution reaction was not complete , and some formation of thioether linkages was observed . a heterogeneous reaction in which sulfur nucleophiles were bonded to whatman filter paperwas carried out by initial chlorination followed by nucleophilic substitution by treatment with thiourea or cysteine in suspension in a dmf / water mixture . it is perhaps worth noting that in monosaccharides , the introduction of thiol nucleophiles at the secondary positions of pyranosides by triflate displacement is relatively trivial , but related work has not been done to date in polysaccharides . also in monosaccharides , selenoethers have been introduced in a protecting - group - minimised approach , similar to those described here for thioethers . butagain , no related work with selenium nucleophiles appears to have been done to date in the polysaccharide series . polysaccharides may be oxidised in different ways to produce structures of different types ( scheme 9 ) . where there is a free primary alcohol ( e.g. , at c - 6 in cellulose or amylose ) , this may be oxidised simply to give the aldehyde or further to the carboxylic acid level . oxidation to the carboxylic acid level would result in a polysaccharide based on uronic acids , which would then resemble the structure of natural polyuronic acids such as pectin or alginates . chemical and enzymatic methods have both been used for oxidation of the primary alcohols of polysaccharides . where this structural motif occurs in a polysaccharide ( e.g. , at c - 2 and c - 3 in cellulose , amylose , or xylose ) it may be possible to undergo a ring - opening oxidative c c bond cleavage to give dicarbonyl compounds . with these different possible oxidation modes come issues of selectivity when carrying out an oxidative derivatisation of a native ( unprotected ) polysaccharide , it would be desirable to have either one of these oxidation modes operating but not both . when oxidising primary alcohols , it may also be desirable to avoid potential simple oxidation of unprotected secondary alcohols to give ketones and also to be able to choose conditions that result in either oxidation to the aldehyde or the carboxylic acid levels . the periodate oxidation of polysaccharides and the oxidation of cellulose have recently been reviewed . a method that has been used for the oxidation of c - 6 of monosaccharide glycosides to the uronic acid level is treatment with oxygen over a heterogeneous platinum metal surface as a catalyst . in many respects , this is an attractive method , since molecular oxygen is used as the oxidising agent , water is the sole by - product , and in principle , heterogeneous catalysts can be easily recovered and reused . however , this method has a significant disadvantage when it comes to the oxidation of polysaccharides : as the catalyst is heterogeneous , the degree of oxidation ( dsox ) can be quite low . it is generally true that homogeneous catalysts will give better results for the modification of insoluble polymeric substrates . nevertheless , inulin with a dp of ca 30 could be oxidised to the uronic acid level at the primary positions ( c - 6 ) with a dsox of ca 0.20 under such conditions , and c - 6 oxidation of a galactan over platinum to the uronic acid level with a dsox of ca 0.15 has also been achieved . purification was carried out by precipitation followed by membrane filtration . in the early 1990s , van bekkum found that a homogeneous catalyst , tempo [ i.e. , ( 2,2,6,6 - tetramethyl - piperidin -1-yl ) oxyl ] , could be used for the regioselective oxidation of the primary alcohols in polysaccharides ( starch and inulin were included in the initial report ) to give the corresponding polyuronic acids with essentially complete conversion , ( i.e. , dsox ca 1.0 ) . in a typical oxidation procedure , the polysaccharide ( 20 mmol glc units ) , a catalytic amount of tempo ( 0.65 mol - % ) , and nabr ( 0.4 equiv . ) were dissolved in water . a ph - adjusted solution of the stoichiometric oxidant , naocl ( 1.1 equiv . ) , was added at 0c . the reaction mixture was kept at 0c , and the ph was kept at ca 10 by the addition of naoh . the reaction was complete after 1 - 2 h , after which etoh was added to quench the reaction and to precipitate the polysaccharide , which could then be collected by filtration . the method is catalytic in tempo and is selective for primary alcohols , with secondary alcohols remaining unaffected . in the reaction mechanism , the persistent radical tempo is initially oxidised to give the active oxidant , an oxoammonium species . this species then oxidises the polysaccharide primary alcohol to the aldehyde , being itself reduced to the hydroxylamine . the polysaccharide aldehyde must then be hydrated , and the hydrate is then oxidised to the acid by a second molecule of the oxoammonium reagent . the stoichiometric oxidant is naocl / nabr , naobr , or naocl , and this is responsible for the initial oxidative activation of tempo and the subsequent reoxidation of the hydroxylamine to the active oxoammonium species . this method was suitable for the very selective oxidation of c - 6 of soluble potato starch and of pullulan . the three glc ( a ) environments of the oxidised pullulan can be clearly seen and distinguished in the c nmr spectra of the product . amylodextrin , which is a short amylose structure with a dp of ca 20 , was oxidised selectively at c - 6 , but some overoxidation at the reducing ends became significant at the shorter polymer chain length . dextran , which is basically a ( 16 ) - linked polymer without free primary hydroxyl groups except for end - groups , was oxidised only at the level of background oxidation of the secondary alcohols by naocl ( or naobr ) , which occurred much more slowly than the tempo - catalysed oxidation of the primary alcohols . apparently , the selectivity for the primary alcohols was less good in inulin , based on furanoside residues , but when the reaction was quenched after 20 min , the a c nmr spectrum of the product was clean and 90 % selectivity was reported . water - soluble polysaccharides were investigated initially , but this c - 6 oxidation to the carboxylic acid ( carboxylate ) level greatly increased the water solubility of the polysaccharide products , and in fact , the method was found to be broadly applicable . the polysaccharides that have been successfully oxidised using the tempo method include starch , amylose , amylopectin , amylodextrin , dextran , regular comb dextran , pullulan , alternan , inulin , chitin , chitosan , and cellulose . normally , excellent selectivity for oxidation of the primary alcohol was seen , and normally dsox values close to 1.0 ( i.e. , complete conversion ) were obtained . some reports indicate that the selectivity for the primary alcohols was lower in chitin , and some oxidation of secondary alcohols also occurred , while others found that chitin could be oxidised to give a polyuronic acid with a quite clean c nmr spectrum . different celluloses were investigated , including microcrystalline cellulose ( dp = 200 ) , linters ( dp = 800 ) , bleached kraft pulps ( dp = 9001200 ) , and amorphous regenerated celluloses . the oxidation procedure was essentially identical to that described above , except that all of the celluloses were , of course , initially insoluble in the aqueous reaction medium . when the oxidation was complete , the polysaccharide had dissolved and purification could be carried out again by precipitation from etoh . the regenerated celluloses were completely oxidised at c - 6 within 2 h , whereas the native celluloses did not form homogeneous solutions , even after long reaction times , presumably due to the crystallinity and the resulting inaccessibility of some of the c - 6 hydroxyl groups . an essentially completely regioselective ( c - 6 ) oxidation of these insoluble polysaccharides ( i.e. , the regenerated or mercerised cellulose samples ) was achieved under these conditions , as shown by the c nmr spectra of the products . it was found that under these reaction conditions , some depolymerisation occurred , presumably by a e1cb elimination mechanism across c - 4c - 5 ; the reaction time , temperature , and amounts of reagents are all important factors to be considered if this depolymerisation is to be minimized . a variant of the tempo oxidation method in which the sodium bromide is omitted , but still using naocl as the stoichiometric oxidant , has been used for the oxidation of potato starch . this variant method gave similar reaction rates and selectivities when the reaction was carried out at room temperature , and when the ph was kept below 9.5 . tempo is a persistent stable radical to the extent that it is a commercially available solid . related methods for the oxidation of polysaccharides using shorter - lived n o radicals have been investigated briefly . an example of such a method uses catalytic n - hydroxysuccinimide , naocl as stoichiometric oxidant , and nabr . another related reaction is the oxidation with n2o4 . this reagent oxidises the primary position of carbohydrates regioselectively to give the uronic acids , but the regioselectivity is not perfect , and some oxidation of the secondary positions can take place . normally then , it is necessary to include a borohydride reduction step after the oxidation to reduce any ketones back to the alcohol level ( clearly this would introduce issues of diastereoselectivity and inhomogeneity in the products ) . depolymerisation can also occur ( by e1cb elimination resulting in chain cleavage at c - 4 , see above ) under the basic conditions of this reaction . the side - reactions that are found with this reagent mean that it is less suitable for the preparation of pure polyglucuronic acid polysaccharides than the other methods discussed here . the enzyme galactose -6-oxidase ( ec 1.1.3.9 ) catalyses the c - 6 oxidation of galactose to the aldehyde level , using oxygen as the oxidant and generating hydrogen peroxide as the reduced by - product ( 3 ) . thus , the reaction is complementary to the tempo oxidation , where the product of c - 6 oxidation is the carboxylic acid rather than the aldehyde . the enzyme is highly selective for c - 6 of galactose , although it does tolerate substituents at the anomeric position of the galactose ( i.e. , the formation of glycosides ) . possible galactose - derived by - products include the uronic acid ( from overoxidation ) or the , - unsaturated aldehyde ( from e1cb elimination across c - 4c - 5 ) . the oxidation of polysaccharides with galactose -6-oxidase has been investigated , but first , an optimisation of the reaction conditions was carried out on a monosaccharide model system , methyl - d - galactopyranoside . the best results were obtained using a combination of three enzymes ( viz galactose -6-oxidase , catalase , and horseradish peroxidase ) in water rather than buffer . catalase ( ec 1.11.1.6 ) was added to catalyse the decomposition of the h2o2 formed in the reaction , as otherwise h2o2 can poison the activity of the galactose -6-oxidase . horseradish peroxidase was added to activate the oxidase enzyme by oxidising it to its active form . the same group went on to investigate the oxidation of polysaccharides using galactose -6-oxidase in some detail . the general oxidation procedure was as follows : the polysaccharide was stirred in water at 4c or rt for 112 h until it had dissolved . then the enzymes were added , and the mixture was stirred for 48 h. the oxidation of several galactose - containing polysaccharides was investigated using the same three - enzyme system . these included spruce galactoglucomannan [ a ( 14 ) - linked backbone of glucose and mannose residues with pendant galactose residues linked ( 16 ) ] , guar gum [ a ( 14 ) - mannan backbone with pendant galactose residues linked ( 16 ) ] , larch arabinogalactan [ a ( 13 ) - linked galactan backbone with pendant arabinofuranose units linked ( 16 ) , and galactose and galactobiose units , linked to the backbone by ( 16 ) - linkages ] , corn arabinoxylan [ a ( 14 ) - linked xylan with various appendages , mostly arabinofuranose ] , and xyloglucan from tamarind seeds [ a ( 14 ) - linked glucan with pendant ( 16 ) - linked xylose units ; about half of the xylose residues are galactosylated ] . hence the polysaccharides had different galactose contents and different presentations of the galactose units due to branching , and the efficiency of the oxidation reaction varied between the different polysaccharides . xyloglucan was the most efficiently oxidised ( up to dsox 0.8 based on the galactose residues ) , followed by galactoglucomannan ( dsox ca 0.65 ) and guar gum ( dsox ca 0.4 ; scheme 10 ) . there are also some further earlier reports on the oxidation of polysaccharides by galactose -6-oxidase in the literature . the galactose residues in guar gum were converted into the corresponding uronic acids in a two - step process consisting of enzymatic oxidation at c - 6 with galactose -6-oxidase , followed by chemical oxidation ( with i2 / ki ) . a synthetic polysaccharide consisting of chitosan to which lactose had been attached by reductive amination was also a substrate for galactose -6-oxidase , and the appended galactose units could be oxidised enzymatically at c - 6 . the ( 1 - deoxy - lactit -1-yl ) chitosan was dispersed in phosphate buffer to give a soft glassy gel , which was purged with o2 for 1 min . catalase and galactose -6-oxidase solutions were added and a viscous material formed after a few hours . after 2 d , the mixture was diluted with water , and the polysaccharide was precipitated from absolute ethanol to give a product with a dsox of ca 0.7 . periodate may be used as an oxidising agent to achieve the ring - opening cleavage of the 1,2 - diols at c - 2 and c - 3 of polysaccharides very efficiently and selectively . the initial product is the dialdehyde and is then usually oxidised further to give the dicarboxylate . the best results were obtained using a two - step procedure of periodate oxidation - cleavage ( to the dialdehyde ) followed by chlorite oxidation ( to the dicarboxylate ) . under the same conditions , it was also confirmed that ( as expected ) the ring - opened polymers are more susceptible than the parent unoxidised polysaccharides to acid - catalysed depolymerisation ( i.e. , acetal hydrolysis ) . for cellulose , the efficiency of this oxidation reactionmay be improved by the addition of metal salts to disrupt intermolecular hydrogen bonding and improve the solubility . initially formed aldehyde products were subjected to reductive amination with long - chain alkylamines to give hydrophobically modified derivatives ( scheme 11 ) . several natural polysaccharides , including alginates and pectins , use uronic acid residues as structural components . in a uronic acid derivative , this section covers the reactions of these carboxylic acids ( scheme 12 ) , both electrophilic and nucleophilic reactions , including esterification , amide formation , and multicomponent reactions . as well as natural uronic - acid - containing polysaccharides , this chemistry may be applicable to synthetic c - 6 oxidised polysaccharides ( see above ) . the modification of the carboxylic acid ( uronic acid ) functionality of alginates has been reviewed . carboxylic acids can react either as electrophiles or nucleophiles to form esters . in the first scenario , the acid must first be activated , which may happen prior to the esterification ( e.g. , by formation of an acid chloride ) , or in situ by using a coupling reagent such as dcci , or by using a strong - acid catalyst ( fischer esterification ) . the activated acid should then be attacked by an alcohol nucleophile to give the ester . however , this approach has some disadvantages that mean it does not appear to have been widely used for the modification of polysaccharide uronic acids : ( i ) in aqueous solution , the water can effectively compete with the intended alcohol nucleophile , hydrolysing the activated acid intermediates and restoring the carboxylic acid starting material ; ( ii ) where the other hydroxyl groups of the polysaccharide are unprotected , they too could compete as nucleophiles with the added alcohol , and possible cyclised products could result ; ( iii ) in a fischer ( acid - catalysed ) esterification , there is significant risk of depolymerisation of a polysaccharide substrate . in the second approach , the carboxylic acid can be deprotonated by a weak base to generate a carboxylate . the hydroxyl groups of the polysaccharide will not normally react under these conditions , and so this approach has been more widely used for the preparation of esters of polysaccharide uronates . treatment of the tba salt of ( completely demethylated ) pectin with benzyl bromide and tbai in dmso at rt gave the benzyl ester with a ds of up to 0.73 . the same method has been used for the preparation of esters of pectin with lower ds ( 0.1 ) and of alginates and hyaluronates , again with lower ds ( 0.1 ) . uronic acids must be activated to react as electrophiles with amine nucleophiles to generate amides . classically , this can be achieved using a coupling ( dehydrating ) agent such as dcci or the water - soluble edci , but even esters can be used as electrophilic carboxylic acid derivatives in amide - forming reactions . the conversion of the uronic acids of alginate into amides has been achieved by reaction with amines in water using edci , a water - soluble coupling agent . alginate amides with ds of 0.10.3 were synthesised in this way by the reaction of sodium alginate with octylamine and edci in water . thus , alginate amides with ds of up to 0.2 were prepared by the reaction of an alginate tba salt with decylamine and cmpi ( 2 - chloro -1-methylpyridinium iodide ; the coupling agent ) in dmf . esters react directly with amines to form amides in a reaction termed aminolysis . in a polysaccharide context , highly methylated pectin ( methyl esters ; dsmethyl = 0.73 ) was treated with various alkylamines ( n - butyl up to n - octadecyl ) in dmf under heterogeneous conditions ( 8 , 25 , or 45c ) , and the amide products were formed with dsamide = 0.40.55 . a concept that has been used to rapidly generate molecular diversity is that of multicomponent reactions , in which condensation / addition products are generated from three or more starting materials in a single reaction . one example is the ugi four - component reaction between an aldehyde ( or ketone ) , an amine , an isocyanide , and a carboxylic acid to form a diamide . it has been shown that the uronic acids of alginate can undergo the ugi reaction ( scheme 13 ) . thus , an aqueous solution of alginate was treated with formaldehyde , octylamine , and cyclohexyl isocyanide for 24 h. purification was achieved by dialysis . this section concerns the reactions of polysaccharide amines such as chitosan , which carries a free basic nitrogen at c - 2 , but the methods should also be applicable to other synthetic aminated polysaccharides , for example , c - 6 aminated cellulose . amines can react with electrophiles to give amides ( i.e. , acylation ) , higher order amines or ammonium salts ( i.e. , alkylation ) , or imines ( schiff bases ) . the different reactivity of nitrogen and oxygen nucleophiles means that it is often possible to carry out these derivatisations in aqueous solution , and without protection of any free hydroxyl groups in the saccharide derivative . of course , o - alkylation and o - acylation may take place under some conditions , but with an appropriate choice , it should be possible to find conditions that favour chemoselective derivatisation at nitrogen . ( 4 ) the alkylation of amines can be complex in that the initial products , which are also amines , can react further to form higher order amines or , under direct alkylation conditions , eventually ammonium salts . this can be particularly problematic in direct alkylation reactions with very reactive electrophiles ( sterically , e.g. , methyl ; electronically , e.g. , benzyl ; or with special reactivity , e.g. , allyl ) and with reactive nucleophiles . as a result , direct alkylation is not normally used for the preparation of amines , even though when the reactants are more sterically hindered , as is the case with saccharide amine nucleophiles and moderately hindered electrophiles , the barrier to oversubstitution increases . the reductive amination reaction is widely regarded as the alkylation method of choice for amines . in this method , the amine first condenses with a carbonyl compound ( normally an aldehyde ) to give an imine . a reducing agent , normally nabh4 , nacnbh3 , or na ( oac ) 3bh , reduces the imine to give the amine product . overalkylation can be minimised by this method , but in fact , it is still often seen to a greater or lesser extent ( see below ) . but quaternisation to form ammonium salts can not occur under these conditions and neither can o - alkylation to form ethers , and these are definite advantages over a direct alkylation method . a standard procedure for the preparation of n - alkylated derivatives of chitosan by reductive amination has been widely used over the years ( scheme 14 ) . even here , though , overalkylation occurs and products with homogeneous structures are often not obtained . depending on the ratio of glcn / aldehyde used , the polysaccharide products were composed of mixtures of mainly monoalkylated and unalkylated glucosamines or mainly dialkylated and monoalkylated glucosamines , according to the h nmr spectra of the products . the general procedure is as follows : chitosan was dissolved ( i.e. , reactions are homogeneous ) in either a mixture ( 1 : 1 , ph 5.5 ) of an alcohol ( normally methanol or ethanol ) and 1 % aq . acetic acid or in 1 % aq . acetic acid alone . a solution containing the carbonyl compound and nacnbh3 ( 7 equiv . ) was added , and the reaction mixture was stirred at room temperature , usually until gel formation was observed ( ca 124 h ) . the solid product is then obtained by filtration and washing with methanol and et2o . further purification by soxhlet extraction into etoh / et2o ( 1 : 1 ) has also been done in some cases . when no alcohol cosolvent is added , the reaction takes place in essentially aqueous solution . the role of the alcohol is to solubilise the aldehyde component , which can often be hydrophobic . this procedure has been used with many different carbonyl components , including reducing monosaccharides , disaccharides , ketosugars , other oxidised sugars , and noncarbohydrate carbonyls . aldehydes bearing straight - chain alkyl groups with chain lengths from c3c12 have been used . chitosan underwent n - alkylation under reductive amination conditions with benzylic ( heterocyclic ) aldehydes : furfural , methylfurfural , pyridine -3-carboxaldehyde , and so forth . the ds of the products was between 0.30 and 0.43 , and the broad h nmr spectra showed two sets of signals , presumably due to the monoalkylated and the unalkylated glucosamines . chitosan underwent n - alkylation by reductive amination with aliphatic aldehydes c2c12 ( 0.1 to 1 equiv . ) to give products with ds between 0.03 and 0.3 , and with twelve substituted benzaldehydes ( 1 equiv . ) a fluorescence label was installed into chitosan by the reductive amination method with 9 - anthraldehyde as the carbonyl component , aiming for very low ds ( values between 0.00001 and 0.01 ) . imines , the c = n intermediates in the reductive amination procedure , are liable to hydrolyse their formation is reversible . this is clearly a disadvantage when designing a stable product , but in cases where the reversible formation of semistable covalent compounds is beneficial , in supramolecular chemistry , for example , imines can be useful compounds . the conversion of chitosan into imines ( without reduction ; scheme 15 ) has been investigated in solution ( to give products with ds of ca 0.9 ) and under heterogeneous conditions on prespun polysaccharide fibres ( to give products with ds of 0.91.0 ) . typical conditions for imine formation under homogeneous conditions are as follows : chitosan was dissolved in a mixture of 2 % aq . this mixture was left overnight , and then the imine ( a solid / gel ) was then purified by filtration and washing with methanol . imine formation on prespun chitosan fibres was simply carried out by suspending the fibres in methanol and adding the aldehydes , and after the mixture had been left overnight , the derivatised fibres were washed with methanol . repeated alkylation of the free amine base of chitosan eventually gives quaternary salts ( scheme 16 ) . according to a very recent review covering the formation of quaternary salts ( quaternisation ) of chitosan , better synthetic routes that do not requiremuch research into the quaternisation of chitosan has focussed on trimethyl derivatives . in this transformation , the chitosan nitrogen must act as a nucleophile , attacking an alkylating agent ( methylating agent ) three times . the oxygen nucleophiles in chitosan ( i.e. , oh - 3 and oh - 6 ) could also be alkylated in a potential undesired side process . the ph of the reaction mixture can affect the rate and outcome of the reaction . when no base is added , the basic nitrogens in the starting material and partially alkylated products will be protonated , decreasing their nucleophilicity and resulting in products with low ds . the methylation of chitosan with the aim of tri - n - methylation to form the quaternary ammonium salt without concomitant o - methylation has been investigated in some detail , and errors in a published method were found . thus , when alkylation was carried out with mei and naoh in 1 - methyl -2-pyrrolidinone at 60c , the major product was found to be the dialkylated product ( i.e. , the tertiary amine ) , and significant quaternisation did not occur . a polysaccharide with a dsquat of 0.7 was obtained in a two - step procedure in which the initial product ( containing the n , n - dialkylated material as its major component ) was isolated and then resubjected to the same reaction conditions . but for higher dsquat values , looking towards complete quaternisation , concomitant o - alkylation started to become significant . a recent paper describes how a change of solvent can suppress o - methylation , enabling a one - pot synthesis of essentially uniform ( ds ca 0.9 ) quaternised trimethyl chitosan . in this approach , dmf / h2o ( 1 : 1 ) was used as solvent , and several separate additions of naoh and mei were necessary for complete quaternisation to be achieved . a two - step approach to the synthesis of quaternised chitosan using reductive amination followed by alkylation opens the possibility of installing two different r groups onto the nitrogen atoms . subsequently , alkylation was carried out with mei and naoh in nmp as solvent , and purification was by precipitation from acetone . the chitosan derivatives obtained by this method were found electrochemically to have dsquat values between 0.8 and 0.9 . the acylation of amines to give amides ( scheme 17 ) is a very well investigated reaction , due to its importance in peptide synthesis . here , i am covering the reaction of polysaccharide amines with nonpolysaccharide acylating agents to give amides ; the related amide - forming reactions between polysaccharide carboxylic acid ( uronic acid ) derivatives and nonpolysaccharide amines following similar principles are covered above . the reaction may be carried out ( in water or alcohol solvents ) using acylating agents such as acyl chlorides or acid anhydrides , or using carboxylic acids and dehydrating agents . it can be beneficial to use a reactive o - nucleophile , such as water , methanol , or ethanol , as solvent or cosolvent so as to suppress o - acylation of the polysaccharide , a possible side - reaction that can occur when a polar aprotic solvent ( such as dmf , nmp ) is used . acoh and methanol ( 1 : 1 ) using different carboxylic anhydrides as acylating agents . a solution of the anhydride in methanol was added to the chitosan solution , and the reaction was quenched after 15 min by pouring into ammonia solution ( 7 : 3 , v / v ) . the precipitated polysaccharides were filtered and washed with methanol and ether . fibres of the polysaccharide were suspended in methanol , and a carboxylic acid anhydride ( 5 equiv . ; acetic , propionic , butyric , or hexanoic anhydride ) was added . the mixture was shaken at 40c for 24 h , and then the derivatised fibres were washed with methanol . the ds of the products were between 0.65 and 0.85 , as determined by elemental analysis . polysaccharide derivatives in which the monosaccharide constituents contain c = c double bonds have been prepared . cellulose derivatives of this type have been termed cellulosenes , and they should be classified as one of two types - enol ethers or alkenes depending on whether one of the carbons of the c = c double bond is directly bonded to an oxygen or not ( figure 4 ) . the enol ether and alkene types of unsaturated polysaccharides may be expected to have different properties and reactivities .5,6 - cellulosene is unsaturated between c - 5 and c - 6 it is formed by simple elimination ( i.e. , a formal elimination of water from cellulose ) , and the c = c double bond is part of an enol ether . in 2,3 - cellulosene , unsaturated between c - 2 and c - 3 , the c = c double bond represents an alkene ( olefin ) functionality and must be formed by a reductive elimination from cellulose . xylan and amylose , two more common ( 14 ) - linked polysaccharides , have both been transformed into their 2,3 - unsaturated olefinic derivatives . the 5,6 - unsaturated ( enol ether ) derivative of amylose has also been investigated of course , as xylose is built up of pentose monomers , a corresponding 5,6 - unsaturated derivative of this polysaccharide can not exist . further possibilities for both the enol ether and alkene types of unsaturated polysaccharide can be envisaged . for ( 16 ) - linked structures , olefinic unsaturation in the ringcould be located either between c - 2 and c - 3 or between c - 3 and c - 4 , although the regioselective synthesis of such compounds may not be straightforward . in ( 13 ) - linked pyranose - based polysaccharides , an alkene structure is impossible , as all of c - 1 , c - 3 , and c - 5 must bear an oxygen atom . ( 12 ) - linked pyranose - based polysaccharides are not common . for both simple elimination and reductive elimination reactions , it will normally be necessary for the two groups that will undergo the elimination reaction to adopt an antiperiplanar or synperiplanar relationship . free rotation about the exocyclic c - 5c - 6 bond should allow a favourable conformation to be reached in the synthesis of 5,6 - unsaturated polysaccharides . for the synthesis of compounds with endocyclic unsaturation , though , the stereochemistry of the hydroxyl groups in the pyranose ring can be important . as stated above , the formal overall process for the synthesis of an enol - ether - based unsaturated derivative of a polysaccharide is elimination of water . for 5,6 - unsaturated derivativesthis means elimination of water across c - 5 and c - 6 . in a two - step process , oh - 6 is converted into a good leaving group , and then treatment with a base will promote the elimination reaction . processes for the regioselective conversion of oh - 6 into a good leaving group are quite well described ( see the section on nucleophilic substitution , above ) . such competing processes are typically minimised by using a nonnucleophilic ( e.g. , sterically hindered ) base . however , in polysaccharide systems , when the polysaccharide is unprotected , any base could deprotonate the free hydroxyl groups in the pyranose rings to generate intramolecular nucleophiles that could attack the carbon bearing the leaving group to form a new ring . the undesired intramolecular cyclisation of o - 3 onto c - 6 in particular has been a problem in the synthesis of 5,6 - cellulosene . a solution to this problem has been reported in a synthesis of 5,6 - cellulosene that gave a ds as high as 0.7 ( scheme 18 ) . dbu is a strong , nonnucleophilic base that is able to induce elimination without acting as a nucleophile on c - 6 or removing the acetate protection from o - 2 or o - 3 .2,3 - unsaturated derivatives of the ( 14 ) - linked polysaccharides cellulose , amylose , and xylan have all been mentioned in the literature . the stereochemistry at c - 2 and c - 3 of all these polysaccharides is the same , i.e. , trans diequatorial , which means that they may be expected to form 2,3 - unsaturated polysaccharides under similar conditions ( scheme 19 ) . the conversion of amylose into its 2,3 - unsaturated derivative was achieved by the following reaction sequence : protection of o - 6 as a trityl ether ; conversion of o - 2 and o - 3 into tosylates ; reductive elimination with zinc and sodium iodide . the reactivity of the alkene functionality was also briefly investigated , undergoing dibromination or hydrogenation . the number of published methods for the synthesis of alkene - containing polysaccharides by reductive elimination is limited , but studies of similar reactions on simpler monosaccharide systems can be relevant for the further development of this chemistry . a one - step procedure to convert pyranoside 2,3 - diols into alkenes seems particularly relevant . treatment of the diols with chlorodiphenylphosphine , iodine , and imidazole ( reflux , 1 h ) gave 2,3 - unsaturated derivatives in 7589 % yields starting from glucose ( 2,3 - trans ) derivatives , and in 52 % yield from a mannose ( 2,3 - cis ) derivative . alternatively , vic - diols were first converted into vic - halocarboxylates , which were then treated with a reducing agent such as zinc or nash to give the alkenes . as well as summarising the achievements in this field , also the gaps are highlighted , and this will hopefully inspire further developments . many of the methods that have been developed for the modification of polysaccharides are inefficient and wasteful , as stoichiometric amounts of waste products may be formed and several steps may be required . the use of a renewable resource loses a lot of its meaning and significance if it must undergo many manipulations with nonrenewable materials before reaching its final goal . thus , future research in this area would do well to focus on catalytic transformations .\noutput:\n" }, { "from": "agent", "value": "this review covers methods for modifying the structures of polysaccharides . the introduction of hydrophobic , acidic , basic , or other functionality into polysaccharide structures can alter the properties of materials based on these substances . the development of chemical methods to achieve this aim is an ongoing area of research that is expected to become more important as the emphasis on using renewable starting materials and sustainable processes increases in the future . the methods covered in this review include ester and ether formation using saccharide oxygen nucleophiles , including enzymatic reactions and aspects of regioselectivity ; the introduction of heteroatomic nucleophiles into polysaccharide chains ; the oxidation of polysaccharides , including oxidative glycol cleavage , chemical oxidation of primary alcohols to carboxylic acids , and enzymatic oxidation of primary alcohols to aldehydes ; reactions of uronic - acid - based polysaccharides ; nucleophilic reactions of the amines of chitosan ; and the formation of unsaturated polysaccharide derivatives ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: chronic periodontitis ( cp ) is the infection of highly vascularizing supporting periodontal tissues with episodes of active destruction and periods of quiescence . earlier reports indicated that in the region of the periodontal pocket , there was a positive relationship between an increase in the number of blood vessels and progression of the disease , especially affecting capillaries and venules . angiogenesis ( neovascularization ) is defined as the process of budding of new capillaries and formation of new blood vessels , considered to be the integral component in the development of chronic inflammatory disease . angiogenesis can increase the severity of the inflammation by virtue of the new blood vessels that can transport pro - inflammatory cells and supply nutrients and oxygen to the inflamed tissues . of the various cytokines and growth factors that are involved in the regulation of angiogenesis , the most potent agent that acts specifically on vascular endothelium is vascular endothelial growth factor ( vegf ) . vegf is a multifunctional angiogenic cytokine of importance and an endothelial - specific growth factor that potently increases microvascular permeability , stimulates endothelial cell ( ec ) proliferation , and induces proteolytic enzyme expression and the migration of ecs , monocytes , and osteoblasts , all of which are essential for angiogenesis . vegf shares homology with platelet - derived growth factor and placenta growth factor ( plgf ) and has recently attracted attention as a potential inducer of vascular permeability and angiogenesis . several members of the vegf family have been described during the past few years , including vegf - a , plgf , vegf - b , vegf - c , vegf - d , and vegf - e . vegf has been detected in human periodontal tissues and gingival crevicular fluid ( gcf ) in variable quantity in healthy and diseased sites . in periodontal tissues , vegf is detectable within ec , plasma cells , macrophages and in junctional , sulcular , and gingival epithelium . diabetes mellitus ( dm ) is a metabolic disease usually characterized by the classic triad of polydipsia , polyuria , and polyphagia , the consequences of homeostasis disruption , due to impaired glucose metabolism . periodontal disease has been proposed as the sixth complication of diabetes , based on the frequent presence of both diseases in the same patient . mechanisms such as vascular changes , neutrophil dysfunction , altered collagen synthesis , and genetic predisposition , which are observed in dm , may contribute to periodontitis . vegf not only appears to play a central role in mediating diabetic vasculopathy in many organs but also affects glucose levels , and ultimately , the extent of diabetic complications . thus , this study aimed at estimating the gcf levels of vegf in healthy controls and cp patients with and without dm and also to evaluate the effect of periodontal therapy ( scaling and root planing [ srp ] ) in these patients . the null hypothesis stated that there was no difference in gcf levels of vegf in healthy controls and cp patients with and without dm , and phase - i periodontal therapy does not affect these levels in cp patients with and without dm . the research hypothesis stated that there was a difference in gcf levels of vegf in healthy controls and cp patients with and without dm , and phase - i periodontal therapy does affect these levels in cp patients with and without dm . for this study , 105 patients ( 35 systemically healthy , 35 cp , and 35 cp patients with type ii dm ) in the age range of 3060 years ( mean age 41.37.8 years ) were recruited from the outpatient department of periodontics , from may 2013 to november 2013 table 1 . the study was approved by the institutional review board , and all study patients were given a detailed verbal and written description of the study and signed an informed consent form before commencement of the study . demographic variables the diagnosis of healthy and cp patients was made on the basis of clinical and radiographic criteria proposed by the 1999 international world workshop for a classification of periodontal diseases and conditions . the most severely affected tooth was used as test site for the evaluation of the clinical parameters and gcf sampling . all the selected 105 patients were divided into three groups of 35 each : healthy subject ( group 1 ) , cp patients without dm ( group 2 ) , and cp with well - controlled type ii dm ( hba1c level 68 % ) ( group 3 ) . during the study , patients with any history of a systemic disease , those having taken any antibiotic therapy or underwent any form of periodontal treatment in the past 6 months , pregnant or lactating females , smokers , and those on antiviral or immunosuppressive drugs , were excluded from the study . all the selected cases were subjected to recording of clinical parameters such as plaque index ( pi ) , gingival index ( gi ) , probing pocket depth ( pd ) , and clinical attachment level ( cal ) . probing pd was performed at six sites per tooth . for group 2 and group 3 patients , hba1c levels of diabetic patients were assessed by using chairside test kit ( bayer a1cnow + , ontario , canada ) . after a brief and precise case history recording , the site showing the greatest attachment loss was selected for gcf sample collection in groups 2 and 3 . in the healthy group , one of the maxillary teethsupragingival plaque was removed gently without touching the marginal gingiva , to avoid contamination and blocking of the microcapillary pipette . gcf was collected by placing white color - coded 15 l calibrated volumetric microcapillary pipettes ( sigma - aldrich , st . the test sites , which did not express standard volume ( 1 l ) of gcf , or micropipette contaminated with blood / saliva / plaque were excluded or discarded . samples of gcf were collected at the initial visit in group 1 , group 2 , and group 3 patients . srp was performed for group 2 and group 3 patients at the same appointment after gcf collection . srp was done using ultrasonic scalers and area specific gracey curettes ( osung , gyeonggi , south korea ) . after 6 weeks , gcf was collected from same site of the patients in group 2 and group 3 . collected samples were immediately transferred to plastic tubes and stored at 80c until the time of the assay . for this 6 - week study , patients were called at 1 - week interval to monitor oral hygiene status . the concentration of vegf was determined by quantitative sandwich enzyme - linked immunosorbent assay kit ( krishgen biosystems , mumbai , india ) . standards and samples were pipetted into the wells , and vegf present in a sample was bound to the wells by the immobilized antibody . the wells were washed and biotin - conjugated anti - human vegf antibody is added . after washing away unbound biotin - conjugated antibody , horseradish peroxidase - conjugated streptavidin was pipetted to the wells . the wells were again washed , 3,3 ' ,55 ' - tetramethylbenzidine substrate solution was added to the wells and color developed in proportion to the amount of vegf bound . the stop solution changed the color from blue to yellow , and the intensity of the color was measured at 450 nm . the concentrations of vegf in the tested samples were estimated using the standard curve plotted using the optical density values with the standards . data were analyzed using a software program ( spss statistical package [ pc version 19.0 ] , spss , chicago , il , usa ) . anova tukey 's test was performed to compare gcf vegf level of the three groups at baseline . wilcoxon 's signed rank test was performed to determine whether there was any difference between gcf vegf level before and after treatment . for this study , 105 patients ( 35 systemically healthy , 35 cp , and 35 cp patients with type ii dm ) in the age range of 3060 years ( mean age 41.37.8 years ) were recruited from the outpatient department of periodontics , from may 2013 to november 2013 table 1 . the study was approved by the institutional review board , and all study patients were given a detailed verbal and written description of the study and signed an informed consent form before commencement of the study . demographic variables the diagnosis of healthy and cp patients was made on the basis of clinical and radiographic criteria proposed by the 1999 international world workshop for a classification of periodontal diseases and conditions . the most severely affected tooth was used as test site for the evaluation of the clinical parameters and gcf sampling . all the selected 105 patients were divided into three groups of 35 each : healthy subject ( group 1 ) , cp patients without dm ( group 2 ) , and cp with well - controlled type ii dm ( hba1c level 68 % ) ( group 3 ) . during the study , patients with any history of a systemic disease , those having taken any antibiotic therapy or underwent any form of periodontal treatment in the past 6 months , pregnant or lactating females , smokers , and those on antiviral or immunosuppressive drugs , were excluded from the study . all the selected cases were subjected to recording of clinical parameters such as plaque index ( pi ) , gingival index ( gi ) , probing pocket depth ( pd ) , and clinical attachment level ( cal ) . probing pd was performed at six sites per tooth . for group 2 and group 3 patients , hba1c levels of diabetic patients were assessed by using chairside test kit ( bayer a1cnow + , ontario , canada ) . after a brief and precise case history recording , the site showing the greatest attachment loss was selected for gcf sample collection in groups 2 and 3 . in the healthy group , one of the maxillary teeth was selected for gcf sample collection . the selected site was air dried and isolated with cotton rolls . supragingival plaque was removed gently without touching the marginal gingiva , to avoid contamination and blocking of the microcapillary pipette . gcf was collected by placing white color - coded 15 l calibrated volumetric microcapillary pipettes ( sigma - aldrich , st . the test sites , which did not express standard volume ( 1 l ) of gcf , or micropipette contaminated with blood / saliva / plaque were excluded or discarded . samples of gcf were collected at the initial visit in group 1 , group 2 , and group 3 patients . srp was performed for group 2 and group 3 patients at the same appointment after gcf collection . srp was done using ultrasonic scalers and area specific gracey curettes ( osung , gyeonggi , south korea ) . after 6 weeks , gcf was collected from same site of the patients in group 2 and group 3 . collected samples were immediately transferred to plastic tubes and stored at 80c until the time of the assay . for this 6 - week study , patients were called at 1 - week interval to monitor oral hygiene status . the concentration of vegf was determined by quantitative sandwich enzyme - linked immunosorbent assay kit ( krishgen biosystems , mumbai , india ) . standards and samples were pipetted into the wells , and vegf present in a sample was bound to the wells by the immobilized antibody . the wells were washed and biotin - conjugated anti - human vegf antibody is added . after washing away unbound biotin - conjugated antibody , horseradish peroxidase - conjugated streptavidinthe wells were again washed , 3,3 ' ,55 ' - tetramethylbenzidine substrate solution was added to the wells and color developed in proportion to the amount of vegf bound . the stop solution changed the color from blue to yellow , and the intensity of the color was measured at 450 nm . the concentrations of vegf in the tested samples were estimated using the standard curve plotted using the optical density values with the standards . data were analyzed using a software program ( spss statistical package [ pc version 19.0 ] , spss , chicago , il , usa ) . anova tukey 's test was performed to compare gcf vegf level of the three groups at baseline . wilcoxon 's signed rank test was performed to determine whether there was any difference between gcf vegf level before and after treatment . manna total of 175 samples were collected ( 105 samples at baseline and 70 samples 6 weeks postperiodontal therapy from groups 2 and 3 ) from 105 volunteers . all the samples collected tested positive for the presence of vegf . a significant ( p 0.001 ) reduction in pi , gi , probing pd , and cal in both group 2 and group 3 occurred at 6 weeks after phase - i treatment , compared with baseline [ table 2 ] . however , when the clinical parameters were compared between group 2 and group 3 at baseline and at 6 weeks after phase - i therapy , no statistically significant change was seen [ table 3 ] . comparative evaluation of clinical parameters at baseline and 6 weeks after periodontal treatment intergroup comparison of clinical parameters and gingival crevicular fluid vascular endothelial growth factor levels at baseline and 6 weeks after phase - i therapy the mean gcf vegf levels in all the three groups are presented in table 2 . at baseline , there was a significant difference in gcf vegf levels between groups 1 and 2 and groups 1 and 3 ( p 0.001 ) . furthermore , there was a statistically highly significant difference in the gcf vegf level at baseline and 6 weeks posttherapy in groups 2 and 3 ( p 0.001 ) [ table 2 ] . when the mean gcf vegf levels of groups 2 and 3 were compared at baseline , no statistically significant changes were seen . however , when the levels were compared 6 weeks after phase - i therapy , a statistically significant change was seen [ table 3 ] . the mean gcf vegf levels in all the three groups are presented in table 2 . at baseline , there was a significant difference in gcf vegf levels between groups 1 and 2 and groups 1 and 3 ( p 0.001 ) . furthermore , there was a statistically highly significant difference in the gcf vegf level at baseline and 6 weeks posttherapy in groups 2 and 3 ( p 0.001 ) [ table 2 ] . when the mean gcf vegf levels of groups 2 and 3 were compared at baseline , no statistically significant changes were seen . however , when the levels were compared 6 weeks after phase - i therapy , a statistically significant change was seen [ table 3 ] . periodontitis is a chronic inflammatory disease with episodes of active destruction and periods of quiescence . however , patients vary in their response to chronic gingival inflammation . some are highly susceptible to rapidly destructive disease and others , who have a similar extent of periodontal inflammation , are more resistant to destructive disease . the periodontal vasculature is profoundly affected during progression of periodontal disease . angiogenesis refers to a process by which new blood vessels are produced by sprouting from established vessels . angiogenesis can contribute to the severity of the inflammation as a result of the ability of new blood vessels to transport pro - inflammatory cells to the lesion and supply nutrients and oxygen to the inflamed tissue . numerous cytokines and growth factors are involved in the regulation of angiogenesis ; however , most potent agent that act specifically on vascular endothelium is vegf . periodontitis which is an inflammatory response to a bacterial challenge represents a portal of entry for periodontal pathogens , bacterial endotoxins , and pro - inflammatory cytokines . thus , the local oral inflammatory disease , periodontitis , may induce and perpetuate a systemic inflammation that may aggravate systemic diseases such as cardiovascular disease , pulmonary disease , rheumatoid arthritis , and dm . periodontitis is frequently mentioned among the oral problems observed in dm , which may contribute to periodontitis by mechanisms such as vascular changes , neutrophil dysfunction , altered collagen synthesis , and genetic predisposition . vegf is one of the major factors promoting diabetic complications and is implicated in the development of neovascularization and endothelial dysfunction in diabetic vascular complications . considering the important role of vegf in the pathogenesis of cp , it is important to control the vegf level in the local inflammatory lesion by periodontal treatment to inhibit the disease progression successfully in periodontitis model . studies have shown that srp is an effective means of slowing or arresting the periodontal disease progression and severity . vegf is a multifunctional cytokine that plays a pivotal role during inflammation by mediating neovascularization . studies have shown that the volume of gcf and total amount of vegf were greater in diseased sites compared to clinically healthy sites . reported a higher concentration of vegf in gcf of healthy patients than periodontally diseased sites , and explained their observation with two possible mechanisms : first , the presence of subclinical levels of inflammation or healing after the microbial assault that may interfere with vegf expression , and second , physiological angiogenesis in the gingival / periodontal environment . however , our results did not match this finding probably due to differences in patient selection criteria and comparison methods . in this study , the difference in the mean gcf concentration of vegf of group 2 and group 3 was statistically highly significant compared to group 1 . this is in agreement with the findings presented in the study conducted by mohamed et al . however , there was no statistically significant difference in the mean gcf concentration of vegf between group 2 and group 3 even though the clinical parameters recorded in group 3 at baseline was comparable to that recorded for group 2 . therefore , it can be interpreted that the presence of well - controlled diabetes does not have an effect on the expression of vegf in gcf of cp patients and that it is the clinical parameters that would dictate its expression . these findings are consistent with the observations made by gneri et al . , prapulla et al . , and booth et al . in addition , sakallioglu et al . in his recent study stated that the level of vegf may increase in periodontitis patients which is in agreement with the findings of our study . there was a statistically highly significant reduction in the mean gcf vegf level 6 weeks after phase - i periodontal therapy ( srp ) in groups 2 and 3 . this finding is consistent with the results published by padma et al . in their study . the reduction in the gcf vegf level after phase - i periodontal therapy can be attributed to the resolution of gingival inflammation and reduction in pd due to tissue shrinkage . moreover , when the gcf vegf levels of groups 2 and 3 were compared 6 weeks after phase - i therapy , a statistically significant difference was seen . this finding can be interpreted as that , even though the presence of diabetes in cp patients may not have an effect on expression of vegf in gcf , the effectiveness of phase - i therapy in controlling vegf levels is poorer in patients with both diabetes and cp . taken together , these results indicate that gcf vegf expression is higher in periodontitis patients than in healthy patients , which is in agreement with the studies done by gneri et al . andprapulla et al . where they reported progressive increase in gcf mean concentrations of vegf from healthy to periodontitis patients . the variability of gcf vegf levels within the cp group can be attributed to the different stages of disease process at the time of gcf collection . further , the presence of well - controlled dm in cp patients did not influence the level of vegf in gcf . furthermore , the treatment aimed at arresting periodontal disease progression resulted in statistically significant reduction in the levels of vegf in gcf . the limitations of this study however that is , a limited sample size was included . a specific analysis will further throw light on the role vegf may play in the periodontal pathophysiology . further , longitudinal prospective studies involving larger sample population are needed to confirm these findings and to better understand the role of vegf in periodontal health and disease . taking all these into consideration , gcf vegf can be considered a potential biomarker for periodontal disease and deserves further considerations in the development of preventive and therapeutic methods for treating periodontal disease .\noutput:\n" }, { "from": "agent", "value": "aim : to estimate the gingival crevicular fluid ( gcf ) level of vascular endothelial growth factor ( vegf ) in periodontally healthy controls and chronic periodontitis ( cp ) patients with and without diabetes mellitus ( dm ) and also to investigate the effect of scaling and root planing ( srp ) on the gcf vegf level.materials and methods : one hundred and five patients were divided into three groups : healthy ( group 1 ) , cp ( group 2 ) , and cp with dm ( group 3 ) . group 2 and group 3 patients underwent srp planning , and the cases were followed for 6 weeks . periodontal clinical parameters such as plaque index , gingival index , probing pocket depth , and clinical attachment level were recorded at baseline and 6 - week posttherapy . gcf samples collected from each patient were quantified for vegf level using enzyme - linked immunosorbent assay.results : the mean gcf vegf level was increased in cp patients with and without dm compared to healthy patients and srp therapy caused a statistically significant ( p < 0.001 ) reduction in gcf vegf level.conclusion : vegf is increased in gcf of cp patients with and without dm and that srp substantially reduces its level in gcf ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: magnesium is the most abundant divalent cation in the cell , with numerous roles that are essential for cellular function . the estimated total concentration of mg in mammalian cells varies between 14 and 20 mm , the majority of it bound to atp and a lesser extent to proteins , phospholipids , and various phosphometabolites . the concentration of free cytosolic magnesium , [ mg ] i , not associated with macromolecules , is estimated to be in the sub - millimolar range . abnormal levels of magnesium are associated with a number of age - related and neuronal diseases ranging from hypertension to alzheimer s disease . the mechanisms by which mg concentration is regulated at the cellular level and the implications in human health , however , remain poorly understood due to the scarcity of efficient chemical tools for the study of this ion . most detection methods employed thus far do not offer the combination of selectivity and spatiotemporal resolution required to study magnesium in the complex chemical environment offered by the cell . the use of fluorescent indicators has emerged as a powerful approach to detect free magnesium in biological samples . most fluorescent indicators available commercially at this time are based on o - aminophenol - n , n , o - triacetic acid ( aptra ) chelators ( figure 1 ) , which afford a rapid response and dissociation constant in the low millimolar range , optimal for measurements of free mg . nevertheless , the aptra binding group suffers from low selectivity against ca and zn ( e.g. , kd , ca = 20 m and kd , zn = 11 nm for mag - fura - 2 ) , which may give rise to artifacts in the detection of mg in the cellular milieu . alternative chelators based on - keto - acids and related - dicarbonyl bidentate binding motifs have been incorporated recently into fluorescent probes for the detection of mg . significantly , these chelators form magnesium complexes with typical dissociation constants in the low millimolar range and exhibit dissociation constants the same or 1 order of magnitude higher when complexed to ca . as a result , they are practically insensitive to biological concentrations of ca and show great promise for the development of fluorescent probes with an improved metal selectivity profile for biological applications . unlike the pentadentate aptra - based sensors , - dicarbonyl species may occupy only two sites in the coordination sphere of mg , leaving room for coordination of further charged or neutral ligands and formation of ternary species . the formation of these species and its effect in the performance of fluorescent sensors have been long overlooked and warrant further investigation . in this paper , we provide evidence for the formation of ternary complexes from interaction of bidentate fluorescent indicators with mgatp , the most abundant form of bound mg in the cell , and investigate its effect on the optical properties of the indicators under conditions relevant to fluorescence imaging of biological magnesium . magnesium - binding chelators o - aminophenol - n , n , o - triacetic acid ( aptra , 1 ) and 4 - oxo - 4h - quinolizine -3-carboxylic acid ( 2 ) employed in the design of fluorescent probes such as furaptra ( mag - fura - 2 , 3 ) and kmg - 301 ( 4 ) for imaging of mg . compounds kmg - 301,2 , and 2a ( 15 ) were prepared according to reported procedures , and their purity ( 98 % ) was verified by reverse phase c - 18 hplc . high - purity piperazine - n , n - bis ( 2 - ethanesulfonic acid ) ( pipes ) , 37 % hcl , 45 % koh , and 99.999 % anhydrous mgcl2 were purchased from aldrich . deuterium oxide ( d , 99.9 % ) , sodium deuteroxide ( d , 99.5 % , 40 % w / w in d2o ) , and deuterium chloride ( d , 99.5 % , 35 % w / w in d2o ) were obtained from cambridge isotope laboratories . all aqueous solutions for fluorescence experimentsaqueous buffers were treated with chelex resin ( bio - rad ) according to the manufacturer s protocol to remove adventitious metal ions . fluorescence spectra were acquired on a quantamaster 40 photon technology international spectrofluorometer equipped with xenon lamp source , emission and excitation monochromators , excitation correction unit , and pmt detector . all measurements were conducted at 25.00.1 c controlled with quantum northwest cuvette holders . fluorescence measurements at ph 7.0 were conducted in aqueous buffer containing 50 mm pipes and 100 mm kcl . stock solutions of compounds 2 and 2a , 1.0 mm , were prepared in pipes buffer at ph 7.0 . all stock solutions for fluorescence measurements were stored at 20 c in 20200 l aliquots and thawed immediately before each experiment . excitation for compound 2 was provided at 385 nm and for compound 2a at 395 nm . excitation for kmg - 301 was provided at 540 nm , and corrected emission spectra were integrated in the 545750 nm range . apparent kd values for a 1:1 binding model ( probe / mg or probe / mgatp ) were obtained from nonlinear fit of integrated florescence intensity or fluorescence ratio plots ( see supporting information for details ) . nmr spectroscopic data were acquired on a bruker avance - 400 nmr or bruker avance iii - 600 nmr spectrometer equipped with a 5 mm sample diameter inverse quadruple resonance probe . h nmr shifts were calibrated based on the protio impurity of the solvent peak . changes of the chemical shift of the indicator s protons as a function of total magnesium concentration were fitted using a model including two sequential dissociation equilibria as described in the supporting information . diffusion measurements were conducted on a bruker avance iii - 600 nmr using the ledbpgp2s pulse program , with a longitudinal eddy current delay of 5 ms , diffusion time = 100 ms , and effective gradient duration = 3600 s . the gradient power of the probe was calibrated from the diffusion coefficient of water . diffusion experiments were run with 16 , 32 , or 64 scans ; more scans were used for samples with broad peaks ( concentrations of mgatp above 10 mm ) . linear gradient strength ramps from 8 % to 50 % were employed for samples of sensors 2 and 2a with and without mg . the intensities of non - overlapping peaks were analyzed using the relaxation module in the bruker topspin version 3.2 software ( supporting information ) . diffusion coefficients are reported as averages of the values obtained from analysis of the different peaks corresponding to one given compound . samples for nmr spectroscopy were prepared by mixing appropriate amounts of na2atp and mgcl2 solutions in d2o with a sensor stock solution containing tris buffer in d2o . the mixture was adjusted to pd 7.40 with small amounts of 37 % dcl in d2o , and diluted to a final concentration of 2.5 mm compound 2 in 10 mm tris or 5.0 mm compound 2a in 25 mm tris . na2atp was added from a 100 mm stock solution in d2o , adjusted to pd 7.40 with naod . magnesium was added from 100 mm or 1.00 m stock solutions prepared by dissolving high purity anhydrous mgcl2 beads in d2o . crystals of 2 mg ( oh2 ) 2 were obtained as follows : a 25 mm solution of chelator 2 in dmso ( 50 l ) at 60 c was treated with aqueous pipes buffer at ph 7.0 containing 50 mm mgcl2 ( 250 l ) , layered atop the first solution . the warm mixture was allowed to cool slowly and diffuse over a period of 16 h protected from light . single crystals suitable for x - ray analysis were coated with paratone - n oil and mounted on fiber loops for analysis . diffraction data were collected at 100 ( 2 ) k on a bruker apexii ccd x - ray diffractometer performing scans using graphite - monochromated mo k radiation . structure was solved by direct methods and standard difference map techniques and was refined by full - matrix least - squares procedures on f with shelxtl ( version 6.12 ) . crystallographic data collection and refinement parameters are summarized in table s1 , supporting information . levy and co - workers developed a series of 4 - oxo - 4h - quinolizine -3-carboxylic acid derivatives ( figure 1 ) that bind mg with dissociation constants in the low millimolar range and show negligible response to ca . based on these chelators , oka s group developed fluorescein and rosamine fluorescent compounds kmg - 104 and kmg - 301 that perform as turn - on sensors with excitation and emission in the visible range . in our study , we first employed the most recently reported rosamine probe , kmg - 301 , as a representative example of a bidentate dicarbonyl - based chelator that would allow us to investigate the formation of ternary complexes in conditions akin to those employed in fluorescence bioimaging experiments . treatment of kmg - 301 with increasing mg concentrations in aqueous buffer at ph 7.0 leads to an increase in the fluorescence emission ( figures 2 and s1 ) for an overall 24-fold turn on . nonlinear fit of the integrated fluorescence as a function of magnesium concentration , obtained under our experimental conditions , results in an apparent dissociation constant kd = 3.790.04 mm for the 1:1 complex of the chelator with mg at 25 c . significantly , a titration employing increasing concentrations of mg as a 1:1 complex with atp ( figure 2b ) , leads to a 58 % larger increase in emission intensity compared to that observed in the titration with mgcl2 over the same concentration range . the intensity increase is accompanied by a slight red shift in the fluorescence maximum . a control experiment conducted with the addition of atp , in the absence of mg ( figure s1 , supporting information ) , shows a similar red shift but only a slight increase in the fluorescence intensity , thus supporting the notion that the fluorescence turn on in each case involves magnesium coordination . nonlinear fit of the binding isotherm for the titration with mgatp yields an apparent dissociation constant kd = 14.20.3 mm at 25 c for a 1:1 binding model . a similar value is obtained for a titration conducted in the presence of a 1:2 ratio mg to atp ( data not shown ) . with an apparent dissociation constant in the mid - micromolar range for mgatp under physiological conditions , the quinolizine - based chelator is not expected to displace the atp from the coordination sphere of magnesium . accordingly , the formation of a ternary atpmgprobe species is the most likely origin of the observed changes in fluorescence . fluorescence emission of 1.0 m solutions of kmg - 301 in response to increasing concentrations of mg ( a ) or mgatp complex ( b ) . titrations were conducted in 50 mm aqueous pipes buffer , 100 mm kcl , ph 7.0 , 25 c . insets correspond to the integrated emission ( squares ) and nonlinear fit ( red line ) as a function of [ mg ] or [ mgatp ] using a 1:1 binding model . we also investigated the interaction between mgatp and the simpler 4 - oxo - 4h - quinolizine -3-carboxylate chelator 2 . unlike kmg - 301 , compound 2 is fluorescent in both mg - free and - bound states , which facilitates the study of the binding process and allows for ratiometric determination of mg . treatment of 2 with increasing mg concentrations in aqueous buffer at ph 7.0 ( figure 3a ) led to a blue shift in the fluorescence emission maximum , from 435 to 408 nm . the ratio of emission at these two wavelengths , f408 / f435 , was employed to calculate an apparent dissociation constant , which resulted in a value of kd = 1.550.05 mm for the 1:1 complex of the chelator with mg under our experimental conditions . treatment of 2 with increasing concentrations of mgatp over the same range ( figure 3b ) also led to a blue shift in the fluorescence emission maximum , from 435 to 412 nm . employing the ratio of emission at these two wavelengths , f412 / f435 , an apparent constant kd = 1.810.09 mm for the dissociation of the fluorescent probe from a 1:1:1 atpmgprobe ternary complex was obtained . a control experiment conducted with the addition of atp in the absence of mg only led to a slight decrease in the fluorescence of the sensor with no significant blue shift ( data not shown ) , presumably due to mild quenching effect of the purine base . therefore , the wavelength shift observed in the presence of mgatp can be attributed to coordination of the magnesium center to the bidentate chelator . fluorescence emission of 1.0 m solutions of 4 - oxo - 4h - quinolizine -3-carboxylate , compound 2 , in response to increasing concentrations of mg ( a ) or mgatp complex ( b ) . all titrations were conducted in 50 mm pipes buffer , 100 mm kcl , ph 7.0 , 25 c . insets correspond to the ratio of fluorescence intensity at two wavelengths , f408 / f435 ( f412 / f435 for mgatp titration , squares ) and nonlinear fit ( red line ) as a function of added magnesium or mgatp using a 1:1 binding model . the apparent affinities of 2 for mg and mgatp are surprisingly similar and , in comparison to those of the rosamine probe kmg - 301 , indicate that the xanthene moiety has an electronic effect on the apparent binding properties of the chelator . with either sensor , however , the mgatp - induced optical changes are expected to contribute significantly to the overall fluorescence response obtained in cell or tissue imaging experiments . this contribution can not be neglected in the interpretation of imaging studies of mg , as it does not allow for a clear distinction between the detection of free mg from its nucleotide - bound forms at typical physiological levels , based on steady state fluorescence intensity or ratio measurements . in short , the - dicarbonyl - based sensors tested herein do not report on levels of free mg , as presumed in previous studies , but their optical response may reflect changes in concentration of various forms of mg ( e.g. free + nucleotide bound ) . this limitation may affect the performance of other low - denticity chelators and must be considered carefully . however , the role of mg in mediating the interaction is not clear in every case . the use of other metals such as zn and cu has allowed for the isolation and structural characterization of various ternary complexes in which the phosphate backbone of the nucleotide and a second chelator share the coordination sphere of the metal center ; similar magnesium - containing ternary complexes with fluorescent chelators are not unlikely . to gain further insight into the interaction of the fluorescent probe with mgatp , we investigated the complex formation by nmr spectroscopy ( figure 4 ) . for this purpose , we employed a derivative of 2 , 1 - ( 2,2 - dicarboxyethyl ) -4-oxo-4h - quinolizine -3-carboxylic acid 2a , which displays similar fluorescence response to both mg and mgatp ( figure s2 , supporting information ) but offers increased solubility in water compared to 2 . treatment of a 5.0 mm solution of compound 2a in aqueous buffer with increasing concentrations of mg reveals a gradual shift and broadening of the aromatic signals , which sharpen at high concentrations of mg ( figure 4a ) . analysis of the chemical shift as a function of total magnesium concentration suggests at least two metal - binding steps , and a model considering the formation of both 2:1 and 1:1 chelator / mg species provides the best fit ( figure 5 and supporting information ) . from this analysis , two apparent dissociation constants are obtained , one of kd1 = 121 mm for the chelator dissociation from the 2:1 complex , and the second kd2 = 0.90.3 mm for the dissociation of the 1:1 species . h nmr spectra ( 600 mhz , d2o , 25 mm tris buffer , pd = 7.40 , 25 c ) of a 5.0 mm solution of chelator 2a after treatment with increasing concentrations of mgcl2 ( a ) or mgatp ( b ) . ( a ) changes in chemical shift of aromatic protons of chelator 2a ( 5.0 mm in d2o , 25 mm tris buffer , pd = 7.40 , 25 c ) as a function of total concentration of magnesium , obtained from the h nmr spectroscopic titrations . ( b ) nonlinear fit of the changes in chemical shift for ha in response to increasing concentrations of magnesium , employing a model that includes both the formation of complexes with 2:1 and 1:1 chelator - to - mg stoichiometry . the limited water solubility of the simple chelator 2 at millimolar concentrations facilitated the isolation and structural characterization of the complex 2 mg ( oh2 ) 2 , as shown in figure 6 . the solid - state structure exposes a - [ o2 ] coordination mode for two of the quinolizine - derived fluorophores forming almost perpendicular six - membered chelates around a pseudo - octahedral magnesium center . the concentration of this 2:1 chelator / mg species in solution is negligible at the low chelator concentration and high [ mg ] / [ chelator ] ratio involved in typical fluorescence sensing experiments . its formation at high concentrations , however , illustrates the ability of small low - denticity chelators to share the coordination sphere with other multidentate ligands , such as another molecule of 2 or potentially a biologically relevant ligand such as atp . a second titration experiment was conducted with a 5.0 mm solution of compound 2a in aqueous buffer treated with increasing concentrations of mgatp and followed by h nmr and p nmr spectroscopy ( figures 4b and s10 and s11 , supporting information ) . with the exception of the signal corresponding to proton he , all the aromatic signals of compound 2a shift upfield in the h nmr spectrum indicating the formation of a complex that is electronically different from that formed upon treatment of the chelator with mgcl2 alone . furthermore , these signals remain broad even at close - to - saturating concentrations of mgatp , likely due to the effect of conformational changes of the atp ligand in a ternary complex . further evidence for the formation of ternary species upon interaction of the bidentate fluorescent probes with mgatp was obtained through nmr diffusion studies . specifically , the translational self - diffusion coefficient of quinolizine - based chelator 2a was determined via pulsed gradient spin echo ( pgse ) diffusion h nmr spectroscopy experiments in the absence and presence of near - saturating concentrations of mg or mgatp ( table 1 ) . upon treatment with mgcl2 , the diffusion coefficient of the chelator decreases , thus reflecting an increase in the overall size of the molecule as a result of metal complexation . the change in diffusion coefficient is , however , more pronounced upon treatment with mgatp . at high concentration of the nucleotide - bound magnesium source , the diffusion coefficient of the chelator drops to a value lower than that obtained upon complexation with magnesium and even lower than that of mgatp alone , thus consistent with the formation of a larger species . additionally , a marked decrease in diffusion coefficient was observed for chelator 2 in the presence of mgatp ( table s2 , supporting information ) ; the low solubility of the compound in the presence of high concentration of magnesium , however , prevented further studies . samples containing 5.0 mm of chelator 2a in d2o , with 25 mm tris buffer adjusted to pd = 7.40 , 25 c. sample containing 10 mm mgatp in tris buffer adjusted to pd = 7.40 , 25 c . at 55 mm mgatp , the coefficient is , within error , the same as the coefficient at 40 mm . much of our understanding of metal homeostasis and its implications in health and disease stems from the use of fluorescent metal indicators that enable optical tracking of ion accumulation and fluxes in the complex matrix provided by the cell . sensor development endeavors typically devote substantial effort to the fine - tuning of dissociation constants as to provide maximum dynamic range , avoid competitive binding of other metals , and prevent displacement of typical biological chelators , thereby enabling the selective detection of the free or ionized forms of the cation under physiological conditions . our results highlight the need for a deeper understanding of the coordination properties of the chelator , and the consideration of binding schemes beyond the simple formation of binary species , to provide a more complete depiction of the selectivity of fluorescent metal chelators . we hereby provide spectroscopic evidence for the formation of ternary complexes from - keto - acid fluorescent chelators , namely , 4 - oxo - 4h - quinolizine -3-carboxylic acid and kmg - 301 , with mgatp , the most abundant bound form of biological magnesium . the formation of such ternary species elicits comparable or greater optical changes than those attributed to the formation of binary complexes alone , with equilibrium constants that are similar for the binding of the chelator to either free magnesium or its nucleotide complex . as a result , these low - denticity chelators do not afford a clear distinction between free ( ionized ) mg and mgatp from simple ratio - or intensity - based steady - state fluorescence measurements . instead , they may co - report various magnesium - containing species , thus posing challenges in the interpretation of results obtained from fluorescence imaging of magnesium in nucleotide - rich biological samples . being a consequence of the mismatch between the typical coordination number of mg and the denticity of the sensor , the formation of ternary complexes is likely to influence the performance of other low - denticity chelators and must be considered carefully .\noutput:\n" }, { "from": "agent", "value": "fluorescent indicators based on - keto - acid bidentate coordination motifs display superior metal selectivity profiles compared to current o - aminophenol - n , n , o - triacetic acid ( aptra ) based chelators for the study of biological magnesium . these low denticity chelators , however , may allow for the formation of ternary complexes with mg2 + and common ligands present in the cellular milieu . in this work , absorption , fluorescence , and nmr spectroscopy were employed to study the interaction of turn - on and ratiometric fluorescent indicators based on 4 - oxo - 4h - quinolizine -3-carboxylic acid with mg2 + and atp , the most abundant chelator of biological magnesium , thus revealing the formation of ternary complexes under conditions relevant to fluorescence imaging . the formation of ternary species elicits comparable or greater optical changes than those attributed to the formation of binary complexes alone . dissociation of the fluorescent indicators from both ternary and binary species have apparent equilibrium constants in the low millimolar range at ph 7 and 25 c . these results suggest that these bidentate sensors are incapable of distinguishing between free mg2 + and mgatp based on ratio or intensity - based steady - state fluorescence measurements , thus posing challenges in the interpretation of results from fluorescence imaging of magnesium in nucleotide - rich biological samples ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: mr h is a 70 - year - old black male with a history significant for dementia associated with chronic hydrocephalus . he also had urinary outflow obstruction , producing chronic bilateral hydronephrosis requiring a chronic indwelling urinary catheter . his family noticed decreased interactions and decreased oral intake developing over the course of 2 weeks . in the facility , he was found to have a urinary tract infection and was treated with sulfamethoxazole / trimethoprim without improvement in his symptoms . subsequent laboratory investigation revealed a serum sodium ( sna ) level of 177 mmol / l , and the patient was administered intravenous fluids and admitted to our hospital . his other medications on admission were bisacodyl and docusate . on admission , he was a cachectic , chronically ill - appearing man who was in no acute distress . he was tachycardic at 110 beats per minute ; his vital signs were otherwise normal . laboratory studies ( roughly 8 hours after nursing home labs were drawn ) revealed a white blood cell count of 18,500 , sna of 167 mmol / l , k of 3.5 mmol / l , and cl of 139 mmol / l ; blood urea nitrogen level was 56 mg / dl , and creatinine level was 2.3 mg / dl . urinalysis revealed a specific gravity of 1.016 and confirmed the presence of a urinary tract infection . initially , the patient was diagnosed with hypovolemic hypernatremia secondary to urinary tract infection and sepsis in the setting of impaired access to free water in the facility , and there was a strong suspicion of neglect by the facility . he was treated with broad - spectrum intravenous antibiotics . because he had past admissions for hypernatremia coming from multiple different facilities , unfortunately , the initiation of the workup was delayed , only beginning after hydration had corrected his sna to 150 mmol / l . at that point , he was requiring 34 l intravenous fluids to maintain his sna between 145148 mmol / l , with a urine output of 34 l daily ( table 1 ) . his serum osmolality was 335 mosm / kg , urine osmolality was 241 mosm / kg , urine specific gravity was 1.0121.016 , and urine sodium was 46the inappropriately normal urine specific gravity and urine - to - plasma osmolality ratio of 0.7 indicate water excretion despite a relative water deficit in the setting of hypernatremia . a 12 hours water deprivation test was performed ( table 2 ) that also documented no response to administered desmopressin , confirming a diagnosis of nephrogenic diabetes insipidus . ultimately , his nephrogenic diabetes insipidus was managed with free water via percutaneous endoscopic gastrostomy tube ; treatment with hydrochlorothiazide was not attempted because of borderline hypotension . this case illustrates the importance of considering diabetes insipidus among other conditions when a nursing home resident presents with hypernatremia , especially recurrent hypernatremia , so that evaluation and therapy are not delayed . hypernatremia is termed as a deficit of total body water relative to total body salt and is defined by a sna concentration greater than 145 mmol / l. 1,2 hypernatremia is a common disorder associated with significant morbidity and mortality for older people . in nursing home residents , hypernatremia and dehydration are considered preventable and are markers of substandard care . the residents often are dependent on help to maintain adequate hydration . as hypernatremia and dehydration developing in the nursing homeare considered indicators of neglect , some jurisdictions require investigation and reporting .3 this case illustrates the importance of consideration of alternate explanations for hypernatremia in a nursing home resident . the prevalence of hypernatremia in older patients living in the community may be as high as 3.7 % , depending on the diagnostic criteria used ( the range for hypernatremia threshold varied between studies from 140150hypernatremia is present in approximately 2 % of older patients admitted to hospital , but in almost 5 % of those older than 75 years in one large survey .4 hypernatremia was present in roughly 30 % of elderly patients admitted to a geriatric hospital with a febrile illness .5 hypernatremia is a frequent complication of hospitalization . in a study involving 8,441 consecutive patients ( primarily elderly ) admitted to the intensive care unit , roughly 3.5 % had hypernatremia on admission , and another 15 % developed hypernatremia during hospitalization .6 hypernatremiais associated with high morbidity and mortality rates . in the 8,441 primarily elderly intensive care unit patients described earlier , mortality in those admitted with hypernatremia was approximately 33 % .6 in comparison , those without hypernatremia had a mortality of 15 % .6 if the patients had normal sna on admission and developed mild or moderate to severe hypernatremia while in the intensive care unit , mortality increased to 30 % and 45 % , respectively .6 other studies confirm these findings : mortality increases with serum sodium , and even mild hypernatremia is associated with significant mortality in hospitalized elders , even after accounting for confounders .610 at the time of this review , all available literature includes data in hospitalized patients ; however , data about hypernatremia in the ambulatory setting are lacking . mortality from hypernatremia does not increase with age but does increase with recurrent episodes .11 the mortality from hypernatremia may be increased by delays in diagnosis or inappropriate management .12 in fact , a previous review on hypernatremia suggests the most serious complications occur from treatment of the hypernatremia , rather than the elevated sna itself .1 older patients are predisposed to hypernatremia . sodium and water balance is regulated by thirst , arginine vasopressin ( avp ) , and the central renin - angiotensin - aldosterone system .13 in transient hypernatremic states , thirst is such a strong stimulant for water intake that sustained hypernatremia almost never occurs unless the thirst mechanism is impaired or access to water is restricted .1 in the nursing home , both impaired thirst and limited access to water may be common challenges for the residents and may predispose them to hypernatremia . those unable to care for themselves are more likely to have limited access to water and rely on the facility s staff to get that access . this provides the rationale for the link between dehydration / hypernatremia and substandard care . however , there are multiple studies showing that even healthy elders have an impaired thirst mechanism . phillips et al showed that after 24 hours of water deprivation , elderly subjects were not as thirsty as younger subjects and did not drink enough water to dilute plasma to predeprivation sodium levels .14 this also held true in response to hypertonicity , produced by infusing hypertonic saline , without extracellular fluid depletion .15 in both studies , these cognitively intact elderly subjects had a thirst response that was inadequate for the degree of hypernatremia they were experiencing .15 the risk is even greater in patients with severe dementia , as many are unable to indicate their need for water . the effects of interfering with the central renin - angiotensin system or , less commonly , with avp pathways may exaggerate the aging effects on thirst .16 multiple studies have demonstrated a renal concentrating impairment with age .14,15,1720 the longest nephrons , those most critical for concentrating urine , seem the most depleted with aging .2 this can lead to a decrease in sodium excretion in response to a sodium load .21 healthy older persons can achieve a maximum urinary concentration of 700800 mosm / kg , whereas a healthy young adult can achieve 1,200 mosm / kg .2 after 24 hours water deprivation , elderly subjects had higher plasma osmolality and serum sodium concentration , in large part because of this inability to conserve water by concentrating the urine . these patients had higher plasma avp levels , suggesting normal central response to osmolality and hypernatremia but an impairment in tubular response to avp .14 this impaired responsiveness partially accounts for nocturia in older persons .22 in addition , the effects of diuretics , especially furosemide , which is commonly used in elder patients , decrease urine concentrating ability . lastly , this population is prone to hypernatremia because of a physiologic decrease in total body water . in young adults , water accounts approximately 60 % 65 % of body weight , whereas in older persons , it is closer to 50 % , and it may be even lower in women .22 having lower total body water predisposes patients to dehydration with smaller losses of fluid , and therefore can increase the tendency to become hypernatremic . the symptoms include lethargy , weakness , and in more severe cases , changes in consciousness and seizures .2 few symptoms may be present until sodium levels exceed 160 mmol / l. 1 as noted earlier , many older patients may be hypodipsic , whereas others may have more intense thirst that diminishes as hypernatremia worsens .1,8 in patients with chronic hypernatremia , symptoms will be milder because of adaptation at the cellular level , especially in the central nervous system .1,2 signs and symptoms may be even more vague in patients developing hypernatremia in the hospital .1 a recent change in consciousness is often a marker for sodium dysnatremia in the correct clinical context ; however , this is a poor prognostic indicator .12 initial workup in a patient with hypernatremia is essential because a delay in diagnosis or management can lead to higher mortality . in addition to a review of medications , laboratory workup should include serum electrolytes , including calcium , serum blood urea nitrogen and creatinine levels , serum and urine osmolality , and urine sodium .2 a head computed tomography scan will help , as hypernatremia induces shrinkage of brain cells , which may cause vascular rupture and lead to cerebral bleeding or subarachnoid hemorrhage .1,2 there are several approaches to hypernatremia , but it is essential to determine volume status as a prudent first step . dry oral mucosa , abnormal supraclavicular or thigh skin turgor , absent axillary moisture , orthostasis or hypotension , and low urine output are clinical signs of hypernatremic dehydration12 but are much less useful for the elderly . laboratory signs that suggest dehydration as a cause of hypernatremia include an elevated blood urea nitrogen level and / or creatinine level , with an increased blood urea nitrogen to creatinine ratio , metabolic alkalosis , hemoconcentration resulting in increased hematocrit , and low urine sodium .2 it is also important to exclude states such as hyperglycemia , in which excess circulatory osmoles can cause diuresis , resulting in water loss and development of hypernatremia .2 cases of hypernatremic dehydration resulting from disorders such as diabetes insipidus are typically unmasked whenever a patient becomes incapacitated or does not readily have access to water .1 rarely , the thirst mechanism can be interrupted as a result of medication23 or trauma ,2 resulting in dysregulation and development of hypernatremia . adrogu et al1 and al - absi et al24 have described excellent comprehensive management strategies of hypernatremia , and we discuss some of the elements in the consideration of older patients . in hemodynamically unstable patients , administration of isotonic normal saline is essential , irrespective of sna .1 in dehydrated patients , the most appropriate method for rehydration is hypotonic saline .1 using hypotonic saline instead of isotonic normal saline is crucial , as this will aid in the correction of both volume status and sodium in a shorter time , given the constraints described here .1 in euvolemic patients , any hypotonic fluid should suffice .1 last , hypervolemic hypernatremia is the least common type at time of hospital presentation and usually stems from excessive administration of sodium ( eg , hypertonic sodium bicarbonate , hypertonic saline , etc ) during the hospital course .24 in patients with hypervolemic hypernatremia , hypotonic fluid administration coupled with loop diuretics will aid in correcting volume status without worsening hypernatremia .24 although management with the first step will invariably help acutely correct volume status and show some improvement in sodium levels , the second step requires some further considerations for ongoing treatment , including whether the hypernatremia is acute ( occurred within a few hours ) or chronic . if hypernatremia is unequivocally known to be acute , usually identified when symptoms develop rapidly , sodium correction can be rapid ( approximately 1 mmol / l / hour ) , as the brain has not had enough time to adapt .1 cell shrinkage occurs when high plasma osmolality draws water out of brain cells .1 to counteract this shrinkage , the brain cells accumulate additional solutes ( initially inorganic ions , followed by organic osmolytes ) .1 this cellular adaptation takes 2448 hours .1 as a consequence , when a patient has chronic hypernatremia , to prevent cerebral edema from occurring with correction , the maximal recommended correction rate is 0.5 mmol / l / hour .1 correcting hypernatremia too slowly also has negative consequences . correction at 0.5 mmol / l / hour in the first 24 hours25 and the complete correction of hypernatremia within 4 days11 improves level of cognition and mortality . correction extended beyond 4 days may lead to permanent loss of cognitive function and higher mortality .11 therefore , we recommend correcting hypernatremia slowly at 0.5 mmol / l / hour for the first 1224 hours ( rapid correction at 1 mmol / l / hour initially if severe symptoms are present ) , followed by correction to the normal range within the next 4872 hours . if the history is unclear ( the duration of hypernatremia is uncertain ) , a slower correction rate is likely to be safer . attention to ongoing fluid losses and concurrent electrolyte abnormalities will improve outcomes .1 for example , hypokalemia can cause a concentrating defect in the kidney and potentially worsen dehydration .26,27 the final step for management is establishing the underlying reason for development of hypernatremia . otherwise , the patient remains at risk for recurrence . it is crucial to consider concomitant disorders , as exemplified in the patient described in the case presented earlier . as noted earlier , the elderly have a physiologic decrease in the thirst mechanism ; however , there can be a pathological decrease in free water intake as well . primary hypodipsia results from an injury to the hypothalamus from vascular occlusion or hemorrhage , traumatic brain injury , brain tumor , or infiltrative disease .2 a computed tomography and / or magnetic resonance image of the brain can help aid in diagnosing these conditions . in which the threshold for thirst and avp release have been reset to a higher level .2 these patients will have a high urine osmolality .2 a major cause of hypernatremia in the elderly is from hypotonic fluid losses . loop or thiazide diuretics are common medications that create a urinary concentrating defect that generates diuresis .2 osmotic diuresis secondary to nonabsorbable solutes such as glucose ( as in hyperglycemia ) can create a relative concentrating defect .2 lastly , the recovery phase from acute tubular necrosis or postobstructive nephropathy is characterized by a concentrating defect resulting from tubular injury .2 this renal concentrating defect can be identified by a urinary osmolality lower than 700 mosm / kg and an elevated urine sodium level greater than 20 mmol / dl .2 diabetes insipidus can be characterized by a severe renal concentrating defect caused by central or renal lesions . in these patients , there is consistent polyuria associated with diluted urine , indicated by urine osmolality that can be lower than 200 mosm / kg .2 in diabetes insipidus , a water deprivation test will reveal increasing serum sodium without significant change in urine osmolality ( table 2 ) . the central versus nephrogenic origin can be distinguished by good response to administered desmopressin in patients with a central defect .2 central causes are similar to ones leading to hypodipsia and are a result of injury to the hypothalamus by surgery , traumatic brain injury , vascular occlusion , or hemorrhage .2 nephrogenic causes are from drugs ( lithium , foscarnet , amphotericin b , carbamazepine , or clozapine are some examples ) , hypercalcemia , hypokalemia , obstructive nephropathy , or renal failure ( acute or chronic ) .2,23 hypotonic fluid depletion can also result from insensible fluid losses or gastrointestinal losses . significant insensible hypotonic fluid losses can result from fever , diaphoresis , or tachypnea .2 common gastrointestinal fluid losses in the elderly include diarrhea , vomiting , nasogastric drainage , and use of osmotic agents such as lactulose .2 if hypotonic fluid loss is considered , as long as kidney function is intact , there should be a renal response to retain sodium ; therefore , urine osmolality should be elevated and urine sodium level reduced .2 age - related changes may limit the extent of the elevation in urine osmolality and the decrease in urine sodium . lastly , rarer causes of hypernatremia in the elderly population include sodium overload from iatrogenic excessive administration of sodium bicarbonate or hypertonic saline , primary hyperaldosteronism , or cushing s syndrome .1 any altered mental state , dementia or delirium , can cause a patient to decrease free water intake . nursing home patients may be dependent on caretakers for adequate hydration . according to the nursing home reform act of 1987 , these facilities can be held liable for inadequate nutrition and hydration of a patient because of neglect .28 in patients with hypernatremic dehydration resulting from neglect , there may be no laboratory abnormalities other than the hypernatremia , and the deficits may be corrected with appropriate measures . the prevalence of hypernatremia in older patients living in the community may be as high as 3.7 % , depending on the diagnostic criteria used ( the range for hypernatremia threshold varied between studies from 140150hypernatremia is present in approximately 2 % of older patients admitted to hospital , but in almost 5 % of those older than 75 years in one large survey .4 hypernatremia was present in roughly 30 % of elderly patients admitted to a geriatric hospital with a febrile illness .5 hypernatremia is a frequent complication of hospitalization . in a study involving 8,441 consecutive patients ( primarily elderly ) admitted to the intensive care unit , roughly 3.5 % had hypernatremia on admission , and another15 % developed hypernatremia during hospitalization .6 hypernatremia is associated with high morbidity and mortality rates . inthe 8,441 primarily elderly intensive care unit patients described earlier , mortality in those admitted with hypernatremia was approximately 33 % .6 in comparison , those without hypernatremia had a mortality of 15 % .6 if the patients had normal sna on admission and developed mild or moderate to severe hypernatremia while in the intensive care unit , mortality increased to 30 % and 45 % , respectively .6 other studies confirm these findings : mortality increases with serum sodium , and even mild hypernatremia is associated with significant mortality in hospitalized elders , even after accounting for confounders .610 at the time of this review , all available literature includes data in hospitalized patients ; however , data about hypernatremia in the ambulatory setting are lacking . mortality from hypernatremia does not increase with age but does increase with recurrent episodes .11 the mortality from hypernatremia may be increased by delays in diagnosis or inappropriate management .12 in fact , a previous review on hypernatremia suggests the most serious complications occur from treatment of the hypernatremia , rather than the elevated sna itself .1 older patients are predisposed to hypernatremia . sodium and water balance is regulated by thirst , arginine vasopressin ( avp ) , and the central renin - angiotensin - aldosterone system .13 in transient hypernatremic states , thirst is such a strong stimulant for water intake that sustained hypernatremia almost never occurs unless the thirst mechanism is impaired or access to water is restricted .1 in the nursing home , both impaired thirst and limited access to water may be common challenges for the residents and may predispose them to hypernatremia . those unable to care for themselvesare more likely to have limited access to water and rely on the facility s staff to get that access . this provides the rationale for the link between dehydration / hypernatremia and substandard care . however , there are multiple studies showing that even healthy elders have an impaired thirst mechanism . phillips et al showed that after 24 hours of water deprivation , elderly subjects were not as thirsty as younger subjects and did not drink enough water to dilute plasma to predeprivation sodium levels .14 this also held true in response to hypertonicity , produced by infusing hypertonic saline , without extracellular fluid depletion .15 in both studies , these cognitively intact elderly subjects had a thirst response that was inadequate for the degree of hypernatremia they were experiencing .15 the risk is even greater in patients with severe dementia , as many are unable to indicate their need for water . the effects of interfering with the central renin - angiotensin system or , less commonly , with avp pathways may exaggerate the aging effects on thirst .16 multiple studies have demonstrated a renal concentrating impairment with age .14,15,1720 the longest nephrons , those most critical for concentrating urine , seem the most depleted with aging .2 this can lead to a decrease in sodium excretion in response to a sodium load .21 healthy older persons can achieve a maximum urinary concentration of 700800 mosm / kg , whereas a healthy young adult can achieve 1,200 mosm / kg .2 after 24 hours water deprivation , elderly subjects had higher plasma osmolality and serum sodium concentration , in large part because of this inability to conserve water by concentrating the urine . these patients had higher plasma avp levels , suggesting normal central response to osmolality and hypernatremia but an impairment in tubular response to avp .14 this impaired responsiveness partially accounts for nocturia in older persons .22 in addition , the effects of diuretics , especially furosemide , which is commonly used in elder patients , decrease urine concentrating ability . lastly , this population is prone to hypernatremia because of a physiologic decrease in total body water . in young adults , water accounts approximately 60 % 65 % of body weight , whereas in older persons , it is closer to 50 % , and it may be even lower in women .22 having lower total body water predisposes patients to dehydration with smaller losses of fluid , and therefore can increase the tendency to become hypernatremic . the symptoms include lethargy , weakness , and in more severe cases , changes in consciousness and seizures .2 few symptoms may be present until sodium levels exceed 160 mmol / l. 1 as noted earlier , many older patients may be hypodipsic , whereas others may have more intense thirst that diminishes as hypernatremia worsens .1,8 in patients with chronic hypernatremia , symptoms will be milder because of adaptation at the cellular level , especially in the central nervous system .1,2 signs and symptoms may be even more vague in patients developing hypernatremia in the hospital .1 a recent change in consciousness is often a marker for sodium dysnatremia in the correct clinical context ; however , this is a poor prognostic indicator .12 initial workup in a patient with hypernatremia is essential because a delay in diagnosis or management can lead to higher mortality . in addition to a review of medications , laboratory workup should include serum electrolytes , including calcium , serum blood urea nitrogen and creatinine levels , serum and urine osmolality , and urine sodium .2 a head computed tomography scan will help , as hypernatremia induces shrinkage of brain cells , which may cause vascular rupture and lead to cerebral bleeding or subarachnoid hemorrhage .1,2 there are several approaches to hypernatremia , but it is essential to determine volume status as a prudent first step . dry oral mucosa , abnormal supraclavicular or thigh skin turgor , absent axillary moisture , orthostasis or hypotension , and low urine output are clinical signs of hypernatremic dehydration12 but are much less useful for the elderly . laboratory signs that suggest dehydration as a cause of hypernatremia include an elevated blood urea nitrogen level and / or creatinine level , with an increased blood urea nitrogen to creatinine ratio , metabolic alkalosis , hemoconcentration resulting in increased hematocrit , and low urine sodium .2 it is also important to exclude states such as hyperglycemia , in which excess circulatory osmoles can cause diuresis , resulting in water loss and development of hypernatremia .2 cases of hypernatremic dehydration resulting from disorders such as diabetes insipidus are typically unmasked whenever a patient becomes incapacitated or does not readily have access to water .1 rarely , the thirst mechanism can be interrupted as a result of medication23 or trauma ,2 resulting in dysregulation and development of hypernatremia . adrogu et al1 and al - absi et al24 have described excellent comprehensive management strategies of hypernatremia , and we discuss some of the elements in the consideration of older patients . inhemodynamically unstable patients , administration of isotonic normal saline is essential , irrespective of sna .1 in dehydrated patients , the most appropriate method for rehydration is hypotonic saline .1 using hypotonic saline instead of isotonic normal saline is crucial , as this will aid in the correction of both volume status and sodium in a shorter time , given the constraints described here .1 in euvolemic patients , any hypotonic fluid should suffice .1 last , hypervolemic hypernatremia is the least common type at time of hospital presentation and usually stems from excessive administration of sodium ( eg , hypertonic sodium bicarbonate , hypertonic saline , etc ) during the hospital course .24 in patients with hypervolemic hypernatremia , hypotonic fluid administration coupled with loop diuretics will aid in correcting volume status without worsening hypernatremia .24 although management with the first step will invariably help acutely correct volume status and show some improvement in sodium levels , the second step requires some further considerations for ongoing treatment , including whether the hypernatremia is acute ( occurred within a few hours ) or chronic . if hypernatremia is unequivocally known to be acute , usually identified when symptoms develop rapidly , sodium correction can be rapid ( approximately 1 mmol / l / hour ) , as the brain has not had enough time to adapt .1 cell shrinkage occurs when high plasma osmolality draws water out of brain cells .1 to counteract this shrinkage , the brain cells accumulate additional solutes ( initially inorganic ions , followed by organic osmolytes ) .1 this cellular adaptation takes 2448 hours .1 as a consequence , when a patient has chronic hypernatremia , to prevent cerebral edema from occurring with correction , the maximal recommended correction rate is 0.5 mmol / l / hour .1 correcting hypernatremia too slowly also has negative consequences . correction at 0.5 mmol / l / hour in the first 24 hours25 and the complete correction of hypernatremia within 4 days11 improves level of cognition and mortality . correction extended beyond 4 days may lead to permanent loss of cognitive function and higher mortality .11 therefore , we recommend correcting hypernatremia slowly at 0.5 mmol / l / hour for the first 1224 hours ( rapid correction at 1 mmol / l / hour initially if severe symptoms are present ) , followed by correction to the normal range within the next 4872 hours . if the history is unclear ( the duration of hypernatremia is uncertain ) , a slower correction rate is likely to be safer . attention to ongoing fluid losses and concurrent electrolyte abnormalities will improve outcomes .1 for example , hypokalemia can cause a concentrating defect in the kidney and potentially worsen dehydration .26,27 the final step for management is establishing the underlying reason for development of hypernatremia . otherwise , the patient remains at risk for recurrence . it is crucial to consider concomitant disorders , as exemplified in the patient described in the case presented earlier . as noted earlier , the elderly have a physiologic decrease in the thirst mechanism ; however , there can be a pathological decrease in free water intake as well . primary hypodipsia results from an injury to the hypothalamus from vascular occlusion or hemorrhage , traumatic brain injury , brain tumor , or infiltrative disease .2 a computed tomography and / or magnetic resonance image of the brain can help aid in diagnosing these conditions . in which the threshold for thirst and avp release have been reset to a higher level .2 these patients will have a high urine osmolality .2 a major cause of hypernatremia in the elderly is from hypotonic fluid losses . loop or thiazide diuretics are common medications that create a urinary concentrating defect that generates diuresis .2 osmotic diuresis secondary to nonabsorbable solutes such as glucose ( as in hyperglycemia ) can create a relative concentrating defect .2 lastly , the recovery phase from acute tubular necrosis or postobstructive nephropathy is characterized by a concentrating defect resulting from tubular injury .2 this renal concentrating defect can be identified by a urinary osmolality lower than 700 mosm / kg and an elevated urine sodium level greater than 20 mmol / dl .2 diabetes insipidus can be characterized by a severe renal concentrating defect caused by central or renal lesions . in these patients , there is consistent polyuria associated with diluted urine , indicated by urine osmolality that can be lower than 200 mosm / kg .2 in diabetes insipidus , a water deprivation test will reveal increasing serum sodium without significant change in urine osmolality ( table 2 ) . the central versus nephrogenic origin can be distinguished by good response to administered desmopressin in patients with a central defect .2 central causes are similar to ones leading to hypodipsia and are a result of injury to the hypothalamus by surgery , traumatic brain injury , vascular occlusion , or hemorrhage .2 nephrogenic causes are from drugs ( lithium , foscarnet , amphotericin b , carbamazepine , or clozapine are some examples ) , hypercalcemia , hypokalemia , obstructive nephropathy , or renal failure ( acute or chronic ) .2,23 hypotonic fluid depletion can also result from insensible fluid losses or gastrointestinal losses . significant insensible hypotonic fluid losses can result from fever , diaphoresis , or tachypnea .2 common gastrointestinal fluid losses in the elderly include diarrhea , vomiting , nasogastric drainage , and use of osmotic agents such as lactulose .2 if hypotonic fluid loss is considered , as long as kidney function is intact , there should be a renal response to retain sodium ; therefore , urine osmolality should be elevated and urine sodium level reduced .2 age - related changes may limit the extent of the elevation in urine osmolality and the decrease in urine sodium . lastly , rarer causes of hypernatremia in the elderly population include sodium overload from iatrogenic excessive administration of sodium bicarbonate or hypertonic saline , primary hyperaldosteronism , or cushing s syndrome .1 any altered mental state , dementia or delirium , can cause a patient to decrease free water intake . nursing home patients may be dependent on caretakers for adequate hydration . according to the nursing home reform act of 1987 , these facilities can be held liable for inadequate nutrition and hydration of a patient because of neglect .28 in patients with hypernatremic dehydration resulting from neglect , there may be no laboratory abnormalities other than the hypernatremia , and the deficits may be corrected with appropriate measures . hypernatremia in the elderly is not unusual and is associated with significant morbidity and mortality . the geriatric population is predisposed to developing hypernatremia as a result of physiologic changes in thirst sensitivity , urinary concentrating ability , and total body water . the causes for hypernatremia may be elusive , and initial workup is essential to prevent delay in diagnosis and management . as in the case presented , it is essential to consider multiple causes of hypernatremia to prevent recurrence and significant morbidity and mortality and to prevent false accusations of substandard care .\noutput:\n" }, { "from": "agent", "value": "hypernatremia in the geriatric population is a common disorder associated with significant morbidity and mortality . older people are predisposed to developing hypernatremia because of age - related physiologic changes such as decreased thirst drive , impaired urinary concentrating ability , and reduced total body water . medications may exacerbate this predisposition . hypernatremia and dehydration occurring in nursing homes are considered indicators of neglect that warrant reporting , but there are other nonavoidable causes of hypernatremia , and consideration at time of presentation is essential to prevent delay in diagnosis and management . we describe a case illustrating the importance of the consideration of alternate explanations for hypernatremia in a nursing home resident , followed by a review of hypernatremia in the elderly population , to underscore that neglect is the etiology of exclusion after alternatives have been considered ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: healthcare systems are characterized by shared and distributed decision making and management of care . the distributed nature of the knowledge among different healthcare locations implies that a request may not be completely satisfied at a specific location or that one or more healthcare location may contain information similar to , though not exactly the same as , that required by the request . many initiatives and programs have been established to promote the development of less costly and more effective healthcare networks and systems at national and international scales . the objectives of these healthcare networks are to improve diagnosis through online access to medical specialists , online reservation of analysis and hospital services by practitioners extended on wide global scale , transplant matching , and so forth . a complete electronic medical patient - case file , which might be shared between specialists andcan be interchanged between hospitals and with general practitioners ( gps ) , will be crucial in diagnosing diseases correctly , avoiding duplicative risky and expensive tests , and developing effective treatment plans . however , medical patient - case files may contain some sensitive information about critical and vital topics such as abortions , emotional and psychiatric care , sexual behaviors , sexually transmitted diseases , hiv status , and genetic predisposition diseases . privacy and the confidentiality of medical records have to be especially safeguarded . without broad trust in medical privacyhealthcare professionals and care providers prefer to have the ability of controlling the collection , retention , and distribution of information about themselves . on the other hand , healthcare service providers need to effectively manage and prevent any abuse of the information or service they provide in addition to the ability of protecting their identities . an important feature of the various healthcare sectors is that they share similar problems and are faced with challenges that can be characterized as follows . ( i ) in open - distributed healthcare environments , it is no longer practical to expect healthcare clinicians , staff , care providers , and patients to determine and keep track of the information and services relevant to his / her requests and demands . for example , a patient will be ubiquitously able to access his / her medical record from anywhere at any time or may request medical services offered by available healthcare centers in a particular city without being aware of the distributed sources and irrespective of their locations . in addition , an application should be able to manage distributed data in a unified fashion . this involves several tasks , such as maintaining consistency and data integrity among distributed data sources , and auditing access . ( ii ) the distributed nature of the knowledge among multiple healthcare locations may require collaboration for information gathering . for example , each unit in a hospital keeps its own information about patients ' records . ( iii ) the solution of specific medical problem includes complex activities and requires collaborative effort of different individuals who posses distinct roles and skills . for example , the provision of care to hospitalized patients involves various procedures and requires the coordinated interaction amongst various staff and medical members . it is essential that all the involved medical staff and professionals must coordinate their activities in a manner that will guarantee the best appropriate treatment that can be offered to the patient . ( iv ) a recent survey shows that 67 % of the american national respondents are concerned about the privacy of their personal medical records , 52 % fear that their health insurance information might be used by employers to limit job opportunities , while only 30 % are willing to share their personal health information with health professionals not directly involved in their case . as few as 27 % are willing to share their medical records with drug companies . to explore such issues , distributed healthcare systems need to have an access to a service that can enable collaboration between different healthcare service requesters and providers . brokering facilitates achieving better coordination among various healthcare service requesters and providers , and permits healthcare personnel to get access to different services managed by various providers without having to be aware of the location , identities , access mechanisms , or the contents of these services . the proactive health systems have the potential to improve healthcare access and management which significantly lower the associated incurred costs through efficiently controlled information flow between various physicians , patients , and medical personnel , yet threaten to facilitate data sharing beyond any privacy concerns . the high degree of collaborative work needed in healthcare environments implies that developers and researchers should think of other venues that can manage and automate this collaboration efficiently . however , privacy concerns over inappropriate use of the information make it hard to successfully exploit and achieve the gains from sharing such information . this dilemma restricts the willingness of individuals and personnel to disseminate or publicize information that might lead to adverse outcomes . this paper presents an agent privacy - based information brokering architecture that supports ad hoc system configurations emphasizing the strategies for achieving privacy in healthcare environments . within the context of brokering , we view privacy as the ability of entities to decide upon revealing or hiding information related to their identities , requests and capabilities in open distributed environments . legislation to protect personal medical information was proposed and put in effect to help building a mutual confidence between various participants in the healthcare domain . privacy - based brokering protocols were proposed in many application domain such as e - auctions , data mining , and e - commerce . different techniques were used to enable collaboration among heterogeneous cooperative agents in distributed systems including brokering via middle agents . these middle agents differ from the role they play within the agent community . the work in has proposed an agent - based mediation approach , in which privacy has been treated as a base for classifying the various mediation architectures only for the initial state of the system . in another approach , agents capabilities and preferences are assumed to be common knowledge , which might violate the privacy requirements of the involved participants . other approaches such as in have proposed frameworks to facilitate coordination between web services by providing semantic - based discovery and mediation services that utilize semantic description languages such as owl - s and rdf . another recent approach distinguishes a resource brokering architecture that manages and schedules different tasks on various distributed resources on the large - scale grid . however , none of the above - mentioned approaches has treated privacy as an architectural element that facilitates the integration of various distributed systems of an enterprise . several approaches were proposed for integration of distributed information sources in healthcare . in oneapproach , the focus was on providing management assistance to different teams across several hospitals by coordinating their access to distributed information . the brokering architecture is centralized around a mediator agent , which allocates the appropriate medical team to an available operating theatre in which the transplant operation may be performed . other approach attempts to provide agent - based medical appointments scheduling , in these approaches the architecture provides matchmaking mechanisms for the selection of appropriate recipient candidates whenever organs become available through a matchmaking agent that accesses a domain - specific ontology . other approaches proposed the use of privacy policies along with physical access means ( such as smartcards ) , in which the access of private information is granted through the presence of another trusted authority that mediate between information requesters and information providers . a european ist project , telemediacare , lincoln , uk , developed an agent - based framework to support patient - focused distant care and assistance , in the architecture composes two different types of agents , namely , stationaryweb service - based tools were developed to enable patients to remotely schedule appointments , doctor visits , and to access medical data . different approaches had been suggested to protect the location privacy in open - distributed systems . location privacy is a particular type of information privacy that can be defined as the ability to prevent other parties from learning one 's current or past location . some approaches focus on using anonymity by unlinking user personal information from their identity . the service protects the internet protocol ( ip ) address or the identity of the user who views web pages or submits information ( including personal preferences ) to a remote site . the solution uses anonymous proxies ( gateways to the internet ) to route user 's internet traffic through the tool . however , this technique requires a trusted third party because the anonymizer servers ( or the user 's internet service provider , isp ) can certainly identify the user . other tools try not to rely on a trusted third party to achieve complete anonymity of the user 's identity on the internet , such as crowds , onion routing , and mix networks . various programs and initiatives have proposed a set of guidelines for secure collection , transmission , and storage of patients ' data . some of these programs include the initiative for privacy standardization in europe ( ipse ) and the health insurance portability and accountability act ( hipaa ) . yet , these guidelines need the adoption of new technology for healthcare requester / provider interaction . brokering enables collaboration between different service requesters and providers , and allows the dynamic interpretation of requests for the determination of relevant service providers . for service providers , the brokering services permit dynamic creation of services ' repositories after suitable assembly of service advertisements available from the various providers , or other additional activities ( i ) provision of registration services : the registration and naming service allows building up a knowledge base of the environment that can be utilized to facilitate locating and identifying the relevant existing service sources and their contents for serving a specific request . it is crucial to be able to identify the subset of relevant information at a source , and to combine partially relevant information across different sources ; this requires the process of identification and retrieval of a subset of required service at any source . it is clear that in such environment , different sources would provide relevant information to a different extent . the most obvious choice of the source from which information will be retrieved is the one which returns most ( or all ) of the relevant request . in that case , the user will have to keep track of which source has the most relevant information . ( ii ) the acceptance of providers ' service descriptions : to enable the dynamic discovery of services , a mechanism is required to describe the capability aspects of services , such as the functional description of a service , the conditions and the constraints of the service , and the nature of the results . ( iii ) receiving services ' requests : to enable requesters to define and describe the required parameters that are needed to represent a request . ( iv ) interaction : brokers may engage ( on behalf of requesters ) in the process of negotiation with various service providers to serve a request . the interaction requires a set of agreed messages , rules for actions based upon reception of various messages . ( v ) communication : the communication capability allows the entities to exchange messages with the other elements of the environment , including users , agents , and objects . in order to perform their tasks , these entities need to depend heavily on expressive communication with others not only to perform requests , but also to propagate their capabilities , advertise their own services , and explicitly delegate tasks or requests for assistance . developing the brokering services comprises the automation of privacy to enhance the overall security of the system and accordingly entities should be able to define the desired degree of privacy . in fact , the brokering service permits entities to participate in the environment with different roles , and hence be capable of automating their privacy concerns and select a particular privacy . the challenge here is how to architect a service that could provide means and mechanisms by which entities would be able to interact with each other and determine any privacy degree that suits a particular situation . such interaction is characterized by the nondeterministic aspect in addition to the dynamic nature of the environment , where these entities exist and operate for which they require to be able to change configurations to participate in different roles . we strongly believe that agent orientation is an appropriate design paradigm for providing coordination services and mechanisms in such settings . indeed , such a paradigm is essential to modeling open , distributed , and heterogeneous environments in which an agent should be able to operate as a part of a community of cooperatively distributed systems environments , including human users . a key aspect of agent orientation is the ability to design artifacts that are able to perceive , reason , interact , and act in a coordinated fashion . here , we view agent orientation as a metaphorical conceptualization tool at a high level of abstraction ( knowledge level ) that captures supports and implements features that are useful for distributed computation in open environments . these features include cooperation , coordination , interaction , as well as intelligence , adaptability , economic and logical rationalities . we define an agent as an individual collection of primitive components that provide a focused and cohesive set of capabilities . we focus on the notion of agenthood as a metaphorical conceptualization tool at a high level of abstraction ( knowledge level ) that captures supports and implements features that are useful for distributed computation in open environments . architecturally , the brokering service is viewed as a layer of services and is modeled as an agent with a specific architecture and interaction protocol that are appropriate to carry the required privacy degree . the challenge in this context is how to architect the brokering layer with the appropriate set of services that enable cooperation across the different degrees of privacy . the interaction protocols represent both the message communication and the corresponding constraints on the content of messages . they describe the sequence of messages among agents , and illustrate various protocols that satisfy a desired privacy requirement . the focus for designing these patterns is to provide a mechanism to reduce the costs and risks that might be a result of violating privacy requirements . the patterns provide mechanisms allowing users ( human / agents ) to adjust the privacy attributes , and allowing these users to achieve and accomplish their tasks in addition to protecting their desired privacy attributes . the agent interaction requires a set of agreed messages , rules and assumption of communication channels . these rules and constraints can be abstracted as agents ' patterns that define various protocols for every possible privacy requirement . using these protocols , agents would be able to protect the privacy aspects of the most concern . from the privacy standpoint , the brokering services are categorized into different roles that are classified according to the participants ' ( providers and requesters ) desired degree of privacy . these degrees of privacy control the proper interaction patterns and will vary from a specific scenario to another . the brokering layer takes in consideration the protection of any privacy desires required by requesters , providers , or both . here , we define the degree of privacy in terms of three attributes : the entity identity , capability , and goals . therefore , an agent can categorize its role under several privacy degrees . formally , an agent can be represented as a 2 - tuple ag ( ra : i d , g ) ; ( pa : i d , cap ) , where ra and pa refer to the agent role as requester and provider while i d , g , and cap , respectively , refer to the agent identity , goals , and capabilities , which might have a null value . for example , an agent might participate with a privacy degree that enables the hiding of its identity as a requester by setting the value of i d to null . tables 1 , 2 summarize the different scenarios and roles that might be played by the brokering layer categorized by the possible privacy concern of the requester ( ra ) and provider ( pa ) agents . the layer permits various entities to participate in the environment with different roles , and hence be capable of automating their privacy concerns and select a particular degree . each layer role is represented as a special broker with a specific architecture and interaction protocol that is appropriate to serve requests from various participants while maintaining the required privacy degree . an agent role is an abstract description of an entity with the specified functionalities . the brokering layer has the ability to interact , solicit help , and delegate services ' requests from other available brokering agents who support different privacy degrees . responsibilities are separated and defined according to the roles played and the required degree of privacy . within the layer two sets of brokering agents are available to service requesters and providers . the first set handles interactions with requesters according to the desired privacy degree that is appropriate to their preferences while the other set supports privacy degrees required by service providers . figure 1 shows a logical view of the brokering services and the relevant entities that are involved in any brokering scenario . every brokering pattern is accomplished by the composition of the requester role , brokering agents , and the provider role , in which the interaction scenarios are produced automatically . a complete brokering session is divided into several stages , starting from requester - to - brokering layer interaction , brokering layer intra - interaction , and broker layer - to - provider interaction . note that in the figure a negation on a specific privacy attribute variable exemplifies that the corresponding privacy attribute is hidden from the environment . the brokering protocols describe a cooperative multibrokering system , which provides the solution for interaction among participants in a dynamic and heterogeneous environment of service providers and requesters . each brokering entity performs basic brokering functionality , such as service discovery , dynamic service composition , and knowledge sharing with the community according to a required privacy degree . a brokering entity within the layerbrokers within the layer might represent a set of services in which providers can advertise their service capability . the brokering protocols regulate and govern service knowledge discovery and sharing of acquired knowledge by defining interaction patterns that are composed of a set of messages that can be exchanged by other brokers within the layer or other registered entities that might benefit of the functionalities supported by the overall brokering service . the architecture permits the brokering agents to have various combinations with other brokering entities which support different privacy degrees . the following section describes the different interaction patterns supported by the brokering layer for entities that might play either a requester or a provider role . it assists service requesters to achieve their goals without exposing their identities to the environment . for example , information about the number of patients who have hepatitis b in a specific city and wanted by a doctor can be assessed by the broker agent without revealing , neither the doctor nor the patients identities . however , agents playing the role of requesters and wanting to benefit from such a service are required to reveal their identities and goals to the relevant broker within the layer . note that each privacy degree is described in terms of two main interactions : an interaction amongst the various brokers within the brokering layer ( intra - interaction ) and the interaction between the domain ( i.e. , a requester or a provider ) with the relevant broker that supports a particular privacy degree ( inter - interaction ) . intra - interactionas shown in figure 2 , the broker might extend the pattern to include interaction with various brokers associated with supporting other privacy degrees of service providers , consequently the broker solicit help and forward request to all available provider - related brokers within the layer incorporating various interaction compositions . note that for every potential composition , the provider - related brokers receive only a notification of a service request , and accordingly carry on its own interaction pattern to satisfy that request without exaggerating , overstressing , or overemphasizing any incurred rights or privileges ( e.g. , cost ) . as shown in figure 2 , the broker might extend the pattern to include interaction with various brokers associated with supporting other privacy degrees of service providers , consequently the broker solicit help and forward request to all available provider - related brokers within the layer incorporating various interaction compositions . note that for every potential composition , the provider - related brokers receive only a notification of a service request , and accordingly carry on its own interaction pattern to satisfy that request without exaggerating , overstressing , or overemphasizing any incurred rights or privileges ( e.g. , cost ) . inter - interactionthe typical interaction pattern for this particular privacy degree comprises that the layer engages in performing the following : ( 1 ) accepting and interpreting service requests from pertinent requesters ; ( 2 ) identifying and contacting a set of available providers , forwarding service requests , and controlling appropriate transactions to fulfill any required service request . these transactions should adhere to agreed appropriate interaction mechanism ( e.g. , auction , negotiation , etc . ) ; ( 3 ) receives result of a service request and delivers it back to the relevant requester . the typical interaction pattern for this particular privacy degree comprises that the layer engages in performing the following : ( 1 ) accepting and interpreting service requests from pertinent requesters ; ( 2 ) identifying and contacting a set of available providers , forwarding service requests , and controlling appropriate transactions to fulfill any required service request . these transactions should adhere to agreed appropriate interaction mechanism ( e.g. , auction , negotiation , etc . ) ; ( 3 ) receives result of a service request and delivers it back to the relevant requester . requesters such as patients with fatal diseases may wish to access services or seek further assistance without revealing their identities . the brokering service dynamically identifies relevant service providers , and acts on behalf of those requesters to fulfill their goal ( s ) . as shown in figure 3 , requesters will be responsible of checking the availability of the service result , which implies that requesters should be aware of a designated result location . system performance is clearly dependent on number of parameters , including the number of providers willing to carry out the request and the time needed by each provider to fulfill that request . intra - interactionas described in the previous case , the broker might extend its pattern to include an interaction composition with various brokers associated with supporting other privacy degrees for service providers . upon receiving a service result , the broker stores the result in a dedicated repository ( result repository ) to be retrieved by the relevant requester . as described in the previous case , the broker might extend its pattern to include an interaction composition with various brokers associated with supporting other privacy degrees for service providers . upon receiving a service result , the broker stores the result in a dedicated repository ( result repository ) to be retrieved by the relevant requester . inter - interactionrequesters may wish to access services or seek further assistance without revealing their identities . the interaction pattern for this particular privacy degree is as follows : ( 1 ) requesters are required to store services requests in a predefined service repository along with preferred parameters . ( 2 ) as shown in figure 3 , requesters are responsible of checking the availability of the service result and hence retrieve it ; this implies that requesters are able to link a service result to their own requests . requesters may wish to access services or seek further assistance without revealing their identities . the interaction pattern for this particular privacy degree is as follows : ( 1 ) requesters are required to store services requests in a predefined service repository along with preferred parameters . ( 2 ) as shown in figure 3 , requesters are responsible of checking the availability of the service result and hence retrieve it ; this implies that requesters are able to link a service result to their own requests . there might be certain situations where requesters prefer to hide their goals from the environment ; the layer functionality entails the forwarding of every advertised service out to every registered requester with unknown preferences or interests . for example , clinician might benefit from variety of service advertisements regarding new medications , tools , medical equipments , and health - related notifications . the brokering service permits these clinicians to check a service repository for further information or to browse other service offerings that have been previously posted and accordingly determine an appropriate and interested service . intra - interactionprovider - related brokers representing providers with known capabilities will have the possibility to advertise existing service offerings to the broker which in turn promotes forwarding every received advertisement to the relevant requester . it is to be noted that whenever a requester decides on a particular service offering , the inter - interaction is not restricted only to contacting those who had offered such services , but might extend to all available provider - related brokers supporting other privacy degrees . for example , the same advertised service offering might be achieved by other providers in the environment who had the interest of hiding their own capabilities . provider - related brokers representing providers with known capabilities will have the possibility to advertise existing service offerings to the broker which in turn promotes forwarding every received advertisement to the relevant requester . it is to be noted that whenever a requester decides on a particular service offering , the inter - interaction is not restricted only to contacting those who had offered such services , but might extend to all available provider - related brokers supporting other privacy degrees . for example , the same advertised service offering might be achieved by other providers in the environment who had the interest of hiding their own capabilities . inter - interactionthey broker permits healthcare requesters to check a service repository for further information or to browse other service offerings that have been previously posted and accordingly determine an appropriate and interested service as shown in figure 4 . once a requester selects a particular service advertisement and forwards that request to the broker , then it is the broker responsibility to determine the most suitable service provider that fulfills that request . upon achieving the requester goal , the broker delivers back the service result to the requester . in an open environment , where many different services providers are in continual increase and with a competitive manner to sell their services , requesters have to determine whether the service advertised to them is of an interest or not . clearly , this process implies that a significant time is required to assess every single - service notification . the broker sends the notifications along with any related parameters required for providing the service ( such as name of the service , cost , and location ) . they broker permits healthcare requesters to check a service repository for further information or to browse other service offerings that have been previously posted and accordingly determine an appropriate and interested service as shown in figure 4 . once a requester selects a particular service advertisement and forwards that request to the broker , then it is the broker responsibility to determine the most suitable service provider that fulfills that request . upon achieving the requester goal , the broker delivers back the service result to the requester . in an open environment , where many different services providers are in continual increase and with a competitive manner to sell their services , requesters have to determine whether the service advertised to them is of an interest or not . clearly , this process implies that a significant time is required to assess every single - service notification . the broker sends the notifications along with any related parameters required for providing the service ( such as name of the service , cost , and location ) . requesters would have the possibility to hide their identities and goals from the entire environment ; as shown in figure 5 , they have the option either to post their want ads to the layer service repository directly , or might check for any services that would be of an interest . for example , patients with narcotic - related problems ( such as drug or alcohol addiction ) can seek services that provide information about rehabilitation centers , specialized psychiatrists , or programs that will help overcoming a particular critical situation without revealing either their identities nor the desired information . inter - interactionrequesters will have the option to either post their want ads to a service repository directly , or might check for any service offerings that would be of an interest . in both cases , requesters will be permitted to store their service requests and retrieve services results . the broker identifies and interprets the required requests , and accordingly will determine the applicable provider which is capable of achieving and fulfilling the requester goal . note that , for this degree of privacy , it is the requester responsibility to check for the availability of the service result , and hence retrieve it . requesters will have the option to either post their want ads to a service repository directly , or might check for any service offerings that would be of an interest . in both cases , requesters will be permitted to store their service requests and retrieve services results . the broker identifies and interprets the required requests , and accordingly will determine the applicable provider which is capable of achieving and fulfilling the requester goal . note that , for this degree of privacy , it is the requester responsibility to check for the availability of the service result , and hence retrieve it . providers with this degree of privacy will have the ability to register their presence along with the capability of the service they offer . although providers with this privacy degree are required to reveal their privacy attributes to the relevant broker , the protocol will suppress any other entity from knowing the provider attributes . intra - interactionthe interaction between the broker and other requester - related brokers is accomplished through sending and receiving messages related to service proposals , service offerings , and services results . the interaction between the broker and other requester - related brokers is accomplished through sending and receiving messages related to service proposals , service offerings , and services results . inter - interactionas shown in figure 6 , a service provider registers itself with the broking service , along with the description of its service capabilities which is stored as an advertisement in a repository maintained by the broker and contains all available service descriptions . assigning requests to providers with known capabilities and identitiescan be based on either broadcasting or focusing , however , the interaction is neither restricted to specific service providers nor committed to a fixed number of them . this ability is particularly useful in which a brokering agent acts in a dynamic environment in which entities may continually enter and leave the society unpredictably . for every received service request , the broker matches the most applicable providers that are appropriate to fulfill that request , and thus maintains a pertinent queue that contains the capable providers along with their identities . as shown in figure 6 , a service provider registers itself with the broking service , along with the description of its service capabilities which is stored as an advertisement in a repository maintained by the broker and contains all available service descriptions . assigning requests to providers with known capabilities and identitiescan be based on either broadcasting or focusing , however , the interaction is neither restricted to specific service providers nor committed to a fixed number of them . this ability is particularly useful in which a brokering agent acts in a dynamic environment in which entities may continually enter and leave the society unpredictably . for everyreceived service request , the broker matches the most applicable providers that are appropriate to fulfill that request , and thus maintains a pertinent queue that contains the capable providers along with their identities . healthcare providers can have the option to hide their identities from the environment and advertise their service offerings to the relevant brokering agent . protection for the core identity prevents service abuses that impact availability of service and hence improving the ability to consistently deliver reliable access . since the service capabilities are known to the broker , service requests that are believed to be fulfilled by such providers will be posted to a dedicated repository for which providers will have the possibility to browse such requests and select whichever of an interest . intra - interactionthe broker interacts with other entities in the layer to engage in receiving and sending messages related to service requests and offerings . the broker task includes ( 1 ) receiving service requests ; ( 2 ) determining whether these requests are within the provider capabilities ; ( 3 ) storing service requests to be browsed by authorized registered providers ( providers hiding identities ) ; ( 4 ) retrieving and delivering back service result . a broker supporting this privacy case will have the ability to advertise registered provider capabilities , and hence engage in various interaction patterns of available requester - related brokers . the broker interacts with other entities in the layer to engage in receiving and sending messages related to service requests and offerings . the broker task includes ( 1 ) receiving service requests ; ( 2 ) determining whether these requests are within the provider capabilities ; ( 3 ) storing service requests to be browsed by authorized registered providers ( providers hiding identities ) ; ( 4 ) retrieving and delivering back service result . a broker supporting this privacy case will have the ability to advertise registered provider capabilities , and hence engage in various interaction patterns of available requester - related brokers . inter - interactiona provider can participate in any interaction mechanism and may respond to call - for - proposal requests by proposing service offerings that are stored in a queue - structured repository . upon assigning and delegating a service request to a provider with this degree of privacy , it is the provider responsibility to store pertinent service result to be retrieved by the broker , and thus delivered to the proper destination as shown in figure 7 . a provider can participate in any interaction mechanism and may respond to call - for - proposal requests by proposing service offerings that are stored in a queue - structured repository . upon assigning and delegating a service request to a provider with this degree of privacy , it is the provider responsibility to store pertinent service result to be retrieved by the broker , and thus delivered to the proper destination as shown in figure 7 . the brokering services allow providers that do not wish to reveal their own capabilities to participate in fulfilling a service request . after receiving a request , the brokering interaction protocol exemplifies the forming out of requests to every registered provider with unknown capability . it is noteworthy that , for every advertised request , providers have to determine whether the request is within their capabilities and / or of an interest . clearly , such an interaction implies that a considerable elapsed time will be spent on evaluating every single request . therefore ( under the assumption of an open dynamic environment ) , providers would be deluged by a variety of service requests , which significantly impact performance and efficiency . intra - interactionthe broker interacts with other entities in the layer to engage in receiving and sending messages related to service requests and offerings . the broker task includes ( 1 ) receiving service requests from requester - related brokers ; ( 2 ) receiving service proposals ; ( 3 ) delivering back service result . the broker interacts with other entities in the layer to engage in receiving and sending messages related to service requests and offerings . the broker task includes ( 1 ) receiving service requests from requester - related brokers ; ( 2 ) receiving service proposals ; ( 3 ) delivering back service result . inter - interactionafter receiving a service request , the broker sends out requests in the form of broadcasting to every registered provider with unknown capabilities . once a provider selects a particular service request , it forwards a service proposal to the broker who controls the remaining transaction according the appropriate negotiation mechanisms similar to what has been described in the former patterns . after receiving a service request , the broker sends out requests in the form of broadcasting to every registered provider with unknown capabilities . once a provider selects a particular service request , it forwards a service proposal to the broker who controls the remaining transaction according the appropriate negotiation mechanisms similar to what has been described in the former patterns . providers will have the ability to browse a special request repository and consequently determine the relevant requests that might be of an interest and within their capabilities . as shown in figure 9 , the broker - provider side agent responds back with the service result ( a result location within the layer has to be identified to the provider upon registration within the brokering layer ) . intra - interactionthe broker intra - interaction comprises the following : ( 1 ) receiving service requests from requester - related brokers ; ( 2 ) storing service requests ; ( 3 ) accessing and evaluating service proposals ; ( 4 ) retrieving and delivering back service result . the broker intra - interaction comprises the following : ( 1 ) receiving service requests from requester - related brokers ; ( 2 ) storing service requests ; ( 3 ) accessing and evaluating service proposals ; ( 4 ) retrieving and delivering back service result . inter - interactionin this protocol , the brokering functionality is mainly seen as a directory service , in which the broker maintains a repository of service requests along with any required preferences . providers will have the ability to browse this repository to determine applicable relevant requests that might be fulfilled . as shown in figure 9 , providers with this degree of privacy have to take in consideration linking the result of the service to the request . in this protocol , the brokering functionality is mainly seen as a directory service , in which the broker maintains a repository of service requests along with any required preferences . providers will have the ability to browse this repository to determine applicable relevant requests that might be fulfilled . as shown in figure 9 , providers with this degree of privacy have to take in consideration linking the result of the service to the request . it is clear that the development of coordination solutions in open and distributed healthcare environments requires a new design paradigm , improved integration architectures and services . a cooperative distributed systems ( cdss ) approach is an ideal and appropriate design paradigm which allows the various healthcare entities to exercise some degree of authority in sharing their information and capabilities . the architecture must describe the organization and the interconnection among the software entities . in this architecture , the environment can be envisioned as a cooperative distributed system ( cds ) comprised of a collection of economically motivated software agents that interact competitively or cooperatively , find and process information , and disseminate it to humans and other agents . it also enables common services that facilitate the coordination and the cooperation activities amongst various domain entities and support ad hoc and automated configurations . in our proposed model , a cdsis conceptualized as a dynamic community of agent and nonagent entities that contribute with different services . based on the above view , an agent might play different roles and be able to coordinate cooperatively or competitively with other agents , including humans . ( i ) service requester : is a domain specific entity that can interact with the environment and request services . ( ii ) service provider : a domain entity that provide application - specific services . ( iii ) brokering entity : is an agent that provides common coordination services , and facilities for the generic cooperative distributed systems environment . the representative agents of domain and brokering entities within the context of healthcare - based cds are built on the foundation of cir - agent architecture with focuses on utilizing the model to capture the participants ' individual behavior toward achieving a desirable goal while maintaining a required privacy degree . the cir - agent is an individual collection of primitive components that provide a focused and cohesive set of capabilities . the basic components include problem - solving , interaction , and communication components , as shown in figure 10 ( b ) . a particular arrangement ( or interconnection ) of componentsthis arrangement reflects the pattern of the agent mental state as related to its reasoning about achieving a goal . however , no specific assumptions need to be made on the detailed design of the agent components . therefore , the internal structure of the components can be designed and implemented using object oriented or another technology , provided that the developer conceptualizes the specified architecture of the agent as described in figure 10 . the knowledge includes the agent self - model , other agents ' model , goals that need to be satisfied , possible solutions generated to satisfy each goal , and the local history of the world that consists of all possible local views for an agent at any given time . the agent knowledge also includes the agent desires , commitments , and intentions toward achieving each goal . the capability package includes the reasoning component ; the domain actions component which contains the possible set of domain actions that when executed , the state of the world will be changed ; the communication component where the agent sends and receives messages to and from other agents and the outside world . the problem solver component represents the particular role of the agent and provides the agent with the capability of reasoning about its knowledge to generate appropriate solutions directed to satisfy its goal . during the interaction processes , the agents engage with each other while resolving problems that are related to different types of interdependencies . the coordination mechanisms are meant to reduce and resolve the problems associated with interdependencies . interdependencies are goal - relevant interrelationships between actions performed by various agents . as argued in , the agent interaction module identifies the type of interdependencies that may exist in a particular domain . consequently , agents select an appropriate interaction device that is suitable to resolve a particular interdependency . ( interaction device is an agent component by which it interacts with the other elements of the environment through a communication device . a device is a piece or a component with software characteristics that is designed to service a special purpose or perform a special function ) . negotiation based includes resource scheduling , conflict resolution , synchronization , and redundancy avoidance devices . contract based includes the assignment device . negotiation based includes resource scheduling , conflict resolution , synchronization , and redundancy avoidance devices . within the context of brokering , the interdependency problem is classified as capability interdependency , and the interaction device is the assignment . the basic characteristics of the assignment device are problem specifications , evaluation parameters , and the subprocesses . the problem specifications might include , for example , the request , the desired satisfying time , and the expiration time . a collection of basic components comprises the structure of the agent model and represents its capabilities . the agents architectures are based on the cir - agent model as shown in figure 11 . a brokering session mainly recognizes two types of agents , namely , domain agent ( requester or provider ) and brokering agent ( reqbroker or provbroker ) . service providers and requesters are modeled as domain agents as shown in figure 12 . the requester agent can participate with various privacy degrees and request services from the brokering layer . a requester delegates the service request ( s ) to the relevant brokering agent according to the interaction protocol of the selected privacy degree . the knowledge includes the model of the brokering agents in terms of the supported privacy degree , self - model , and the local history . the capability is categorized into three components : reasoning that includes problem - solving and coordination , communication , and a set of domain actions . a domain agent playingthe role of a service provider can select the appropriate privacy degree , and thus participate in providing the capability that meets the needs of another domain entity . the problem solver of the domain agent hiding any of the privacy attributes encompasses the accessing of different storage repositories . for example , the problem solver of a requester includes functionalities related to formulating service requests , checks for available service offerings , and accesses various storage repositories to store requests or to retrieve service results . on the other hand , the problem solver of a provider hiding its identity and capability attributes consists of modules related to accessing storage repositories to check for stored service requests that might be fulfilled and hence participating in storing service proposals and service results . the coordination component of a requester comprises the interaction device which entails soliciting service from the relevant reqbroker agent . the interaction device of the provider agent manages the coordination activities which involve proposing services to specific cfp messages and engage in bidding processes . a brokering agent is composed of two components , namely , the knowledge and capability . the knowledge component contains the information in the agent memory about the environment and the expected world . as shown in figure 13 , this includes the agent self - model , models of the domain agents in terms of their roles ( requester / provider ) and / or capabilities , and the local history of the world . the knowledge includes all possible local views for an agent at any given time ( such as the knowledge of physical repositories , available services requests , services offerings , and service results ) . in this section , we show an example of our proposed model applied to healthcare environments to support information - gathering capabilities . we describe the implementation of one pattern associated with an information requester hiding identities and goals and with three information providers ; one is revealing privacy attributes , the second hiding its identity , while third is hiding its own privacy attributes ( identities and capabilities ) . the broker agent ( called reqbroker henceforth ) protects the privacy of requesters , understands the preferences , routes requests , and replies appropriately . all the inter - interactions utilize the fipa contract net protocol as a negotiation mechanism . the three providers offer medical - related information , healthcare guidelines , and clinical diagnosis procedures that can be supplied to various medical students , clinicians , staff , doctors , and physicians in various formats ( online delivery , hard copies , or access to online medical repositories ) . all the three companies decided to register and subscribe to the brokering service and make use of the various privacy degrees . e - virtualmedinfo registered with the brokering service while revealing it privacy attributes , e - virtualdiagnosis comprises diagnosis capabilities jointly derived retired medical doctors and had selected hiding its identity , whereas futuredocassistants , a company that can also provide various online samples of medical exams and virtual evaluation assessments for different medical specialties , decided to hide both the identity and the capabilities . upon registration , a dedicated brokering agent ( provbroker ) alice , a four - year medical student , is conducting a research on the most top fatal diseases in canada , the mortality and death rates of each and the possible diagnosis and prevention procedures that would help a trainee - student in examining and diagnosing patients with such diseases . deciding to hide her own identity , alice anonymously requests this information by posting the required information in special repository dedicated to such privacy degree . after storing the request , alice 's assigned broker ( reqbroker ) interacts with various provbrokers associated with supporting other privacy degrees of service providers ( including the three mentioned companies ) and consequently ( acts as a manager ) issues , and announces a call - for - proposals ( cfps ) to those provbrokers ( act as potential contractors ) informing them of alice 's request specifications ( note that alice 's identity is anonymous to each participant including its own supporting reqbroker ) . the announcement includes task abstraction , a brief description of the required information ; bid specification , a description of the expected format of the information ; expiration time , a specified time interval during which the required information is valid . each provbroker working on behalf of each company contacts the registered company agent and sends the request . note that for the futuredocassistants company , the request is dispatched in special dedicate storing repository allowing its own agent to browse this repository and retrieve the request ( if interested ) . every company ( through its representing agent ) determines the evaluation parameters ( such as information quality , expiration time , and cost ) and accordingly submits a bid along with the offer parameters ( such as quality , cost , and availability ) . the e - virtualmedinfo and e - virtualdiagnosis agents will send the bids directly to their assigned provbrokers , while the futuredocassistants agent stores the bid in a repository that will be retrieved by the relevant provbroker . alice 's dedicated reqbroker receives those bids from every provbroker and carries on the evaluation process and accordingly determines the most bid ( or bids ) that fulfills alice 's request for all the interested , and sends back an acceptance - proposal message to the potential companies ( winners ) and a rejection - message to the bids that do not meet the evaluation parameters . after receiving the information that alice was requesting , the reqbroker stores it in a special repository for which she has a valid access to retrieve it without having to reveal her own identity or being exposed to the identity and the capabilities of the three companies which had participated in fulfilling her requesta web - based prototype of the proposed system has been implemented using jade , an fipa compliant , and java web services development pack ( jwsdp ) platform to support and provide information - gathering capabilities to different participants in healthcare environments , where the accessibility of private information is a desirable feature to various categories of the healthcare personnel , patients , and clinicians . the proposed architecture has been implemented using coordinated intelligent , rational agent ( cir - agent ) . as shown in figure 14 , three relational databases represent various medical data for three distributed locations , each being managed by a dedicated agent that can play both roles of an information requester as well as a provider . upon the required privacy degree and the role desired , the a web interface is available for healthcare participants to select and register their desired privacy degree along with any information capability they might posses ( medical data , patient diagnosis and treatment reports , pharmaceutical data reports , etc . ) . based on the privacy degree required by the both the requester and information provider , a dedicated broker agent within the brokering layer will handle all the interaction required to fulfill an information request . current advances in nowadays technologies coupled with the rapidly evolving healthcare paradigms allow us to foresee novel applications and services for improving the quality of daily life health activities . the increasing demand and dependency on information in healthcare organizations has brought the issues of privacy to every aspect of the healthcare environments . it is expected and with no doubt that medical data such as genome information , medical records , and other critical personal information must be respected and treated with a great concern . as awareness of the threats that organizations face becomes more well understood , the need for additional privacy specifications for open , distributed , and heterogeneous systems grows clear . tremendous efforts have been devoted to privacy and security issues in distributed systems for the last few decades to find technological means of guaranteeing privacy by employing state - of - the - art encryption and anonymization technology . the proposed architecture provides feasible solution to privacy protection in open environments , and presents myriad of additional privacy and security opportunities without negative impact to the utilization of these services . architecturally , the proposed model is viewed as a layer of services , where different roles can be played by the various entities ( requesters , brokers , and providers ) . while existing approaches provide traditional information brokering by incorporating agent - based solutions to make healthcare information more accessible to individuals , the proposed architecture classifies the brokering role into several subroles based on the attributes designated to describe the privacy - desired degree of both the information provider and the information requester . each role is modeled as an agent with a specific architecture and interaction protocol that are appropriate to support a required privacy degree . within the layer , the first set handles interactions with requesters according to the desired privacy degree that is appropriate to their preferences , while the other set supports privacy degrees required by service providers . a brokering pattern is realized by the different roles played by the domain entities and their corresponding brokering agent . a complete brokering scenario is accomplished by performing different levels of interaction , namely , ( 1 ) requester - to - broker interaction , ( 2 ) broker - to - broker interaction , and ( 3 ) broker - to - provider interaction . the proposed layered architecture provides an appropriate separation of responsibilities , allowing developers and programmers to focus on modeling solutions and solving their particular application problems in a manner and semantics most suitable to the local perspective . agent technology has been viewed as one of the key technologies for supporting information brokering in heterogeneous open environments . the use of agent technology provides high degree of decentralization of capabilities , which is the key to system scalability and extensibility . another important aspect of the model is that it treats the privacy as a design issue that has to be taken into consideration in developing healthcare information brokering systems . in healthcare environments , the proposed model provides feasible solution to the problem of information overload and privacy concerns . it enables transparent integration amongst different participants of healthcare cds , and provides querying ability and coordination solutions that enhance the overall connectivity of distributed , autonomous , and possibly heterogeneous information sources ( databases ) of different healthcare sectors . it can efficiently govern different types of health - oriented information and critical medical data such as genetic , hiv , mental health , and pharmacy records from not distributed , disseminated , or abused . based on the level and the amount of information that can be released , patients , clinicians , service providers , and medical staff members can securely translate their privacy policies to an applicable - related privacy case in the proposed model . the proposed approach is innovative in the sense that it treats the privacy as a design issue for information brokering systems , and it supports ad hoc and automated configurations among distributed , possibly autonomous , and heterogeneous entities with various degrees of privacy requirements . the multilayer architecture minimizes the architecture complexity encountered in direct - interaction architectures ( where interactions between agents often take more complex processes for encompassing series of message exchange and forming a single point of failure ) , and makes it less vulnerable to failures . the proposed layered architecture provides an appropriate separation of responsibilities , letting developers and programmers focus on solving their particular application problems in a manner and semantics most suitable to the local perspective .\noutput:\n" }, { "from": "agent", "value": "healthcare industry is facing a major reform at all levels locally , regionally , nationally , and internationally . healthcare services and systems become very complex and comprise of a vast number of components ( software systems , doctors , patients , etc . ) that are characterized by shared , distributed and heterogeneous information sources with varieties of clinical and other settings . the challenge now faced with decision making , and management of care is to operate effectively in order to meet the information needs of healthcare personnel . currently , researchers , developers , and systems engineers are working toward achieving better efficiency and quality of service in various sectors of healthcare , such as hospital management , patient care , and treatment . this paper presents a novel information brokering architecture that supports privacy - based information gathering in healthcare . architecturally , the brokering is viewed as a layer of services where a brokering service is modeled as an agent with a specific architecture and interaction protocol that are appropriate to serve various requests . within the context of brokering , we model privacy in terms of the entities ability to hide or reveal information related to its identities , requests , and / or capabilities . a prototype of the proposed architecture has been implemented to support information - gathering capabilities in healthcare environments using fipa - complaint platform jade ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: nuclear medicine is a branch of medical imaging that uses small amounts of radioactive material to diagnose and determine the severity of or treat a variety of diseases , including many types of cancers , heart disease , gastrointestinal , endocrine , neurological disorders and other disorders . given the ability of nuclear medicine procedures to pinpoint molecular activity within the body , it has a potential role in an early diagnosis as well as patient 's immediate response to therapeutic interventions . pet and ct are established imaging modalities that have been validated and extensively utilized in routine clinical practice . integrated pet / ct combines pet and ct in a single imaging device and allows morphological and functional imaging to be carried out in a single sitting . at the same time , there is greater awareness that the quantitative features of pet may have a major impact in oncology trials and clinical practice . in some developing countries ( with middle - income economies ) , where there has not been a reference unit cost and / or standard hospital costing system for medical services , individual hospitals conduct cost analysis employing different methods . the adoption of different methodologies results in non uniform cost outcomes , which can not be compared or utilized by other organizations . the information on unit costs of medical services is needed for performance based budgeting systems and financing methods of different types of insurance schemes . the public sector , especially in developing nations , has suffered from poor accounting and management systems for quite long time . in hospitals , there is a need for better cost management systems arising from efficiency problems and lack of resources . the cost associated with the provisioning of pet services depends on the unit costs of the resources consumed . pet / ct scan services are one of the major capital intensive and revenue - generating centres of a hospital . imaging technology represents a sizeable investment of resources in the hospital leading to an increase in the patient care costs . with the advancement of new technology and with more sophisticated tests and procedures , it is important to understand the utilization of resources , to bring cost consciousness and rational use of resources . hence , it becomes imperative to study various cost centres and costs involved in the delivery of pet / ct scan services . there are limited , if any , studies with regard to costing of pet / ct scan facility in india . aiims , being an apex healthcare institute in the country , it is essential that the costing of radio - imaging service is done as calculating the unit cost of services . this study aims to determine the cost of providing pet / ct scan services in a hospital . this study will help in understanding the resource consumption pattern , which can guide for future allocations / redistribution of allocations as well as for reviewing the policy guidelines on budgeting of the centres . further cost analysis of establishing new pet / ct scan services will facilitate better value of the services as well as bench mark for replicating developmental activities in the future elsewhere . this study was carried out in the department of nuclear medicine at a tertiary apex referral hospital in new delhi , india from june 2014 to july 2015 . the traditional ( syn - average or gross ) costing methodology was used to arrive at the unit cost of pet scan from the providers perspective for the year 2014 - 15 . equipment not related to cyclotron ( spect / ct , gamma camera and gallium module ) , land cost ( donated by government of india ) , insignificant cost attributable towards provisioning of supportive services that is cssd , laundry , and medical records departments were not included in the study . to arrive at the annualized cost of the capital assets , replacement cost was calculated by multiplying procurement cost with cost inflation multiplication factor ( cost inflation index for 2014 - 2015 / cost inflation index of procurement year ) . thereafter , the annualized method of depreciation was applied to arrive at the annual cost by dividing replacement cost of the asset in the year 2014 - 15 by the annualization factor . the formula for calculating the annualization factor is ( 1 / r ) [ 1 - 1 / ( 1 + r ) n ] where : r is the real interest rate , which is calculated by the following formula : [ ( 1 + nominal interest rate ) / ( 1 + annual inflation ) - 1 ] nominal interest rate is the prevailing national bank savings rate for the year 2014 . n is the number of years of life years ,10 years ( 15 years ) for building , and machinery and equipment ( fixed ) , respectively . following the above - mentioned methodology , equipment cost was calculated . similarly , annualized equipment cost was calculated for pet / ct scan services and same was obtained for furniture and fixtures . equipments which were only dedicated for pet / ct scan facility was taken into account . for building , furniture and fixed machineries , straight line method of depreciation was applied . building cost was calculated using central public works department ( a central agency prescribing the construction rates ) manual plinth area rate . unstructured interviews were held with the hospital staff of nuclear medicine department for pet / ct scan facility , and departmental records were also studied to gain an insight into the functioning of pet / ct scan services . it was done to calculate the time devoted by various categories of staff to apportion their salaries . to calculate floor area of nuclear medicine department , records from the engineering department were studied . the cost of consumables was taken for a period of 1 year to account for the fluctuation in consumption . it was assumed that consumables indented by the staff in the year of study were consumed in the same year . actual quantity as per indent book was considered and the cost of the same was taken from different rate contracts of the hospital . electricity cost was derived by recording total number of equipment and machineries dedicated for pet / ct scan facility , and per day consumption was calculated which was later on multiplied by per unit cost to derive the annual cost of electricity consumption . the proportion of ot terminal manifold units to the total terminal units of medical gases , compressed air and vacuum was used as an apportioning criterion for various costs ( capital and operating cost ) . the cost was also calculated to set up a new pet facility with the cost was also calculated to set up a new pet facility with ( model 1 ) and without ( model 2 ) cyclotron . for this , cost references were taken from aiims cost centres including capital cost and operating cost for 5 years . similar method of depreciations were taken into account and for model 2 , total area and total furniture / fixtures were assumed to be 50 % of model 1 facility and the cost for cyclotron and chemistry models were excluded in this facility . unstructured interviews were held with the hospital staff of nuclear medicine department for pet / ct scan facility , and departmental records were also studied to gain an insight into the functioning of pet / ct scan services . it was done to calculate the time devoted by various categories of staff to apportion their salaries . the actual salary of employees was taken from the accounts section . to calculate floor area of nuclear medicine department , the cost of consumables was taken for a period of 1 year to account for the fluctuation in consumption . it was assumed that consumables indented by the staff in the year of study were consumed in the same year . actual quantity as per indent book was considered and the cost of the same was taken from different rate contracts of the hospital . electricity cost was derived by recording total number of equipment and machineries dedicated for pet / ct scan facility , and per day consumption was calculated which was later on multiplied by per unit cost to derive the annual cost of electricity consumption . the proportion of ot terminal manifold units to the total terminal units of medical gases , compressed air and vacuum was used as an apportioning criterion for various costs ( capital and operating cost ) . the cost was also calculated to set up a new pet facility with the cost was also calculated to set up a new pet facility with ( model 1 ) and without ( model 2 ) cyclotron . for this , cost references were taken from aiims cost centres including capital cost and operating cost for 5 years . similar method of depreciations were taken into account and for model 2 , total area and total furniture / fixtures were assumed to be 50 % of model 1 facility and the cost for cyclotron and chemistry models were excluded in this facility . this leading apex tertiary referral hospital in new delhi was established as an institution of national importance by an act of parliament . it 's objectives were to develop patterns of teaching in undergraduate and post - graduate medical education in all its branches so as to demonstrate a high standard of medical education in india ; to bring together in one place educational facilities of the highest order for the training of personnel in all important branches of health activity ; and to attain self - sufficiency in post - graduate medical education . pet / ct scan facility is located at ground floor of hospital and was started in year the 2005 . it is spread over an area of 200 square meters and has one cyclotron , one chemistry module with 2 pet / ct scanner to provide diagnostic facility . the centre also acts as a referral hospital for delhi national capital region and neighbouring states , where patients are sent by regional public hospitals for the diagnosis of various diseases including oncology , cardiology , gastroenterology , and neurological disease . a total of 6785 pet / ct scans were performed in the nuclear medicine department in the year 2014 - 15 [ table 3 ] . on an average , daily 30 pet / ct scans were performed in a year , and cost estimates were calculated for the financial year 2014 - 15 . the annualization factor for capital assets was calculated to be 8.3 and 19.60 for equipments and cyclotron , respectively . for building , fixed machineries , furniture / fixtures , straight line depreciation method was used assuming useful life year 100 , 15 and 5 respectively . cost summary of pet / ct scan facility at nuclear medicine department , aiimspet / ct scan census for year 2014/15 at aiims , new delhi depreciated pet / ct scan facility building cost and engineering maintenance cost for 2014 - 15 was calculated to be inr 96,904 ( $ 1,514 ) and inr 1,020,800 ( $ 15,950 ) , respectively [ table 2 ] . total annualized cost of pet / ct scan facility equipment was calculated to be inr 49,194,701 ( $ 768,667 ) [ table 2 ] . equipment maintenance cost was not included , as cost of comprehensive annual maintenance / annual maintenance was loaded in the cost of the equipment . depreciated cost for furniture / fixtures for the year 2014 - 15 was calculated to be inr 272,052 ( $ 4,250 ) [ table 2 ] . depreciated hvac cost and its annual operating and maintenance cost was calculated to be inr 140,000 ( $ 2,187 ) and inr 1,100,000 ( $ 17,187 ) , respectively [ table 2 ] . human resource cost of the pet / ct scan facility was calculated to be inr 7,430,667 ( $ 116,104 ) per year . the yearly cost of chemicals and supplies for radioisotopes for the year 2014 - 2015 was found to be inr 2,346,689 ( $ 36,667 ) and for consumables was found to be inr 334,978 ( $ 5,234 ) [ table 2 ] . electricity cost for the year 2014 - 15 was calculated to be inr 3,337,400 ( $ 52,147 ) [ table 2 ] . support services cost pet / ct scan facility manifold terminal units are only two and were derived from the per terminal cost , which were derived from the previous study at aiims . the total cost of manifold terminal for 2014 - 2015 was calculated to be inr 37,328 ( $ 583 ) . capital and operating cost was calculated to be inr 49,703,657 ( $ 776619 ) and 15,608,062 ( $ 243875 ) , respectively [ table 2 ] . [ table 2 ] gives the detailed information on the capital and operating cost of the pet / ct scan services . annual cost of providing pet / ct scan services at aiims , new delhi was calculated to be inr 65,311,719 ( $ 1020495 ) . of the total operating room cost , the pet / ct scan facility expenditure mainly comprised of three major components contributing to more than 95 % of the cost that is equipment cost , manpower cost and the cost of electricity [ figure 2 ] . proportion of operating and capital cost of pet / ct scan at aiims cost breakdown of pet / ct scan facility unit cost was derived using formula : total number of pet / ct scan done in study period ( july 2014 - june 2015 ) was 6875 . therefore , unit cost of pet / ct was calculated to be inr 9,625.22 ( $ 150 ) for establishment of pet / ct facility with cyclotron ( model 1 ) and pet / ct scan facility without cyclotron ( model 2 ) total cost was calculated to be inr 610,873,517 ( $ 9,544,899 ) and inr 226,745,158 ( $ 3,542,893 ) respectively , where all the cost were derived with reference to pet / ct facility of aiims and operating cost was taken for 5 years . in the public sector , for establishing any new facility in india , it requires projection of operating cost of next 5 years along with the capital cost of establishing it to secure funds from the government under the plan budget . [ table 4 ] and [ table 5 ] provides total capital and operating cost required for establishing model 1 and model 2 facility , respectively [ figure 3 ] and [ figure 4 ] . total cost required for establishment of model 1 pet / ct facility total cost required for establishment of model 2 pet / ct facility total capital and operating cost required for model 1 pet / ct facility total capital and operating cost required for model 2 pet / ct facilitydepreciated pet / ct scan facility building cost and engineering maintenance cost for 2014 - 15 was calculated to be inr 96,904 ( $ 1,514 ) and inr 1,020,800 ( $ 15,950 ) , respectively [ table 2 ] . total annualized cost of pet / ct scan facility equipment was calculated to be inr 49,194,701 ( $ 768,667 ) [ table 2 ] . equipment maintenance cost was not included , as cost of comprehensive annual maintenance / annual maintenance was loaded in the cost of the equipment . depreciated cost for furniture / fixtures for the year 2014 - 15 was calculated to be inr 272,052 ( $ 4,250 ) [ table 2 ] . depreciated hvac cost and its annual operating and maintenance cost was calculated to be inr 140,000 ( $ 2,187 ) and inr 1,100,000 ( $ 17,187 ) , respectively [ table 2 ] . human resource cost of the pet / ct scan facility was calculated to be inr 7,430,667 ( $ 116,104 ) per year . the yearly cost of chemicals and supplies for radioisotopes for the year 2014 - 2015 was found to be inr 2,346,689 ( $ 36,667 ) and for consumables was found to be inr 334,978 ( $ 5,234 ) [ table 2 ] . electricity cost for the year 2014 - 15 was calculated to be inr 3,337,400 ( $ 52,147 ) [ table 2 ] . support services cost pet / ct scan facility manifold terminal units are only two and were derived from the per terminal cost , which were derived from the previous study at aiims . the total cost of manifold terminal for 2014 - 2015 was calculated to be inr 37,328 ( $ 583 ) . capital and operating cost was calculated to be inr 49,703,657 ( $ 776619 ) and 15,608,062 ( $ 243875 ) , respectively [ table 2 ] . [ table 2 ] gives the detailed information on the capital and operating cost of the pet / ct scan services . annual cost of providing pet / ct scan services at aiims , new delhi was calculated to be inr 65,311,719 ( $ 1020495 ) . of the total operating room cost , 76 % is capital cost while 24 % is operating cost [ figure 1 ] . the pet / ct scan facility expenditure mainly comprised of three major components contributing to more than 95 % of the cost that is equipment cost , manpower cost and the cost of electricity [ figure 2 ] . proportion of operating and capital cost of pet / ct scan at aiims cost breakdown of pet / ct scan facility unit cost was derived using formula : total number of pet / ct scan done in study period ( july 2014 - june 2015 ) was 6875 . therefore , unit cost of pet / ct was calculated to be inr 9,625.22 ( $ 150 ) for establishment of pet / ct facility with cyclotron ( model 1 ) and pet / ct scan facility without cyclotron ( model 2 ) total cost was calculated to be inr 610,873,517 ( $ 9,544,899 ) and inr 226,745,158 ( $ 3,542,893 ) respectively , where all the cost were derived with reference to pet / ct facility of aiims and operating cost was taken for 5 years . in the public sector , for establishing any new facility in india , it requires projection of operating cost of next 5 years along with the capital cost of establishing it to secure funds from the government under the plan budget . [ table 4 ] and [ table 5 ] provides total capital and operating cost required for establishing model 1 and model 2 facility , respectively [ figure 3 ] and [ figure 4 ] . total cost required for establishment of model 1 pet / ct facility total cost required for establishment of model 2 pet / ct facility total capital and operating cost required for model 1 pet / ct facility total capital and operating cost required for model 2 pet / ct facilitydepreciated pet / ct scan facility building cost and engineering maintenance cost for 2014 - 15 was calculated to be inr 96,904 ( $ 1,514 ) and inr 1,020,800 ( $ 15,950 ) , respectively [ table 2 ] . total annualized cost of pet / ct scan facility equipment was calculated to be inr 49,194,701 ( $ 768,667 ) [ table 2 ] . equipment maintenance cost was not included , as cost of comprehensive annual maintenance / annual maintenance was loaded in the cost of the equipment . depreciated cost for furniture / fixtures for the year 2014 - 15 was calculated to be inr 272,052 ( $ 4,250 ) [ table 2 ] . depreciated hvac cost and its annual operating and maintenance cost was calculated to be inr 140,000 ( $ 2,187 ) and inr 1,100,000 ( $ 17,187 ) , respectively [ table 2 ] . human resource cost of the pet / ct scan facility was calculated to be inr 7,430,667 ( $ 116,104 ) per year . the yearly cost of chemicals and supplies for radioisotopes for the year 2014 - 2015 was found to be inr 2,346,689 ( $ 36,667 ) and for consumables was found to be inr 334,978 ( $ 5,234 ) [ table 2 ] . electricity cost for the year 2014 - 15 was calculated to be inr 3,337,400 ( $ 52,147 ) [ table 2 ] . support services cost pet / ct scan facility manifold terminal units are only two and were derived from the per terminal cost , which were derived from the previous study at aiims . the total cost of manifold terminal for 2014 - 2015 was calculated to be inr 37,328 ( $ 583 ) . capital and operating cost was calculated to be inr 49,703,657 ( $ 776619 ) and 15,608,062 ( $ 243875 ) , respectively [ table 2 ] . [ table 2 ] gives the detailed information on the capital and operating cost of the pet / ct scan services . annual cost of providing pet / ct scan services at aiims , new delhi was calculated to be inr 65,311,719 ( $ 1020495 ) . of the total operating room cost , 76 % is capital cost while 24 % is operating cost [ figure 1 ] . the pet / ct scan facility expenditure mainly comprised of three major components contributing to more than 95 % of the cost that is equipment cost , manpower cost and the cost of electricity [ figure 2 ] . proportion of operating and capital cost of pet / ct scan at aiims cost breakdown of pet / ct scan facility unit cost was derived using formula : total number of pet / ct scan done in study period ( july 2014 - june 2015 ) was 6875 . therefore , unit cost of pet / ct was calculated to be inr 9,625.22 ( $ 150 ) for establishment of pet / ct facility with cyclotron ( model 1 ) and pet / ct scan facility without cyclotron ( model 2 ) total cost was calculated to be inr 610,873,517 ( $ 9,544,899 ) and inr 226,745,158 ( $ 3,542,893 ) respectively , where all the cost were derived with reference to pet / ct facility of aiims and operating cost was taken for 5 years . in the public sector , for establishing any new facility in india , it requires projection of operating cost of next 5 years along with the capital cost of establishing it to secure funds from the government under the plan budget . [ table 4 ] and [ table 5 ] provides total capital and operating cost required for establishing model 1 and model 2 facility , respectively [ figure 3 ] and [ figure 4 ] . total cost required for establishment of model 1 pet / ct facility total cost required for establishment of model 2 pet / ct facility total capital and operating cost required for model 1 pet / ct facility total capital and operating cost required for model 2 pet / ct facilitylimited studies are done for the cost analysis of pet / ct scan . some studies done in the different parts of the worldeven indicates that the cost of performing pet / ct scan is comparatively less with references to our study . previous study done in iran found that the total cost required to set up a model 1 pet scan facility with average 3000 scan per year is 8.2 million us $ and 3.7 million us $ for model 2 pet / ct scan facility resulting in us $ 300 - us $ 450 per pet scan performed ; where as in our study the cost per pet / ct performed is only $ 150 . the costs for pet and pet / ct are decreasing as number of examination performed are increasing . in germany , costs per examination range between approximately $ 885 - $ 1,474 , the amount for production and delivery of radiopharmaceuticals is approximately $ 265 - $ 383 per scan . similar survey in done in great britain , costs per pet scan were derived to be $ 1,030 - $ 2,109 . in the united states , reimbursement for pet and pet / ct is provided by the medicare program , which reimburses a median amount of $ 952.83 . the amount consists of $ 855.43 for the examination and $ 97.40 for the analysis . these comparison of surveys from different parts of the world even shows that the cost of pet / ct scan in india is relatively low . in india , there has been a tremendous increase in the number of imaging systems since 2004 . majority of the pet / ct scanners and cyclotrons are in the private setup and scanners situated in different locations share the isotope produced from one cyclotron .6000 whereas in private sectors , the cost for a whole body pet / ct scan is rs . the studies in government institutes are higher in number than those done in private centres . in a government institutional setupabout 15 - 25 whole - body studies are done in a day . in the private sectorthe number is 5 - 15 , with eight per day being a good average . various strategies for cost cutting can be applied both in terms of capital cost and operating cost of pet / ct scan , which can even decrease the unit cost of pet / ct scan . in capital cost , cyclotron can be used in cooperative basis with many of the other institute or radioisotopes can be procured in cooperative basis . similarly instead of building a separate facility , it can be incorporated in the same institute following the regulatory and legal formalities . equipments , furniture and supplies can be procured in a bulk to reduce the cost . the strategies for reducing operating cost may involve reducing excessive service levels , utilizing the staffs in optimal level , changing processes through adopting automation , altering timing , periodic equipment and energy audit , and eliminating exceptions . a well planned contract formulation including service contract , composite cost , warranty on spares and turnkey installation are also the strategies for cost cutting . the study was carried out at a government institute ; hence , data availability was one of the major weaknesses of this study . the study considered the major cost centres towards the provisioning of pet / ct scan services . the results of this study also suffer from the disadvantages associated with traditional or average costing methodology . however , in a developing country like india , it is difficult to carry out activity - based costing due to lack of awareness and record keeping issues and accounting methods . this study at a tertiary apex referral centre of india was conducted to gain an insight regarding the amount of resources being dedicated towards the provisioning of pet / ct scan services at one of the apex tertiary care centre in the country . the results of this costing will act as rough estimates for planning for pet / ct scan facility in a similar setting in india and neighbouring countries . a large amount of resources were devoted towards equipment ( 75 % ) followed by manpower cost ( 11 % ) , cost of electricity ( 5 % ) , consumables and supplies ( 4 % ) , engineering maintenance cost ( 3.24 % ) , building , furniture and hvac capital cost ( 0.76 % ) , and manifold cost ( 0.05 % ) . the average number of scan performed in the aiims hospital per day with 2 pet / ct scanners is 30 . the hospital , being a matrix organisation , may require huge resources and time to arrive at the apportioning of the resources not only in terms of equipment and human resources but in other resources as well . land cost was excluded from the study since the land where the nuclear medicine service is located was donated by the government . the cost contributed by the excluded departments would have a minimal insignificant impact on the final outcome of this study . however , this costing of pet / ct facility may be an under - estimation of the real cost .\noutput:\n" }, { "from": "agent", "value": "context : pet / ct scan service is one of the capital intensive and revenue - generating centres of a tertiary care hospital . the cost associated with the provisioning of pet services is dependent upon the unit costs of the resources consumed.aims : the study aims to determine the cost of providing pet / ct scan services in a hospital.methods and material : this descriptive and observational study was conducted in the department of nuclear medicine at a tertiary apex teaching hospital in new delhi , india in the year 2014 - 15 . traditional costing methodology was used for calculating the unit cost of pet / ct scan service . the cost was calculated under two heads that is capital and operating cost . annualized cost of capital assets was calculated using methodology prescribed by who and operating costs was taken on an actual basis.results : average number of pet / ct scan performed in a day is 30 . the annual cost of providing pet / ct scan services was calculated to be 65,311,719 indian rupees ( inr ) ( us $ 1,020,496 ) , while the unit cost of pet scan was calculated to be 9625.92 inr ( us $ 150 ) . 3 / 4th cost was spent on machinery and equipment ( 75.3 % ) followed by healthcare personnel ( 11.37 % ) , electricity ( 5 % ) , consumables and supplies ( 4 % ) engineering maintenance ( 3.24 % ) , building , furniture and hvac capital cost ( 0.76 % ) , and manifold cost ( 0.05 % ) . of the total cost , 76 % was capital cost while the remaining was operating cost.conclusions : total cost for establishing pet / ct scan facility with cyclotron and chemistry module and pet / ct scan without cyclotron and chemistry module was calculated to be inr 610,873,517 ( us $ 9944899 ) and 226,745,158 ( us $ 3542893 ) , respectively . ( us $ 1 = inr 64 )" } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in recent years , several papers have noted important modifications in the epidemiology of sepsis and septic shock . in the usa , the annual incidence of sepsis increased 8.7 % , with sepsis more frequent among non - white people and men . possible reasons for the real increase in the incidence of sepsis include the increased number of immunocompromised patients ; hiv infected patients represent more than 10 % of patients hospitalized in teaching hospitals with severe sepsis and 6 % of patients hospitalized with septic shock . in industrialized countries , the introduction of highly active antiretroviral therapy ( haart ) has significantly reduced the morbidity and mortality associated with hiv infection . the combination of a stable rate of new hiv cases with the longer survival of hiv - infected patients has increased the prevalence of hiv / aids . although the rate of hospital admissions has decreased in the hiv - infected population , the proportion of hospitalized patients admitted to intensive care units ( icus ) did not change or increased . between 1990 and 1996 ( the beginning of haart therapy ) , in - icu mortality [ 6 - 9 ] improved moderately or did not change , but the three - month and long - term outcome of hiv / aids patients admitted to the icu improved dramatically . for example , in the claude - bernard bichat experience , in - icu mortality was 20.6 % in 1990 to 1992 , 27 % in 1995 to 1996 and 25 % in 1998 to 2000 . in contrast , six - month mortality was 49 % in 1990 to 1992 , 38 % in 1995 to 1996 and 30 % in 1998 to 2000 . the unmodified icu prognosis is obviously not related to the absence of improvements in icu care , but is largely due to modifications in the case - mix and attitudes toward the use of icu care . compared to the pre - haart period , two distinct categories of hiv / aids patients are now admitted . the most common of these is a particular subgroup of patients with problems in hiv screening , access to healthcare and compliance with the treatment . these patients are more frequently women , intravenous drug abusers , or foreigners with undiagnosed hiv infection at icu admission and are more likely to be admitted through the emergency room . the second and less common group comprises patients with a known hiv infection who are admitted with frequent non - aids associated admission diagnoses , such as cardiac ( myocardial infarction ) and gastro - intestinal ( bleeding , cirrhosis ) disorders , and drug overdose as well as complications of haart therapy . in this issue of critical care , mrus et al . studied the epidemiology and cost of severe sepsis in hiv infected patients . in a very large cohort of patients hospitalized in six us states in 1999 , they found that patients with hiv / aids had a greater mortality and a lower rate of icu admission compared to other patients with severe sepsis . the major limitation of the study is the use of administrative data to define severe sepsis . the method used has been validated without using individual data and its accuracy could be largely questioned . the use of icd - 9 codes to diagnose infection and organ dysfunction is not sufficiently accurate . moreover , although the definitions of severe sepsis combined infection with organ dysfunction within the same admission , a causal link between organ dysfunction and infection could only be speculated at as no time frames between infection and organ dysfunction were defined . furthermore , confounding factors could have biased the final results . in the mrus et al . admission for surgery could , therefore , act as a confounder in the relationship between icu non - admission and hiv / aids status . similarly , admission type has been associated with hospital mortality of icu patients ( scheduled surgery has a better hospital prognosis than patients admitted for a medical problem or after an emergency surgery ) , but was not taken into account in estimating the relationship between hiv / aids status and hospital mortality . the study was based on a very large database , however , and , if its findings are confirmed , suggests that icu admission of hiv / aids patients is delayed or not accepted and is associated with a poorer prognosis . this would raise important questions about triage policies and / or access to care for hiv - infected patients , even after the dramatic improvement in the prognosis of hiv disease resulting from haart therapy . for a patient to be admitted to the icu , where they should benefit from aggressive therapythe preferred use of palliative care in hiv infected patients seems unlikely , however , except in cases of haart failure and multiresistant viruses , and icu physicians might still be reluctant to admit hiv infected patients to the icu . icu prognosis of immunocompromised , especially cancer patients , improves , however , if patients are admitted early and if supportive techniques such as non - invasive ventilation are begun quickly . as access to care becomes more and more difficult for hiv - aids patients , referrals for icu admission might be delayed , which would subsequently explain the absence of improvement in the icu outcome . the outcome for septic hiv / aids patients should , therefore , be improved in two different ways : the screening of hiv infection in populations who find access to care difficult should be facilitated ; and icu admission of non - palliative care patients should be encompassing and should not be delayed .\noutput:\n" }, { "from": "agent", "value": "severe sepsis is more and more frequent , especially because of an increased rate of immunocompromised patients . despite the improvement in the overall prognosis of hiv / aids patients and the improvement of global icu care , the prognosis of hiv / ads patients hospitalized in icu with severe sepsis remained poor . this situation is partly due to the increased proportion of hiv / aids patients with limited access to health care and to a reluctance of icu physicians in admitting hiv infected patients . however , medical literature suggests that icu prognosis of immunocompromised ( especially cancer ) patients should be largely improved by early icu admission and by an early institution of supportive techniques . this strategy should be used in hiv / aids patients with severe sepsis ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: infantile hemangiomas ( ihs ) are common , benign vascular tumors of infancy , 5060 % of which affect the head and neck area . although usually innocuous and self - limiting , they can cause serious complications such as airway compromise , visual loss , severe anemia , and high - output cardiac failure . till recently , treatment modalities included steroids , bleomycin , vincristine , etc . reported the effect of propranolol in ihs , which provoked a paradigm shift in its management . however , important questions remain unanswered , and doubts exist among clinicians regarding use in neonates and small infants , optimal dose , duration of treatment , monitoring for side effects , resolution rate , and long - term follow - up . we present a 2 - month - old male infant with extensive hemangioma , involving the face , orbit , buccal mucosa , and palate with potential life - threatening complications of airway compromise , aspiration of blood , and loss of vision which we treated with high - dose propranolol under the strict monitoring and had rapid , excellent response with no side effects . a 2 - month - old male infant presented with the complaints of red patch over the entire right side of the face and right side of the palate . the baby was unable to open the right eye due to the involvement of the right upper eyelid and had difficult in breastfeeding due to the involvement of the upper lip . there were no other lesions elsewhere on the body and no associated symptoms of bleeding , airway compromise , or cardiovascular complications . examination revealed a large 10 cm 12 cm bright red hemangioma involving the right hemiface , including the right orbit , the right half of upper lip , [ figure 1 ] and extending intraorally to involve the right buccal mucosa , the right half of uvula and mucosa of right half of hard , and soft palate . ( a and b ) large , bright red hemangioma involving the right hemiface , including the right frontotemporal region , right orbit , right cheek , and right half of the upper lip blood investigations were normal . magnetic resonance imaging showed a t1 - iso , t2 - hyperintense 15 mm 15 mm 15 mm lesion in the extraconal , and conal space of the right orbit with postcontrast intense homogenous enhancement suggestive of low - flow vascular malformation . magnetic resonance - angiogram showed prominent branches of the right middle meningeal and lacrimal branches of the right ophthalmic arteries [ figure 2 ] . ( a ) magnetic resonance imaging showing t1 - iso , t2 - hyperintense 15 mm 15 mm 15 mm lesion ( white arrow ) in extraconal and conal space of right orbit ( b ) magnetic resonance - angiogram showing prominent branches of the right middle meningeal and right ophthalmic arteries ( yellow arrows ) oral propranolol was planned after explaining risks and benefits to the parents . pretreatment evaluation involved a thorough personal and familial history for atopy , asthma , recurrent wheezing , and elaborate clinical examination for multiple hemangiomas , electrocardiography , blood pressure , and blood glucose levels . after hospital admission , propranolol was initiated at 2 mg / kg body - weight / day as a single oral dose with hourly monitoring of heart rate , respiratory rate , and blood pressure . to avoid the potential side effect of hypoglycemia with propranolol , it was administered soon after feeding , and blood glucose was measured after 4 h of the first dose and then 12 hourly for 2 days . rapid response was observed within 48 h evident by the immediate cessation of growth , softening , and fading of erythema [ figure 3 ] . baby was discharged after 48 h with detailed instructions regarding dose , administration after feeds , warning signs ( wheeze , lethargy , etc . , ) , and to bring the child immediately if any of the signs noted . ( a ) response at 48 h evident by cessation of growth , softening , and fading of erythema ( b ) 2 weeks : paleness of lesion and decrease in bulkiness of right upper eyelid ( c ) 2 months : facial and orbital lesions decreased more than 30 % and able to open right eye with ease ( d ) 7 months : complete disappearance of the orbital hemangioma and normal eye movements ( e ) 8.5 months : near - total ( ~ 95 % ) resolution with excellent cosmesis and no residual scarring the baby was followed up in the outpatient clinic for the 1 month on a 2 - weekly basis , then onward at a monthly interval . significant response was noted at 2 weeks with paleness of the lesion and disappearance of about 25 % of the oral lesions . the baby was also able to open the right eye and even feed easily . by 2 month , oral ( palatal and buccal ) lesions completely disappeared with no residual scar while the facial and orbital lesions decreased more than 30 % . at 4 - month follow - up , there was 50 % resolution and at 7 - month , there was complete disappearance of the orbital hemangioma and normal eye movements . at 8.5 months , there is near - total ( ~ 95 % ) resolution with 100 % parental satisfaction , excellent cosmesis , and no residual scarring [ figure 3 ] . gradual tapering and stoppage of propranolol is planned over next 2 months with continued monthly surveillance for 6 more months for any relapse . infantile capillary hemangiomas are benign vascular tumors with typical clinical course , characterized by rapid proliferative phase in early infancy , followed by an involutional phase . female : male ratio is 3:15:1 with higher incidence in prematurity , low birth - weight , placentary anomalies and multiple pregnancies . ihs present as small tumors at birth or first 23 months too , proliferate during 1 year ( most prominent growth during first 46 months ) , and involute over 57 years . as a thumb - rule , 50 % of ihs involute by 5 years , 70 % by 7 years of age , and remainingeven after involution , permanent residues may present as scars , telangiectasia , or redundant skin . while most are innocuous and spontaneously resolving , some ihs can cause major complications such as airway compromise , serious visual loss through induction of strabismic , deprivational , or anisometropic astigmatism , severe anemia , kasabach meritt syndrome , and high - output cardiac failure . feeding difficulties due to oral hemangiomas can lead to poor sucking as was noted in our patient or bleeding during sucking resulting in malnutrition and anemia in infants causing extreme parental anxiety . various pharmacological agents such as steroids ( systemic or intralesional ) , interferon , vincristine , bleomycin , cyclophosphamide , or imiquimod have been used in the treatment of ih with no single uniformly safe and effective treatment . the report about the impressive effect of propranolol in treating ihs provoked a paradigm shift in their management with several reports since then . one explanation is the induction of vasoconstriction , which is immediately visible as a change in color , and palpable softening of the hemangioma . beta - blockers could also influence signal - transduction - pathway of angiogenic factors ( basic fibroblast - growth - factor , vascular - endothelial - growth - factor , thereby effecting the proliferative phase . propranolol 's ability to trigger apoptosis in capillary endothelial cells in rat lung tissue might also be applicable to hemangioma endothelial cells . in a large systematic review of ihs treated with propranolol , marqueling et al . reported the most common adverse events as changes in sleep and acrocyanosis seen in 11.4 % and 5.1 % patients and rare incidence of serious adverse events such as symptomatic hypotension in 0.4 % , hypoglycemia in 0.3 % , and symptomatic bradycardia in 0.08 % patients , respectively . likewise , restless sleep , constipation , and cold extremities were also observed by de graaf et al . but they concluded that side effects such as symptomatic hypoglycemia , hypotension , and bronchial hyperreactivity that needed intervention and / or close monitoring were infrequent and not dose - dependent . xu et al . noted that fluctuations from the normal range of cardiovascular parameters occurred frequently with initiating propranolol , but were clinically asymptomatic . similarly , our patient also did not develop any major or minor side effects despite initiating a relatively higher dose of propranolol . it has also been suggested quite wisely that as propranolol may blunt clinical features of hypoglycemia , it should be avoided in neonates in their 1 week of life when symptomatic hypoglycemia is more likely to develop . reviewed ihs of the airway and concluded that while propranolol was effective in 90 % of the cases , 8.6 % patients were classified as nonresponders . nearly 9.8 % patients relapsed while weaning of propranolol or after discontinuation , and 1.2 % cases appeared resistant to re - initiation of therapy . despite several reports since 2008 , , , even now several doubts exist among clinicians regarding use in neonates and small infants , dosing and duration , monitoring for side effects , and parental counseling . further research should focus on the optimal treatment protocol , optimal dose range , duration of treatment , resolution rate , predictors of relapse , long - term follow - up , and the actual percentage of nonresponders . nevertheless , only a minority of patients with life - threatening situations or severe functional impairment require active medical intervention . administering systemic medication to an infant with a benign condition requires careful consideration and should be advised only by experienced clinicians trained in handling neonates and infants . close monitoring of the babies is required , considering the risk of serious side effects , relapse , and resistance to propranolol . the authors certify that they have obtained all appropriate patient consent forms . in the form the patient ( s ) has / have given his / her / their consent for his / her / their images and other clinical information to be reported in the journal . the patients understand that their names and initials will not be published and due efforts will be made to conceal their identity , but anonymity can not be guaranteed . the authors certify that they have obtained all appropriate patient consent forms . in the form the patient ( s ) has / have given his / her / their consent for his / her / their images and other clinical information to be reported in the journal . the patients understand that their names and initials will not be published and due efforts will be made to conceal their identity , but anonymity can not be guaranteed .\noutput:\n" }, { "from": "agent", "value": "infantile hemangiomas ( ihs ) are common , benign vascular tumors of infancy , with more than half affecting the head and neck region . ihs involving the lips and oral cavity can often present to the oral surgeon and the pedodontist . till date , several doubts exist among clinicians regarding the use of propranolol to treat infantile hemangiomas in neonates and small infants , appropriate dose , treatment duration , side effects , response , and long - term follow - up . we present a 2 - month - old male infant with extensive hemangioma involving the face , orbit , buccal mucosa and palate with feeding difficulties , and risk of life - threatening complications such as airway compromise , aspiration , and visual loss which showed excellent response with high - dose propranolol and had no side effects . we also reviewed literature for the mechanism of action of propranolol and possible minor and serious side effects ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: rapidly rising life expectancy is forcing many of the world s societies to see neurodegenerative diseases as a wider social and economic issue . such diseases have always been devastating for sufferers and their carers , but aging societies are facing a broader burden resulting from the lack of effective treatments . there is hope for disorders such as alzheimer disease ( ad ) , where now we have a good understanding of pathogenesis and novel treatments are on the horizon . however , two neurodegenerative disorders that remain in urgent need of attention , and that mainly but not exclusively affect the aging population , are amyotrophic lateral sclerosis ( als ) and frontotemporal lobar degeneration ( ftld ) . als is the third most common neurodegenerative cause of adult death after ad and parkinson disease ( http://www.statistics.gov.uk/statbase ) and the lifetime risk of dying from als lies between 1/400 and 1/1000 ( boillee et al .2006 ; pasinelli and brown 2006 ) , and in the uk 1 in 400 death certificates is issued for motor neuron diseasethe upper motor neurons that run from the brain into the spinal cord and the lower motor neurons that extend from the spinal cord out to the muscles degenerate , leading inexorably to paralysis and death , typically within 35 years of diagnosis ( boillee et al . ; valdmanis and rouleau 2008 ) . intellect usually remains intact and no effective treatments are available . up to approximately 10 % of alsis familial ( fals ) , usually autosomal dominant , and mutations in the ubiquitously expressed enzyme superoxide dismutase 1 ( sod1 ) are causative in less than 20 % of fals ( deng et al .1993 ) and in approximately 1 % of sporadic als ( sals ) ( pasinelli and brown 2006 ) . other rare als mutant genes are known , usually associated with variants of als rather than the classic typical midlife onset disease ( boillee et al . 2006 ; pasinelli and brown 2006 ; schymick et al . ftld is the most common cause of presenile ( below 65 years of age ) dementia after ad ( forman et al . affected individuals have a range of characteristic traits that reflect degeneration in the frontal and temporal lobes of the brain the areas that control behavior , emotions , and language . early symptoms typically manifest as language difficulties and inappropriate behavior ( neary et al . 1998 ) . up to 40 % of ftldcausative mutations have been identified in several genes , including those encoding tau ( hutton et al .1998 ; spillantini et al . 1998 ) , charged multivesicular body protein 2b ( chmp2b ) ( skibinski et al . 2005 ) , and progranulin ( grn ) ( baker et al . 2006 ; cruts et al . 2006 ) , and others remain to be found . mutations have also been identified in the valosin - containing protein ( vcp ) gene in inclusion body myopathy associated with paget disease of bone and frontotemporal dementia , in which frontotemporal dementia can be , but is not always , a feature ( watts et al . appear to be different disorders ; however , clinicians have noted for some time that there are overlaps . ftld symptoms are reported in up to 20 % of als cases ( valdmanis and rouleau 2008 ; van deerlin et al .2008 ) and there are other intriguing connections such as families that segregate both disorders ( morita et al .2006 ; valdmanis et al . 2007 ) and imaging studies which show frontal deficits in als patients ( kato et al . 1993 ) . a recent study has shown that progranulin is a modifier of als disease progression ( sleegers et al .2008 ) , although this was not replicated in another study ( pickering - brown et al . importantly , in common with several other neurodegenerative disorders , als and ftld both present with aggregates of misfolded proteins in the cytoplasm and / or nucleus of neurons . ubiquitinated inclusion bodies have been reported in the cytoplasm of neurons of both sals and fals cases and in mutant sod1 transgenic mice that model fals ( for further discussion see boillee et al . ftld is subdivided into two classes based on the content of the inclusion bodies : ( 1 ) those with tau - positive and ubiquitin - negative inclusions ( tauopathies ) and ( 2 ) more common forms with ubiquitinated but tau - negative inclusions known as ftld - u , including pgrn , vcp , and chmp2b mutations ( reviewed in mackenzie and rademakers 2007 ) . als and ftld - u cases both present with cytoplasmic ubiquitin - positive , tau - negative inclusions indicating that there are at least some common pathway ( s ) involved in the pathogenesis of these diseases . research into als and ftld - u was radically redirected by the appearance of a new player in 2006 . in that year , neumann , trojanowski , lee , and colleagues provided a molecular connection between these disorders by finding that a protein called the tar dna - binding protein ( tdp - 43 ) is the major protein in the inclusion bodies in both disorders ( neumann et al .2006 ) , which was quickly confirmed ( arai et al . 2006 ) . some authors now refer to the tdp - 43 inclusion positive types of als and ftld - u as different forms of the same neurodegenerative disorder : tdp - 43 proteinopathy ( cairns et al . 2007 ; kwong et al . 2008 ; winton et al . 2008 ) . tdp - 43 positive inclusions have now also been reported in cases of alzheimer disease , pick disease , dementia with lewy bodies , and other neurodegenerative disorders , and are seen in glia as well as neurons ( amador - ortiz et al . 2007 ; 2008 ; hasegawa et al . 2007 ; higashi et al . 2007 ; nakashima - yasuda et al . 2007tdp - 43 is a 414 - residue , 43 - kda protein , first identified as a binding partner of the tar dna element of the human immunodeficiency virus ( ou et al .1995 ) . currently we know that tdp - 43 is a ubiquitously expressed , highly conserved nuclear protein encoded by a 6 - exon gene ( tardbp on human chromosome 1p36 .2 ) . the protein consists of two rna recognition motifs and a glycine - rich domain ( fig . 1 ) . it is found in nuclear bodies , colocalized with smn and gemin proteins , and may function as a transcriptional repressor and as an activator of exon skipping , or in other roles such as in mirna biogenesis , apoptosis , and cell division ( ayala et al .2008 ) . in the tdp - 43 proteinopathies tdp - 43 is depleted from the nucleus and is sequestered as hyperphosphorylated insoluble aggregates in the nucleus , perikarya , and dystrophic neurites ( neumann et al . perturbation of the trafficking of tdp - 43 between the nucleus and cytoplasm is thought to lead to the formation of these aggregates ; brain samples from both als and ftld - u are enriched for a smaller ( 25 kda ) phosphorylated c - terminal fragment and high - molecular - weight ubiquitinated species ( neumann et al . inhibition of autophagy can also lead to the relocalization of tdp - 43 from the nucleus to the cytoplasm in vitro ( filimonenko et al . tdp - 43 is encoded by a 6 - exon gene , of which exons 2 - 6 are protein coding ( top ) . the tdp - 43 protein contains four known functional domains : a nuclear localization sequence , two central rna recognition motifs ( rrm1 and rrm2 ) , and a c - terminal glycine - rich domain , predicted to mediate protein - protein interactions . all disease mutations so far are found in the glycine - rich domain ( encoded by exon 6 ) , with the exception of one mutation in rrm1 ( encoded by exon 4 ) . a mutation in the nuclear localization domain has been reported in two unaffected controls ( data compiled from gitcho et al . tdp - 43 is encoded by a 6 - exon gene , of which exons 2 - 6 are protein coding ( top ) . the tdp - 43 protein contains four known functional domains : a nuclear localization sequence , two central rna recognition motifs ( rrm1 and rrm2 ) , and a c - terminal glycine - rich domain , predicted to mediate protein - protein interactions . all disease mutations so far are found in the glycine - rich domain ( encoded by exon 6 ) , with the exception of one mutation in rrm1 ( encoded by exon 4 ) . a mutation in the nuclear localization domain has been reported in two unaffected controls ( data compiled from gitcho et al .2008 ) intriguingly , while tdp - 43 is deposited in sporadic and familial ftld - u and in sporadic and non - sod1 familial als ( kwong et al . 2008 ; neumann et al .2006 ) , it is not found in inclusions in sod1 fals ( mackenzie et al .2007 ; tan et al . 2007 ) or in the sod1 , sod1 , and sod1 transgenic mouse models of fals ( robertson et al . the identification of tdp - 43 in als and ftld - u inclusion bodies immediately led to surveys of patient cohorts to find either association with or mutations in the gene .2007 ; rollinson et al . 2007 ; schumacher et al . 2007 ) , leading to the reasonable conclusion that tdp - 43 deposition may simply be a consequence of disease and therefore possibly of less interest in providing novel insight into the cause of these diseases . however , in 2008 all this has changed with the publication of five articles , all of which report rare tdp - 43 mutations in sporadic and familial als in patients of different ethnicities ( mainly but not exclusively caucasian ) ( gitcho et al .2008 ) . in summary ( fig . 1 , table 1 ) , the fals cases are autosomal dominant with some variability in presentation , bulbar and limb onset cases , some with more or less lower motor neuron loss and different ages of onset and rates of progression , but all fairly classic fals . ( 2008 ) report apathy , major anxiety , and agitation in two individuals . for cases in which postmortems have been carried out , tdp - 43 deposition has been found in the brains of affected individuals ( van deerlin et al . table 1novel mutations in the gene encoding tdp - 43sals = sporadic amyotrophic lateral sclerosis ; fals = familial amyotrophic lateral sclerosis ; mnd = motor neuron disease ; grn = progranulin ; sod1 = cu / zn superoxide dismutase 1 ; mapt = microtubule - associated protein tau ; chmp2b = chromatin modifying protein 2b ; vapb = synaptobrevin - associated membrane protein b ; ang = angiogenin ; dctn1 = dynactin.each mutation is absent in the control group . fourteen missense mutations lie in the glycine - rich domain of the protein encoded by exon 6 of tardbp and one mutation lies in the first rna binding domain ( d169g ) mean age of onset , ftld and related disorders , see text for details , all exons sequenced , only the specific variants were analyzed , full sequencing was not performed , only exon 6 sequenced , method of detection not described , mutation found in familial als , or individuals with no known family history of als novel mutations in the gene encoding tdp - 43 sals = sporadic amyotrophic lateral sclerosis ; fals = familial amyotrophic lateral sclerosis ; mnd = motor neuron disease ; grn = progranulin ; sod1 = cu / zn superoxide dismutase 1 ; mapt = microtubule - associated protein tau ; chmp2b = chromatin modifying protein 2b ; vapb = synaptobrevin - associated membrane protein b ; ang = angiogenin ; dctn1 = dynactin . fourteen missense mutations lie in the glycine - rich domain of the protein encoded by exon 6 of tardbp and one mutation lies in the first rna binding domain ( d169 g ) mean age of onset , ftld and related disorders , see text for details , all exons sequenced , only the specific variants were analyzed , full sequencing was not performed , only exon 6 sequenced , method of detection not described , mutation found in familial als , or individuals with no known family history of als the mutations are already starting to give some insight into pathogenesis ( gitcho et al . most mutations lie in the c - terminal , a glycine - rich region that may mediate interactions with proteins , including heterogeneous ribonucleoproteins . also , some of the mutations found in this region could increase phosphorylation by substituting threonine or serine residues or through the creation of a new protein kinase a site ( sreedharan et al . this may result in disruption of protein interactions and / or disruption of transport through the nuclear pore complex . in transfected cell lines and patient lymphocytes some variants also show a clearly increased propensity to aggregate and to produce a lower - molecular weight , detergent - insoluble protein product ( kabashi et al . one mutation , d169 g , lies in the first rna - binding motif and may affect rna binding ( kabashi et al . when mutant tdp - 43 is electroporated into the neural tube of developing chick embryos , two different mutations showed a reduction in rate of maturation of the neural tube with an increase in apoptotic nuclei , suggesting a toxic gain of function or dominant negative effect ( sreedharan et al . it is noteworthy that just one mutation lies in exon 4 , within the first rna recognition motif ( rrm 1 ) , whereas the other 13 mutations identified so far occur in exon 6 , in the putative protein interaction domain . this raises the question of whether the exon 4 mutation ( d169 g ) is a genuine pathogenic mutation and , if so , if it leads to disease via a different effect on tdp - 43 function than the other mutations .2008 ) and the mutation was absent in 360 ethnically matched controls from france ( kabashi et al .2008 ) , as well as in 872 nonethnically matched controls ( 700 british , 172 australian ) for which all exons of tdp - 43 were sequenced in the study of sreedharan et al . the absence of the mutation in a large number of controls and the evolutionary conservation of the amino acid argue for a pathogenic role ; however , absence in a larger number of ethnically matched controls and functional data or the identification of further mutations in rrm 1 will be required to fully resolve this issue . if d169 g is pathogenic , then it suggests that mutations in the c - terminal domain , and the rrm1 domain , which has been shown to be essential for the rna - binding ability of tdp - 43 ( buratti and baralle .2001 ) , affect the function of tdp - 43 in a similar way , such as a general loss of function , or that there are different ways to disrupt tdp - 43 function and still lead to disease . the identification of the major protein in neurodegenerative disease inclusion bodies , followed by finding rare mutations in the gene encoding this protein , is a powerful route to understanding pathogenesis and is turning into a surprisingly common approach in neurodegenerative diseases . it is exemplified by the classic example of finding mutations in the amyloid precursor protein ( app ) gene that encodes the abeta peptide deposited in the plaques of alzheimer disease ; it revolutionized our understanding of ad ( hardy and selkoe 2002 ) . similar rare dominant single - gene mutations have also been found in the proteins that aggregate in parkinson disease , prion diseases , and tauopathies , for example , also giving us great insight into the pathogenesis of these disorders . the articles that reported on tdp - 43 mutations in als have shifted the focus of attention on this protein from being deposited as a by - product of disease processes to actually being a causative agent that triggers the processes resulting in neuronal death . from this point investigationswill proceed using transgenic and knockout mice and a variety of different cellular systems to understand the link between mutation and disease . many questions need to be addressed , such as does tdp - 43 take on a toxic gain of function when mutated in als , as happens with sod1 mutations in als ? will tdp - 43 mutations be found in cases of ftld - u , and if not , why not ? how important is timing ? does having a germline tdp - 43 mutation give rise to als which might develop into ftld - u if individuals lived long enough ? these two diseases are very similar at a clinical level , but clearly different pathways are affected for at least some of the pathogenesis . we assume that there are many parallel cellular pathways , which , if disrupted can lead to the same outcome . the new mutations found in tdp - 43 are a breakthrough for als and ftld - u research and we are looking forward to seeing what new discoveries they herald to help us treat and ultimately cure these terrible neurodegenerative diseases .\noutput:\n" }, { "from": "agent", "value": "in 2006 the protein tdp - 43 was identified as the major ubiquitinated component deposited in the inclusion bodies found in two human neurodegenerative diseases , amyotrophic lateral sclerosis and frontotemporal lobar degeneration . the pathogenesis of both disorders is unclear , although they are related by having some overlap of symptoms and now by the shared histopathology of tdp - 43 deposition . now , in 2008 , several papers have been published in quick succession describing mutations in the tdp - 43 gene , showing they can be a primary cause of amyotrophic lateral sclerosis . there are many precedents in neurodegenerative disease in which rare single - gene mutations have given great insight into understanding disease processes , which is why the tdp - 43 mutations are potentially very important ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: acute lymphoblastic leukemia ( all ) is a heterogeneous group of malignancies of committed precursor lymphoid cells characterized by the clonal proliferation of t - cell or b - cell lineage lymphoblasts . all is primarily a disease of children , with a peak incidence of 7.7 per 100,000 between the ages of one and 4 years . sixty percent of all cases are diagnosed before 20 years of age .1 while the rate begins to decline after the first decade of life , the incidence increases again in the fifth decade of life , with a smaller peak observed in patients older than 85 years .2 in adults , approximately 30 % of all cases are associated with a biologically and clinically distinct variant characterized by the philadelphia chromosome , a reciprocal translocation between chromosomes 9 and 22 , designated as t ( 9 ; 22 ) ( q34 ; q11 .2 ) , which results in a constitutively active fusion tyrosine kinase protein , bcr - abl .3,4 in contrast with children with all , the prognosis for adults diagnosed with all remains poor .2,57 compared with children with all , in whom long - term survival approaches 90 % ,8 the leukemia - free survival of adults with all ranges from 30 % to 40 % in large series with 37 years of follow - up .911 despite an initial complete remission rate of up to 90 % following induction chemotherapy , a majority of adults will relapse and die of all .9,12,13 the high rate of relapse in adults with all as compared with children likely relates to many factors , including decreased response to regimens less toxic than pediatric induction chemotherapy regimens .1416 for patients who relapse after initial induction chemotherapy , allogeneic hematopoietic stem cell transplantation ( hsct ) remains the best treatment option , although only a minority of patients makes it to transplant due to disease resistance , toxicity of salvage therapy , and comorbidities .7 however , in such patients , achievement of a second complete remission is a priority for optimal long - term outcome following allogeneic transplantation . currently , there is no uniformly accepted standard salvage treatment for relapsed all , and novel therapies to improve outcome without increasing toxicities are required . recently , there has been growing interest in liposome - encapsulated drugs for delivery of more efficacious treatment with less toxicity . the clinical utility of most conventional chemotherapeutics is limited either by the inability to deliver therapeutic drug concentrations to the target tissues or by severe and harmful toxic effects on normal organs and tissues .17 liposome - encapsulated drugs represent a potential way to overcome these limitations . liposomes are small , spherical , and enclosed compartments separating an aqueous medium from another biphospholipid bilayer .17 figure 1 illustrates how drugs can be packaged for delivery to target tissues within a liposome . liposomes were first discovered by the british hematologist , alec bangham ,18 and the first liposomal pharmaceutical product , liposomal doxorubicin ( doxil , johnson & johnson , brunswick , nj , usa ) , received united states food and drug administration ( fda ) approval in 1995 for the treatment of chemotherapy - refractory acquired immune deficiency syndrome - related kaposi s sarcoma .17 doxil is currently approved for use in recurrent ovarian cancer and in relapsed or refractory multiple myeloma . given the activity of liposome - encapsulated doxorubicin and other drugs ,17 investigators have looked at additional drugs with activity in all that could also be encapsulated . vincristine , like the other vinca alkaloids , is very active against many of the lymphoid malignancies , including aggressive non - hodgkin s lymphoma and all .19 in adults with all , vincristine remains an integral component of induction chemotherapy regimens .2023 vincristine acts by binding to tubulin during active mitosis , resulting in microtubule depolymerization and metaphase arrest , leading to apoptosis .24,25 however , vincristine also binds to neuronal tubulin , disrupts axonal microtubules , and thus causes severe neurotoxicity , which has led to the clinical practice of capping the total dose of vincristine to 2.0 mg regardless of body surface area , potentially reducing clinical efficacy . the high affinity of vincristine to both mitotic and neuronal microtubules suggests that it may be difficult to prevent neurotoxicity without reducing clinical efficacy .26 the dosing limitations of vincristine have led researchers to investigate the use of liposomes to deliver vincristine with an increased half - life of the drug while decreasing toxicity . liposome - encapsulated vincristine appears to be less neurotoxic in animal models as well as in humans .26 this review discusses current therapies for relapsed philadelphia chromosome - negative all , focusing on liposome - encapsulated vincristine as a novel approach to a potentially more efficacious and safer means of delivering the drug . from a therapeutic perspective , it is useful to subclassify all according to the presence or absence of the philadelphia chromosome . while philadelphia chromosome - positive all is associated with a poor prognosis , the use of molecularly targeted therapy with imatinib or other tyrosine kinase inhibitors , in combination with chemotherapy , has improved the outcome of this disease variant .2831 currently , there are no similar molecularly targeted agents approved for the treatment of philadelphia chromosome - negative all variants . allogeneic hsct may improve the survival of adults when performed in first complete remission ,32 and remains the best curative modality for patients with relapsed disease .3335 while the vast majority of adults with all will achieve complete remission with primary induction chemotherapy , most will relapse . the goal of therapy in relapse is to obtain a remission without undue toxicity and to move to allogeneic transplantation as rapidly as possible if the patient is eligible . however , a vast majority of all patients , who are otherwise eligible for transplantation , die shortly after relapsing , and many do not achieve a second complete remission .36 this is emphasized by a study of 609 relapsed patients where the overall survival at 5 years was only 7 % ,12 highlighting the need for improved treatment of relapsed disease . currently , there is no uniformly accepted standard of care for relapse , and outcomes with salvage chemotherapy for adults with relapsed or refractory all have traditionally been poor .5 multiple salvage chemotherapy regimens are used in relapsed all .37 salvage regimens typically can be grouped according to the backbone drugs in a combination , and include : vincristine , corticosteroids , and anthracycline - based combinations ; asparaginase - based combinations with or without methotrexate ; high - dose cytarabine - based combinations ; and miscellaneous combinations or single agents , including clofarabine and nelarabine ( particularly for t - lineage all ) . currently no survival benefit is apparent with any given chemotherapy approach ,12 with drug resistance being a major limitation to successful treatment . as noted above , while intolerance of adult patients to high - intensity pediatric regimens may be partly responsible for the higher relapse rate , molecular and biological mechanisms of drug resistance continue to be described . recently , activating mutations of the gene nt5c2 , encoding the enzyme cytosolic purine 5 - nucleotidase responsible for inactivating the nucleoside analogs 6 - mercaptopurine and 6 - thioguanine , which are commonly used in all treatment , have been shown to be present in a small proportion of b - lineage and t - lineage all .38,39 in addition , multiple preclinical studies have identified abnormal cellular signaling in leukemia cells as a possible mechanism . for example , the immunoglobulin heavy chain binding protein , bip / hspa5 , a pivotal component of the prosurvival axis of the unfolded protein response signaling network , is abundantly expressed in relapsed b - cell all and has been proposed as a chemotherapy - resistance biomarker .40 a murine model also detailed that obesity might be a factor in resistance , with all cells preferentially migrating to a proposed protective microenvironment within adipose cells .41 a number of phase i and ii clinical trials of novel agents are currently underway to investigate novel targeted therapies for relapsed all to improve outcomes .42,43 an alternative approach is to alter the delivery of drugs known to be efficacious against the disease to enhance drug exposure while minimizing limiting toxicity . use of nanoparticle technology to enhance delivery of vincristine is one such promising therapy in all . vincristine is an important and active drug in first - line therapy of all as well as in the treatment of relapsed disease .44 its administration is generally limited to weekly injections , usually for 2 months or less in most regimens because of severe peripheral neuropathy , including autonomic neuropathy that often leads to intestinal complications . because of its narrow therapeutic index , the maximal antileukemia activity of free vincristine is not realized .24 thus , an approach to increasing the dose intensity of vincristine while decreasing its toxicity through the use of liposome encapsulation technology has been investigated . liposomes are artificially prepared vesicles composed of a lipid bilayer that are used as drug delivery vehicles , and have been shown to enhance the therapeutic activity of a number of anticancer drugs .17,4550 liposomes encapsulate a region of aqueous solution inside a hydrophobic membrane ( figure 1 ) , and can be used to overcome suboptimal pharmaceutical properties of certain drugs , including low solubility , instability , and rapid metabolism , and may reduce systemic toxicity by allowing selective delivery of the drug to the tumor site . the extent of encapsulation of a dissolved aqueous drug , such as vincristine sulfate , and subsequent retention of the drug within the liposome , both in vitro and in vivo , has been shown to depend on the lipid composition of the liposome and on the magnitude of the transmembrane ph gradient .51 multiple lipids have been used to construct liposomes . most utilize a phosphatidylglycerol or phosphatidylcholine base , while some are derived from egg or soy .17 doxil is a pegylated liposome using distearoylphosphatidylethanolamine bound to polyethylene glycol .52 liposomes containing a low ph can be constructed such that dissolved aqueous drugs will be charged in solution , and because the ph naturally neutralizes within the liposome through transmembrane passage of protons , the drug will also be neutralized , allowing it to pass freely through the membrane . appropriately designed liposomes also have the ability to accumulate passively in tissues with fenestrated vasculature ( eg , bone marrow , spleen , liver , lymph nodes , and within solid tumors ) ,53 resulting in enhanced exposure of tumor tissue to drug to a greater extent than can be achieved by administration of free drug . also , retention of the drug in the liposome can increase its duration of exposure to cancer cells , while minimizing the concentration of free drug in the circulation , which can contribute to toxicity .54 the earliest work focused on liposomal encapsulation of anthracyclines ,45,46 eventually leading to approval of liposome - encapsulated doxorubicin ( doxil ) by the fda , and subsequently liposome - encapsulated daunorubicin ( daunoxome , galen pharmaceuticals , craigavon , northern ireland ) . in both cases , the liposomal anthracycline formulation retained the efficacy of the free drug but was associated with reduced toxicity in clinical trials in a variety of cancers ,5558 including all , where the use of liposomal daunorubicin in place of free doxorubicin in the hyper - cvad ( fractionated cyclophosphamide , vincristine , doxorubicin , and dexamethasone ) regimen was well - tolerated in relapsed or refractory all .57 the development of these two drugs helped to establish the paradigm for approval that if a liposomal - encapsulated drug could be shown to be comparable in efficacy to its free counterpart while causing less adverse events , then it could be approved for use . liposomal cytarabine ( depocyt , pacira pharmaceuticals inc , san diego , ca , usa ) is another drug active in all which , after encapsulation , showed improved outcomes when used intrathecally to treat leptomeningeal disease .59 the systemic use of liposomal cytarabine was investigated in a phase i study using a fixed molar ratio formulation of cytarabine and daunorubicin ( cpx - 351 ) in 48 patients with relapsed or refractory acute myeloid leukemia or high - risk myelodysplastic syndrome .60 pharmacokinetic data showed that the intended plasma ratio of 5:1 was maintained at all dose levels , while nearly all of the detectable cytarabine and daunorubicin in the circulation was liposome - encapsulated .61 although not tested in all , a randomized phase ii trial is currently ongoing using cpx - 351 for the treatment of high - risk patients with untreated myelodysplastic syndrome or acute myeloid leukemia , and is attempting to improve the treatment - related mortality rate while at least keeping the complete remission rate constant ( clinicaltrials.gov identifier , nct01804101 ) . these studies continue to support further investigation of drugs active in hematologic malignancies in newly developed liposome - encapsulated versions . vincristine is a vinca alkaloid with activity against a broad range of cancers , including hodgkin s and non - hodgkin s lymphoma , chronic lymphocytic leukemia , all , and a variety of solid tumors . as noted above , vincristine exerts its cytotoxic activity by attaching to the growing end of microtubules and preventing their assembly , arresting cell growth in metaphase . therefore , as a cell - cycle specific cytotoxic drug , prolonging exposure time to the drug is expected to be therapeutically advantageous ; perhaps even more so than prolonged exposure to anthracyclines which do not act in a cell cycle - specific manner . in leukemia cell lines , exposure to vincristine from one to 72 hours resulted in a 10-fold reduction in the drug concentration needed to cause 50 % cytotoxicity ( ic50 ) , compared with only a 40-fold reduction in the ic50 for doxorubicin following prolonged exposure to the same extent .48,51 pharmacokinetic data with free vincristine detailed rapid tissue binding , low serum concentrations after intravenous administration , and extensive tissue distribution in vivo ,62,63 limiting its potential therapeutic efficacy . while continuous intravenous infusion of vincristine has been investigated as a way to increase drug exposure , significant neurotoxicity still occurred .64 furthermore , conventional vincristine is limited by significant peripheral and central nervous system neurotoxicity , which occurs at doses higher than 1.4 mg / m . therefore , it was hypothesized that if liposomal encapsulation and delivery results in higher levels of drug at tumor sites for longer periods of time , greatly improved efficacy may be expected with a cell cycle - specific drug like vincristine ,51 and retention of drug in the liposome would result in lower drug concentrations in tissues where toxicity occurs , including the peripheral and central nervous systems .24 the earliest investigations of liposomal encapsulation of vincristine failed to demonstrate a therapeutic advantage over free vincristine sulfate in murine leukemia models .65 indeed , the low solubility of vincristine in aqueous solution at physiologic ph and its relatively high permeability to membranes , resulting in poor retention of drug in the liposome , initially presented significant limitations to development of a stable liposomal vincristine formulation . subsequent work identified that transmembrane ph gradients , with the inside of the vesicle being acidic , can result in significantly improved trapping of drug in the liposome .6668 furthermore , maintenance of the ph gradient is affected , at least in part , by the lipid composition of the liposome .47 utilizing such transmembrane ph gradient drug uptake processes , almost 100 % trapping of vincristine was achieved inside egg phosphatidylcholine / cholesterol and distearoylphosphatidylcholine ( dspc ) / cholesterol liposomes , when the internal ph of the liposome was lowered to 4.0.47 however , while both dspc / cholesterol and egg phosphatidylcholine / cholesterol preparations had similar vincristine trapping efficiency , the ph gradient across the membrane was significantly more sustained in dspc / cholesterol vesicles with better retention of vincristine in the liposome ,47 resulting in a longer drug circulation time and enhanced tumor delivery and antitumor activity compared with free vincristine .47,48 in murine models of lymphocytic leukemia , the dspc / cholesterol liposome formulation showed greater antitumor efficacy compared with either free vincristine or the egg phosphatidylcholine / cholesterol formulation ,47,48 and the ld50 ( median lethal dose ) was significantly higher with dspc / cholesterol liposome - encapsulated vincristine formulation ( ld504 .8 mg / kg ) compared with free vincristine ( ld501 .9 mg / kg ) , indicating that liposomal encapsulation increased drug delivery with less toxicity .47 the observation that the antitumor efficacy of liposome - encapsulated vincristine increases with liposome circulation time and increased retention of the drug within the liposome after intravenous administration47 ,48,69 led to further attempts at optimizing the liposome formulation . however , because lowering the ph buffer within the liposome to increase the ph gradient and improve vincristine retention resulted in increased acid - catalyzed hydrolysis of the phosphatidylcholine component of the liposome , more chemically stable lipids were investigated .69,70 this led to identification of sphingomyelin / cholesterol liposomes , which were more resistant to acid - mediated hydrolysis , and also had a longer in vivo circulation time compared with dspc / cholesterol liposomes , likely related to lower adsorption of serum proteins to the sphingomyelin / cholesterol liposomes , which contributes to clearance of the liposomes by the mononuclear phagocytic system .70 in mouse leukemia models , it was confirmed that sphingomyelin / cholesterol formulations were significantly more effective at reducing tumor progression than free vincristine or vincristine encapsulated in dspc / cholesterol formulations .70 pharmacokinetic data also confirmed that sphingomyelin / cholesterol liposome - encapsulated vincristine had a longer half - life ( 6.6 hours versus 1.36 hours ) , a higher area under the plasma concentration - time curve ( 213 gh / ml versus 0.59 gh / ml ) , and a smaller volume of distribution ( 2.0 ml versus 145 ml ) compared with free vincristine .54 as indicated in figure 1b , chemically attachment of water - soluble polymers , such as polyethylene glycol , to the lipid polar heads of the liposome has been used to limit removal of liposomes by phagocytic cells in vivo .71,72 however , while the addition of polyethylene glycol to sphingomyelin / cholesterol liposomes increased liposome circulation longevity , it also resulted in significant leakage of vincristine from the liposomes , resulting in no added benefit .70 preclinical models also confirmed that vincristine encapsulated in sphingomyelin / cholesterol liposomes accumulated preferentially at tumor sites , which correlated with antitumor activity .54,70,73 furthermore , this was related to liposomal extravasation into the tumor rather than uptake by tumor cells of free vincristine that had been released from liposomes in the circulation .70 in a murine model with human breast cancer xenografts , sphingomyelin / cholesterol liposome - encapsulated vincristine resulted in targeted delivery of the drug , with a four - fold increase in concentration of drug in tumor tissue and a three - fold increase in bone marrow , with maintenance of significant tissue drug concentrations for several days compared with free vincristine , and without increased toxicity .73 the antitumor efficacy of sphingomyelin / cholesterol liposome - encapsulated vincristine has also been confirmed in several preclinical murine and human tumor xenograft models , representing several cancer types ,54,70,7376 including human all .24 the aggregate of the above studies supports the utility of encapsulating vincristine in sphingomyelin / cholesterol liposomes to increase drug delivery while limiting release in the central blood compartment to decrease drug toxicity . based on the efficacy of liposome - encapsulated vincristine and the decreased toxicity observed in preclinical studies , clinical trials were initiated in humans with solid tumors and relapsed hematologic malignancies . the first open - label , dose - escalation phase i clinical trial of liposomal vincristine was conducted using a dspc / cholesterol liposomal formulation of vincristine sulfate ( onco - tcs ; british columbia cancer agency , vancouver , bc , canada ) in 25 patients with previously treated solid tumors .77 patients were treated with escalating doses of vincristine from 0.5 mg / m to 2.8 mg / m intravenously over 60 minutes every 3 weeks . dose - limiting toxicities , including myalgias , peripheral neuropathy , and constipation , were observed at the highest dose level of 2.8 mg / m . overall grades 34 toxicities observed across all dose levels were constipation ( 12 % ) , fatigue ( 8 % ) , anemia ( 8 % ) , and alopecia ( 8 % ) . one partial response was seen in a patient with pancreatic cancer , and tumor response not meeting partial response criteria was seen in two other patients .77 pharmacokinetic studies , which measured total plasma ( both liposome - entrapped and nonencapsulated ) vincristine concentrations , indicated that plasma elimination of vincristine after injection best fits a two - compartment model , suggesting that this formulation protects vincristine from the early phase of rapid elimination seen with the standard nonencapsulated drug formulation .77,78 in addition , total vincristine plasma concentrations were significantly greater following liposomal administration than described previously following nonencapsulated vincristine injection .77,78 it should be noted , however , that the plasma concentration of free vincristine released from the liposome into the circulation was too low to be quantified . subsequent clinical investigation , including clinical development in all patients , was performed using the optimized liposome formulation , ie , vincristine sulfate liposome for injection ( vsli , marqibo , talon therapeutics inc , san francisco , ca , usa ) . marqibo is a proprietary nanoparticle formulation of vincristine in an aqueous core of sphingomyelin and cholesterol liposomes developed for clinical use . evaluation of vsli in patients with all followed encouraging results in 16 adult patients with relapsed and refractory all who were enrolled on an extension study of a phase ii trial in patients with relapsed , aggressive non - hodgkin s lymphoma .26 eight of these patients had philadelphia chromosome - positive all . patients received vsli 2 mg / m intravenously over 60 minutes every 2 weeks until rapid disease progression or dose - limiting toxicity occurred . of 14 patients evaluable for response , two responded ( one complete remission , one partial response ) and four further patients had transient reduction in bone marrow blasts . toxicity was minimal , although treatment was limited , with only a median two ( range 15 ) doses delivered . two patients developed grade 1 peripheral neuropathy after two and four doses , respectively , and one patient developed grade 3 seizure that was not attributed to vsli .79 the observed antileukemic activity of vsli in this refractory group of patients , and the minimal toxicity observed , warranted further investigation of this agent in relapsed all . to optimize dosing and betterdefine the toxicity of vsli in adult patients with relapsed or refractory all , a multicenter phase i trial was conducted to determine the maximum tolerated dose .80 thirty - six patients of median age 32 years with relapsed or refractory all , all pretreated with conventional vincristine , received at least one dose of vsli . in a 3 + 3 dose - escalation design , five dose levels of intravenous vsli were tested , including 1.5 mg / m , 1.825 mg / m , 2.0 mg / m , 2.25 mg / m , and 2.4 mg / m . vsli was administered weekly , together with dexa methasone ( 40 mg ) on days 14 and 1114 of each 4 - week cycle , with therapy continued until progression or dose - limiting toxicity . the maximum tolerated dose of vsli was 2.25 mg / m based on dose - limiting toxicities of grade 3 motor neuropathy , grade 4 seizure , and grade 4 hepatotoxicity in one patient each at the 2.4 mg / m dose level . the most common toxicities attributed to vsli included peripheral neuropathy ( 55 % ) and constipation ( 53 % ) . seven of 36 ( 19 % ) patients achieved a complete remission based on intent - to - treat analysis , and four of 14 ( 29 % ) patients receiving vsli as their first salvage attempt achieved complete remission . additionally , four of the seven patients who achieved complete remission underwent subsequent allogeneic hsct in remission .80 the results indicated that vsli plus dexamethasone is an effective salvage treatment for patients for relapsed or refractory all , and may be used as a well - tolerated , successful option as abridge to allogeneic transplantation . based on the encouraging activity in the phase i trial , and the clear unmet need of patients with relapsed or refractory all , for whom no accepted standard therapy exists , a multinational , pivotal , single - arm , open - label , phase ii trial of weekly vsli monotherapy was conducted in patients with relapsed and refractory b - cell or t - cell lineage philadelphia chromosome - negative all . the results of this trial have recently been reported ,81 and have served as the basis for accelerated approval of vsli in the us by the fda on august 9 , 2012 . sixty - five adult patients , of median age 31 ( range 1983 ) years , with clinically advanced and heavily pretreated relapsed or refractory all , received intravenous vsli 2.25 mg / m weekly on days 1 , 8 , 11 , and 22 of each 28 - day cycle until disease progression , toxicity , or a decision to pursue other treatment , such as allogeneic hsct , was made . most patients had a large disease burden at the time of study treatment , with median bone marrow or peripheral blood blast content of 82 % , and more than half of the patients had received at least three lines of prior therapy . forty - five percent of the patients were also refractory to their immediate prior line of therapy . after a median of four ( range 118 ) doses of vsli , a complete remission ( or complete remission with incomplete count recovery [ cri ] ) was observed in 20 % of patients , and an additional 15 % achieved a partial response for an overall response rate of 33 % . of note , eight patients who achieved complete remission / cri were also in molecular remission by minimal residual disease assessment . the median duration of complete remission / cri was 23 ( range 566 ) weeks . importantly , 12 of the 13 patients who achieved complete remission / cri were successfully bridged to allogeneic hsct . thirty - seven patients ( 58 % ) experienced at least one grade 3 or 4 treatment - related adverse event . grade 3 peripheral neuropathy occurred in 15 patients , and one patient developed grade 4 neuropathy . other serious adverse events included febrile neutropenia ( 5 % ) , tumor lysis syndrome ( 5 % ) , and constipation ( 3 % ) . the results of the pivotal phase ii trial of vsli monotherapy compare well with other salvage therapies in patients with clinically advanced relapsed or refractory all . unfortunately , no randomized , comparative phase iii trials in this population have been reported . currently , only limited comparisons with small studies of other agents in comparable populations can be made . in a retrospective analysis of a subgroup of 56 patients with clinically advancedrelapsed and refractory philadelphia chromosome - negative all treated with non - vsli single agents , only 4 % achieved complete remission / cri , with 17 of 56 patients dying within 30 days of treatment .5,82 single - agent clofarabine induced complete remission in only one of eight relapsed all patients ( 13 % ) in need of third - line therapy , with all remission being short - lived .83 in a study of the combination of clofarabine plus cytarabine , three of 16 ( 19 % ) all patients in need of third - line or higher treatment achieved complete remission / cri .84 finally , single - agent nelarabine was reported to result in complete remission in five of 28 patients with relapsed or refractory t - cell lineage all or lymphoblastic lymphoma .85 the earliest investigations of liposomal encapsulation of vincristine failed to demonstrate a therapeutic advantage over free vincristine sulfate in murine leukemia models .65 indeed , the low solubility of vincristine in aqueous solution at physiologic ph and its relatively high permeability to membranes , resulting in poor retention of drug in the liposome , initially presented significant limitations to development of a stable liposomal vincristine formulation . subsequent work identified that transmembrane ph gradients , with the inside of the vesicle being acidic , can result in significantly improved trapping of drug in the liposome .6668 furthermore , maintenance of the ph gradient is affected , at least in part , by the lipid composition of the liposome .47 utilizing such transmembrane ph gradient drug uptake processes , almost 100 % trapping of vincristine was achieved inside egg phosphatidylcholine / cholesterol and distearoylphosphatidylcholine ( dspc ) / cholesterol liposomes , when the internal ph of the liposome was lowered to 4.0.47 however , while both dspc / cholesterol and egg phosphatidylcholine / cholesterol preparations had similar vincristine trapping efficiency , the ph gradient across the membrane was significantly more sustained in dspc / cholesterol vesicles with better retention of vincristine in the liposome ,47 resulting in a longer drug circulation time and enhanced tumor delivery and antitumor activity compared with free vincristine .47,48 in murine models of lymphocytic leukemia , the dspc / cholesterol liposome formulation showed greater antitumor efficacy compared with either free vincristine or the egg phosphatidylcholine / cholesterol formulation ,47,48 and the ld50 ( median lethal dose ) was significantly higher with dspc / cholesterol liposome - encapsulated vincristine formulation ( ld504 .8 mg / kg ) compared with free vincristine ( ld501 .9 mg / kg ) , indicating that liposomal encapsulation increased drug delivery with less toxicity .47 the observation that the antitumor efficacy of liposome - encapsulated vincristine increases with liposome circulation time and increased retention of the drug within the liposome after intravenous administration47 ,48,69 led to further attempts at optimizing the liposome formulation . however , because lowering the ph buffer within the liposome to increase the ph gradient and improve vincristine retention resulted in increased acid - catalyzed hydrolysis of the phosphatidylcholine component of the liposome , more chemically stable lipids were investigated .69,70 this led to identification of sphingomyelin / cholesterol liposomes , which were more resistant to acid - mediated hydrolysis , and also had a longer in vivo circulation time compared with dspc / cholesterol liposomes , likely related to lower adsorption of serum proteins to the sphingomyelin / cholesterol liposomes , which contributes to clearance of the liposomes by the mononuclear phagocytic system .70 in mouse leukemia models , it was confirmed that sphingomyelin / cholesterol formulations were significantly more effective at reducing tumor progression than free vincristine or vincristine encapsulated in dspc / cholesterol formulations .70 pharmacokinetic data also confirmed that sphingomyelin / cholesterol liposome - encapsulated vincristine had a longer half - life ( 6.6 hours versus 1.36 hours ) , a higher area under the plasma concentration - time curve ( 213 gh / ml versus 0.59 gh / ml ) , and a smaller volume of distribution ( 2.0 ml versus 145 ml ) compared with free vincristine .54 as indicated in figure 1b , chemically attachment of water - soluble polymers , such as polyethylene glycol , to the lipid polar heads of the liposome has been used to limit removal of liposomes by phagocytic cells in vivo .71,72 however , while the addition of polyethylene glycol to sphingomyelin / cholesterol liposomes increased liposome circulation longevity , it also resulted in significant leakage of vincristine from the liposomes , resulting in no added benefit .70 preclinical models also confirmed that vincristine encapsulated in sphingomyelin / cholesterol liposomes accumulated preferentially at tumor sites , which correlated with antitumor activity .54,70,73 furthermore , this was related to liposomal extravasation into the tumor rather than uptake by tumor cells of free vincristine that had been released from liposomes in the circulation .70 in a murine model with human breast cancer xenografts , sphingomyelin / cholesterol liposome - encapsulated vincristine resulted in targeted delivery of the drug , with a four - fold increase in concentration of drug in tumor tissue and a three - fold increase in bone marrow , with maintenance of significant tissue drug concentrations for several days compared with free vincristine , and without increased toxicity .73 the antitumor efficacy of sphingomyelin / cholesterol liposome - encapsulated vincristine has also been confirmed in several preclinical murine and human tumor xenograft models , representing several cancer types ,54,70,7376 including human all .24 the aggregate of the above studies supports the utility of encapsulating vincristine in sphingomyelin / cholesterol liposomes to increase drug delivery while limiting release in the central blood compartment to decrease drug toxicity . based on the efficacy of liposome - encapsulated vincristine and the decreased toxicity observed in preclinical studies , clinical trials were initiated in humans with solid tumors and relapsed hematologic malignancies . the first open - label , dose - escalation phase i clinical trial of liposomal vincristine was conducted using a dspc / cholesterol liposomal formulation of vincristine sulfate ( onco - tcs ; british columbia cancer agency , vancouver , bc , canada ) in 25 patients with previously treated solid tumors .77 patients were treated with escalating doses of vincristine from 0.5 mg / m to 2.8 mg / m intravenously over 60 minutes every 3 weeks . dose - limiting toxicities , including myalgias , peripheral neuropathy , and constipation , were observed at the highest dose level of 2.8 mg / m . overall grades 34 toxicities observed across all dose levels were constipation ( 12 % ) , fatigue ( 8 % ) , anemia ( 8 % ) , and alopecia ( 8 % ) . one partial response was seen in a patient with pancreatic cancer , and tumor response not meeting partial response criteria was seen in two other patients .77 pharmacokinetic studies , which measured total plasma ( both liposome - entrapped and nonencapsulated ) vincristine concentrations , indicated that plasma elimination of vincristine after injection best fits a two - compartment model , suggesting that this formulation protects vincristine from the early phase of rapid elimination seen with the standard nonencapsulated drug formulation .77,78 in addition , total vincristine plasma concentrations were significantly greater following liposomal administration than described previously following nonencapsulated vincristine injection .77,78 it should be noted , however , that the plasma concentration of free vincristine released from the liposome into the circulation was too low to be quantified . subsequent clinical investigation , including clinical development in all patients , was performed using the optimized liposome formulation , ie , vincristine sulfate liposome for injection ( vsli , marqibo , talon therapeutics inc , san francisco , ca , usa ) . marqibo is a proprietary nanoparticle formulation of vincristine in an aqueous core of sphingomyelin and cholesterol liposomes developed for clinical use . evaluation of vsli in patients with all followed encouraging results in 16 adult patients with relapsed and refractory all who were enrolled on an extension study of a phase ii trial in patients with relapsed , aggressive non - hodgkin s lymphoma .26 eight of these patients had philadelphia chromosome - positive all . patients received vsli 2 mg / m intravenously over 60 minutes every 2 weeks until rapid disease progression or dose - limiting toxicity occurred . of 14 patients evaluable for response , two responded ( one complete remission , one partial response ) and four further patients had transient reduction in bone marrow blasts . toxicity was minimal , although treatment was limited , with only a median two ( range 15 ) doses delivered . two patients developed grade 1 peripheral neuropathy after two and four doses , respectively , and one patient developed grade 3 seizure that was not attributed to vsli .79 the observed antileukemic activity of vsli in this refractory group of patients , and the minimal toxicity observed , warranted further investigation of this agent in relapsed all . to optimize dosing and betterdefine the toxicity of vsli in adult patients with relapsed or refractory all , a multicenter phase i trial was conducted to determine the maximum tolerated dose .80 thirty - six patients of median age 32 years with relapsed or refractory all , all pretreated with conventional vincristine , received at least one dose of vsli . in a 3 + 3 dose - escalation design , five dose levels of intravenous vsliwere tested , including 1.5 mg / m , 1.825 mg / m , 2.0 mg / m , 2.25 mg / m , and 2.4 mg / m . vsli was administered weekly , together with dexa methasone ( 40 mg ) on days 14 and 1114 of each 4 - week cycle , with therapy continued until progression or dose - limiting toxicity . the maximum tolerated dose of vsli was 2.25 mg / m based on dose - limiting toxicities of grade 3 motor neuropathy , grade 4 seizure , and grade 4 hepatotoxicity in one patient each at the 2.4 mg / m dose level . the most common toxicities attributed to vsli included peripheral neuropathy ( 55 % ) and constipation ( 53 % ) . seven of 36 ( 19 % ) patients achieved a complete remission based on intent - to - treat analysis , and four of 14 ( 29 % ) patients receiving vsli as their first salvage attempt achieved complete remission . additionally , four of the seven patients who achieved complete remission underwent subsequent allogeneic hsct in remission .80 the results indicated that vsli plus dexamethasone is an effective salvage treatment for patients for relapsed or refractory all , and may be used as a well - tolerated , successful option as abridge to allogeneic transplantation . based on the encouraging activity in the phase i trial , and the clear unmet need of patients with relapsed or refractory all , for whom no accepted standard therapy exists , a multinational , pivotal , single - arm , open - label , phase ii trial of weekly vsli monotherapy was conducted in patients with relapsed and refractory b - cell or t - cell lineage philadelphia chromosome - negative all . the results of this trial have recently been reported ,81 and have served as the basis for accelerated approval of vsli in the us by the fda on august 9 , 2012 . sixty - five adult patients , of median age 31 ( range 1983 ) years , with clinically advanced and heavily pretreated relapsed or refractory all , received intravenous vsli 2.25 mg / m weekly on days 1 , 8 , 11 , and 22 of each 28 - day cycle until disease progression , toxicity , or a decision to pursue other treatment , such as allogeneic hsct , was made . most patients had a large disease burden at the time of study treatment , with median bone marrow or peripheral blood blast content of 82 % , and more than half of the patients had received at least three lines of prior therapy . forty - five percent of the patients were also refractory to their immediate prior line of therapy . after a median of four ( range 118 ) doses of vsli , a complete remission ( or complete remission with incomplete count recovery [ cri ] ) was observed in 20 % of patients , and an additional 15 % achieved a partial response for an overall response rate of 33 % . of note , eight patients who achieved complete remission / cri were also in molecular remission by minimal residual disease assessment . the median duration of complete remission / cri was 23 ( range 566 ) weeks . importantly , 12 of the 13 patients who achieved complete remission / cri were successfully bridged to allogeneic hsct . thirty - seven patients ( 58 % ) experienced at least one grade 3 or 4 treatment - related adverse event . grade 3 peripheral neuropathy occurred in 15 patients , and one patient developed grade 4 neuropathy . other serious adverse events included febrile neutropenia ( 5 % ) , tumor lysis syndrome ( 5 % ) , and constipation ( 3 % ) . the results of the pivotal phase ii trial of vsli monotherapy compare well with other salvage therapies in patients with clinically advanced relapsed or refractory all . unfortunately , no randomized , comparative phase iii trials in this population have been reported . currently , only limited comparisons with small studies of other agents in comparable populations can be made . in a retrospective analysis of a subgroup of 56 patients with clinically advancedrelapsed and refractory philadelphia chromosome - negative all treated with non - vsli single agents , only 4 % achieved complete remission / cri , with 17 of 56 patients dying within 30 days of treatment .5,82 single - agent clofarabine induced complete remission in only one of eight relapsed all patients ( 13 % ) in need of third - line therapy , with all remission being short - lived .83 in a study of the combination of clofarabine plus cytarabine , three of 16 ( 19 % ) all patients in need of third - line or higher treatment achieved complete remission / cri .84 finally , single - agent nelarabine was reported to result in complete remission in five of 28 patients with relapsed or refractory t - cell lineage all or lymphoblastic lymphoma .85 vsli represents a significant advance in nanotechnology for liposomal delivery of chemotherapy drugs to improve efficacy and reduce toxicity . currently , vsli is approved by the fda for treatment of philadelphia chromosome - negative all in second or greater relapse or where disease has progressed following two or more chemotherapy regimens . however , despite the significant clinical antileukemic activity seen in the pivotal phase ii trial that led to its approval , the role of vsli remains unclear in all . phase iii trials need to be completed to demonstrate improvements in overall survival or rate of complete remission when compared with other second or third salvage regimens to establish fully the role of liposomal vincristine in philadelphia chromosome - negative all . possessing a clear advantage over conventional vincristine , vsli is likely to find its optimal role in combination chemotherapy regimens , where it can be substituted for conventional vincristine in earlier phases of the disease . to this end , a randomized phase iii study to evaluate the substitution of vsli for standard vincristine in the treatment of patients 60 years or older with newly diagnosed philadelphia chromosome - negative all is about to open . the trial will compare vsli with free vincristine in the standard calgb 8811 regimen21 with the study arm incorporating vsli dosed at 2.25 mg / m without a dose cap , with overall survival as the primary endpoint .86 by comparing the overall survival as well as neurotoxicity profile between the two arms in this study , the suggested benefits of greater efficacy with less toxicity of liposome - encapsulated vincristine observed in earlier studies will hopefully be confirmed . while vsli represents an important advance in the treatment of patients with relapsed all , the response rate and duration of response remain modest , with much room remaining for improvement . future improvements in its liposomal formulation may allow greater delivery of vincristine to leukemic cells . for example , increasing the drug - to - lipid ratio in sphingomyelin / cholesterol liposomes has been associated with enhanced antitumor activity in animal models of human cancers by further prolonging the half - life of vincristine .87 the use of a more saturated phospholipid , dihydrosphingomyelin , in sphingomyelin / cholesterol liposomes may further improve vincristine retention and result in a longer circulation half - life with potentially improved antitumor efficacy .88 finally , applying a calcium phosphate nanoshell to the liposome has resulted in higher cellular uptake in tumor cells compared with uptake from uncoated liposomes , attributed to improved drug release at the ph of the tumor interstitium .89 however , beyond improved delivery , future dosing recommendations for all vincristine formulations should take into account differences in drug metabolism in different patient populations . for example , patients who express the cyp3a5 genotype , found in 70 % of african americans , suffer less neurotoxicity following treatment with vincristine ,90 and therefore may be able to tolerate higher doses of the drug , even when encapsulated in liposomes . finally , it is clear that all drug resistance in all will not be overcome simply by enhanced drug delivery or dose optimization of vincristine , and further investigation of novel agents and approaches are still urgently required to improve the outcome of all .\noutput:\n" }, { "from": "agent", "value": "acute lymphoblastic leukemia ( all ) remains a disease with poor outcomes in adults . while induction chemotherapy achieves a complete remission in almost 90 % of patients , the majority will relapse and die of their disease . relapsed all is associated with a high reinduction mortality and chemotherapy resistance , with allogeneic hematopoietic stem cell transplantation offering the only therapy with curative potential . however , there is no efficacious and well tolerated standard regimen accepted as a bridge to allogeneic stem cell transplantation or as definitive treatment for patients who are not transplant candidates . vincristine is an active drug in patients with all , but its dose intensity is limited by neurotoxicity , and its full potential as an anticancer drug is thus not realized . encapsulation of vincristine into sphingomyelin and cholesterol nanoparticle liposomes facilitates dose - intensification and densification to enhanced target tissues with reduced potential for toxicity . vincristine sulfate liposome injection ( vsli ) is associated with significant responses in clinically advanced all , and has recently been approved by the us food and drug administration for treatment of relapsed and clinically advanced philadelphia chromosome - negative all . this review provides an overview of the preclinical and clinical studies leading to the approval of vsli for the treatment of relapsed and refractory all , and suggests potential areas of future clinical development ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in the literature , the devastating effects of cancer treatment on the cardiovascular system are often referred to as so - called cardiotoxicity . so far , no standardized definition of cardiovascular toxicity that would precisely explain its nature has been adopted . what is certain is that , regardless of whether the anticancer therapy is physical ( ionizing radiation ) , chemical , hormonal or biological ( targeted therapy ) , it has a negative effect on the cardiovascular system . drugs administered and radiation can damage the cardiovascular system , both at the central level , by the deterioration of cardiac function , and at the peripheral level , by increasing the hemodynamic and thrombotic changes . it is worth noting that the level of toxicity of anticancer therapy may be increased by the impact of cardiovascular disease risk factors , as well as those related to the method of anti - tumor therapy itself ( table 1 ) . risk factors for cardiovascular cardiotoxicity , pathogenesis , and cardiovascular pathological manifestations caused , in regard of the method of treatment used younger age at exposure overall dose ( 3035 gy ) division into fractions ( 2 gy ) the heart was exposed to ionizing radiation ( toxicity increases with increasing volume ) use of cytotoxic chemotherapy irradiation technique ( teleradiotherapy is more toxic than brachytherapy ) radiation in the morning hours ( between 6 am and noon ) longer time since exposure acute pericarditis 2 . fibrosis of the conduction system complete or incomplete heart block patient age 18 years of age and 6570 years of age overall drug dose ( doxorubicin 550 mg / m , epirubicin 900 mg / m , idarubicin 90 mg / m ) division of the total dose into sessions female gender ( especially in the pediatric population ) manner of administration of the drug combination of drugs administered sequence of administration of medicines prior or concomitant radiotherapy ( in particular of left side of chest and mediastinum ) prior therapy with anthracyclines concurrent therapy with other anti - cancer drugs ( drug interaction ) genetic peculiarities left ventricular dysfunction suter and ewer have proposed two types of cardiotoxicity in anticancer treatment . it is characterized by irreversible changes in cardiomyocytes , leading to apoptosis , and is dependent upon the dose of the drug and ionizing radiation used . the second type , however , relates to trastuzumab ( herceptin ) monoclonal - antibody therapy and , unlike type i , is not dose - dependent . it is believed that the cardiotoxicity may be reversible upon cessation of treatment . the childhood cancer survivor study research experiment has shown that the risk of cardiovascular events in patients with cancer is probably greater than the risk of another tumor , especially in those treated with anthracyclines and radiotherapy . the results of those studies have shown that in children who have survived cancer the incidence of congestive heart failure is fifteen - fold higher , the incidence of cardiovascular diseases is ten - fold higher , and the incidence of stroke has increased nine - fold in comparison with the control group . similar numbers were observed in the study from scandinavia , which showed that these patients have a 5 - year cardiac mortality of 5.9 % . in view of these reports of serious and irreversible changes in the circulatory system that may be the result of treatment with anthracyclines and radiotherapy , the subject of this paper is to analyze the impact of radiotherapy and anthracyclines on the cardiovascular system . it should be noted , however , that a comprehensive evaluation of data published on the subject is difficult to perform , as the studies investigating the effects of cancer treatment on the cardiovascular system differ in regard to methodology and the definition of cardiotoxicity ; therefore it is not always possible to draw reliable conclusions . irradiation - induced cardiovascular diseases include a number of dangerous effects , ranging from subclinical histopathological symptoms to clinically overt diseases . the spectrum of these complications can be manifested in a variety of structures , such as pericardium , ventricles , cardiac muscle , cardiovascular system and the conduction system . it is estimated that radiotherapy - induced cardiovascular diseases occur in 10 % to 30 % of patients within 510 years following treatment . in 88 % of patientsthe abnormalities are asymptomatic , and thus the disclosure of pathological cardiovascular lesions is often delayed , and as such can often be misleading . it is important that patients treated with ionizing radiation are systematically monitored by methods of cardiac diagnosis recommended for these patients ( table 2 ) , as radiation can cause a wide variety of pathological cardiovascular manifestations ( table 1 ) . recommended methods for monitoring patients undergoing radiotherapy or chemotherapy to diagnose cardiovascular abnormalities coronary artery disease : lipid profile , exercise stress test , radionuclide , angiography , echocardiogram , electrocardiography pericarditis : electrocardiography , chest x - ray and echocardiogram cardiomyopathy : electrocardiography , echocardiogram , and radioisotopic angiography arrhythmias : electrocardiography and 24 - h electrocardiography valvular disease : echocardiogram , electrocardiography , cardiac catheterization left ventricular dysfunction : electrocardiography , magnetic resonance imaging , multiple - gated acquisition scan , sampling of serial troponin and / or nt - probnp levels there are two mechanisms causing tissue damage during radiation therapy ( table 1 ) . it is believed that the radiolysis of water may be the key mechanism contributing to the occurrence of peroxidation processes in cell membranes . the often - described result of exposure to ionizing radiation is the fibrosis of the pericardium , causing it to become rigid and constricted . this pathology is caused by the accumulation of collagen fibers in the mesothelium of the epicardium , visceral pericardium and in the interstitium . this accumulation leads to the replacement of the peripheral pericardial fat pad , increasing the thickness of the fibrous layer . production of protein - rich fluid inside the pericardial sac occurs and its rapid accumulation may even lead to lethal cardiac tamponade . the most frequently observed form of pericardial radiation syndrome is its chronic inflammation , appearance of which is often delayed . it occurs in about 420 % of patients within 10 years after the termination of radiotherapy . a literature review has shown that acute pericarditis is rare , but may occur within several weeks after irradiation . it can manifest itself with a fever , tachycardia , chest pain and pericardial sac effusion . it is believed that acute pericarditis is mainly caused by the inflammation and the necrosis of large tumors in the mediastinal area , rather than directly by the toxic effects of thoracic irradiation . abnormalities affecting cardiovascular valves can be caused by ionizing radiation or fibrosis of the cardiac muscle , which is adjacent to their rings . it is worth noting that radiation - induced valvular dysfunction frequently affects the left side of the cardiac muscle . studies reveal that the aortic valve pathology is diagnosed more often than mitral or right - chamber pathology . this is explained by the fact that higher intracardiac pressure occurs there , and also by accompanying higher intracardiac blood flow velocities . it is possible that such location of the pathology may also result from the irradiation techniques applied . the literature states that the average time of detection of asymptomatic valvular pathology is 11.5 years , and 16.5 years for symptomatic pathology . thus , the process is slow , but gradually progressing . myocardial damage may contribute to the development of progressive diastolic dysfunction and hemodynamic instability ( 1 year after irradiation ) . these complications correlate with extensive fibrosis and microvascular damage leading to occlusion of capillaries , whereas systolic myocardial dysfunction may occur following combined treatment with anthracyclines . radiation damage in the circulatory system may concern the capillaries , veins , and small and large arteries . there are two hypotheses explaining the biological mechanisms that lead to a higher incidence and mortality due to blood vessel diseases resulting from ionizing radiation treatment . the first states that radiation increases the occurrence of myocardial infarction by intravascular proliferation and accelerated development of atherosclerosis in the arteries . the second hypothesis is that the radiotherapy - induced increased mortality is related to the decrease in myocardial tolerance to the above - mentioned acute ischemic necrosis induced by microvascular disorders . it is worth noting that these hypotheses are not mutually exclusive , and the mechanisms described may occur simultaneously , contributing to the development of clinical cardiac diseases . all major ionizing radiation - induced coronary diseases presumably include processes such as increased vascular permeability , intimal hyperplasia , fibroblast proliferation , collagen deposition , fibrosis and scarring of the vascular wall outer membrane . however , in comparison to atherosclerosis occurring in the general population , irradiation leads to the formation of plate which is more fibrotic and is characterized by a lower content of lipid components . their growth occurs as a result of exposure to ionizing radiation , leading to occlusion of the capillaries and lumen and density loss . impairment of microcirculatory function can cause extensive damage , leading to ischemia , necrosis of myocardial cells and finally their fibrosis . heart rate , being controlled by the autonomic nervous system , is an important predictor of cardiovascular disease . it is believed that fibrosis of the myocardial tissue resulting from radiotherapy may explain the pathological changes in its functioning . it causes certain changes in the electrocardiography , including premature re - polarization abnormalities and premature ventricular complexes . thus , the sympathetic nervous system is activated , and the level of catecholamines and density of adrenergic receptors are changed . consequently , the nervous system causes the heart muscle to be more intensively stimulated to work and compensate for its own impairment . anthracyclines are a group of antibiotics that are among the most active representatives of chemotherapeutics , and since the 1960s have been a key component in many cytotoxic anticancer regimens . it has been known since the 1970s that anthracycline therapy is associated with increased risk of a heart failure . treatment with these drugs , compared to the treatment without their use , increases the risk of clinical cardiotoxicity 5.43-fold , subclinical 6.25-fold and the risk of death related to cardiac problems 4.94-fold . it is important that the patients subject to this treatment are systematically diagnosed for cardiovascular diseases . cardiological biopsies and modern imaging techniques suggest that myocardial damage may already have occurred at the start of exposure to the anthracyclines , regardless of whether it had been diagnosed using standard non - invasive techniques . data obtained from biopsies and charts showing dose - response relationships provide strong evidence that the damage occurs at the beginning of the exposure , despite the fact that cardiac reserve does not allow them to be diagnosed until it is completed . thus , there is no specified period for the onset of pathological post - anthracycline changes in the circulatory system . therefore , three types of post - anthracycline cardiotoxicity have been distinguished : acute , chronic and delayed . acute cardiotoxicity ( not related to the dose of the drug ) can occur during or immediately after a single dose of an anthracycline . it can be characterized by transient arrhythmia or electrocardiographic changes ( nonspecific st - and t - wave changes ) and pericardial effusion . in some cases it can cause pericarditis , myocarditis and heart failure . it is believed , however , that cardiac toxicity is not a serious therapeutic problem , but it should be noted that it is often asymptomatic . it is probably the consequence of direct damage caused by anthracycline and excessive discharge of catecholamines and histamine caused by these drugs . however , the most serious type of cardiotoxicity is the chronic type ( associated with drug dose ) , as it causes irreversible changes in the circulatory system . this type of cardiotoxicity usually occurs within a year after treatment with anthracyclines , and can result in development of congestive heart failure ( chf ) , refractory to medical therapy . if the lesions show up years or decades after exposure to the drug , they are referred to as delayed cardiotoxicity and are characterized by arrhythmias such as paroxysmal ventricular tachycardia and paroxysmal supraventricular tachycardia , and atrioventricular block . exacerbation of chronic heart failure , de novo chf or sudden cardiac death can also occur . the pathomechanism ( table 1 ) of post - anthracycline cardiotoxicity is controversial and still not completely understood . it is believed , however , that anthracyclines may become cardiotoxic immediately after the reduction of one or two electrons . one - electron reduction ( of the quinone moiety of anthracyclines and the subsequent semiquinone redox cycling ) leads to the formation of reactive oxygen species ( ros ) , which cause oxidative stress and loss of energy in the cells of the myocardium . two - electron reduction ( of the side - chain c - 13 carbonyl group ) leads to the creation of secondary alcohol metabolites that are responsible for the disruption of homeostasis of calcium and iron in the organism . it is worth noting that ros are responsible for the occurrence of early cardiac abnormalities , including impairment of dna repair pathways . this leads to irreversible changes in the myocardial cells , which have limited capacity for regeneration due to a low level of antioxidant enzymes in the myocardium . secondary alcohol metabolites , however , may have a key role in the progression of cardiomyopathy - causing cardiotoxicity and chf . post - anthracycline cardiomyopathy may occur in the form of severe myocardial damage or be asymptomatic . the prognosis for post - anthracycline cardiomyopathy is significantly worse than in infarct heart failure or idiopathic cardiomyopathy . the primary cause of impaired intracellular metabolism is free radicals , as they cause dna , cell membrane and endoplasmic reticulum damage , among others . the mitochondria also become impaired , and changes occurring within them are responsible for the release of cytochrome c , aif protein ( apoptosis inducing factor ) and intramitochondrial caspases from the inter - membrane space . cell membrane structure , its transport properties and transport enzyme activity may be modified as a result . the mechanism of damage to the structure and impaired cardiac function by anthracycline is multifactorial . it consists of processes such as inhibition of the synthesis of nucleic acids and proteins , reducing the amount of gsh , atp and creatine phosphate , pathological adenine , amino acids and glucose absorption , inhibition of enzymatic activity of the na and k atpase , inhibition of ion pumps ( with consequent disruption of the metabolism of iron ) , myocyte calcium overload , inhibition of ion exchange of sodium / calcium , inhibition of adenylate cyclase , impairment of oxidative phosphorylation , blocking the activity of topoisomerase ii , abnormal metabolism of sphingolipids , a sudden release of catecholamines and histamine , disturbance in the sympathetic system , activation of signaling pathways and gene expression alteration . kaczmarek - borowska and co - authors emphasize that the activity of coenzyme q10 in the respiratory chain may be impaired its inhibition may result in shortage of energy . all metabolic and ultrastructural changes in the cardiac muscle lead to its pathological mechanical and electrical activity . it is worth noting that doxorubicin , through the generation of mediators of oxidative stress , not only causes apoptosis of cardiomyocytes , but can also have a damaging effect on the endothelium of blood vessels . przybyszewski and co - authors believe that the pathology of the endothelium may result in the early stage of development of post - anthracycline atherosclerosis of coronary arteries . galderisi and co - authors state that treatment with these substances may also cause cardiac muscle valvular pathologies . nowadays , the high efficiency of anticancer therapy increases the rate of survival in patients treated for breast cancer . it should be emphasized , however , that these treatments damage not only the affected tissue , but also the healthy tissue . consequently , with the increase of the survival rate in these patients , the number of patients with complaints concerning many organs and systems also increases , which is the result of earlier treatment . it seems appropriate at this moment to ask whether the reduction in the risk of relapse is tantamount to prolonging overall survival in these patients . in patients with cancer , the principle of primum non nocere should be of particular significance , and therefore the number of studies on the effects of cancer treatment on the human body is constantly increasing . this issue is not to be underestimated , as the pathology of the cardiovascular system leads to reduction in the quality of life in these patients . the awareness of the need to balance the oncologist 's objectives ( maximum elimination of cancer cells or inhibiting their division ) with the objectives that impact the quality of life is of paramount importance .\noutput:\n" }, { "from": "agent", "value": "the subject of this paper is to analyze the impact of radiotherapy and anthracyclines on the cardiovascular system , based on a survey of contemporary literature . currently , high efficiency of anticancer therapies has increased the rate of survival in patients treated for cancer . it should be emphasized , however , that these treatments damage not only the affected but also the healthy tissue . consequently , with the increase of survival rate in these patients , the number of patients with complaints regarding numerous organs and systems also increases as a result of earlier treatment . thus , during the first decade of the 21st century , a number of concerns about the relationship between cancer treatment and dysfunction of the cardiovascular system were resolved . anthracyclines , as well as radiotherapy , are capable of damaging the cardiovascular system , both at the central level , by the deterioration of cardiac function , and at peripheral levels , by increasing the hemodynamic and thrombotic changes ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the anterior belly of the digastric muscle ( abdm ) originates from the digastric fossa of the mandible and inserts at an intermediate tendon that serves as a shared attachment site with the posterior belly of the digastric muscle . when contracting together , these muscles function as synergists to depress of the mandible against resistance and elevate and stabilize the hyoid during deglutition and phonation . the abdms are typically considered to be symmetric bilaterally ; however , diverse anatomical variations have been documented to occur , including duplications , triplications and quadrifications of the abdm . abdm bellies have been demonstrated to insert into the mylohyoid raphe or cross the midline and insert contralaterally . the abdm has also been documented to present as a fractal , with one digastric giving rise to another smaller digastric from which other , even smaller digastric muscles originate . in addition to the many types of abdm variants , there is wide prevalence of abdm variants , ranging from of 2.7 to 69.6 % . during routine dissection of a 66 - year - old caucasian female cadaver , a duplication of the right - sided abdm was observed ( fig . 1 ) . abdms were measured by taking a high resolution photograph ( canon powershot sx50 hs , 12.1 megapixel ) with a digital caliper in the frame [ mitutoyo 08 in ( 0203.2 mm ) absolute digimatic caliper series 500 , accuracy 0.001 in ( 0.025 mm ) ] . the photograph was then analyzed with the imagej software ( nih ) calibrated according to the digital caliper . muscle belly lengths , muscle belly widths , angles formed between the digastric muscle bellies and the area of each muscle belly as viewed from the inferior were measured . figure 1 : inferior view of the variant digastric musculature demonstrating an oblique digastric belly variant crossing from the left digastric fossa of the mandible to the right intermediate tendon of the right digastric muscle . ab , anterior belly of the digastric muscle ; ob , oblique belly of the anterior digastric muscle ; mh , mylohyoid muscle ; it , intermediate tendon of the digastric muscle . inferior view of the variant digastric musculature demonstrating an oblique digastric belly variant crossing from the left digastric fossa of the mandible to the right intermediate tendon of the right digastric muscle . ab , anterior belly of the digastric muscle ; ob , oblique belly of the anterior digastric muscle ; mh , mylohyoid muscle ; it , intermediate tendon of the digastric muscle . the length of the muscle belly , from the mandible to the intermediate tendon measured 33 mm . the breadth of the muscle , measured through the middle of the length of the muscle belly , was 10 mm . on the right side , there were two muscle bellies inserting at the intermediate tendon . the typical anterior muscle belly was , more or less , mirrored in its orientation to that of the right - sided muscle belly . its length was 31 mm , width 13 mm , and visible area 340 mm . an oblique muscle belly traveled between the right - sided intermediate tendon , sharing some muscle fibers with the right - sided anterior digastric belly , and the contralateral digastric fossa , sharing some muscle fibers with the left - sided muscle belly . the length of the oblique muscle belly was 41 mm , width 10 mm and visible area 220 mm . at the intermediate tendon , the oblique belly formed an angle of 27 with the right - sided anterior belly . an angle of 38 was formed between the oblique muscle belly and the left abdm at the mandible . abdm variations have been reported in as few as 2.7 % to as many as 69.6 % of individuals . therefore , it is important to understand the anatomical diversity of abdm variants , particularly with regard to head and neck surgery . the described variant has implications in procedures including submental lipectomy , rhytidectomy , surgical alteration of the cervicomental angle via partial resection of the abdm , muscle transfer for reanimation of the mouth and submental artery flap procedures . likewise , the abdm is used as a surgical landmark for location of the lingual nerve and submandibular salivary duct . it is also important to understand the diversity of abdm variants in order to differentiate between anatomical and pathological structures common to the submental region including normal muscle tissue , submental lymph nodes , space occupying lesions and muscular asymmetries due to trigeminal nerve lesions .\noutput:\n" }, { "from": "agent", "value": "anterior belly of the digastric muscle ( abdm ) variations have been reported to occur in as few as 2.7 % to as many as 69.6 % of individuals . therefore , it is important to understand the anatomical diversity of abdm variants , particularly with regard to head and neck surgery . the report documents a unilateral duplication of the abdm with an oblique belly which crosses the midline . measurements of muscle length , width , orientation and inferior surface area are documented . abdm variants may cause confusion during surgeries , including submental lipectomy , rhytidectomy , surgical alteration of the cervicomental angle via partial resection of the abdm , muscle transfer for reanimation of the mouth and submental artery flap procedures . therefore , knowledge of this particular variant may aid in surgical planning as well as prevent confusion and disorientation during operations in the submental region ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: in 1978 allgrove and colleagues described 2 unrelated pairs of siblings with achalasia and acth insensivity , three had impaired lacrimation and one also had autonomic dysfunction . this triad ( achalasia , adrenal insufficiency and alacrima ) became known as ttriple a syndrome . during the following years several reports in the literature have focused on more global autonomic disturbances associated with allgrove syndrome leading one author to recommend the name 4a syndrome ( adreno - cortical insufficiency , achalasia of cardia , alacrima and autonomic abnormalities ) . incidence is unknown and only few numbers of families and case reports exist in literature . inheritance is autosomal recessive and most patients have consanguineous parents , but autosomal dominant forms with incomplete penetrance have also been reported . mutations in the aaas gene , which encodes the product aladin , on chromosome 12q13 have been implicated as a cause of this disorder . this gene belongs to wd - repeat regulatory protein family which exhibits wide functional diversity . the encoded protein , aladin , may help regulate nucleo - cytoplasmic transport of other proteins . high expression of this protein is seen in the adrenal gland , brain and gastrointestinal tract , the organs in which the main pathologic manifestations of disease occur . some authors believed that the pathology of this condition may be due to a progressive loss of cholinergic function throughout the body . age at onset of symptoms is variable but patients usually present during the first decade of life with hypoglycemia , adrenal crisis or dysphagia . this article reports two pairs of siblings in two related families with broad clinical features of the syndrome with particular attention to premature loss of permanent teeth in two siblings . case 1 : a 13 year - old girl with unremarkable birth history was referred to our endocrinology clinic for further follow up . she was diagnosed with familial gluococorticoid insufficiency at age 4 after a hypoglycemic seizure with low cortisol and elevated acth level and was discharged on oral prednisolone . review of systems was positive for crying without tears from early infancy and darkening of skin at age 4 . by age 7there was loosening of permanent teeth when she was l0 years old , and became near totally edentulous by the age of 13 years . blood pressure was normal without orthostatic hypotension , weight 25 kg ( z score -3 sd ) , height 132 cm ( z score -4 sd ) according to nchs growth chart . pubertal stage : breast smr ( sex maturity rating ) 1 and pubic hair smr 2 according to tanner 's staging system . she had a distinct facial appearance consisting of narrow upper lip and down turned mouth with nasal speech . there was distal wasting in the arms , lower limb , and significant weakness of the legs . her past hospital records - before treatment with prednisolone showed normal thyroid function tests and routine biochemical and hematological tests . serum cortisol was 1.5 g / dl ( normal range 5 - 20 ) before , 3 g / dl 30 minutes and 2 g / dl 4 hours after intramuscular injection of 250 g long acting acth . ( normal response : peak plasma cortisol level greater than 19 g / dl ) . case 2 : this 15 - year - old girl was second sibling of case 1 who was born of consanguineous parents . she first presented with vomiting and difficulty in swallowing at age 5 and subsequently underwent esophageal dilatations for achalasia . she also was noted to have learning difficulties , poor school performance and hearing deficit . on examinationadditional findings were muscular wasting , weakness and alacrima . bilateral hearing loss was confirmed by hearing evaluation . routine biochemical , hematological and serum cortisol level before and after acth stimulation test were normal . neither of the two patients had significant dental caries or periodontal disease , we did not find abnormal results in clinical and laboratory investigations for their teeth loss . case 3 : a 6 - year old boy born to consanguineous parents ( cousin to cases 1 and 2 ) was referred to our clinic with darkening of skin , developmental delay and photophobia . hyperpigmentation over the knuckles of the hands and feet had developed gradually over the last 12 months . the patient 's past medical history was significant for esophageal surgery and cardiomyotomy for achalasia manifested by recurrent vomiting . on physical examinationlong thin face with long philtrum , narrow upper lip characteristic of allgrove syndrome was observed . the weight was 16.5 kg ( z score -2.5 standard deviation ) and the height was 103 cm ( z score -3 standard deviation ) . heart rate was 90 / min and blood pressure 100/60 mmhg in supine position , but he had marked postural fall in both . schirmer 's test revealed right eye 4 mm and left eye 2 mm of wetting ( alacrima was confirmed ) . serum na , k , aldosterone , renin , thyroid function tests , bun , and creatinine were normal . serum acth level was high normal ( 53 pg / ml ; reference range 9 - 52 pg / ml ) . serum cortisol was 2.6 g / dl before , 4 g / dl 30 minutes and 2 g / d 4 hours after acth stimulation respectively . plasma levels of cortisol was measured by chemiluminescence , serum aldosterone and acth by radioimmunoassay , and rennin by immunochemiluminescence assay . based on these findings , allgrove syndrome diagnosis was established . case 4 : this 10 - year - old patient is older sister of case 3 and was born with unremarkable birth history . she was evaluated because of reduced tear production and positive history of allgrove syndrome in her brother . at age 2she was noted to have prominent neuro - developmental delay ( delay in sitting , walking and speech ) . clinical findings included distinct facial appearance characteristic of allgrove syndrome , nasal voice , dysarthria , mental retardation , ataxia ( tandem gait and finger - to - nose testing was disturbed ) . slit lamp examination and ophtalmoscopy were normal , but schirmer 's test typically showed alacrima . biochemical , hormonal and hematological screening were negative except for low cortisol and blood sugar and high acth ( serum glucose 40 mg / dl , serum cortisol 3.4 g / dl , 4 g / dl , and 2.4 g / dl , immediately before , 30 minutes and 4 hours after intramuscular injection of 250 g long acting acth , respectively ) . acth level was 60 pg / ml . in the light of these findings a diagnosis of allgrove syndrome was considered . case 1 : a 13 year - old girl with unremarkable birth history was referred to our endocrinology clinic for further follow up . she was diagnosed with familial gluococorticoid insufficiency at age 4 after a hypoglycemic seizure with low cortisol and elevated acth level and was discharged on oral prednisolone . review of systems was positive for crying without tears from early infancy and darkening of skin at age 4 . by age 7there was loosening of permanent teeth when she was l0 years old , and became near totally edentulous by the age of 13 years . blood pressure was normal without orthostatic hypotension , weight 25 kg ( z score -3 sd ) , height 132 cm ( z score -4 sd ) according to nchs growth chart . pubertal stage : breast smr ( sex maturity rating ) 1 and pubic hair smr 2 according to tanner 's staging system . she had a distinct facial appearance consisting of narrow upper lip and down turned mouth with nasal speech . there was distal wasting in the arms , lower limb , and significant weakness of the legs . her past hospital records - before treatment with prednisolone showed normal thyroid function tests and routine biochemical and hematological tests . serum cortisol was 1.5 g / dl ( normal range 5 - 20 ) before , 3 g / dl 30 minutes and 2 g / dl 4 hours after intramuscular injection of 250 g long acting acth . ( normal response : peak plasma cortisol level greater than 19 g / dl ) . case 2 : this 15 - year - old girl was second sibling of case 1 who was born of consanguineous parents . she first presented with vomiting and difficulty in swallowing at age 5 and subsequently underwent esophageal dilatations for achalasia . she also was noted to have learning difficulties , poor school performance and hearing deficit . on examinationadditional findings were muscular wasting , weakness and alacrima . bilateral hearing loss was confirmed by hearing evaluation . routine biochemical , hematological and serum cortisol level before and after acth stimulation test were normal . neither of the two patients had significant dental caries or periodontal disease , we did not find abnormal results in clinical and laboratory investigations for their teeth loss . case 3 : a 6 - year old boy born to consanguineous parents ( cousin to cases 1 and 2 ) was referred to our clinic with darkening of skin , developmental delay and photophobia . hyperpigmentation over the knuckles of the hands and feet had developed gradually over the last 12 months . the patient 's past medical history was significant for esophageal surgery and cardiomyotomy for achalasia manifested by recurrent vomiting . on physical examinationlong thin face with long philtrum , narrow upper lip characteristic of allgrove syndrome was observed . the weight was 16.5 kg ( z score -2.5 standard deviation ) and the height was 103 cm ( z score -3 standard deviation ) . heart rate was 90 / min and blood pressure 100/60 mmhg in supine position , but he had marked postural fall in both . schirmer 's test revealed right eye 4 mm and left eye 2 mm of wetting ( alacrima was confirmed ) . serum na , k , aldosterone , renin , thyroid function tests , bun , and creatinine were normal . serum acth level was high normal ( 53 pg / ml ; reference range 9 - 52 pg / ml ) . serum cortisol was 2.6 g / dl before , 4 g / dl 30 minutes and 2 g / d 4 hours after acth stimulation respectively . plasma levels of cortisol was measured by chemiluminescence , serum aldosterone and acth by radioimmunoassay , and rennin by immunochemiluminescence assay . based on these findings , allgrove syndrome diagnosis was established . case 4 : this 10 - year - old patient is older sister of case 3 and was born with unremarkable birth history . she was evaluated because of reduced tear production and positive history of allgrove syndrome in her brother . at age 2she was noted to have prominent neuro - developmental delay ( delay in sitting , walking and speech ) . clinical findings included distinct facial appearance characteristic of allgrove syndrome , nasal voice , dysarthria , mental retardation , ataxia ( tandem gait and finger - to - nose testing was disturbed ) . slit lamp examination and ophtalmoscopy were normal , but schirmer 's test typically showed alacrima . biochemical , hormonal and hematological screening were negative except for low cortisol and blood sugar and high acth ( serum glucose 40 mg / dl , serum cortisol 3.4 g / dl , 4 g / dl , and 2.4 g / dl , immediately before , 30 minutes and 4 hours after intramuscular injection of 250 g long acting acth , respectively ) . acth level was 60 pg / ml . in the light of these findings a diagnosis of allgrove syndromewhen adrenal insufficiency is seen in conjunction with reduced lacrimation , achalasia of cardia and autonomic neuropathy , the condition is referred to as 4a syndrome . it is a form of primary adrenal insufficiency , commonly without mineralo - corticoid deficiency . affected patients have between two and four of these main criteria , but a wide spectrum of associated features have been described including progressive central , peripheral and autonomic nervous system abnormalities , amyotrophic lateral sclerosis , pyramidal syndrome , distal motor neuropathy , dystonia , chorea , micro - cephaly , angular cheilitis , pes cavus , short stature , hearing deficit , xerostomia , and palmo - plantar hyper - keratosis . most cases present with classic symptoms of adrenocortical insufficiency including hypoglycemic seizures or hypotensive attacks , less frequently , a child may be evaluated initially for recurrent vomiting , hyperpigmentation , or developmental delay . we believe that clinical evaluation met the criteria for the diagnosis of allgrove syndrome in our patients . impaired intelligence , similar facial appearance characteristic of allgrove syndrome and alacrima were the most consistent clinical signs of the syndrome in our patients . lack of lacrimation was frequently present from early infancy and almost invariably before age 5 years . in review of literature alacrima was the earliest and most consistent clinical sign of allgrove syndrome . we identified a spectrum of associated neurologic features in our cases including : impaired intelligence in all cases , significant autonomic dysfunction in case 3 , muscular wasting and weakness in case 1 and , 2 , ataxia in case3 , 4 , dysarthria in case 3 and 4 . kimber described two families who exhibited signs of multisystem neurological disease including hyperreflexia , muscle wasting , dysarthria , ataxia , optic atrophy , and intellectual impairment . kurca reported epilepsy , autonomic neuropathy and damages of central and peripheral nervous system in two brothers . chvez et al described a 21 - year - old man with hyper - reflexia and muscle weakness with allgrove syndrome . our cases are remarkable in that all patients show evidence of intellectual impairment which was suggested by clinical history and confirmed by neuropsychometry . cognitive problems have been reported in some pediatric patients with allgrove syndrome in literature ( kimber et al 2003 , grant et al 1993 , moore 1991 , khalifa 1988 ) , but it is unclear if this is a primary feature of the allgrove syndrome or simply a reflection of recurrent hypo - glycemia . with one exception all patients had adrenal insufficiency . glucocorticoid deficiency is hallmark of this syndrome and develops during the first two decades of life , progression from normal adrenal function to adrenal insufficiency has been described in a number of individuals . it remains to be seen if case 2 will go on to develop adrenal insufficiency . lack of adrenal insufficiency or achalasia does not negate this diagnosis . . two of our cases differed from other cases with premature loss of permanent teeth . we did not find possible causes of premature loss ( trauma , osteomyelitis , peri - odontal infection , xerostomia , dental caries were ruled out ) . the literature was reviewed for loss of teeth associated with this condition but it has not been described by previous investigators . chu has reported periodontal disease , multiple caries , and dry mouth in a 16 - year - old hispanic boy . case 3 and 4 are currently on treatment with hydrocortisone and topical ocular lubrication with periodically follow up visits . case 1 who was the first diagnosed patient died at age 14 after a heavy stress condition ( status epilepticus ) although she received stress doses of hydrocortisone ) . by case 2we suspect that in addition to known previous manifestations , 4 - a syndrome can particularly present with loss of permanent teeth without dental caries . this could be the first report of an unusual presentation of allgrove syndrome in literature .\noutput:\n" }, { "from": "agent", "value": "backgroundallgrove syndrome is a rare autosomal recessive condition characterized by adrenal insufficiency , achalasia , alacrima and occasionally autonomic disturbances . mutations in the aaas gene , on chromosome 12q13 have been implicated as a cause of this disorder.case ( s ) presentationwe present various manifestations of this syndrome in two related families each with two affected siblings in which several members had symptoms including reduced tear production , mild developmental delay , achalasia , neurological disturbances and also premature loss of permanent teeth in two of them.conclusionthe importance of this report is dental involvement ( loss of permanent teeth ) in allgrove syndrome that has not been reported in literature ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: various methods are available for treatment of cervical spondylosis . these include anterior and posterior approaches with or without fixation of the affected segments . the technique involves facetal distraction and indirect decompression of the spinal cord and the roots without removal of any bone , disc or ligaments . to use this technique effectively knowledge of the anatomy of the cervical facetsthe quantitative anatomy , orientation of the facet joints and the movements occurring at these joints has been discussed on occasions . the mechanical strength and the thick quality of the bone of the facetshave been therapeutically exploited only infrequently due to its close proximity to the vertebral artery and the nerve roots . moreover , the anatomy of facets was poorly delineated on the relatively inferior quality radiological images that were available earlier . there are only a few studies in literature discussing the orientation and morphometry of the cervical facets . in the present analysis , the physical characters of the cervical sub - axial facets has been evaluated and their suitability for insertion of goel facetal spacers has been discussed . the effects and safety of technique are elaborated on the basis of this anatomic review . ten dried cadaveric c3 to c7 vertebrae were procured from the anatomy department of our institution [ figures 15 ] . the shape , orientation , dimensions , inclination , and relationship of the facets with the adjoining spinal and intervertebral root canal and vertebral artery foramina were studied . a micro caliper was used for linear measurements and a goniometer was used for angular measurements . the heights of the facets were measured from superior to inferior , the width was measured in a lateral to medial direction and the thickness of the facets was measured in an anteroposterior direction . the inclination of the facets was measured in the transverse plane with the vertebra held in the position that it lies in the body . the inclination of the facet in the transverse plane was measured as the angle between a line drawn along the length of the facet and a line drawn through the inferior edge of the facet parallel to the transverse plane [ figure 1c ] . the distance between the anterior margins of the inferior facet to the posterior margin of the foramen transversarium was also measured . after these preliminary measurements , the facetal height and inter spinous distances were measured before and after insertion of facetal spacers . spacers used were goel inter - facetal titanium spacers and ranged from 2 to 4 mm in height and 8 mm in diameter . the facetal height was measured from the anterior lip of the inferior facet of the rostral vertebra to the anterior lip of the superior facet of the caudal vertebra . the interspinous distance was measured as the distance between the tips of the spinous processes . the safety of facetal spacer insertion with respect to the vertebral artery and exiting nerve roots was evaluated . the lines ab and cd show the measured height and width respectively of the superior articular facet inferior view of the c3 vertebra showing the inferior articular facets view of the c3 vertebra as it lies in the prone position in the human body . the angles a and b denote the angle of the superior and inferior respectively facets with the transverse plane posterior view of the c4 vertebra showing the superior articular facets . note that the facets are smaller in size as compared to c3 and the other lower cervical vertebra inferior view of the c4 vertebral body showing the inferior articular facets posterior view of the c5 vertebra showing the superior articular facets inferior view of the c5 vertebral body showing the inferior articular facets posterior view of the c6 vertebra showing the superior articular facets inferior view of the c6 vertebral body showing the inferior articular facets posterior view of the c7 vertebra showing the superior articular facets inferior view of the c7 vertebral body showing the inferior articular facets the measured parameters of the superior facet of the sub - axial vertebrae the measured parameters of the inferior facet of the sub - axial vertebraethe results of measurements of various parameters from c3 to c7 are shown in tables 1 and 2 . the height decreased from c4 to c5 and then again increased from c6 to c7 . the inclination with the transverse plane ranged from 22 to 45 . the largest transition of the angle was seen at the c6 vertebra where the angle became more acute . the shape of the superior facet was vertically oval at c3 and c4 level and horizontally oval at c5 and c6 levels and again becoming more toward the vertical at c7 level . the superior facets of c3 and c4 had a posteromedial orientation , whilst those of c5 to c7 faced posteriorly . the height of the inferior facet was maximum at c3 level then decreased at c4 level and then again increased at c5 and was nearly the same at c6 and c7 levels . the width of the inferior facet was maximum at c7 level and least at c4 level . the shape of the inferior facet was vertically oval at c3 , circular at c4 level and horizontally oval at c5 to c7 levels . the inclination of the facet with the transverse plane ranged from 29 to 53 . the most acute angle was seen at c6 level . thus , the facets had the greatest height at c3 level and the greatest width at c7 level . the c6 superior and inferior facet showed the most sudden transition in angles with respect to the transverse plane . the inter - facetal height was maximum at c3 level then decreased from c4 to c6 and then again increased at c7 level . the thickness at the inter - facetal region was maximum at c3 level and then decreased from c3 to c7 . the distance of the anterior margin of the inferior facet from the posterior margin of the foramen transversarium ranged from 5 to 7 mm and was maximum at c3 level , then decreased at c4 and remained constant from c5 to c7 . in the normal position , the superior and inferior facets lie close to each other with just a thin articular cartilage lining between them . the facetal height ( distance between the superior and inferior facets before and after insertion of spacers ) ranged from 5 to 8 mm prior to insertion of facetal spacers , after insertion the height ranged from 7.5 to 12 mm . the interspinous height ranged from 1.8 to 2.1 cm prior to spacer insertion and increased to 2.13 cm after spacer insertion . insertion of the spacers distracted the cervical vertebrae and led to an increase in the intervertebral neural foramen height and in the inter spinous distances . this in turn indirectly decompresses the exiting nerve root and also causes the buckled ligamentum flavum to become tauter . the increase in the intervertebral height was difficult to measure on the dried bones , but this has already been shown by us radiologically in our prior publication where there was an average of 2.2 mm increase in foraminal height [ figures 6a and b ] . pre - operative 3d ct scan showing the facets and the alignment post - operative ct scan showing goel intrafacetal spacersthe largest height of the superior facet was found at c3 level . the height decreased from c4 to c5 and then again increased from c6 to c7 . the inclination with the transverse plane ranged from 22 to 45 . the largest transition of the angle was seen at the c6 vertebra where the angle became more acute . the shape of the superior facet was vertically oval at c3 and c4 level and horizontally oval at c5 and c6 levels and again becoming more toward the vertical at c7 level . the superior facets of c3 and c4 had a posteromedial orientation , whilst those of c5 to c7 faced posteriorly . the height of the inferior facet was maximum at c3 level then decreased at c4 level and then again increased at c5 and was nearly the same at c6 and c7 levels . the width of the inferior facet was maximum at c7 level and least at c4 level . the shape of the inferior facet was vertically oval at c3 , circular at c4 level and horizontally oval at c5 to c7 levels . the inclination of the facet with the transverse plane ranged from 29 to 53 . the most acute angle was seen at c6 level . thus , the facets had the greatest height at c3 level and the greatest width at c7 level . the c6 superior and inferior facet showed the most sudden transition in angles with respect to the transverse plane . the inter - facetal height was maximum at c3 level then decreased from c4 to c6 and then again increased at c7 level . the thickness at the inter - facetal region was maximum at c3 level and then decreased from c3 to c7 . the distance of the anterior margin of the inferior facet from the posterior margin of the foramen transversarium ranged from 5 to 7 mm and was maximum at c3 level , then decreased at c4 and remained constant from c5 to c7 . in the normal position , the superior and inferior facets lie close to each other with just a thin articular cartilage lining between them . the facetal height ( distance between the superior and inferior facets before and after insertion of spacers ) ranged from 5 to 8 mm prior to insertion of facetal spacers , after insertion the height ranged from 7.5 to 12 mm . the interspinous height ranged from 1.8 to 2.1 cm prior to spacer insertion and increased to 2.13 cm after spacer insertion . insertion of the spacers distracted the cervical vertebrae and led to an increase in the intervertebral neural foramen height and in the inter spinous distances . this in turn indirectly decompresses the exiting nerve root and also causes the buckled ligamentum flavum to become tauter . the increase in the intervertebral height was difficult to measure on the dried bones , but this has already been shown by us radiologically in our prior publication where there was an average of 2.2 mm increase in foraminal height [ figures 6a and b ] . pre - operative 3d ct scan showing the facets and the alignment post - operative ct scan showing goel intrafacetal spacersanatomy of the cervical vertebrae has been described on occasions , but most of these studies are focused on the dimensions of the pedicle for transpedicular fixation . very few studies are available on the quantitative anatomy of the sub - axial cervical facets . orientation of the cervical facets and its significance to spinal movements also has been studied . pal et al . in their study noted the orientation of the facet joints at the cervical and upper thoracic region . the sub - axial cervical facet joints were studied and their suitability was assessed for goel facet distraction arthrodesis technique using facetal spacers . the superior facet lies rostrally with its articular facet facing dorsally and the inferior facet lies caudally with its articular facet facing ventrally . the articular processes of the cervical spine are inclined approximately 45 from the horizontal plane with steeper inclinations in the lower segments . the orientation of these facets allows flexion and extension , lateral bending and rotation of the lower cervical spine . panjabi et al . have reported posteromedial orientation of all the superior facets from c3 to c7 , whereas there was posterolateral orientation from c5 in the studies by ebraheim et al . and pal et al . in this study , the facets of c3 and c4 were found to be posteromedially oriented and those of c5 , c6 and c7 were posteriorly oriented . this orientation of the facetal joints in the cervical region is such that their distraction leads to an increase in not only the inter - facetal height , but also the interspinous height and the intervertebral body height . this distraction leads to a decrease in the ligamentous buckling in the region , thus decompressing the cord . the height of the superior facet ranged from 7 to 12 mm and that of the inferior facet ranged from 7 to 13.5 mm . the width of the superior facet ranged from 7.5 to 12 mm and that of the inferior facet ranged from 8 to 15 mm . the width and height of the facets were almost the same at c3 and c4 level . from c5 to c7 , the width was more than the height . in a study performed by francis , the mean facet joint widths for males ranged from 10.1 to 12.3 mm and from 9.9 to 11.7 mm for females . in 1991 , milne disarticulated human cadaver vertebrae and determined facet joint widths from c3 to t1 levels . data from this study ranged from 8.5 to 10.4 mm . in 1993 , panjabi et al . reported a higher range ( 10.2 - 13.9 mm ) in the c3 to t1 facet joint widths . . found the widths to range from 8.6 to 9.6 mm for c3 to c7 levels of the spine . the angle of inclination of the superior and inferior facets was measured with the vertebra kept in the position as it lies in the human prone position . this angle gave the angle of insertion of the spacers between the superior and inferior facets . the mechanical strength , oblique profile , shape , and relatively large size of the facets can be used quite safely and effectively for facetal spacer insertion . the sizes of the spacers used varied from 2 to 4 mm in height and 8 mm in diameter . the distance of the inferior articular facet from the foramen tranversarium was more than 5 mm at all levels , thus keeping the vertebral artery at a safe distance from facetal spacers . measuring the facetal and interspinous height before and after spacer insertion demonstrated a mean increase of 3 mm in the facetal height and a mean increase of 4 mm in the interspinous distance . this increase gives credence to the philosophy of decompression of the root and spinal cord using the technique of facetal distraction . tan et al . in a recent publication studied the effects of machined allograft spacers on the cervical foraminal height and area . the use of the spacers increased the cervical foraminal height and area and caused indirect decompression of the exiting nerve root . it is generally believed that spinal degenerative disease initiates in the disc and osteophyte formation and retrolisthesis of the facets are secondary phenomenon . it has been proposed by us that the spondylotic disease may actually commence in the facet joints leading to subtle facetal instability and retrolisthesis , secondarily involving the intervertebral discs . this retrolisthesis can lead to a decrease in the inter - facet height and a reduction in the foraminal and intervertebral canal height causing radiculopathy and myelopathy . impaction of the spacers within the intra - articular space causes several structural changes , which can result in reversal of the pathological effects of cervical spondylosis . the impacted spacer also provided firm stability to the region and is safe with respect to the vertebral artery and the exiting nerve root . goel intra - articular spacers can be effectively used in the cervical facets for treatment of cervical spondylotic disease . they can be used as a stand - alone method of treatment or in combination with other methods of fixation .\noutput:\n" }, { "from": "agent", "value": "aim : quantitative anatomy of the facets of the sub - axial cervical spine was performed . the purpose of the evaluation was to determine the feasibility of insertion of goel inter - facetal articular spacers in the sub - axial cervical spine . only few studies detailing the morphometry of the facets are available in the literature.materials and methods : ten cervical vertebrae from c3 to c7 with a total of 20 facets were evaluated by the author . the anatomic parameters studied were the height , width , thickness , shape , orientation , and inclination of each of the superior and inferior facets . the alterations in a number of intervertebral segmental distances were measured before and after spacer insertion . the distance of the inferior facet from the foramen tranversarium , spinal canal , and neural foramina was measured to assess safety of spacer insertion with respect to the vertebral artery and neural structures.results : the height , width and thickness of the superior facets from c3 to c7 ranged from 6 to 12 mm , 8 to 12 mm , and 2.5 to 6 mm , respectively . the inferior facets had an average height of 10.5 mm , average width of 11.2 mm and average thickness of 3.5 mm . the inclination of the superior facets with respect to the transverse plane ranged from 22 to 45 and that of the inferior facets ranged from 29 to 53 . the distance of the anterior margin of the inferior facet from the posterior border of the foramen transversium ranged from 5 to 7 mm . this distance was maximum at c3 level , then decreased at c4 and remained constant from c5 to c7.conclusion : this anatomic evaluation aided in understanding the morphology of the cervical facets and the suitability of the cervical facetal articular cavity for insertion of spacers ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: appendiceal intussusception with a leading point in appendix is a very rare disease occurring only in 0.01 % of appendectomy patients .1 clinical symptoms vary from acute appendicitis symptoms such as right lower quadrant pain to repetitive right lower quadrant crampy pain to intermittent lower gastrointestinal bleeding .2,3 some patients are asymptomatic . children could be treated with barium enema or air reduction , while it is agreed that adult patients need operative treatment .4 there is still some debate about how to perform the reduction , but there are also reports that colonoscopic reduction could be considered for patients with good condition .5 - 7 we report a case of appendiceal intussusception that was diagnosed and reduced by colonoscopy , and histologically confirmed as a mucinous cystadenoma after the operation , together with a literature review . a 69 - year - old male visited the hospital for diarrhea and abdominal discomfort lasting about 2 weeks . he did not have a medical history of hypertension or diabetes mellitus , but had a past medical history of tuberculosis diagnosis and complete recovery 1 year before the visit . he did not have any history of operation in the abdomen nor a symptom during defecation . diarrhea and abdominal discomfort started 2 weeks before the visit , without other specific symptoms . vital signs at admission were measured as blood pressure 120/70 mm hg , pulse rate 68 / min , respiration rate 20 / min , and body temperature 36.5 . not pale conjunctiva and anicteric sclera was found at physical examination . cbc result showed wbc 3,220 / mm , hemoglobin 13.0 g / dl , hematocrit 38.0 % , platelet 263,000 / mm , pt 12.7 seconds ( inr 1.09 ) , and aptt 29.8 seconds . the blood chemistry was analyzed as total bilirubin 0.75 mg / dl , total protein 7.5 g / dl , albumin 4.1 g / dl , ast 25 iu / l , alt 19 iu / l , alp 66 iu / l , - gtp 42iu / l , triglyceride 72 mg / dl , cholesterol 149 mg / dl , bun 28 mg / dl , and creatinine 0.9 mg / dl . electrolyte was measured as na 135 mmol / dl , k 3.9 mmol / dl , and cl 101 mmol / dl . colonoscopy was performed for the suspected infectious colitis , where a huge mass was found protruding to the middle of lumen of the sigmoid colon toward the anus . this mass was migrated toward the proximal by the air infusion and was cleared through the colonoscopy . ileocecal lesion was found to have an edematous and erythematous mucosal change , and a cystic submucosal mass was found at the appendiceal orifice from histological examination after the colonoscopy ( fig . an abdomen - pelvis computed tomography was performed , then , for it was suspected of an intussusception reduced by colonoscopy , and a wall enhancing cystic lesion was found at the appendiceal base ( fig . when a follow - up colonoscopy was performed on day 4 , ileocecal mucosal lesion appeared to have improved ( fig . a laparoscopic appendectomy was performed on day 9 , and a histologic examination shows appendiceal cyst is lined by columnar mucinogenic cells and inflamed wall ( fig . appendiceal intussusception is a very rare disease that is appearing often as acute appendicitis , making it very difficult to diagnose before operation . recent development of radiologic examination and colonoscopy increased the possibility of diagnosis before operation , though .8 appendiceal intussusception is caused by irregular appendiceal peristalsis developed by local irritation , and is more likely to occur in mobile mesoappendix wide appendicular lumen , and thin and mobile appendix .2 leading contributing factors include endometriosis , mucocele , villus adenoma , carcinoid , and adenocarcinoma ; other less often factors include papilloma , hamartoma , mucosa - associated lymphoma , juvenile polyp , crohn 's disease , and melanosis coli .9 gross10 defined chronic intussusception as the disease lasting more than 5 days to 2 weeks . adult patients tend to show chronic or subacute clinical symptoms , generally of long - term intermittent partial intestinal obstruction . adult intussusception , especially appendiceal intussusception , varies from acute appendicitis symptoms such as right lower quadrant pain to repetitive right lower quadrant crampy pain to intermittent lower gastrointestinal bleeding . some patients are even asymptomatic .2,3 the most common symptom is the regular , intermittent abdominal pain . our patient was hard to be suspected as intussusception only from physical examination , since he did not show any particular symptoms except for the abdominal discomfort and diarrhea that had started 2 weeks ago . there is no finding for definite diagnosis of appendiceal intussusception , but several radiologic examinations might be useful . ' coiled spring ' sign of cecum or filling defect of appendix on double - contrast barium enema could be helpful for the diagnosis .11 on abdominal ultrasonography , cecum might appearing as concentric loop pattern or the appendix invaginated into the cecum .12 cecum appearing as a bulls - eye shape , sausage shape , or kidney shape are the characteristic findings of appendiceal intussusception on abdomen - pelvis computed tomography .13 our patient did not show such findings on abdomen - pelvis computed tomography , but a wall enhancing cystic lesion was found at the appendiceal base as the leading point of intussusception . radiologic examination is therefore considered as a useful tool not only for the definite diagnosis of apppendiceal intussusception but also for determining the presence and type of leading point and the possibility of malignancy . children could be treated with barium enema or air reduction , while it is agreed that adult patients need operative treatment .4 there is still some debate about how to perform the reduction , but there are also reports of intussusception cases reduced by colonoscopy ,5,6 suggesting that colonoscopic reduction by non - operative air infusion could be a possibility . such colonoscopic reduction accompanies the risk of dissemination of malignant lesion , peritoneal seeding , or venous embolism by excessive manipulation and the risk of bowel perforation accompanied by edema and ischemic change .14,15 there are also reports , however , that pre - operation colonoscopy might be useful for it could find a leading point of intussusception and the air infused during the procedure could often induce the reduction of intussusception .5 - 7,16 it is considered , therefore , that pre - operational reduction could be attempted for intussusception patients without severe bowel ischemia or malignancy . our case was first suspected as infectious colitis at admission ; following the colonoscopy , however , he was diagnosed as intussusception , which was reduced by the injected air during the advancing of the scope following the mass . the ileocecal mucosal lesion was confirmed to have improved on the clinical symptom and follow - up colonoscopy after the reduction . the possibility of malignancy was found unlikely on abdomen - pelvis computed tomography , and laparoscopic appendectomy , not laparotomy , was performed later to improve the prognosis and shorten the hospitalization period . when an appendiceal intussusception does not accompany the possibility of other malignancies , colonoscopic reduction followed by an operationthis strategy is also deemed to minimize the extent of operation of the leading point , thereby enabling the patient to recover more rapidly . we found that colonoscopy could play an important role in the diagnosis and treatment of appendiceal intussusception . more case reports on adult appendiceal intussusception reduced by colonoscopy and further studies on criteria for reduction are required .\noutput:\n" }, { "from": "agent", "value": "appendiceal intussusception is a very rare disease that is found in only 0.01 % of patients who have undergone an appendectomy . clinical symptoms vary but include acute appendicitis symptoms such as right lower quadrant abdominal pain or repetitive right lower quadrant crampy pain . some patients are asymptomatic . operative treatment is necessary to reduce an appendiceal intussusception in adults , but there is a debate about how to perform the reduction . successful colonoscopic reductions have been recently reported for some cases . we report a case of appendiceal intussusception that was diagnosed , reduced by colonoscopy , and histologically confirmed as a mucinous cystadenoma after the operation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: acrylic resins are commonly used for denture fabrication since they exhibit adequate physical , mechanical , and esthetic properties . however , it has been shown that denture base acrylic resins may act as reservoirs for microorganisms and have the potential to support biofilm formation . microbial growth on the denture surface results from the adherence of microbial cells enhanced by surface roughness , and from adhesive interactions between candida species and oral bacteria . several studies have demonstrated an association between c. albicans or other species of candida , and several oral bacteria such as streptococcus sanguis , streptococcus salivarius , streptococcus mutans , fusobacterium nucleatum and actinomyces viscosus . they can induce a chronic inflammatory response in the oral mucosa , described as denture stomatitis , which is the most common infectious disease affecting the oral mucosa and is highly prevalent in denture wearers . c. albicans and staphylococcus aureus have also been associated with lesions in several patients with angular cheilitis , as these microorganisms show a high ability to adhere to oral tissues . to avoid the formation of biofilm on denture base resin surfaces , several attempts to incorporate antifungal agents or antiseptics into tissue conditioners and denture acrylic resins have been reported . however , the materials exhibited antimicrobial activity by releasing antimicrobial agents that could have toxic effects on the oral mucosa , damage the mechanical properties of the materials , and lose their effectiveness over time . a possible alternative to solve this problem could be to substitute these substances with macromolecular antimicrobial agents , such as polycationic polymers with the advantages of reduced toxicity and not causing bacterial resistance . poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) is a functionalized polycationic polymer with pendant amino groups that acts as a very efficient contact biocide . it also has low solubility in water , which makes this biocide especially useful for incorporation into materials designed to be in contact with water , since one can expect very low leachability of ptbaema from polymer blends and compounds . this polymer has been incorporated into a polyethylene with potential fields of application , such as water treatment and inclusion in medical devices . the aim of this study was to evaluate the effect of a denture based acrylic resin containing different percentages of the polymer poly ( 2 - tert - butylaminoethyl ) methacrylate against the biofilm , in vitro , of staphylococcus aureus , streptococcus mutans and candida albicans . the null hypothesis was that denture based acrylic resin containing different percentages of the polymer poly ( 2 - tert - butylaminoethyl ) methacrylate would not inhibit the formation of staphylococcus aureus , streptococcus mutans and candida albicans biofilms . poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) is an antimicrobial polymer in powder form . previously to incorporation in acrylic resin it was necessary to solubilize the commercially available monomer , 2 - tert - butylaminoethyl methacrylate ( evonik degussa brasil ltda , so paulo , sp , brazil ) . the synthesis was performed as described by sosna , et al . first a three - necked flask was charged with 90 ml of 2 - tert butylaminoethyl and 180 ml of ethanol and heated to 65c under a stream of argon . next , 0.745 g of azobisisobutyronitrile ( sigma - aldrich , st louis , mo , usa ) dissolved in 20 ml of ethyl methyl ketone was slowly added drop - wise , with stirring . the mixture was heated to 70c and stirred at this temperature for 72 h. after this time had elapsed , the reaction mixture was stirred into 1l of demineralized water , whereupon the polymeric product was precipitated . after the product was separated by filtration , the filter residue was washed with 100 ml of a 10 % solution of ethanol in water in order to remove any residual monomers still present . initially , a metal mold was used to make disk - shaped silicone patterns ( zetaplus , indurent - zhermack , badia polesine , rovigo , italy ) measuring 15 mm x 2 mm . these silicone patterns were sandwiched between two glass slides and invested in flasks with type iv dental stone ( herodent , vigodent sa ind . com . after the dental stone had set , the flasks were separated and the silicone patterns were removed , leaving disk - shaped cavities . the polymer ptbaema was mixed with the acrylic resin powder ( lucitone 550 , dentsply indstria e comrcio ltda , petrpolis , rj , brazil ) at concentrations : 0 % ( control ) , 10 % and 25 % . the combined powder was then mixed with the resin liquid and the resin dough was put into the disk - shaped cavities . after polymerization , the excess material was carefully removed using a bur ( maxi - cut ; maillefer sa , ballaigues , switzerland ) . after this , the specimens were sterilized using ethylene oxide gas , with a temperature of 50c5c for 4 hours . groups according to the percentage of poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) in order to assay the antimicrobial activity of the experimental specimens , three standard strain microorganisms were tested : staphylococcus aureus atcc 25923 , streptococcus mutans atcc 25175 and candida albicans atcc 90028 . microbial suspensions were obtained from single colonies isolated on agar plates , inoculated in the appropriate broth for overnight cultures at 37c . s. mutans was grown in brain - heart infusion ( bhi ) broth and c. albicans and s. aureus strains were grown in tryptic soy broth ( tsb ) . cells of the resultant cultures were harvested , washed twice with phosphate - buffered saline ( pbs , ph 7.2 ) , centrifuged at 5000x g for 5 min and re - suspended in appropriate fresh broth . microbial suspensions were spectrophotometrically ( biophotometer plus , eppendorf , hauppauge , ny , united states ) standardized to a concentration of 1x10 cells / ml . biofilms of each microorganism ( staphylococcus aureus , streptococcus mutans and candida albicans ) were produced in pre - sterilized , 12 - well polystyrene flat - bottomed microtiter plates . first each sterile acrylic resin specimen was individually placed in each well of a microtiter plate and 2 ml of standard cell suspensions ( 10 cells / ml ) prepared as mentioned above and added to each well containing a specimen . the plate was incubated for 90 min at 37c in an orbital shaker at 75 rpm to promote microorganism adherence to the specimen surfaces ( adhesion phase ) . after the adhesion phase , the specimens were transferred to new wells and the non - adherent cells were removed from the specimen by gently washing twice with 2 ml pbs . to promote biofilm growth ( biofilm phase ) , 2 ml of appropriate fresh broth was added to each well . the plates were covered and incubated at 37c at 75 rpm for 48 h under aerobic conditions ( staphylococcus aureus and candida albicans ) and anaerobic conditions ( streptococcus mutans ) . after incubation , the plates were removed from the incubator and the wells gently washed twice with pbs . after washing , the specimens were transferred to a tube containing distilled water and sonicated for 20 min to disrupt the biofilm cell aggregates . the resultant suspension containing the detached biofilm cells was vortexed , diluted and plated onto sterile petri dishes containing selective media for staphylococcus aureus , streptococcus mutans and candida albicans for 48 h at 37c under aerobic or anaerobic conditions , as deemed appropriate . the media used for plating s. mutans was sb20 , for c. albicans sabouraud dextrose agar was used with 5 g / ml chloranphenicol and s. aureus strains were grown in mannitol salt agar . staphylococcus aureus and candida albicans were cultivated under aerobic conditions and streptococcus mutans under anaerobic conditions . after incubation , colony counts of each petri dish were quantified using a digital colony counter ( cp 600 plus , phoenix ind . no homogeneity of variances was observed for the three species evaluated ( levene test , p 0.05 ) , and nonparametric tests were then performed . s. aureus and s. mutans counts were compared by the mann - whitney test and c. albicans results were compared by the kruskal - wallis test . poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) is an antimicrobial polymer in powder form . previously to incorporation in acrylic resin it was necessary to solubilize the commercially available monomer , 2 - tert - butylaminoethyl methacrylate ( evonik degussa brasil ltda , so paulo , sp , brazil ) . the synthesis was performed as described by sosna , et al . first a three - necked flask was charged with 90 ml of 2 - tert butylaminoethyl and 180 ml of ethanol and heated to 65c under a stream of argon . next , 0.745 g of azobisisobutyronitrile ( sigma - aldrich , st louis , mo , usa ) dissolved in 20 ml of ethyl methyl ketone was slowly added drop - wise , with stirring . the mixture was heated to 70c and stirred at this temperature for 72 h. after this time had elapsed , the reaction mixture was stirred into 1l of demineralized water , whereupon the polymeric product was precipitated . after the product was separated by filtration , the filter residue was washed with 100 ml of a 10 % solution of ethanol in water in order to remove any residual monomers still present . initially , a metal mold was used to make disk - shaped silicone patterns ( zetaplus , indurent - zhermack , badia polesine , rovigo , italy ) measuring 15 mm x 2 mm . these silicone patterns were sandwiched between two glass slides and invested in flasks with type iv dental stone ( herodent , vigodent sa ind . com . after the dental stone had set , the flasks were separated and the silicone patterns were removed , leaving disk - shaped cavities . the polymer ptbaema was mixed with the acrylic resin powder ( lucitone 550 , dentsply indstria e comrcio ltda , petrpolis , rj , brazil ) at concentrations : 0 % ( control ) , 10 % and 25 % . the combined powder was then mixed with the resin liquid and the resin dough was put into the disk - shaped cavities . after polymerization , the excess material was carefully removed using a bur ( maxi - cut ; maillefer sa , ballaigues , switzerland ) . after this , the specimens were sterilized using ethylene oxide gas , with a temperature of 50c5c for 4 hours . in order to assay the antimicrobial activity of the experimental specimens , three standard strain microorganisms were tested : staphylococcus aureus atcc 25923 , streptococcus mutans atcc 25175 and candida albicans atcc 90028 . microbial suspensions were obtained from single colonies isolated on agar plates , inoculated in the appropriate broth for overnight cultures at 37c . s. mutans was grown in brain - heart infusion ( bhi ) broth and c. albicans and s. aureus strains were grown in tryptic soy broth ( tsb ) . cells of the resultant cultures were harvested , washed twice with phosphate - buffered saline ( pbs , ph 7.2 ) , centrifuged at 5000x g for 5 min and re - suspended in appropriate fresh broth . microbial suspensions were spectrophotometrically ( biophotometer plus , eppendorf , hauppauge , ny , united states ) standardized to a concentration of 1x10 cells / ml . biofilms of each microorganism ( staphylococcus aureus , streptococcus mutans and candida albicans ) were produced in pre - sterilized , 12 - well polystyrene flat - bottomed microtiter plates . first each sterile acrylic resin specimen was individually placed in each well of a microtiter plate and 2 ml of standard cell suspensions ( 10 cells / ml ) prepared as mentioned above and added to each well containing a specimen . the plate was incubated for 90 min at 37c in an orbital shaker at 75 rpm to promote microorganism adherence to the specimen surfaces ( adhesion phase ) . after the adhesion phase , the specimens were transferred to new wells and the non - adherent cells were removed from the specimen by gently washing twice with 2 ml pbs . to promote biofilm growth ( biofilm phase ) , 2 ml of appropriate fresh broth was added to each well . the plates were covered and incubated at 37c at 75 rpm for 48 h under aerobic conditions ( staphylococcus aureus and candida albicans ) and anaerobic conditions ( streptococcus mutans ) . after incubation , the plates were removed from the incubator and the wells gently washed twice with pbs . after washing , the specimens were transferred to a tube containing distilled water and sonicated for 20 min to disrupt the biofilm cell aggregates . the resultant suspension containing the detached biofilm cells was vortexed , diluted and plated onto sterile petri dishes containing selective media for staphylococcus aureus , streptococcus mutans and candida albicans for 48 h at 37c under aerobic or anaerobic conditions , as deemed appropriate . the media used for plating s. mutans was sb20 , for c. albicans sabouraud dextrose agar was used with 5 g / ml chloranphenicol and s. aureus strains were grown in mannitol salt agar . staphylococcus aureus and candida albicans were cultivated under aerobic conditions and streptococcus mutans under anaerobic conditions . after incubation , colony counts of each petri dish were quantified using a digital colony counter ( cp 600 plus , phoenix ind . no homogeneity of variances was observed for the three species evaluated ( levene test , p 0.05 ) , and nonparametric tests were then performed . s. aureus and s. mutans counts were compared by the mann - whitney test and c. albicans results were compared by the kruskal - wallis test . the number of viable cells of each microorganism and standard deviations are presented in figures 1 , 2 and 3 . effect of different percentages of poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) incorporated into acrylic resin specimens on the viability of staphylococcus aureus biofilm cells . different capital letters denote signicant differences among groups ( mann - whitney test , p = 0.001 ) effect of different percentages of poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) incorporated into acrylic resin specimens on the viability of streptococcus mutans biofilm cells . different capital letters denote signicant differences among groups ( mann - whitney test , p = 0.001 ) effect of different percentages of poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) incorporated into acrylic resin specimens on the viability of candida albicans biofilm cells . identical capital letters denote no signicant differences among groups ( kruskal wallis test , p = 0.079 ) a strong dose - dependent bactericidal effect against staphylococcus aureus and streptococcus mutans biofilms was observed with a reduction in viable cells according to the percentage of ptbaema incorporated into the acrylic resin . for these microorganisms , significant antimicrobial activity was observed for the acrylic resin containing 10 % ptbaema in comparison with the corresponding control groups ( p 0.05 ) . a decrease in the number of viable biofilm cells of s. aureus ( control group : 7.90.8 ; group 10 % : 3.83.3 ) and s. mutans ( control group : 7.50.7 ; group 10 % : 5.12.7 ) in addition , the number of viable biofilm cells of s. aureus and s. mutans was strongly reduced during contact with the acrylic resin specimens containing 25 % ptbaema , reducing the number of cells to zero . however , for the c. albicans biofilm ( control group : 6.60.2 ; group 10 % : 6.60.4 , 6.40.1 ) , there was no significant difference among the groups ( p 0.05 ) . in this study , a water - insoluble polycationic polymer poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) was incorporated into an acrylic resin , whose biocidal properties resulted from the pendant bulky secondary amine of the methacrylate backbone . the findings of this study showed that the group containing 10 % ptbaema significantly reduced the number of s. aureus and s. mutans biofilms formed on the specimen surfaces when compared with the control group . in the group containing 25 % ptbaema , complete inhibition of s. aureus and s. mutans biofilm formation was observed . these results show a dose - dependent response to ptbaema and were similar to results of others authors . ( 2006 ) investigated the antimicrobial properties of a polyethylene containing different concentrations of ptbaema , which reduced the number of cfu / ml of s. aureus to zero after 24 hours of contact with groups containing ptbaema . ( 2006 ) showed that a stainless steel coated ptbaema reduced the adhesion of s. aureus by 99.9 % . ( 2007 ) after evaluation of the antimicrobial properties against e. coli , of compounds into which ptbaema had been incorporated , showing that the bacteria had been completely eliminated after a certain period of time . although this study did not evaluate mixed species biofilm , it is known that bacteria can significantly influence and modify candidal growth and biofilm formation . this study presented a significant effect of ptbaema against the s. mutans biofilm , which is considered one of the primary colonizers of oral biofilm , and is heavily involved in the initial stages of biofilm formation , producing extra cellular matrix polysaccharide and facilitating the attachment of other microorganisms such as c. albicans . moreover , the reduction in the amount of s. aureus biofilm observed in this study represents a significant result , since s. aureus is a normal colonizer of the oral cavity , and this colonization can be a potential danger to the patient as a source of bacterial dissemination to other sites in the body , and a source of transmission to other people , food or objects . according to lenoir , et al . ( 2008 ) the biocidal action is based on the interaction between the membrane of the bacteria in contact with ptbaema . the divalent cations ca and / or mg that cross - bridge the outer membrane of the bacteria are replaced by the charged amine groups of ptbaema , followed by membrane disorganization and cell lyses . moreover , ptbaema can also act in inducing a phase - separation of charged and uncharged lipids inside the cytoplasma membrane of bacteria . finally , the cytoplasma membrane disintegrates , which causes the death of the microorganism ( apoptosis ) . the results of this study also demonstrated that the denture base acrylic resin with incorporation of ptbaema did not have antifungal activity against candida albicans . ( 2008 ) incorporated methacrylic acid into an acrylic denture base resin and observed a reduction in the number of c. albicans . these conflicting results may be related to the ability of each agent to interact with the cell wall of c. albicans , much like other living cells , has a net negative surface charge , providing an environment of electrostatic repulsion through the negative - negative charge interactions with the polymer . ( 2012 ) incorporated silver nanoparticles ( agnps ) into a denture base acrylic resin and did not observed an effect on c. albicans adherence and biofilm formation . the effect of ptbaema incorporated to denture base acrylic resins against c. albicans is not well - established , since the biocide power of this agent has been evaluated only in polyethylene compounds . the fungus , different from the bacteria , shows a cell wall composed of approximately 80 to 90 % carbohydrate . moreover , the microfibrillar polymers ( b - glucans and chitin ) represent the structural components of the wall . they form a rigid skeleton that provides strong physical properties to the cell . consequently , it might be supposed that this rigid skeleton protects c. albicans against ptbaema and do not allow the antimicrobial agent to displace ca and / or mg ions from the outer wall of the cell . further studies should be conducted to determine the cytotoxicity of this polymer and to assess possible changes in the properties of acrylic resin due to the incorporation of ptbaema , such as flexural strength , surface roughness , vickers hardness and color stability of acrylic resin . according to previous studies that have incorporated antimicrobials agents into acrylic resin , some kind of damage on the mechanical and / or physical properties of the acrylic resinthe characterization of the acrylic resin after the incorporation of ptbaema is not described in this study , since chemical and mechanical tests are being conducted and will be showed in a specific paper on this subject . within the limitations of this study , favorable outcomes were detected indicating that ptbaema might also be successfully associated with other dental materials since streptococcus sp . in addition , staphylococcal infections , particularly those caused by staphylococcus aureus , produce substantial morbidity and mortality in hemodialysis patients . within the limitations of this study , it can be concluded that the denture base acrylic resin combined with 10 % and 25 % ptbaema showed a significant antimicrobial activity against s. aureus and s. mutans biofilm , but had no significant effect on the c. albicans biofilm formation . the authors would like to thank professor adhemar c. ruvollo - filho , of the federal university of so carlos ( ufscar ) for his assistance with the synthesis of poly ( 2 - tert - butylaminoethyl ) methacrylate ; professor raphael freitas de souza of ribeiro preto dental school - university of so paulo ( usp ) for his assistance with the statistical analysis ; evonik - degussa ( so paulo , brazil ) for supplying a research sample of tbaema and fapesp for financial support ( grants no . 2008 / 02602 - 0 and no .\noutput:\n" }, { "from": "agent", "value": "objectivesthe purpose of this study was to evaluate the antimicrobial activity of an acrylic resin combined with an antimicrobial polymer poly ( 2 - tert - butylaminoethyl ) methacrylate ( ptbaema ) to inhibit staphylococcus aureus , streptococcus mutans and candida albicans biofilm formation . material and methodsdiscs of a heat - polymerized acrylic resin were produced and divided according to ptbaema concentration : 0 ( control ) , 10 and 25 % . the specimens were inoculated ( 107 cfu / ml ) and incubated at 37c for 48 h. after incubation , the wells were washed and each specimen was sonicated for 20 min . replicate aliquots of resultant suspensions were plated at dilutions at 37c for 48 h. the number of colony - forming units ( cfu ) was counted and expressed as log ( cfu +1 ) / ml and analyzed statistically with = .05 . resultsthe results showed that 25 % ptbaema completely inhibited s. aureus and s. mutans biofilm formation . a significant reduction of log ( cfu +1 ) / ml in count of s. aureus ( control : 7.90.8 a ; 10 % : 3.83.3 b ) and s. mutans ( control : 7.50.7 a ; 10 % : 5.12.7 b ) was observed for the group containing 10 % ptbaema ( mann - whitney , p < 0.05 ) . for c. albicans , differences were not significant among the groups ( control : 6.60.2 a ; 10 % : 6.60.4 a ; 25 % : 6.40.1 a ) , ( kruskal - wallis , p > 0.05 , p = 0.079 ) . conclusionsacrylic resin combined with 10 and 25 % of ptbaema showed significant antimicrobial activity against s. aureus and s. mutans biofilm , but it was inactive against the c. albicans biofilm ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: qaannaq , upernavik , ummannaq , qeqertarsuaq , ilulissat , sisimiut , nuuk , narsaq , tasiilaq and ittoqqor - toormitt in the period from 19972006 ( fig . participants from nuuk during 20002002 were randomly selected from a cross - sectional study assessing legacy pop exposure on osteoporosis - related ultrasound bone measurements in greenlandic inuit women ( 29 ) , and the rest of the participants were randomly selected from projects in the human health program of the ongoing circumpolar amap ( 21,30,31 ) . map of greenland showing the different districts and sampling periods , including the serum pfaas median levels ( ng / ml ) for each district . the proposed protocols of the studies were accepted by the ethical committee for scientific investigations in greenland and all the participants gave written informed consent . the following compounds were analysed in serum samples : perfluoroheptanoic acid ( pfhpa ) , perfluorooctanoic acid ( pfoa ) , perfluorononanoic acid ( pfna ) , perfluorodecanoic acid ( pfda ) , perfluoroundecanoic acid ( pfuna ) , perfluorododecanoic acid ( pfdoa ) , perfluorotridecanoic acid ( pftra ) , perfluorohexane sulfonate ( pfhxs ) , perfluorooctane sulfonate ( pfos ) and perfluorooctane sulfonamide ( pfosa ) . the following compounds from wellington laboratories were used as surrogate standards : c8 - pfoa , c4pfos and c2 - pfda . instrumental analysis was performed by liquid chromatography - tandem mass spectrometry ( lc - ms - ms ) with electrospray ionization ( esi ) . the analytical method used heremethod performance was tested through participation in inter - laboratory comparison studies organized by the institute nationale de sant publique du qubec for amap ( 33 ) . satisfactory z - scores were obtained in the inter - laboratory comparison studies from our laboratory . serum concentration of pcb congeners cb99 , cb101 , cb105 , cb118 , cb128 , cb138 , cb153 , cb156 , cb170 , cb180 , cb183 and cb187 , and organochlorine pesticides including chlordanes , p , p - dichlorodiphenyldichloroethane ( p , p - dde ) , p , p - dichlorodiphenyltrichloroethane ( p , p - ddt ) , oxychlordane , hexachlorobenzene ( hcb ) , beta - hexachlorocyclohexane ( - hch ) , mirex and toxaphene were measured at the certified laboratory , le centre toxicologie , in sainte foy , quebec , canada ( 21,23,29,30 ) . the fatty acid profiles were determined in plasma phospholipids at the biology department of the university of guelph , ontario , canada ( 23,34 ) . the ratio between n - 3 polyunsaturated fatty acids and n - 6 fatty acids is known to be a strong indicator of seafood intake and thus is a good indicator of the relative consumption of traditional food versus imported food ( 35 ) . the statistical analysis of the data was performed in spss 13.0 ( spss inc . , half of the detection limit values were used in case of concentrations below the detection limit . based on the chemical structure , the analysed pfaas were grouped in perfluorosulfonated acids ( pfsas ) as in , the sum of pfos , pfhxs and pfosa and perfluor - ocarboxylated acids ( pfcas ) , which were made up of the sum of pfhpa , pfoa , pfna , pfda , pfuna , pfdoa and pftra . the legacy pops were grouped in pcbs ( sum of 12 measured pcb congeners ) , pesticides ( sum of 8 measured organochlorine pesticides ) and legacy pops ( sum of 12 pcb congeners and 8 pesticides ) . due to the low number of samples collected from most districts and the different lifestyles among them ( 21 ) , the data from non - nuuk districts were grouped as pooled non - nuuk district data , and the subsequent data analysis was based on the comparison between nuuk and pooled non - nuuk district data . natural logarithm ( ln ) - transformed data improved the normality and homogeneity of variance and the statistical analyses were performed on the ln - transformed data . pearson correlation analysis was performed to assess the bivariate correlation between life - style factors and both pfaas and legacy pops . previous studies reported a correlation between pfaa and both age and n - 3 / n - 6 ratio ( 17,26,36 ) . therefore comparisons of means for pfaas between the districts and genders were also performed by the general linear model procedure under adjustment of age and n - 3 / n - 6 . the following approaches were used : ( 1 ) univariate regression analyses , where age and n - 3 / n - 6 were included individually in the model ; ( 2 ) multi - variate regression analyses , in which pfos , pfoa , sumpfsa sumpfca , age and n - 3 / n - 6 were included and thereby mutually adjusted . multiple linear regression analysis was used to assess the relationship between serum pfaa levels and the serum level of legacy pops under adjustment of age and n - 3 / n - 6 ratio . comparison of the biomarker of seafood intake ( n - 3 / n - 6 ratio ) was also performed under adjustment of age since seafood intake is significantly correlated to age . time pfaa trend analyses were performed on 142 samples from nuuk . only time series with at least 4 years of data were included in the analysis . the analyses of temporal trends followed the procedures used in temporal trend assessments by the international council for the exploration of the sea , a method that employs a robust , regression - based analysis to detect temporal trends ( 37 ) . the total variation in the contaminant index values over time was divided into a linear and a non - linear component . log - linear regression analysis was applied to describe the linear component , and a simple , 3 - point running mean smoother was applied to describe the non - linear component . the linear and non - linear components were tested by means of an anova . the time trend analysis was performed with pia , a statistic analytical tool developed for analysis of amap time trend data sets ( 38 ) . since pfaas was reported to be related to age ( 26 ) , age was also added as a covariate for the adjustment of age in the trend analysis . all participants were of inuit descent , defined as having more than 2 grandparents born in greenland . qaannaq , upernavik , ummannaq , qeqertarsuaq , ilulissat , sisimiut , nuuk , narsaq , tasiilaq and ittoqqor - toormitt in the period from 19972006 ( fig . participants from nuuk during 20002002 were randomly selected from a cross - sectional study assessing legacy pop exposure on osteoporosis - related ultrasound bone measurements in greenlandic inuit women ( 29 ) , and the rest of the participants were randomly selected from projects in the human health program of the ongoing circumpolar amap ( 21,30,31 ) . map of greenland showing the different districts and sampling periods , including the serum pfaas median levels ( ng / ml ) for each district . the proposed protocols of the studies were accepted by the ethical committee for scientific investigations in greenland and all the participants gave written informed consent . the following compounds were analysed in serum samples : perfluoroheptanoic acid ( pfhpa ) , perfluorooctanoic acid ( pfoa ) , perfluorononanoic acid ( pfna ) , perfluorodecanoic acid ( pfda ) , perfluoroundecanoic acid ( pfuna ) , perfluorododecanoic acid ( pfdoa ) , perfluorotridecanoic acid ( pftra ) , perfluorohexane sulfonate ( pfhxs ) , perfluorooctane sulfonate ( pfos ) and perfluorooctane sulfonamide ( pfosa ) . the following compounds from wellington laboratories were used as surrogate standards : c8 - pfoa , c4pfos and c2 - pfda . instrumental analysis was performed by liquid chromatography - tandem mass spectrometry ( lc - ms - ms ) with electrospray ionization ( esi ) . the analytical method used heremethod performance was tested through participation in inter - laboratory comparison studies organized by the institute nationale de sant publique du qubec for amap ( 33 ) . satisfactory z - scores were obtained in the inter - laboratory comparison studies from our laboratory . serum concentration of pcb congeners cb99 , cb101 , cb105 , cb118 , cb128 , cb138 , cb153 , cb156 , cb170 , cb180 , cb183 and cb187 , and organochlorine pesticides including chlordanes , p , p - dichlorodiphenyldichloroethane ( p , p - dde ) , p , p - dichlorodiphenyltrichloroethane ( p , p - ddt ) , oxychlordane , hexachlorobenzene ( hcb ) , beta - hexachlorocyclohexane ( - hch ) , mirex and toxaphene were measured at the certified laboratory , le centre toxicologie , in sainte foy , quebec , canada ( 21,23,29,30 ) . the fatty acid profiles were determined in plasma phospholipids at the biology department of the university of guelph , ontario , canada ( 23,34 ) . the ratio between n - 3 polyunsaturated fatty acids and n - 6 fatty acids is known to be a strong indicator of seafood intake and thus is a good indicator of the relative consumption of traditional food versus imported food ( 35 ) . the statistical analysis of the data was performed in spss 13.0 ( spss inc . , half of the detection limit values were used in case of concentrations below the detection limit . based on the chemical structure , the analysed pfaas were grouped in perfluorosulfonated acids ( pfsas ) as in , the sum of pfos , pfhxs and pfosa and perfluor - ocarboxylated acids ( pfcas ) , which were made up of the sum of pfhpa , pfoa , pfna , pfda , pfuna , pfdoa and pftra . the legacy pops were grouped in pcbs ( sum of 12 measured pcb congeners ) , pesticides ( sum of 8 measured organochlorine pesticides ) and legacy pops ( sum of 12 pcb congeners and 8 pesticides ) . due to the low number of samples collected from most districts and the different lifestyles among them ( 21 ) , the data from non - nuuk districts were grouped as pooled non - nuuk district data , andthe subsequent data analysis was based on the comparison between nuuk and pooled non - nuuk district data . natural logarithm ( ln ) - transformed data improved the normality and homogeneity of variance and the statistical analyses were performed on the ln - transformed data . pearson correlation analysis was performed to assess the bivariate correlation between life - style factors and both pfaas and legacy pops . previous studies reported a correlation between pfaa and both age and n - 3 / n - 6 ratio ( 17,26,36 ) . therefore comparisons of means for pfaas between the districts and genders were also performed by the general linear model procedure under adjustment of age and n - 3 / n - 6 . the following approaches were used : ( 1 ) univariate regression analyses , where age and n - 3 / n - 6 were included individually in the model ; ( 2 ) multi - variate regression analyses , in which pfos , pfoa , sumpfsa sumpfca , age and n - 3 / n - 6 were included and thereby mutually adjusted . multiple linear regression analysis was used to assess the relationship between serum pfaa levels and the serum level of legacy pops under adjustment of age and n - 3 / n - 6 ratio . comparison of the biomarker of seafood intake ( n - 3 / n - 6 ratio ) was also performed under adjustment of age since seafood intake is significantly correlated to age . time pfaa trend analyses were performed on 142 samples from nuuk . only time series with at least 4 years of data were included in the analysis . the analyses of temporal trends followed the procedures used in temporal trend assessments by the international council for the exploration of the sea , a method that employs a robust , regression - based analysis to detect temporal trends ( 37 ) . the total variation in the contaminant index values over time was divided into a linear and a non - linear component . log - linear regression analysis was applied to describe the linear component , and a simple , 3 - point running mean smoother was applied to describe the non - linear component . the time trend analysis was performed with pia , a statistic analytical tool developed for analysis of amap time trend data sets ( 38 ) . since pfaas was reported to be related to age ( 26 ) , age was also added as a covariate for the adjustment of age in the trend analysis . the median age of the green - landic inuit in the study was 50 years , ranged from 18 to 73 years . the included inuit living in nuuk were older than those living in the pooled non - nuuk districts , in terms of both the separate genders and pooled gender data . it should be noted that data for only 5 males were included in the nuuk district data . no significant difference was found in the bmi and the seafood intake biomarker ( n - 3 / n - 6 ) between nuuk and non - nuuk inuit . most participants ( 68.9 % ) were smokers , but no difference was observed between districts . no gender differences were observed for age , bmi , n - 3 / n - 6 and smoking status within nuuk and pooled non - nuuk districts ( p 0.06 ) ( table i ) . pfaa concentrations differed significantly between the studied inuit from nuuk and pooled non - nuuk districts . nuuk inuit had significantly higher pfaa levels than pooled non - nuuk inuit , both for the separate gender data and pooled data . serum levels of pfaas and legacy pops of greenlandic inuit participants p - value of nuuk vs. non - nuuk after adjustment for age and n - 3 / n - 6 ; legacy pops is the summation of pcbs and pesticides ( pcbs + pesticides ) . two subjects from upernavik district had relatively high values of pfaas ( pfos : 91.8 and 74.9 ng / ml ; pfoa : 8.6 and 4.0 ng / ml ; pfsa : 101 and 83.5 ng / ml ; pfca : 12.8 and 9.85 ng / ml ) . the levels of legacy pops were generally higher for nuuk inuit compared to non - nuuk inuit . for the pooled gender data , levels of pcbs , pesticides and legacy pops for nuuk inuit were significantly higher than for pooled non - nuuk inuit ( table ii ) . however , after adjustment for age and n - 3 / n - 6 , pcb levels were not significantly different between the nuuk district and pooled non - nuuk district for the separate genders , whereas pesticides differed between the 2 district groups for both genders . serum pfaa levels in male inuit were significantly higher than those in female inuit both before and after adjustment for age and n - 3 / n - 6 within both nuuk and pooled non - nuuk districts ( figure 2a , 2b ) . significantly higher levels of legacy pops for males were found in the pooled non - nuuk districts only , and a statistically insignificant tendency of higher legacy pops in nuuk males was observed , although the small sample size of nuuk males must be taken intoconsideration ( figure 2c ) . a ) pfsas ( pfos + pfhxs + pfosa ) ; b ) pfcas ( pfhpa + pfoa + pfna + pfda + pfuna + pfdoa + pftra ) ; c ) legacy pops ( pcbs + pesticides ) . p - values were adjusted for age and n - 3 / n - 6 . a significant but weakly positive correlation between age and serum pfaa levels ( r0 .29 , p0 .001 ) was observed in non - nuuk inuit . for the nuuk inuit , in general , pfaas were not significantly correlated to age ( supplementary table i a , www.ijch.fi ) . a relatively weak correlation between serum concentrations of pfsas and pfcas and n - 3 / n - 6 ( r 0.27 , p 0.05 ) was observed for both nuuk and non - nuuk inuit ( supplementary table i a , www.ijch.fi ) . legacy pops significantly correlated with age ( r 0.42 , p 0.0001 ) and n - 3 / n - 6 ( r 0.60 , p 0.0001 ) ( supplementary table i a , www.ijch.fi ) . positive correlations among pfaa levels with both age and seafood intake were also observed for both genders . in general , the correlations found in female inuit were higher than those in male inuit , while the correlations between age , n - 3 / n - 6 and legacy pops between genders were similar ( supplementary table i b , www.ijch.fi ) . for male inuit , the correlation between n - 3 / n - 6 and pfaas was weaker than that between legacy pops and n - 3 / n - 6 ( supplementary table i b , www.ijch.fi ) . to explore whether the sources for the body burden of pfaas and legacy pops in green - landic inuitwere identical , we analysed the correlation between serum pfaas and legacy pops . for the nuuk inuit , positive correlations between serum pfos , pfsas , pfcas and legacy pops were observed . but after adjustment for age and seafood intake ( n - 3 / n - 6 ) , the significant correlations of pfos and pfsas with legacy pops disappeared ( table iii ) . for the non - nuuk inuit , significant correlations between serum pfaas and legacy pops were observed both before and after adjustments for age and n - 3 / n - 6 ( table iii ) . the correlation between pfaas and legacy pops was also different between genders . for the male nuuk inuitno correlations were observed , possibly because of the low number of males in the study ( n = 5 ) . for non - nuuk malesthe significant correlation between pfaas and legacy pops disappeared after adjustment for age and n - 3 / n - 6 . for non - nuuk female inuit and for female inuit in general , serum pfaas significantly correlated to legacy pops both before and after adjustment for age and n - 3 / n - 6 , whereas for nuuk females alone the significance disappeared upon adjustment ( table iii ) . association between serum pfcs and serum legacy pops legacy pop is the regression coefficient of pfaas to legacy pops . temporal trend analysis was performed for the district of nuuk , where a sufficient number of samples were available for the period 19982005 . as shown in table iv , pfos level and pfca level showed 2.2 % and 7.1 % yearly increasing trends , respectively , for female inuit . for the pooled gender data , 28 % , 28 % , 10 % , 13 % and 15 % yearly increasing trends were found for pfna , pfda , pfdoa , pftra and pfcas , respectively . the trends were statistically significant ( p 0.05 ) . however , after adjustment for age , the significant trend disappeared ( table iv ) . no significant time trend was observed for the serum level of pfoa and pfsa before and after adjustment for age ( table iv ) , and neither for pfhxs , pfosa , pfhpa or pfuna ( data not shown ) . time trend of serum concentrations ( ng / ml ) of pfaas in greenlandic inuit from nuuk in the period 19982005 slope : yearly difference ; values in bold indicate that the trend is statistically significant . time trend analysis was not performed for the male inuit because there were only 5 males studied in nuuk . for other test pfaas , no time trend was observed . the median age of the green - landic inuit in the study was 50 years , ranged from 18 to 73 years . the included inuit living in nuuk were older than those living in the pooled non - nuuk districts , in terms of both the separate genders and pooled gender data . it should be noted that data for only 5 males were included in the nuuk district data . no significant difference was found in the bmi and the seafood intake biomarker ( n - 3 / n - 6 ) between nuuk and non - nuuk inuit . most participants ( 68.9 % ) were smokers , but no difference was observed between districts . no gender differences were observed for age , bmi , n - 3 / n - 6 and smoking status within nuuk and pooled non - nuuk districts ( p 0.06 ) ( table i ) . pfaa concentrations differed significantly between the studied inuit from nuuk and pooled non - nuuk districts . nuuk inuit had significantly higher pfaa levels than pooled non - nuuk inuit , both for the separate gender data and pooled data . serum levels of pfaas and legacy pops of greenlandic inuit participants p - value of nuuk vs. non - nuuk after adjustment for age and n - 3 / n - 6 ; legacy pops is the summation of pcbs and pesticides ( pcbs + pesticides ) . two subjects from upernavik district had relatively high values of pfaas ( pfos : 91.8 and 74.9 ng / ml ; pfoa : 8.6 and 4.0 ng / ml ; pfsa : 101 and 83.5 ng / ml ; pfca : 12.8 and 9.85 ng / ml ) . the levels of legacy pops were generally higher for nuuk inuit compared to non - nuuk inuit . for the pooled gender data , levels of pcbs , pesticides and legacy pops for nuuk inuit were significantly higher than for pooled non - nuuk inuit ( table ii ) . however , after adjustment for age and n - 3 / n - 6 , pcb levels were not significantly different between the nuuk district and pooled non - nuuk district for the separate genders , whereas pesticides differed between the 2 district groups for both genders . serum pfaa levels in male inuit were significantly higher than those in female inuit both before and after adjustment for age and n - 3 / n - 6 within both nuuk and pooled non - nuuk districts ( figure 2a , 2b ) . significantly higher levels of legacy pops for males were found in the pooled non - nuuk districts only , and a statistically insignificant tendency of higher legacy pops in nuuk males was observed , although the small sample size of nuuk males must be taken intoconsideration ( figure 2c ) . a ) pfsas ( pfos + pfhxs + pfosa ) ; b ) pfcas ( pfhpa + pfoa + pfna + pfda + pfuna + pfdoa + pftra ) ; c ) legacy pops ( pcbs + pesticides ) . a significant but weakly positive correlation between age and serum pfaa levels ( r0 .29 , p0 .001 ) was observed in non - nuuk inuit . for the nuuk inuit , in general , pfaas were not significantly correlated to age ( supplementary table i a , www.ijch.fi ) . a relatively weak correlation between serum concentrations of pfsas and pfcas and n - 3 / n - 6 ( r 0.27 , p 0.05 ) was observed for both nuuk and non - nuuk inuit ( supplementary table i a , www.ijch.fi ) . legacy pops significantly correlated with age ( r 0.42 , p 0.0001 ) and n - 3 / n - 6 ( r 0.60 , p 0.0001 ) ( supplementary table i a , www.ijch.fi ) . positive correlations among pfaa levels with both age and seafood intake were also observed for both genders . in general , the correlations found in female inuit were higher than those in male inuit , while the correlations between age , n - 3 / n - 6 and legacy pops between genders were similar ( supplementary table i b , www.ijch.fi ) . for male inuit , the correlation between n - 3 / n - 6 and pfaas was weaker than that between legacy pops and n - 3 / n - 6 ( supplementary table i b , www.ijch.fi ) . to explore whether the sources for the body burden of pfaas and legacy pops in green - landic inuit were identical , we analysed the correlation between serum pfaas and legacy pops . for the nuuk inuit , positive correlations between serum pfos , pfsas , pfcas and legacy pops were observed . but after adjustment for age and seafood intake ( n - 3 / n - 6 ) , the significant correlations of pfos and pfsas with legacy pops disappeared ( table iii ) . for the non - nuuk inuit , significant correlations between serum pfaas and legacy pops were observed both before and after adjustments for age and n - 3 / n - 6 ( table iii ) . for the male nuuk inuit no correlations were observed , possibly because of the low number of males in the study ( n = 5 ) . for non - nuuk malesthe significant correlation between pfaas and legacy pops disappeared after adjustment for age and n - 3 / n - 6 . for non - nuuk female inuit and for female inuit in general , serum pfaas significantly correlated to legacy pops both before and after adjustment for age and n - 3 / n - 6 , whereas for nuuk females alone the significance disappeared upon adjustment ( table iii ) . association between serum pfcs and serum legacy pops legacy pop is the regression coefficient of pfaas to legacy pops . temporal trend analysis was performed for the district of nuuk , where a sufficient number of samples were available for the period 19982005 . as shown in table iv , pfos level and pfca level showed 2.2 % and 7.1 % yearly increasing trends , respectively , for female inuit . for the pooled gender data , 28 % , 28 % , 10 % , 13 % and 15 % yearly increasing trends were found for pfna , pfda , pfdoa , pftra and pfcas , respectively . however , after adjustment for age , the significant trend disappeared ( table iv ) . no significant time trend was observed for the serum level of pfoa and pfsa before and after adjustment for age ( table iv ) , and neither for pfhxs , pfosa , pfhpa or pfuna ( data not shown ) . time trend of serum concentrations ( ng / ml ) of pfaas in greenlandic inuit from nuuk in the period 19982005 slope : yearly difference ; values in bold indicate that the trend is statistically significant . time trend analysis was not performed for the male inuit because there were only 5 males studied in nuuk . the range observed for serum pfos and pfoa in all the greenlandic districts in the present study corresponded to the range observed in european biomonitoring studies of general populations ( 14 ) although the pfoa was found slightly lower in inuit ( 11,14 ) . the serum pfos level of nuuk inuit were comparable to those observed in europeans from sweden and from northern bavaria , germany , while non - nuuk inuit had a lower level of pfos similar to that of europeans in southern bavaria , germany , and in tarragona , spain ( 14 ) . the median serum pfos and pfoa concentrations in male greenlandic inuit were lower than the plasma levels of pfos and pfoa in danish men ( 39 ) . very few data are available for pfaa serum concentrations from other arctic locations ; the literature data that are available are summarized in table v. the range of mean concentrations of pfos and pfoa in the other arctic studies were 9.336.9 ng / ml and 1.03.4 ng / ml , respectively , while the mean concentrations of pfos and pfoa of green - landic inuit reported in the present study were 33.3 ng / ml and 2.3 ng / ml , respectively ( table v ) . the size of our data set is larger than most of the other arctic data . moreover , both male and female samples were included in the present study , thus avoiding the bias that could be generated by only including serum samples from one gender . the pfos mean concentration ( 33.3 ng / ml ) of the greenlandic inuit in this study was slightly higher than the value ( 25.7 ng / ml ) reported by chateau - degat et al . , which also included male and female inuit ( 40 ) . pfos concentrations reported in other arctic studies including relatively few female subjects were generally lower than the pfos levels of green - landic inuit observed in the present study ( table v ) . however , the mean pfoa level of the pooled greenlandic inuit in our study was comparable to the other reported arctic studies ( table v ) . we did observe gender differences in pfaa levels ; greenlandic inuit within the same district tended to be in accordance with the majority of studies on gender dependency of pfos serum concentrations ( 14 ) , with higher levels in male donors . this gender difference has been partially explained by increased excretion through menstrual flow ( 41 ) , transplacental transfer of pfos and other pfaas to the developing foetus and transfer via milk during breastfeeding in females of younger ages ( 42 ) . other explanations of lower levels in women rely on higher renal clearance of pfaas in women and longer half - lives in males , based on studies of laboratory rodents ( 14 ) . but the last assumption might not be completely true , as better renal clearance in females was not observed in other species ( dogs , rabbits and mice ) ( 14 ) , and no sex difference was found in the renal clearance of humans ( 41 ) . moreover , our data do not support the hypothesis that the higher pfaa levels in males were due to a higher intake of traditional marine food , because males and females had similar seafood intake ( n - 3 / n - 6 ) . moreover , after adjustment for age and n - 3 / n - 6 , the pfaa differences between genders were still statistically significant . we suggest that other sources must contribute to the higher levels of pfaas in male greenlandic inuit . since pfaas are very persistent , the body burden of pfaas may increase with age . studies investigating the dependency of pfaa serum concentrations on age have given inconsistent results , with some studies reporting statistically significant correlations ( 17,36 ) , and others not observing any correlations ( 16,43 ) . in this study , no correlation was observed between pfaas and age for nuuk inuit , while significant correlation was found for non - nuuk inuit . because the median age of non - nuuk inuit was lower than that of nuuk inuit in this study , this discrepancy may be related to the fact that the lifestyle of younger individuals could pose a higher chance of exposure to pfaas ( via clothing or consumption of food items that have been in close contact with packaging containing pfcs ) ( 26,44 ) . dallaire et al . also observed an age dependency of pfos plasma concentrations , with older individuals having higher concentrations ( 26 ) . this was partially explained by the fact that marine food intake also increases with age . consumption of traditional food has been suggested to be an important source of pfaa exposure for indigenous arctic populations ( 28,45 ) . indicated that consumption of fish and marine mammals , male gender and age were the strongest predictors of pfos plasma concentrations in the investigated inuit population . however , diet , gender and age could account for only 28 % of the variation in pfos concentrations ( 26 ) . in the present study , we observed that the correlation between pfaas and seafood intake was weaker than the correlation between legacy pops and seafood intake , suggesting that seafood intake might be the main source for legacy pops and to a lesser degree for pfaas . thus other factors may contribute to pfaa exposure in the inuit populations , such as consumer products ( e.g. , impregnation spray for outdoor clothing ) and different indoor sources ( e.g. , house dust in carpeted houses ) . moreover , our data are supported by the study of tittlemier and co - workers , which suggested that a diet based on traditional foods does not contribute to higher body burdens of pfaas to the same degree as has been observed for legacy pops ( 27 ) . similarly to the data reported by fromme and co - workers ( 36 ) , the correlation between pfaas and marine food intake observed for male inuit in the present study was weaker than that observed for female inuit , suggesting that sources other than n - 3 / n - 6 might also contribute to the higher pfaa levels in male inuit . moderately positive correlations were observed between legacy pops and age as well as n - 3 / n - 6 , similar to previous reports ( 21,35,46 ) . in male inuit , the correlation between legacy pops and n - 3 / n - 6 was stronger than the correlation between pfaas and n - 3 / n - 6 , further suggesting that other sources might play a more important role than seafood intake in the higher body levels of pfaas in greenlandic male inuit as observed in the present study . no significant association was observed between pfaas and legacy pops , suggesting that sources of serum pfaas and legacy pops in nuuk inuit might vary . for non - nuuk inuit , significant correlations between serum pfaas and legacy pops were observed both before and after adjustments for age and n - 3 / n - 6 , suggesting that there might be common sources for the body burden of pfaas and legacy pops in non - nuuk inuit . the correlation between pfaas and legacy pops was also different between genders ; no correlation was found for male inuit and a significant correlation was observed for females , further suggesting that sources other than seafood intake played an important role in the body burden of pfaas and legacy pops for male greenlandic inuit . overall , our data indicate that the sources contributing to the body burden of pfaas and legacy pops might be different for nuuk inuit when compared to non - nuuk inuit . further studies are needed to clarify the pfaa and legacy pop exposure routes of green - landic inuit . for female nuuk inuit , we observed an age - dependent , increasing trend of pfos and pfcas . we also observed increasing , age - dependent trends for pfna , pfda , pfdoa and pftra in all nuuk inuit during the period between 1998 and 2005 . however , we can not conclude that there was an increasing trend of pfaas in nuuk inuit during 19982005 , since the significant trend disappeared upon adjustment forage and only 4 years of data series were used in the present study . however , neither did we observe an obvious decreasing trend for pfaas in nuuk inuit . further research including more time series is needed to study the time trend of pfaas in greenlandic inuit . in conclusion , the levels of pfos and pfoa of greenlandic inuit were comparable to those found in european populations and were similar to , or slightly higher than , those of other arctic populations . the pfaa serum levels differed between the 2 district groups , with higher levels found in the nuuk district than the pooled non - nuuk districts . within the districts , sources for the body burden of pfaas and legacy pops in greenlandic inuit might differ and sources other than seafood intake should be taken into consideration when assessing the body levels of pfaas in greenlandic inuit , especially for male inuit . an age - dependent , but no obvious increasing trend of serum pfaas in nuuk was observed during 19982005 .\noutput:\n" }, { "from": "agent", "value": "objectivesperfluoroalkyl acids ( pfaas ) have been detected in human blood , breast milk and umbilical cord blood across the globe . pfaas do accumulate in the marine food chain in arctic regions . in greenland , increasing pfaa concentrations were observed during 19822006 in ringed seals and polar bears . however , until now , no data have been reported for pfaas in greenlandic inuit . this study assesses the level and temporal trend of serum pfaas in greenlandic inuit.study designcross - section and temporal time trend survey.methodsserum pfaa levels were determined in 284 inuit from different greenlandic districts using liquid chromatography - tandem mass spectrometry with electrospray ionization . the temporal time trend of serum pfaas in nuuk inuit during 19982005 and the correlation between serum pfaas and legacy persistent organic pollutants ( pops ) were explored.resultsserum pfaa levels were higher in nuuk inuit than in non - nuuk inuit . within the same district , higher pfaa levels were observed for males . an age - dependent , increasing trend of serum pfaa levels in the period from 19982005 was observed for nuuk inuit . for the pooled gender data , no significant association between pfaas and legacy pops was observed for nuuk inuit while for non - nuuk inuit this correlation was significant . no correlation between pfaas and legacy pops was found for male inuit , whereas significant correlation was observed both for pooled female inuit and for non - nuuk inuit females.conclusionswe suggest that sources other than seafood intake might contribute to the observed higher pfaa levels in nuuk inuit compared to the pooled non - nuuk inuit .1" } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: abiotrophia species sometimes cause sepsis and bacteremia , and are especially known as one of the major pathogens of infective endocarditis . a 48 - year - old unemployed woman was admitted to our hospital with a two - week history of severe low back pain . she suffered from parkinson 's disease , but she was not a compromised host . on admission , she was unable to sit up because of the pain . her vital signs were as follows : temperature 38.2 c , pulse 80 beats / min , and blood pressure 100/68 mmhg . physical examination revealed moderate tenderness to palpation on the spinous processes of lower lumbar spine . the peripheral white blood cell count was 11,600 / mm , and her c - reactive protein level was 9.9 mg / dl . plain x - ray showed degenerative changes of the lumbar vertebrae with narrowing of the disk spaces at l3 - 4 , and l4 - 5 . magnetic resonance imaging revealed edema and contrast enhancement of the l4 and l5 vertebral bodies with high signal intensity in the l3 - 4 and l4 - 5 intervertebral discs on the t2 - weighted images ( fig . cultures of disk biopsy samples and blood yielded gram positive cocci in short chains with scanty growth on chocolate agar . further subculture with supplemented medium and subsequent 16s ribosomal rna gene sequencing identified the pathogen as abiotrhophia adiacens . as a result of the survey regarding bacteremia origin , we could detect the dental caries . the patient was treated with intravenous ampicillin ( 8 g / day ) for 6 weeks . the clinical and laboratory test abnormalities improved within 2 weeks . at 6 - month follow - up , spinal infections can be devastating and result in significant pain , deformity , and neurologic deterioration . staphylococcus aureus is the most common etiologic organism of spinal infections , followed by escherichia coli , streptococcus species , s. epidermidis , and pseudomonas species ; however , causative microorganism remain unidentified in 2540 % of the cases . abiotrophia species ( a. adiacens and a. defectiva ) have formerly been referred to as nutritionally variant streptococci because of their fastidious nutritional growth requirements . the organisms grow poorly on conventional solid media , and require pyridoxal or thiol group supplementation . use of brucella hk agar or gam agar plate is helpful for detection of abiotrophia species . prolonged incubation ( at least 72 h ) is also recommended . spinal infection due to abiotrophia species is extremely rare , and only four cases have been reported to date ( table 1 ) . in the previous reports , this organism was identified only from blood sample by using columbia blood and chocolate agar plates . in the present case , we first confirmed the diagnosis by direct identification of abiotrophia adiacens from infected disk . abiotrophia species are one of the major pathogens of infective endocarditis accounting for 5 % of cases . abiotrophia endocarditis carries higher morbidity and mortality than endocarditis caused by other streptococci , reflecting their strong virulence . abiotrophia discitis reported previously occurred concomitantly with infective endocarditis although repeated echocardiography showed normal study in our case . patients with history of infective endocarditis or valve disease may be candidate for exploration of abiotrophia discitis . we were able to detect her dental cavity , and it could be a predisposing factor of bacteremia . considering their fastidious nature , it is likely that most cases of abiotrophia discitis are falsely classified as culture - negative discitis ; therefore , their role in pyogenic discitis may be underestimated . adequate diagnosis and treatment of this entity requires a high index of suspicion for the organism , even if cultures are negative . written informed consent was obtained from the patient for publication of this case report and accompanying images . a copy of the written consent is available for review by the editor - in - chief of this journal on request . k.u . assisted in the surgery , was involved in the preoperative work up and postoperative care of the patient , and wrote the paper . performed the surgery , was involved in the preoperative work up and postoperative care of the patient , and helped in the preparation of the write up . k.t . were involved in the preoperative work up and postoperative care of the patient , and revised the final article . y.h . and k.o .\noutput:\n" }, { "from": "agent", "value": "introductionabiotrophia species have been referred to as nutritionally variant streptococci because of their fastidious nutritional requirements for growth . abiotrophia species are difficult to identify with conventional solid culture.presentation of casea 48 - year - old woman was admitted to our hospital with severe low back pain and body temperature of 38.2 c . magnetic resonance imaging revealed edema and contrast enhancement of the l4 and l5 vertebral bodies with high signal intensity in the l3 - 4 and l4 - 5 intervertebral discs on the t2 - weighted images . the patient underwent needle biopsy of the l3 - 4 disk . cultures of disk biopsy samples and blood yielded gram positive cocci in short chains with scanty growth on chocolate agar . further subculture with supplemented medium and subsequent 16s ribosomal rna gene sequencing identified the pathogen as abiotrhophia adiacens . the patient was treated with intravenous ampicillin . at 6 - month follow - up , the patient was free of symptoms.discussioncausative microorganisms remain unidentified in 2540 % of spinal infection cases . abiotrophia species grow poorly on conventional solid media , and require pyridoxal or thiol group supplementation . use of brucella hk agar or gam agar plate is helpful for detection of abiotrophia species . we first confirmed the diagnosis by direct identification of abiotrophia adiacens from infected disk . abiotrophia species are one of the major pathogens of infective endocarditis accounting for 5 % of cases . considering their fastidious nature , it is likely that most cases of abiotrophia discitis are falsely classified as culture - negative discitis ; therefore , their role in pyogenic discitis may be underestimated.conclusionsubculture using nutritionally supplemented media is crucial for their identification ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: infected dental plaque biofilm and the impaired host response remain the main causes of a wide range of gingival diseases . the ability of the patient to adhere to a proper oral care plan is also a critical factor that controls the tissue reaction and disease progression . the clinical manifestations of gingival inflammation differ according to the severity , distribution , and the response to treatment ranging between being localized and highly responsive to treatment to long standing lesions with persistent redness and massive bleeding on probing with variable degrees of swelling . the efficacy of treatment and the subsequent tissue response vary according to the etiology and idiopathic , local , or systemic cause . under healthy conditions , the neutrophils pass from the gingival connective tissue through the junctional epithelium into the gingival sulcus , providing a dynamic balance between continuously invading microorganisms and the immune response . the antioxidants , either enzymatic or nonenzymatic , play a crucial role in the tissue equilibrium via neutralizing such harmful agents ( ros ) . under certain inflammatory conditions , the total amount of antioxidants decreases to its lowest levels , which necessities their supplementation by external source . one of the most important antioxidant agents is vitamin c ( vit - c ) which has an important role in different body functions . despite its mild acidity ( ph 4.2 ) , it requires an alkaline medium to perform its function as a reducing agent . to be activated , many changes in its structure occur in three successive cycles of oxidation ( figure 1 ) . vitamin c , being a strong reducing agent , can regulate the resolution of the inflammatory process and stimulate the tissue repair . it modulates the release of catabolic inflammatory cytokines , chemotaxis of the immune cells , and activation of the phagocytosis . the neutrophils and lymphocytes containing vitamin c show lower apoptotic potentiality and higher proliferation rate . furthermore , it enhances the synthesis of collagen type i , reduced by inflammatory process , keeps the balance between collagen i and collagen iii , and modifies the rate of fibroblast proliferation . it also reduces the potentiality of scaring via inhibiting cross - linking of collagen fibers and fibrosis . it acts as a cofactor in hydroxyproline synthesis to produce collagen type iv and improves endothelial cell vitality and function . the aim of the present study is to investigate the exact role and efficiency of the locally injected vitamin c in the treatment of persistent gingival inflammation after single or multiple dosing based on clinical and histopathological examination . each patient signed an informed detailed consent form before participation , explaining the benefits , steps , and side effects of the treatment protocol . the study was designed as a single arm , unblinded , and unrandomized trial as the trial did not depend on patient selection but it was rather based on an detection of a chronic persistent phenomenon . only patients with persistent inflammationpatients were recruited among those diagnosed with plaque induced gingivitis in the postgraduate periodontology clinic at cairo university between the years 2013 and 2016 . an initial evaluation , including medical and dental history , clinical examination , and radiographic examination , was conducted by nmy and ara to determine patient eligibility for the study . fifty patients who met the following inclusion criteria were examined : ( 1 ) aged between 20 and 50 y , ( 2 ) medically free , and ( 3 ) generalized plaque induced gingivitis . all the reasons that could provoke an inflammatory reaction were excluded : ( 1 ) systemic diseases , ( 2 ) pregnant and lactating mothers , ( 3 ) treatment with antibiotic medication within 1 month before the trial , and ( 4 ) local causes ( smoking , mouth breathing , local trauma , and periodontitis ) ( figure 2 ) . each patient underwent full - mouth sessions of supragingival debridement using ultrasonic and hand instrumentation and received personalized oral hygiene instructions . about twenty patients achieved a minimal residual inflammation ( 15 % of plaque and bleeding scores according to o'leary 's scoring system ) and optimal soft tissue conditions during two weeks . combination antibiotic therapy ( amoxicillin 500 mg and metronidazole 500 mg / 3 times per day for 7 days ) was administrated in order to control the amount of the condition . after 7 days of the complexion of the antibiotic course , reevaluation of the remaining 30 patients was undergone . at the end of the maintenance period ( 4 weeks ) , the included patients were 20 who suffered from persistent gingival inflammation in the esthetic anterior region ( figure 2 ) . the site of interest was anesthetized using lidocaine - epinephrine 1 : 100,000 . intraepidermal injection ( mesotherapy approach ) of 11.5 ml ( 200300 mg concentration ) of l - ascorbic acid was locally introduced in relation to the keratinized gingival tissues with prevalent extension to the whole target region , respectively , using insulin syringes . the current dose is equivalent to the treated region ( distance extends between six maxillary anteriors ) . during the first injection visitthe same dose was repeated once per week until inflammation subsided . at the end of each session , patients were prescribed a rescue analgesic ( ibuprofen 200 mg ) to be used as needed . the patients were asked to abstain from mechanical oral hygiene procedures in relation to the target region for the day of procedure only . immediately before injection procedure , the following clinical measurements were performed by the same examiners ( nmy and ara ) : plaque and bleeding score using o'leary 's scoring system and local bleeding score using sulcus bleeding index ( sbi ) as a more specific index : score 0 : healthy looking and no bleeding on probingscore 1 : healthy looking and bleeding on probingscore 2 : bleeding on probing , change in color , and no edemascore 3 : bleeding on probing , change in color , and slight edemascore 4 : bleeding on probing , change in color , and obvious edemascore 5 : spontaneous bleeding , change in color , and marked edemathe latter index examined color , swelling , and bleeding tendency . at the completion of the injection visits , patient satisfaction was performed by using a 5 - graded self - assessment analysis : excellent ( 4 ) , improved over 75 % ; good ( 3 ) , improved 5075 % ; moderate ( 2 ) , improved 2550 % ; fair ( 1 ) , improved less than 25 % ; no change or worse ( 0 ) , not improved or darkened . score 0 : healthy looking and no bleeding on probing score 1 : healthy looking and bleeding on probing score 2 : bleeding on probing , change in color , and no edema score 3 : bleeding on probing , change in color , and slight edema score 4 : bleeding on probing , change in color , and obvious edema score 5 : spontaneous bleeding , change in color , and marked edema preoperative and postoperative ( after 1 week of last injection ) gingival biopsies were excised , immediately fixed in 10 % neutral buffered formalin , and then processed in the routine way for preparing a paraffin block . tissue sections were cut and stained with hematoxylin & eosin ( h & e ) for histopathological examination . finally , epidermal and dermal changes before and after ascorbic acid application were assessed using computer image analyzer software leica qwin 515 system ( england ) . the experimental period was between september 2013 and april 2016 ( last follow - up visit ) . twenty sites of localized chronic gingival inflammation were included with no definite cause ranging between marginal gingivitis and diffuse gingivitis . improvement was reported in all cases after maximum 2 injections except 2 cases that needed one more injection . measurement of the sbi was done following phase i therapy and after the completion of the treatment . preoperatively , it was noted that 12 ( 60 % ) out of 20 patients scored 3 and 8 patients ( 40 % ) scored 4 on sbi index . postoperatively , the range changed into 20 patients ( 100 % ) scoring zero with variable degree of response to the applied treatment . seven patients ( 35 % ) out of twenty treated patients were totally free of inflammation with zero sbi score after 1 injection visit . eleven ( 55 % ) patients showed the same results after 2 injection visits . only 2 patients ( 10 % ) out of twenty needed further injection to reach the zero score . all the enrolled patients showed great satisfaction about the treatment results , even the patients who were not fully treated . all patients ( 100 % ) showed great satisfaction with the results ( score 4 ) ( figures 3 and 4 ) . the surface epithelium of parakeratinized stratified squamous type was hyperplastic with broad and elongated rete pegs , forming numerous epithelial arcades . obvious intracellular edema and extracellular edema of epithelial cells disturbing the intercellular desmosomal junctions were seen . an intense acute and chronic inflammatory cells infiltrate was observed dispersed in the whole thickness of connective tissue along with coarse blood capillaries ( table 1 ) . basement membrane was masked in some area by inflammatory cells ( figure 5 ) . microscopic examination revealed lower grade of inflammation . on the contrary to the preoperative sections , the connective tissue was formed of proliferating fibroblasts , collagen fiber formation , and few aggregates of chronic inflammatory cells . the characteristic phenomena were the presence of vacuolated epithelial cells especially in basal cell layer ( at the site of injection ) and the appearance of minute capillaries in subepithelial ct areas ( figure 5 ) . obvious reduction in the epithelial thickness was detected with minimal epithelial rete pegs and epithelial arcades . well - formed collagen fiber bundles with numerous and widely distributed blood vessels were detected in the connective tissue . fewer chronic inflammatory cells were detected but restricted to the deep connective tissue ( figure 5 ) . due to diversity of the gingival diseases , treatment plan should be variably designated based on the associated causative factors . however , one of the embarrassing problems is the presence of chronic or resistant inflammatory conditions with no definite aetiopathogenesis . they are usually characterized by persistent redness and bleeding on probing with different degrees of tissue edema which may be localized or diffused . in these cases , massive antibiotic course or corticosteroids regimens followed by surgical interventionif needed were the conventionally and commonly used protocols . despite the incredible results accompanying corticosteroids , they are usually avoided due to their adverse effects . therefore , there is a need for other safe nonsurgical therapeutic agents in order to control such conditions or , at least , improve the tissue healing and reduce inflammatory manifestations prior to the surgical removal of remaining pseudopocketing . dermal mesotherapeutic techniques using antioxidants such as vit - c showed promising results in the treatment of similar localized inflammatory conditions . the aim of the current study is the regulation of the overresponse of the inflammatory process , promoting healing , increasing the collagen content of the affected tissues , and improving the gingival circulation . in the current study , twenty patients were enrolled and evaluated at the baseline ( after 4 weeks following phase i therapy ) and postoperatively in the recall visit ( after 1 week after the last intraepidermal vitamin c injection ) . the long follow - up period preceding the therapy was essential in order to ensure that gingival inflammation is resistant to the conventional therapy . during inflammation , it was found that the tissue antioxidant level ( vit - c , vit - e , etc . ) decreases rapidly , indicating the need of its supplementation . on the other hand , the free radicals production increases at the site of inflammation . extra doses of antioxidants , especially vitamin c , are essential . in localized inflammatory conditions , the administration of the needed higher doses ( higher than 500 mg ) can not be absorbed by the gastrointestinal tract which easily excreted through urine . moreover , in order to reach this dose at the site of inflammation , administration of very high systemic doses is needed , which could be harmful to the patient . , the incidence of vitamin c deficiency is nearly neglected due to its availability in a wide range of fruits and vegetables . due to the impaired financial status of our patients and the absence of the deficiency conditions , the used technique is much cheaper than providing a long term special food protocol or oral supplementations in order to improve their health status . the local injection of vit - c was preferred rather than the usage of topical vitamin c gel or dentifrice that was previously used by daniels and jefferies and shimabukuro et al . . many studies used different forms of lipid soluble topical vitamin c in order to overcome its limited absorption . these studies met several limitations such as very long term improvement time ( 12 weeks ) , easily dislodged from the oral tissues , limited absorption , instability when exposed to solutions , air , heat , or light , and localized enamel erosions . total numerical evaluation of the gingival inflammation ( using sbi ) was determined , resulting in an average value per each patient . this analysis indicates 100 % reduction in gingival inflammation from the average baseline value over the 721 days . intraepidermal vitamin c injection could be either single or double or triple with one week apart according to the severity of the condition . more cautious handling of the inflamed tissues during the first visit is quite important in order to avoid tearing or necrosis , especially in thin biotype tissues . improvement of the tissue color and form was clearly observed in the recall visits after 2 months . once inflammation subsided , representative tissue biopsies have been obtained 7 days following the last injection from the patients indicated for gingivoplasty or gingivectomy . clinically significant reduction of the pseudogingival enlargement was associated with return of the basal keratinocytes to their normal proliferative pattern which is the main role of vitamin c . the anti - inflammatory action of vit - c was also evident and was detected in our specimens as a reduced intraepithelial edema and inflammatory cells . other characteristic changes which occurred after vit - c administration were in accordance with nusgens et al . . an increased number of fibroblasts were clearly detected forming more collagen fibers that showed more maturation and bundles formation following second injection . these features are consistent with its known essential role in the formation of new connective tissue in a healing wound . this is because it acts as a cofactor for enzymes critical in collagen formation , the main component of the connective tissue that forms the framework around which the new tissue is rebuilt . this is why , despite the increase in number of blood vessels , redness and bleeding tendency markedly decreased clinically . these vessels provide more nutritional and oxygen support to chronically irritated and continuously damaged mucosal areas , improving their healing . they detected that vitamin c promotes the development of an organization of the basement membrane and also restores the epidermal barrier within 2 - 3 weeks . furthermore , it promotes the wound closure and reduces its contraction which limits the incidence of scare formation . histologically , a characteristic cellular vacuolization was observed in all groups . in the preoperative specimens , vacuolated cells appeared as clear cells with small pyknotic dark nucleus representing signs of degeneration . in contrast , vit - c associated vacuolated cells were individually distributed along the epithelial layers with greatest aggregations in basal cells . a similar vacuolization was found in immediate and 15 - minute biopsies excised after intradermal injection of local anesthesia described by kimura et al . . they attributed this phenomenon to the injection procedure itself rather than the used solution spatially with the presence of vacuolization in biopsies . however , the presence of these cells in after - week biopsies may be due to the ability of vitamin c to increase the cell resistance to death . furthermore , the basal localization of vacuolated cells , adjacent to injection , may indicate proper infusibility of vit - c . all these positive clinical changes were met by further patients ' cooperation and resulted in their end - treatment satisfaction . these data suggest a significant enhancement of the gingival health by the usage of the antioxidant approach . finally , we recommend the usage of the intraepidermal vitamin c injection as an adjunctive approach for the conventional nonsurgical treatment modality .\noutput:\n" }, { "from": "agent", "value": "objective . the purpose of this study is to investigate the role and efficiency of the locally injected vitamin c in the treatment of persistent gingival inflammation . design . twenty adult patients with persistent chronic gingival inflammation were included in this study . the same dose of sterile vitamin c was injected in gingival tissues after the completion of phase i therapy . gingival biopsies were taken after total resolution of inflammation . the specimens were examined histologically , using h & e stain . results . clinical evaluation revealed great improvement of the injected sites with recall visits . histopathological results revealed marked decrease in inflammatory cells and epithelial thickness and a higher number of newly formed subbasal capillaries . conclusions . vitamin c is an effective adjunctive treatment in reducing various degrees of chronic gingival inflammation ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: children , because of their inquisitive nature , frequently sustain burn injuries particularly to their hands . unfortunately , it is also the most vulnerable part of the body to be affected by burn injuries . hand burns are common injuries in which early accurate diagnosis of the severity of the injury and active surgical treatment can save it or diminish the permanent disability . scars and contractures are common sequelae of severe burns around joints and they lead to limitation of movement . reconstructive procedures are often necessary to release the contractures and reestablish the complete range of motion . flaps and skin grafting , partial or full thickness , are two common methods of contracture release . the prepuce , or foreskin , has been used as a skin graft for a number of indications , including hypospadias repair , eyelid reconstruction , creation of an anal canal , replacement of conjunctiva , correction of ectropion , reconstruction of burned eyelids , reconstruction of extravasation injury to the foot , syndactyly repair , and resurfacing a first web space burn . preputial skin was used for the coverage of released contractures of fingers in 12 patients of age 2 - 6 years . the average time between the injury and surgery was 48 months ( range , 12 - 70 months ) . the aetiology of burns was \" kangri \" burn ( kangri : an earthen pot containing charcoal commonly used by people in kashmir to keep warm during winters ) in eight patients and scald burn in four patients . the right hand was involved in seven cases , left hand in four cases , and both hands in one case . six patients had contracture in two fingers , four patients in one finger , and two patients had contractures in three fingers . in all these cases , the contracture was not very severe [ figure 1,2 ] . uncircumcised penis with contracture of fingers the operations were performed under general anesthesia , and in tourniquet control . the contractures of the involved fingers were released and scar tissue excised until normal tissue was encountered and full correction of the deformity was achieved [ figure 3 ] . circumcision was performed and the inner and outer layers of the prepuce were separated which allowed spreading of the prepuce [ figure 4 ] . haemostasis was achieved at the recipient site and both the outer and inner layers of the prepuce were used for coverage , in most cases , with a tie - over bolster dressing . post - operative immobilisation was achieved by application of plaster slab , keeping the joints in full extension . first dressing change was done on 10 post - operative day and the plaster slab was replaced by a light - weight thermoplastic splint , which was used during night for additional 3 weeks . none of the patients had graft loss , and all wounds healed within 2 weeks . the stretched out preputial graft was sufficient to cover the defects after contracture release in two as well as three fingers [ figure 5 ] . the largest size of the graft used was 6.54 cm [ table 1 ] . all patients had complete release of contractures without any recurrence . during the 18 - month to 6 - year follow - up , all grafts were stable , pliable , and no patients presented with significant graft contracture [ figure 6 ] . the hand functions were normal , though hyperpigmentation of the grafted skin was seen in three cases , which was accepted well by the parents . pigmentary changes were less in mucosal portion of the grafts as compared to the skin portion . wounds covered with preputial grafts preputial graft sizes used in the patients stable graft without any graft contraction on long - term follow - uppenile circumcision is a common operative procedure . using the prepuce as a donor site for reconstruction of post - burn finger contractures refers to the principle of spare part surgerythe unique advantages of the prepuce over other full - thickness graft donor sites include : ( 1 ) expendable , especially in communities that favour circumcision ; ( 2 ) very thin and pliable ; ( 3 ) nearly no donor site morbidity ; ( 4 ) very low tendency to contract ; ( 5 ) good adaptation and natural colour matching , especially along the mucosal side ; ( 6 ) absence of hair follicles ; ( 7 ) hidden donor site for individuals with a tendency for hypertrophic scarring and keloid formation ; and ( 8 ) maybe the most important , being an extra graft reserve site . contraindications to the use of preputial skin are the same as for circumcision in general , including prematurity , or a family history of bleeding disorders . the major disadvantage of this procedure is hyperpigmentation of the prepuce in some cases as the child grows , which was accepted well by their parents . none of the children had body image problems , though a longer follow - up till their maturity is needed to make a definite conclusion . ours being a muslim - dominated society , and circumcision being a common ritual , we utilised the preputial skin of children who had contractures of not more than three fingers . using the preputial skin fulfilled both the aims : the ritual was performed and , at the same time , the preputial skin was utilised for coverage of the released contracture , obviating the need for a new donor site and second exposure to general anesthesia . in all our patients , there was no graft loss and the restoration of the function of the hand was excellent , by ensuring post - operative physiotherapy and pressure therapy and no recurrent contractures were seen in the follow - up . the use of preputial skin for male children with mild - to - moderate contractures of fingers has proved to be a successful method for restoration of the hand function with minimal donor site morbidity .\noutput:\n" }, { "from": "agent", "value": "objective : hand burns are common injuries . children frequently sustain burn injuries , especially to their hands . contractures are a common sequel of severe burns around joints . the prepuce , or foreskin , has been used as a skin graft for a number of indications . we conducted this study to evaluate the feasibility of utilising the preputial skin for the management of post - burn contractures of fingers in uncircumcised male children.materials and methods : preputial skin was used for the coverage of released contractures of fingers in 12 patients aged 2 - 6 years . the aetiology of burns was kangri burn in eight patients and scalding in four patients . six patients had contracture in two fingers , four patients in one finger , and two patients had contractures in three fingers.results : none of the patients had graft loss , and all the wounds healed within 2 weeks . all patients had complete release of contractures without any recurrence . hyperpigmentation of the grafts was observed over a period of time , which was well accepted by the parents.conclusions : preputial skin can be used successfully for male children with mild - to - moderate contractures of 2 - 3 fingers for restoration of the hand function , minimal donor site morbidity ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the north - west diabetes foot care study ( nwdfcs ) , a population - based investigation of diabetes - related foot problems in the community health care setting , provided the study population ( 6 ) . the study was approved by the local research ethics committees , general practitioner ( gp ) based diabetes teams , and hospital - based diabetes teams in each district and was funded by the department of health . one full - time research podiatrist or research nurse was appointed to screen diabetic patients in the gp practices , diabetes centers , and hospital outpatient clinics for each district . at gp practices , the vast majority of patients were screened while attending for their annual review ; others were screened while attending podiatry clinics . remaining patients were invited to attend a special clinic at the practice , or the patient was visited residentially . each patient was assessed once for symptoms and signs of peripheral neuropathy , peripheral vascular disease ( less than or equal to two palpable pedal pulses ) , demographic data , and medical history during a short ( 2030 min ) screening session . neuropathic deficits in the feet were determined using the nds , derived from inability to detect pin - prick sensation ( using neurotip ) , vibration ( using 128 - hz tuning fork ) , and differences in temperature sensation ( using warm and cool rods ) plus achilles reflex ( using tendon hammer ) ( 6 ) . patients were asked about their experience of pain or discomfort in the legs . if the patient described burning , numbness , or tingling , a score of 2 was assigned ; fatigue , cramping , or aching scored 1 . the presence of symptoms in the feet was assigned a score of 2 , the calves 1 , and elsewhere a score of 0 . nocturnal exacerbation of symptoms scored 2 vs. 1 for both day and night and 0 for daytime alone . a score of 1 was added if the symptoms had ever woken the patient from sleep . the patients were asked if any maneuver could reduce the symptoms ; walking was assigned a score of 2 , standing 1 , and sitting or lying down 0 . the severity of symptoms was graded according to the nss as follows : none ( 02 ) , mild ( 34 ) , moderate ( 56 ) , and severe ( 79 ) ( 2 ) . the nss has been used as part of the assessment of pdn in several previous studies ( 2,9,11,13 ) . we defined pdn as at least moderate symptoms with mild neurologic signs ( nss score 5 and nds score 3 ) ( 9,11 ) . variables were stratified into normal and abnormal categories , and tests were performed for categorical data . normally distributed , continuous data were tested using student t test , whereas nonnormally distributed data were first analyzed using kruskal - wallis , followed by a mann - whitney u test . after obtaining 95 % cis , age - adjusted prevalence rate differences were evaluated between the diabetes type , sex , and ethnic groups . logistic regression was used to obtain odds ratios ( ors ) for neuropathy symptoms between the comparison groups . modifiers of the ors were entered into the final logistic regression models to determine which risk factors may account for symptom differences . neuropathic deficits in the feet were determined using the nds , derived from inability to detect pin - prick sensation ( using neurotip ) , vibration ( using 128 - hz tuning fork ) , and differences in temperature sensation ( using warm and cool rods ) plus achilles reflex ( using tendon hammer ) ( 6 ) . patients were asked about their experience of pain or discomfort in the legs . if the patient described burning , numbness , or tingling , a score of 2 was assigned ; fatigue , cramping , or aching scored 1 . the presence of symptoms in the feet was assigned a score of 2 , the calves 1 , and elsewhere a score of 0 . nocturnal exacerbation of symptoms scored 2 vs. 1 for both day and night and 0 for daytime alone . a score of 1 was added if the symptoms had ever woken the patient from sleep . the patients were asked if any maneuver could reduce the symptoms ; walking was assigned a score of 2 , standing 1 , and sitting or lying down 0 . the severity of symptoms was graded according to the nss as follows : none ( 02 ) , mild ( 34 ) , moderate ( 56 ) , and severe ( 79 ) ( 2 ) . the nss has been used as part of the assessment of pdn in several previous studies ( 2,9,11,13 ) . we defined pdn as at least moderate symptoms with mild neurologic signs ( nss score 5 and nds score 3 ) ( 9,11 ) . variables were stratified into normal and abnormal categories , and tests were performed for categorical data . normally distributed , continuous data were tested using student t test , whereas nonnormally distributed data were first analyzed using kruskal - wallis , followed by a mann - whitney u test . after obtaining 95 % cis , age - adjusted prevalence rate differences were evaluated between the diabetes type , sex , and ethnic groups . logistic regression was used to obtain odds ratios ( ors ) for neuropathy symptoms between the comparison groups . modifiers of the ors were entered into the final logistic regression models to determine which risk factors may account for symptom differences . over 4 years , our community - based screening program assessed 15,692 patients with diabetes within six health care districts of northwest england , representing 60 % of involved gps diabetic patients ( 6,14 ) . the majority ( 70 % ) of patientswere screened while attending their diabetes annual review in primary care , with the remainder ( 30 % ) screened at referral sites in diabetes centers and hospital outpatient clinics . demographic and medical characteristics of the entire community - based diabetic cohort and type 1 and 2 diabetic subcohorts are given in table 1 . the patients with type 2 diabetes were substantially older than those with type 1 diabetes ( 63.611.8 vs. 37.612.9 years , respectively ) and had a greater proportion of south asian / african caribbean patients ( 15.1 vs. 3.9 % , respectively ) . duration of type 2 diabetes was one - quarter that of the type 1 group ( p 0.0001 ) . type 2 diabetic patients were less likely to be current smokers ( 22 vs. 33 % , p 0.0001 ) . despite substantially greater levels of clinical neuropathy , peripheral arterial disease ( pad ) , and foot deformities in the type 2 diabetic patients , foot ulcer rates ( past or present ) were similar between the two groups ( 4.9 vs. 6.0 % , respectively , p = 0.07 ) . paradoxically , lower - limb amputation rate was significantly lower in type 2 compared with type 1 diabetic patients ( 1.2 vs. 1.8 % , p 0.05 ) . demographic and medical characteristics of patient cohorts data are mean sd , n ( % ) , or median ( 25th75th percentiles ) ; p values for type 1 vs. type 2 . the distribution of neuropathy symptom severity within the entire cohort was as follows : no symptoms ( nss 02 ) = 52 % ( 8,073 / 15,638 ) , mild symptoms ( nss 34 ) = 14 % ( 2,254 / 15,638 ) , moderate symptoms ( nss 56 ) = 18 % ( 2,780 / 15,638 ) , and severe symptoms ( nss 79 ) = 16 % ( 2,531 / 15,638 ) . the overall prevalence of painful neuropathy symptoms ( i.e. , nss 5 ) in this cohort was 34 % ( 5,311 / 15,638 ) . the prevalence of painful neuropathy symptoms in the presence of clinical neuropathy ( pdn ) ( i.e. , nss score 5 and nds score 3 ) for all patients was 21 % ( 3,242 / 15,614 ) . the distribution of increasing neuropathy symptoms in patient groups stratified by the severity of clinical neuropathy is given in fig .1 . sixty percent ( 379/629 ) of diabetic patients with severe clinical neuropathy ( nds 8 ) had painful neuropathic symptoms ( nss 5 ) , whereas only 26 % ( 2,060 / 8,016 ) of patients without clinical neuropathy ( nds 2 ) had painful symptoms . there was an emerging pattern of worsening clinical neuropathy scores associated with an increasing proportion of patients with more severe painful neuropathic symptoms ( p 0.0001 ) , and there was a significant , positive correlation between nss and nds ( r = 0.24 , p 0.0001 ) . this relationship between signs and symptoms was stronger in type 1 ( r = 0.37 , p 0.0001 ) than type 2 diabetic subjects ( r = 0.22 , p 0.0001 ) . percentage prevalence of neuropathic symptoms in 15,659 diabetic patients characterized by their level of clinical neuropathy . painful symptoms ( nss 5 ) were more prevalent in type 2 ( 35.0 % [ 4,962 / 14,166 ] ) versus type 1 ( 22.7 % [ 303/1 ,334 ] , p 0.0001 ) diabetic patients , as was pdn ( 21.5 % [ 3,039 / 14,144 ] vs. 13.4 % [ 178/1 ,333 ] , respectively , p 0.0001 ) . the risk of painful neuropathy symptoms in type 2 diabetic patients was 83 % higher than in type 1 patients ( or = 1.8 [ 95 % ci 1.62.1 ] , p 0.0001 ) ; this risk doubled after adjusting for differences in age and diabetes duration ( or = 2.1 [ 1.72.4 ] , p 0.0001 ) . when examining patients with moderate to severe clinical neuropathy ( i.e. , nds 6 ) only , the age - and diabetes duration adjusted risk of painful symptoms in type 2 versus type 1 diabetic patients was still significantly greater ( or = 1.8 [ 1.22.5 ] , p 0.0001 ) . adjustment for type 2 versus type 1 diabetes and differences in severity of neuropathy , insulin use , foot deformities , smoking status , and alcohol intake had no impact on these differences in painful symptoms ( data not shown ) ; i.e. , these variables could not account for the disparity in symptoms between type 1 and type 2 diabetes . increasing age was very weakly associated with nss severity in the entire population ( r = 0.083 , p 0.0001 ) ; however , this relationship was stronger in type 1 ( r = 0.20 , p 0.0001 ) than type 2 diabetes ( r = 0.022 , p = 0.008 ) . indeed , increasing age categories in type 1 diabetic patients showed an almost doubling in prevalence of painful symptoms ( nss 5 ) ( aged 35 years , 17.2 % ; 3554 years , 26.4 % ; 55 + years , 33.1 % ; p 0.0001 ) , with a similar , but less marked , association in type 2 diabetic patients ( aged 35 years , 30.6 % ; 3554 years , 32.7 % ; 55 + years , 35.7 % ; p 0.01 ) . insulin use versus oral hypoglycemic agents ( ohas ) and / or diet had no effect on painful neuropathy symptoms , i.e. , 33 % ( 1,085 / 3,272 ) of patients using insulin had nss 5 compared with 34 % ( 4,206 / 12,303 ) of patients treated with diet and oha ( p = 0.27 ) . however , when treatments were examined individually , symptoms were most prevalent in patients treated with oha ( 37.3 % ) compared with insulin ( 33.2 % ) or diet alone ( 29.1 % ) ( p 0.0001 ) . restricting the analysis to patients with clinical neuropathy , painful symptoms were most prevalent in the insulin - treated group oha group diet - only group ( 54.7 , 50.6 , and 42.1 % , respectively ; p 0.0001 ) . a significantly greater proportion of females ( 38 % [ 2,732 / 7,212 ] ) than males ( 31 % [ 2,578 / 8,423 ] ) reported painful neuropathy symptoms ( p 0.0001 ) , despite fewer females than males having clinical neuropathy ( nds 6 ) ( 19 vs. 23 % , p 0.0001 ) . pdn ( nss 5 and nds 3 ) was , similarly , more prevalent in females than males ( 23 vs. 19 % , respectively , p 0.0001 ) . after adjustments for age , diabetes duration , and differences in clinical neuropathy , women still had a 50 % increased risk of painful symptoms compared with men ( or = 1.5 [ 95 % ci 1.41.6 ] , p 0.0001 ) . despite a lower unadjusted prevalence of clinical neuropathy ( nds 6 ) in south asians ( 14 % ) compared with europeans ( 22 % ) and african caribbeans ( 21 % ) ( p 0.0001 ) , painful neuropathy symptoms ( nss 5 ) were significantly and , conversely , greater in south asians ( 38 % ) compared with europeans ( 34 % ) and african caribbeans ( 32 % ) ( p 0.0001 ) . greater neuropathy symptoms in south asians , however , were only evident in patients without clinical neuropathy ( i.e. , nss 5 and nds 2 : south asians 19 % [ 352/1 ,845 ] , europeans 13 % [ 1667/13 ,354 ] , african caribbeans 10 % [ 36/370 ] ; p 0.0001 ) , whereas pdn ( nss 5 and nds 3 ) was similarly prevalent in all ethnic groups ( 21 % [ 2,803 / 13,354 ] , 19 % [ 349/1 ,845 ] , and 22 % [ 80/370 ] , respectively ; p = 0.11 ) . after adjustments for age and diabetes duration , south asians without significant clinical neuropathy were still 50 % more likely to have painful neuropathy symptoms compared with other ethnic groups ( or = 1.5 [ 95 % ci 1.31.6 ] , p 0.0001 ) . the distribution of neuropathy symptom severity within the entire cohort was as follows : no symptoms ( nss 02 ) = 52 % ( 8,073 / 15,638 ) , mild symptoms ( nss 34 ) = 14 % ( 2,254 / 15,638 ) , moderate symptoms ( nss 56 ) = 18 % ( 2,780 / 15,638 ) , and severe symptoms ( nss 79 ) = 16 % ( 2,531 / 15,638 ) . the overall prevalence of painful neuropathy symptoms ( i.e. , nss 5 ) in this cohort was 34 % ( 5,311 / 15,638 ) . the prevalence of painful neuropathy symptoms in the presence of clinical neuropathy ( pdn ) ( i.e. , nss score 5 and nds score 3 ) for all patients was 21 % ( 3,242 / 15,614 ) . the distribution of increasing neuropathy symptoms in patient groups stratified by the severity of clinical neuropathy is given in fig .1 . sixty percent ( 379/629 ) of diabetic patients with severe clinical neuropathy ( nds 8 ) had painful neuropathic symptoms ( nss 5 ) , whereas only 26 % ( 2,060 / 8,016 ) of patients without clinical neuropathy ( nds 2 ) had painful symptoms . there was an emerging pattern of worsening clinical neuropathy scores associated with an increasing proportion of patients with more severe painful neuropathic symptoms ( p 0.0001 ) , and there was a significant , positive correlation between nss and nds ( r = 0.24 , p 0.0001 ) . this relationship between signs and symptoms was stronger in type 1 ( r = 0.37 , p 0.0001 ) than type 2 diabetic subjects ( r = 0.22 , p 0.0001 ) . percentage prevalence of neuropathic symptoms in 15,659 diabetic patients characterized by their level of clinical neuropathy . painful symptoms ( nss 5 ) were more prevalent in type 2 ( 35.0 % [ 4,962 / 14,166 ] ) versus type 1 ( 22.7 % [ 303/1 ,334 ] , p 0.0001 ) diabetic patients , as was pdn ( 21.5 % [ 3,039 / 14,144 ] vs. 13.4 % [ 178/1 ,333 ] , respectively , pthe risk of painful neuropathy symptoms in type 2 diabetic patients was 83 % higher than in type 1 patients ( or = 1.8 [ 95 % ci 1.62.1 ] , p 0.0001 ) ; this risk doubled after adjusting for differences in age and diabetes duration ( or = 2.1 [ 1.72.4 ] , p 0.0001 ) . when examining patients with moderate to severe clinical neuropathy ( i.e. , nds 6 ) only , the age - and diabetes duration adjusted risk of painful symptoms in type 2 versus type 1 diabetic patients was still significantly greater ( or = 1.8 [ 1.22.5 ] , p 0.0001 ) . adjustment for type 2 versus type 1 diabetes and differences in severity of neuropathy , insulin use , foot deformities , smoking status , and alcohol intake had no impact on these differences in painful symptoms ( data not shown ) ; i.e. , these variables could not account for the disparity in symptoms between type 1 and type 2 diabetes . increasing age was very weakly associated with nss severity in the entire population ( r = 0.083 , p 0.0001 ) ; however , this relationship was stronger in type 1 ( r = 0.20 , p 0.0001 ) than type 2 diabetes ( r = 0.022 , p = 0.008 ) . indeed , increasing age categories in type 1 diabetic patients showed an almost doubling in prevalence of painful symptoms ( nss 5 ) ( aged 35 years , 17.2 % ; 3554 years , 26.4 % ; 55 + years , 33.1 % ; p 0.0001 ) , with a similar , but less marked , association in type 2 diabetic patients ( aged 35 years , 30.6 % ; 3554 years , 32.7 % ; 55 + years , 35.7 % ; p 0.01 ) . insulin use versus oral hypoglycemic agents ( ohas ) and / or diet had no effect on painful neuropathy symptoms , i.e. , 33 % ( 1,085 / 3,272 ) of patients using insulin had nss 5 compared with 34 % ( 4,206 / 12,303 ) of patients treated with diet and oha ( p = 0.27 ) . however , when treatments were examined individually , symptoms were most prevalent in patients treated with oha ( 37.3 % ) compared with insulin ( 33.2 % ) or diet alone ( 29.1 % ) ( p 0.0001 ) . restricting the analysis to patients with clinical neuropathy , painful symptoms were most prevalent in the insulin - treated group oha group diet - only group ( 54.7 , 50.6 , and 42.1 % , respectively ; p 0.0001 ) . a significantly greater proportion of females ( 38 % [ 2,732 / 7,212 ] ) than males ( 31 % [ 2,578 / 8,423 ] ) reported painful neuropathy symptoms ( p 0.0001 ) , despite fewer females than males having clinical neuropathy ( nds 6 ) ( 19 vs. 23 % , p 0.0001 ) . pdn ( nss 5 and nds 3 ) was , similarly , more prevalent in females than males ( 23 vs. 19 % , respectively , p 0.0001 ) . after adjustments for age , diabetes duration , and differences in clinical neuropathy , women still had a 50 % increased risk of painful symptoms compared with men ( or = 1.5 [ 95 % ci 1.41.6 ] , p 0.0001 ) . despite a lower unadjusted prevalence of clinical neuropathy ( nds 6 ) in south asians ( 14 % ) compared with europeans ( 22 % ) and african caribbeans ( 21 % ) ( p 0.0001 ) , painful neuropathy symptoms ( nss 5 ) were significantly and , conversely , greater in south asians ( 38 % ) compared with europeans ( 34 % ) and african caribbeans ( 32 % ) ( p 0.0001 ) . greater neuropathy symptoms in south asians , however , were only evident in patients without clinical neuropathy ( i.e. , nss 5 and nds 2 : south asians 19 % [ 352/1 ,845 ] , europeans 13 % [ 1667/13 ,354 ] , african caribbeans 10 % [ 36/370 ] ; p 0.0001 ) , whereas pdn ( nss 5 and nds 3 ) was similarly prevalent in all ethnic groups ( 21 % [ 2,803 / 13,354 ] , 19 % [ 349/1 ,845 ] , and 22 % [ 80/370 ] , respectively ; p = 0.11 ) . after adjustments for age and diabetes duration , south asians without significant clinical neuropathy were still 50 % more likely to have painful neuropathy symptoms compared with other ethnic groups ( or = 1.5 [ 95 % ci 1.31.6 ] , p 0.0001 ) . we have shown that one - third of all patients with diabetes in the community have painful neuropathic symptomatology , regardless of whether they have clinical neuropathy . these data show a higher prevalence of painful neuropathic symptoms than previously reported in two small population - based studies ( 9,11 ) . in a recent study using the validated dn4 ( a clinician - administered neuropathic pain diagnostic questionnaire ) , the prevalence of pdn in 1,039 diabetic patients in secondary careour current data indicate a large morbidity for neuropathic pain in a community - based diabetic population . they also challenge the dogma that painful neuropathic symptoms improve as the severity of neuropathy worsens and provide support for a previous study that actually demonstrated comparable prevalence of painful neuropathy in diabetic patients with mild and more severe neuropathy ( 12 ) . furthermore , approximately one - quarter of our patients without clinical neuropathy on examination had significant painful neuropathic symptoms , indicating the large disparity between signs and symptoms . but of course even patients with impaired glucose tolerance and no apparent neuropathy develop painful neuropathic symptoms and small nerve fiber damage ( 16 ) . this emphasizes the need to ask all patients about the occurrence of painful neuropathic symptoms , not just those who have clinical neuropathy . painful symptoms were twice as prevalent in type 2 versus type 1 diabetic patients , even after adjusting for differences in age , neuropathy , pad , and other known risk factors for neuropathic pain ( 17 ) . these data are consistent with a previous study that demonstrated a higher prevalence of clinical neuropathy in type 2 compared with type 1 diabetic patients , assessed using a combination of the nss and nds ( 2 ) . previously , the prevalence of pdn has not been found to differ between type 1 and type 2 diabetes , although the proportion of patients with type 1 diabetes was very small ( 9,15 ) . this has also been demonstrated recently in a study from saudi arabia ( 15 ) . this latter study demonstrated no ethnic differences for the incidence of pdn ( 15 ) . in the current study , however , we demonstrate a significantly higher prevalence of painful neuropathic symptoms in south asians compared with europeans and african caribbeans , with a 50 % increased risk of neuropathic pain in south asians in the absence of clinical neuropathy . paradoxically , we have previously demonstrated a lower prevalence of both large and small fiber neuropathy ( 18 ) , as well as incidence of foot ulceration ( 14 ) , in south asians . the major strength of this epidemiological study , compared with others , is that it is substantially larger than any previously published study on the prevalence of pdn . furthermore , it is community based and therefore reflects the magnitude of this problem in a nonselected cohort of diabetic patients . as this study was designed to be totally inclusive for community - based patients with diabetes , we did not exclude patients with neuropathic pain from an etiology other than diabetes , or attempt to identify pain from a different origin . we did not assess the duration of pain , hence the prevalence of chronic pain ( 6 months ) could not be established . we used the nss as it is relatively quick to administer and is weighted toward positive neuropathic symptoms in the lower limbs , consistent with pdn . indeed , three key lower - limb symptoms that characterize neuropathic from nonneuropathic pain are tingling pain , numbness , and increased pain due to touch ( 19 ) and are incorporated in the nss . numbness orcotton wool - like feeling is a positive , identifiable , painful symptom described by patients and thus different to loss of sensation , which patients may or may not be aware of . these symptoms were captured by the nss along with a measure of the distribution , presence of nocturnal exacerbation , and relieving factors . the demonstration that one - third of all diabetic patients have significanttingling / shooting , burning pain , with or without numbness , in the lower limbs indicates a larger morbidity than previously established in relatively small and selective studies in the u.k . ( 9,11 ) and in a recent larger , but selected , population - based study from germany ( 17 ) . our finding that one - quarter of community patients without clinical neuropathy have painful neuropathic symptoms implies that a large proportion of the diabetic community are being neglected in the treatment of their symptoms , and that classic neuropathic , lower - limb symptoms may well be inappropriately considered nonneuropathic if there are no concomitant signs of clinical neuropathy . ( 8 ) also showed that a significant proportion ( 7.4 % ) of subjects with pdn using the toronto clinical scoring system had no clinical signs of neuropathy . we have extended this observation in a large cohort of patients and shown that 40 % of all patients without signs of neuropathy will have at least mild neuropathic symptoms . to conclude , we have observed greater neuropathic pain levels in type 2 diabetes , in women , and in people of south asian origin . these areas demand further investigation and also highlight key groups who may warrant screening for pdn .\noutput:\n" }, { "from": "agent", "value": "objectiveto assess , in the general diabetic population , 1 ) the prevalence of painful neuropathic symptoms ; 2 ) the relationship between symptoms and clinical severity of neuropathy ; and 3 ) the role of diabetes type , sex , and ethnicity in painful neuropathy.research design and methodsobservational study of a large cohort of diabetic patients receiving community - based health care in northwest england ( n = 15,692 ) . painful diabetic neuropathy ( pdn ) was assessed using neuropathy symptom score ( nss ) and neuropathy disability score ( nds ) . resultsprevalence of painful symptoms ( nss 5 ) and pdn ( nss 5 and nds 3 ) was 34 and 21 % , respectively . painful symptoms occurred in 26 % of patients without neuropathy ( nds 2 ) and 60 % of patients with severe neuropathy ( nds > 8 ) . adjusted risk of painful neuropathic symptoms in type 2 diabetes was double that of type 1 diabetes ( odds ratio [ or ] = 2.1 [ 95 % ci 1.72.4 ] , p < 0.001 ) and not affected by severity of neuropathy , insulin use , foot deformities , smoking , or alcohol . women had 50 % increased adjusted risk of painful symptoms compared with men ( or = 1.5 [ 1.41.6 ] , p < 0.0001 ) . despite less neuropathy in south asians ( 14 % ) than europeans ( 22 % ) and african caribbeans ( 21 % ) ( p < 0.0001 ) , painful symptoms were greater in south asians ( 38 vs. 34 vs. 32 % , p < 0.0001 ) . south asians without neuropathy maintained a 50 % increased risk of painful neuropathy symptoms compared with other ethnic groups ( p < 0.0001 ) . conclusionsone - third of all community - based diabetic patients have painful neuropathy symptoms , regardless of their neuropathic deficit . pdn was more prevalent in patients with type 2 diabetes , women , and people of south asian origin . this highlights a significant morbidity due to painful neuropathy and identifies key groups who warrant screening for pdn ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: testing the statistical significance of multiple null hypotheses is a routine practice in epidemiologic and other types of biomedical research . by chance , the probability of wrongly rejecting one or more null hypotheses increases in proportion to the number of comparisons tested . various methods have been presented in the literature for controlling the type i error in the context of multiple hypothesis testing . the classic bonferroni inequality provides a simple distribution - free method for multiplicity p value correction . letting i denote the probability that hypothesis si is incorrect , the bonferroni probability for the joint null hypothesismay be written as : ( 1 ) p ( i = 1nsi ) =p [ ( i = 1nsic ) c ] 1i = 1ni . the bonferroni method rejects the n set of null hypotheses if pii = 1nin for at least one i , where pi denotes the p value corresponding to the i null hypothesis . in the simple case , although the family - wise ( fwer ) and per family ( pfer ) error rates are preserved at the level of significance , the bonferroni procedure is known to be conservative , especially for highly correlated test statistics ( i.e. , type i error probability is less than the nominal level of ) . for example , in the case of a study of multiple genetic polymorphisms , the assumption is that all variants being tested have equal probability of being truly associated with the outcome of interest and leads to overcorrection . the first order bonferroni inequality may be improved upon given knowledge of the joint bivariate probabilities or when the absolute value of the correlation coefficient is greater than 50 % . however , these improvements have been limited in applied practice due to their restrictive nature . several multiple testing procedures based upon the closure method and simes equality have been introduced and shown to be more powerful than the bonferroni method for testing the intersection hypothesis . of the closure methodbased options , the hochberg step - up multiple comparisons procedure has gained popularity as being easier to apply than the more powerful procedures of hommel and rom . the procedure also is uniformly more powerful than the bonferroni - based , sequentially - rejective method of holm in many applied situations , e.g. , when test statistics are uncorrelated , follow a multivariate normal or t distribution , or are model independent . p ( n ) , the hochberg procedure rejects all hypothesis hij if p ( j ) / ( nj +1 ) for any j = 1 , , n. p values are incrementally corrected in order from smallest to largest by multiplying p ( j ) by ( nj +1 ) , wherein the multiplicative factor for the largest p value is unity and thus remains the same after multiplicity correction . many researchers and journal editors increasingly recognize confidence intervals ( ci ) as the preferred measure for conveying statistical uncertainty of effect size estimates such as odds ratios ( or ) , relative risks ( rr ) , and hazard ratios ( hr ) , as p values have been commonly misunderstood and misinterpreted in the literature . similar to hypothesis testing by way of p values , ci also may be corrected for multiplicity to minimize the risk of making false - positive inferences . several authors have provided techniques to correct ci for multiple hypothesis testing . however , most of the methods are computationally intensive or mathematically complex , and more importantly , none provide a way to correct ci when corresponding p values are not provided for the individual hypothesis tests . below , we present a method to compute multiplicity corrected ci for or and by analogy for other measures of relative risk , when no p values have been explicitly provided . this computationally simple method based upon the hochberg step - up procedure only requires knowledge of individual test or and ci , and the number of comparisons being tested . the derivation of multiplicity corrected confidence intervals for a set of n or involves expressing the standard error ( se ) for the logarithm of ori ( i = 1 to n ) in terms of the lower confidence interval ( lci ) for ori . letting : ( 2 ) lci ( ori ) = e { log ( ori ) z ( 1/2 ) se [ log ( ori ) ] } , where z ( 1/2 ) is the 100 % ( 1/2 ) percentile of a standard normal distribution , and solving for se [ log ( ori ) ] we see that : ( 3 ) se [ log ( ori ) ] = { log [ lci ( ori ) ] log ( ori ) } / z ( 1/2 ) . substituting the right hand side of ( 3 ) into the equation for the 2 - tailed z test statistic gives : ( 4 ) zi = | log ( ori ) se [ log ( ori ) ] | = | log ( ori ) { log [ lci ( ori ) ] log ( ori ) } / z ( 1/2 ) | . the corresponding p value is computed as : ( 5 ) pi = 2 [ 1 ( zi ) ] , where : ( 6 ) ( zi ) = ziex2 / 22dx . ordering the p values ( pi s ) from the lowest to highest values i.e. , p ( 1 ) p ( 2 ) ... p ( n ) ( with arbitrary ordering in the case of ties ) , the hochberg multiplicity corrected p values denoted by * are computed as : ( 7 ) p ( j ) * =p ( j ) ( nj +1 ) , where j ranges from 1 to n in a 1:1 identity mapping with the i values and p ( j ) is bounded by unity.rearranging ( 5 ) and solving for se [ log ( ori ) ] in the equation : ( 8 ) [ log ( ori ) se * [ log ( ori ) ] ] + ( p ( j ) * 2 ) 1 = 0gives the hochberg corrected standard error for the logarithm of ori , i.e. : ( 9 ) se * [ log ( ori ) ] = log ( ori ) 1 ( 1p ( j ) * 2 ) . the multiplicity corrected ( 1/2 ) 100 % ci for or ( i ) based upon the hochberg step - up procedure can then be computed by substituting the above standard error from eq . 9 into the following basic equation : ( 10 ) ci ( 1/2 ) = e { log ( ori ) z ( 1/2 ) se * [ log ( ori ) ] } . by analogy , replacing or in the above equations with other relative effect estimates such as rr or hr gives the corresponding multiplicity corrected ci for these measures . when p values are directly available for the individual hypothesis tests , the hochberg multiplicity corrected ci may be computed directly beginning with eq . 7 . furthermore , if the hypothesis test is 1 - sided , then must be multiplied by 2 in the above equations . table 1 below presents or from a case - control study for a hypothetical disease ( d ) and exposure to 3 dichotomously coded environmental risk factors . the or and 95 % ci for ( d ) uncorrected for multiplicity ( n = 3 factors ) are shown in columns 3 and 4 : factor 1 ( or = 1.652 , 95 % ci = 0.5514.953 ) ; factor 2 ( or = 1.151 , 95 % ci = 0.1429.324 ) ; and factor 3 ( or = 6.509 , 95 % ci = 1.64625.743 ) . applying equations 7 , 9 and 10 gives the corresponding multiplicity corrected p values ( 0.740 , 0.895 , 0.024 ; not shown in table ) , standard errors for the logarithm of the or ( 1.513 , 1.068 , 0.830 ) , and 95 % ci ( 0.0932 , 0.149.3 , 1.333 ) . the multiplicity corrected ci for factor 1 and factor 3 are considerably wider than the corresponding uncorrected intervals , thus indicating a greater degree of variability for the estimated or . in the case of factor 2 , the uncorrected and corrected ci is the same since factor 2 had the highest p value of the 3 comparisons when applying the hochberg algorithm . in this example , the conclusions regarding the association ( or lack thereof ) of ( d ) and the exposure do not substantively change after correction for multiplicity , thus lending weight to what otherwise might be only cautious interpretation referencing the possibility of a chance observation due to multiple comparisons . however , in other situations where ci is close to containing unity , a null hypothesis might no longer be rejected at least in strict statistical terms after correction for multiplicity . confidence intervals for or , rr and other relative effect estimates are commonly reported in epidemiologic and public health literature without correction for multiple hypothesis testing . the failure to account for multiplicity may lead to inflation of type i error and over interpretation of any apparently positive findings . in the current paper , we show how ci for relative effect size estimates such as or may be corrected for multiplicity by use of the hochberg step - up procedure , a closed - testingthe corrected ci are simple to compute in standard statistical software packages that have function routines for determining percentiles and areas under a curve for a normal distribution . since p values are not required for the original hypothesis tests , multiplicity corrected ci may be computed post hoc ( when estimates are reported with sufficient precision ) from publications that only report values for effect size estimates and corresponding ci . when the test statistics are uncorrelated , the family - wise type i error probability is theoretically guaranteed by the hochberg step - up procedure . simulation results also show that the hochberg step - up procedure holds for many commonly encountered dependent test statistics . the technique is not applicable when exact sampling distribution methods have been used to make statistical inferences . the hochberg multiplicity correction also will inflate p values and related ci when one or more of the hypothesis tests involve a multi - level , logically related categorical variable ( e.g. , current smoker , former smoker , never smoker ) . in this case , it is unnecessary to correct ci for multiplicity for a logically related variable in multivariate space . the computed multiplicity corrected ci will be an approximate solution when the decimal accuracy is limited for the original or and ci values . accordingly , it is generally recommended that at least 2 or 3 significant digits of accuracy are available for published estimates when using this method in a post hoc manner to compute multiplicity corrected confidence intervals .7 ) in rare cases may lead to an anomaly wherein p ( j ) but not p ( j1 ) will achieve statistical significance . in this situation , one might apply the de facto variation of multiplying p ( j ) and lesser ranked p values by j to obtain the corresponding hochberg corrected p values . and finally , the method should not be used if the logarithm of the effect estimate does not follow a normal distribution , or if the underlying observations are not independent and identically distributed . it also is important to note that correction for multiplicity may not be necessary or even desirable in some situations . for example , correction for multiplicity may be unnecessary when an a priori biologic mechanism of action exists for an independent variable that manifests a linear dose response in relationship to the outcome variable . similarly , multiplicity correction may not be desirable when attempting to control type ii errors as the latter will be inflated by virtue of decreasing type i errors . furthermore , multiplicity correction based upon the universal null hypothesis , which tests that two groups are identical for all comparisons between variables , fails to take into account which and how many variables differ if the joint hypothesis is rejected . methods to correct for multiplicity also do not account for the inclusion of hypotheses that are biologically improbable or otherwise indefensible , which unnecessarily inflate the probability of incorrectly rejecting the joint null hypotheses . philosophically , some researchers believe that the primary purpose for ci are to indicate a range of parameter values consistent with the data rather than for de facto hypothesis testing based on whether or not they include 1.0 . another salient concern regarding the appropriateness of multiplicity correction techniques is how does one choose the universe for the number of comparisons . clearly , multiplicity adjustment remains a debated topic with diverse opinions presented in the literature . in the early days of the development of stepwise and closed tests for the control of type i error in multiple hypothesis testing , epidemiologists and statisticians commonly believed that joint ci could not be constructed for these procedures . however , it has been shown since that standard methods for constructing ci also readily apply to common stepwise multiplicity procedures . here , we have expanded on the seminal work of these researchers to develop a simple method for computing multiplicity corrected ci for standard estimates of effect size . although our derivation has focused on the case of binary predictor variables , it is possible that similar principles might be developed and applied to obtain joint confidence sets in the more complex case of multilevel categorical variables . although the most effective strategy to minimize type i error related to multiple comparisons is to simply reduce the number of comparisons , this in effect penalizes the researcher for conducting a more informative multivariable study . statistical correction for multiple comparisons is not a substitution for the parsimonious and epidemiologically prudent selection - during the design phase of a study - of hypotheses to test . nor should it be used in lieu of careful and informed interpretation of the results , taking into account biological plausibility ( or lack thereof ) and the results of prior studies . however , when statistical correction for multiple comparisons is appropriate , as is the case in many but not all situations , the method we present may have application as a supportive measure . a key advantage of this method is its correspondence with ci , which are typically more informative , and potentially more readily available , than p values .\noutput:\n" }, { "from": "agent", "value": "epidemiological studies commonly test multiple null hypotheses . in some situations it may be appropriate to account for multiplicity using statistical methodology rather than simply interpreting results with greater caution as the number of comparisons increases . given the one - to - one relationship that exists between confidence intervals and hypothesis tests , we derive a method based upon the hochberg step - up procedure to obtain multiplicity corrected confidence intervals ( ci ) for odds ratios ( or ) and by analogy for other relative effect estimates . in contrast to previously published methods that explicitly assume knowledge of p values , this method only requires that relative effect estimates and corresponding ci be known for each comparison to obtain multiplicity corrected ci ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: avaliar as alteraes da mecnica respiratria e do volume corrente ( vc ) em lactentes sibilantes em ventilao espontnea aps a realizao da tcnica de expirao lenta e prolongada ( elpr ) . foram includos no estudo lactentes com histria de sibilncia recorrente e sem exacerbaes nos 15 dias anteriores . para a avaliao da funo pulmonar , os lactentes foram sedados e posicionados em decbito dorsal com mscara facial acoplada a um pneumotacgrafo . as variveis da respirao corrente - vc e fr - e da mecnica respiratria - complacncia do sistema respiratrio ( csr ) , resistncia ( rsr ) e constante de tempo ( psr ) - foram mensuradas antes e aps a realizao de trs sequncias consecutivas de elpr . foram avaliados 18 lactentes , com mdia de idade de 3211 semanas . houve um aumento significante no vc aps elpr ( 79,315,6 ml vs. 85,717,2 ml ; p = 0,009 ) , assim como uma reduo na fr ( 40,66,9 ciclos / min vs. 38,80,9 ciclos / min ; p = 0,042 ) . entretanto , no houve alteraes significantes nos valores da mecnica respiratria ( csr : 11,03,1 ml / cmh2o vs. 11,32,7 ml / cmh2o ; rsr : 29,96,2 cmh2o mls ; e psr : 0,320,11 s vs. 0,340,12 s ; p 0,05 para todos ) . essa tcnica de fisioterapia respiratria capaz de induzir alteraes significativas no vc e na fr de lactentes com sibilncia recorrente , mesmo na ausncia de exacerbaes . a manuteno das variveis da mecnica respiratria indica que a tcnica segura para ser aplicada nesse grupo de pacientes . estudos com lactentes sintomticos so necessrios para quantificar os efeitos funcionais da tcnica . the prolonged , slow expiratory ( pse ) maneuver is a respiratory therapy technique applied in infants with airway obstruction and accumulation of secretion . the benefits of different physiotherapy techniques have been described , and the same occurs with the pse maneuver . during the use of this technique , it was possible to quantify the expiratory reserve volume mobilized , the induction of sighs and maintenance of peak expiratory flow was confirmed and a decreased respiratory distress was observed after application . the evaluation of passive respiratory mechanics - respiratory system compliance ( crs ) , resistance ( rrs ) and its time constant ( prs ) - has been used in studies of various segments in infants , because in addition to obtaining reproducible measurements , it assists in longitudinal monitoring of lung function and evaluation of therapeutic interventions . crs and rrs can also help confirm the benefits of respiratory physiotherapy due to altered pulmonary flow and lung volume after the elimination of secretion . several studies on respiratory therapy in patients under mechanical ventilation in icu used the evaluation of crs and rrs . evaluation of airway resistance can also help detect bronchospasm induced by respiratory therapy techniques . the application of chest vibration and \" tapotement \" ( percussive tapping ) in individuals with lung disease and hypersecretion resulted in no alteration in lung function , proving that this technique is safe and can be applied in subjects with bronchial hyperreactivity . evaluation of tidal volume ( vt ) is one of the oldest and most simple techniques to measure lung function in infants . vt has been studied as an outcome for evaluating the efficacy of unconventional techniques of respiratory therapy . the results so far , however , are controversial , with reports of increased vt in some studies , and of maintenance in others . the evaluation of respiratory mechanics and vt in infants breathing spontaneously is not routinely measured in the clinical practice . these functional variables , however , can be studied in specialized laboratories , and we believe that these consist of objective outcomes and important factors in evaluating the effectiveness of respiratory therapy . the objective of this study was to evaluate changes in respiratory mechanics and vt in wheezing infants in spontaneous ventilation after the application of pse maneuver . we conducted a cross - sectional study evaluation wheezing infants referred for pulmonary function evaluation in the infant pulmonary function laboratory at the allergy , clinical immunology , and rheumatology section of the department of pediatrics , federal university of sao paulo , in so paulo , brazil . we included infants ( between 4 and 24 months of age ) with a history of recurrent wheezing ( at least three episodes ) , without acute respiratory disease manifested in the preceding 15 days . absence of acute respiratory disease was inferred from the absence of corresponding clinical symptoms ( such as cough , wheezing and difficulty in breathing ) and from the lack of consistent findings in the physical examination . we excluded those with upper airway obstruction , preterm infants ( less than 37 weeks of gestational age ) , infants with gastroesophageal reflux disease , infants who underwent thoracic and / or abdominal surgery or who have been diagnosed with heart disease or neuropathy . to perform the pulmonary function testchloral hydrate was administered ( 60 - 80 mg / kg ) , according to the laboratory routine and existing standardization . the infants were monitored using a pulse oximeter ( dx 2405 ; dixtal biomedica , manaus , brazil ) and spo2 and hr were evaluated . the infants were in the supine position with subtle cervical spine extension , using a small pad in the scapular region , without lateralization of the head . a face mask connected to a pneumotachograph ( hans rudolph , kansas city , mo , usa ) was attached to the infants ' face . in technical phase , the pse maneuver was performed with the infant in the supine position , with the hypothenar region of one of the therapist 's hands positioned on the chest , precisely below the suprasternal notch , and the hypothenar region of the other hand placed on the abdomen above the umbilicus . at the end of the expiratory phase , the compression of both hands was made , the hand on the chest being moved in craniocaudal direction and the hand on the abdomen and hand in the caudocranial direction . the next three or four inhalations subsequent to compression were restricted and squeezing motion in the expiratory phase was continued in accordance with the technical description . there were three sequences of pse maneuver ( named a , b and c ) in a continuous period of 120 s ( figure 1 ) . the interval between the sequences was 30 s. the technique was always performed by the same evaluator , trained and qualified to do so . the pse maneuver was performed during the evaluation of vt , so the flow - volume curve was recorded constantly , allowing measurement of the vt and its derivations - rr , pef and the ratio between the time to reach the pef ( tme ) and expiratory time ( te ) . figure 1representation of the acceptability criteria of the expiratory curve obtained in the evaluation of passive mechanics of the respiratory system by the technique of single occlusion . in a , flow - volume curve : segment ad - extrapolation for calculation of the time constant of the respiratory system ; segment bc - linear portion of the curve 60 % of the total , meaning the relaxation of respiratory muscles during expiration . in b , crs , rrs and prs were the analyzed variables of respiratory mechanics using the airway occlusion technique , according to existing recommendations . for these measurements , the respiratory system is considered a one - compartment and linear model . the complete relaxation of the respiratory muscles in infants , necessary for the evaluation of the passive respiratory mechanics , is achieved by inducing the hering - breuer reflex , triggered by the rapid airway obstruction ( 1 s ) at the end of normal inhalation . the presence of the linear segment of at least 60 % of the expiratory loop was inspected visually , as well as the lack of muscular activity by the plateau in the pressure - time curve with a standard deviation 0.1 at 100 ms ( figure 1 ) . at least three acceptable maneuvers were performed as recommended , and the average value was recorded . different variables can be obtained from the analysis of vt , such as inspiratory time , te , total respiratory time , pef , tme , rr and the tme / te ratio . for this group of patients , the evaluation was restricted to vt , rr , pef and the tme / te ratio , as these are variables that can be influenced by respiratory therapy techniques . the tme / te ratio is one of the most studied variables in vt , as it may reflect airway obstruction . the first phase ( pre - technique ) consisted of measuring the vt and its derivations ( rr , pef and tme / te ratio ) for 60 s. after the evaluation of the vt , the measurement of respiratory mechanics was carried out . the second phase ( technique phase ) consisted of applying the pse maneuver in three sequences of compression ( a , b and c ) for a period of 120 s. the technique was performed during the measurement of vt ( figure 2 ) . the third phase ( post - technique ) consisted of the revaluation of the vt for 60 s immediately after the application of the pse maneuver , followed by the evaluation of the respiratory mechanics . figure 2representation of three sequences ( a , b , and c ) of the technique prolonged , slow expiratory ( pse ) maneuver . all continuous variables analyzed presented normal distribution and were evaluated using the shapiro - wilk test and therefore are presented as mean and standard deviation . the mean of the 60 s of evaluation of the vt and the three measurements of respiratory mechanics were used for pre - and post - technique comparison . we used the student t test for dependent samples for the analysis of the tidal breathing ( vt and rr ) and respiratory mechanics ( crs , rrs and prs ) variables between the pre and post technique phases . the program used for the analysis was the statistical package for the social sciences , version 14.0 ( spss inc . , of the 22 infants who started the protocol , 4 did not complete the study : one by coughing during the examination and 3 by technical difficulties ( early awakening and insufficient sedation ) . the mean age of the infants who completed the study was 32.211.4 weeks . variablesresultsage , weeks32 .211.4 height , cm68 .04.3 weight , kg 8.31.0 number of wheezing attacks4 .81.9 sex male / female , n / n9 / 9avalues expressed as mean sd , except where otherwise indicated values expressed as mean sd , except where otherwise indicated during the protocol , no infant showed signs of respiratory distress or expiratory grunting . the spo2 remained over 93 % throughout the tests , and hr remained between 110 and 150 bpm in all infants evaluated . when comparing the pre and post technique phases , we observed a statistically significant mean increase in vt ( p = 0.009 , figure 3 ) and vt corrected by height ( p = 0.01 , table 2 ) . a reduction was observed in rr from 40.66.9 breaths / min to 38.85.9 breaths / min after the technique ( p = 0.04 , table 2 ) . we also observed a significant increase in the tme / te ratio ( p = 0.007 ) . there was no significant change in the mean value of pef when compared to the pre and post - technique phases ( table 2 ) . regarding respiratory mechanics , there was no statistically significant changes in crs , rrs and prs ( table 2 ) . figure 3graphical representation of the variation in tidal volume before ( pre - technique ) and after ( posttechnique ) applying the slow and progressive expiration . table 2variables derived from tidal breathing and respiratory mechanics observed in the pre - and posttechnique protocol . variablesphasesppre - techniquepost - techniquepef , ml / s140 .519.2143.520.60.3 vt , ml79 .315.685.717.20.009 vt , % previsto111 .618.7120.117.70.013 vt , ml / cm1 .160.201.210 .6.938.85.90.04 crs , ml / cmh2o11 .03.111.32.70.4 rrs , cmh2o mls 29.96.230.87.10.4 prs , s0 .320.110.340.120.3 vt : tidal volumetme : time to reach pefte : expiratory timecrs : respiratory system compliancerrs : respiratory system resistanceprs : time constant of the respiratory systemavalues expressed as mean sd . : respiratory system compliance : respiratory system resistance : time constant of the respiratory system values expressed as mean sd . the pse maneuver is a respiratory therapy technique described to promote bronchial clearance in infants . the scientific arguments that prove the effectiveness of the pse maneuver were based , for a long time , on the evaluation of indirect variables , such as hr and spo2 . only recently has the variation in expiratory reserve volume during pse maneuver been described more objectively using the evaluation of pulmonary function variables . however , there are still questions about variations in vt and passive respiratory mechanics immediately after the application of the pse maneuver in subjects breathing spontaneously . after having studied the variations in volume and respiratory wheezing in infants breathing spontaneously , we observed a significant increase in vt and maintenance of the variables crs and rrs and after application of the pse maneuver . one possible explanation for the increase in vt is the reduction of airway obstruction . it has been described that the reduction in the tme / te ratio is an indirect form to determine airway obstruction . thus , we infer that there was a decrease in bronchial obstruction in the patients studied by the increase in the tme / te ratio ( 0.30 ) after the pse maneuver . this reduction in the obstructive process is due to the thoracoabdominal compression performed during the pse maneuvers , where the aim is to prolong the expiratory phase and eliminate the trapped air . if this process is successful , the reduction of the expiratory reserve volume is expected , and it is able to allow an increase in vt . in addition to finding an increase in the tme / te ratio , our group has previously described that the pse maneuver contributes in removing over 50 % of the expiratory reserve volume , confirming the results of the decrease in obstruction . another factor that would justify the increase in vt in the infants studied here is the induction of sighs , characterized as breaths in which there is an increase greater than 100 % in vt . recently , we have shown that the pse maneuver favors the induction of sighs , and that it is already known that sighs act by recruiting alveoli and increasing the vt . it is important to point out that the variation observed in our study in the values of vt , albeit small , is probably clinically relevant . the instability of the rib cage , routinely observed in infants , makes those more susceptible to lung volume reduction , and maneuvers that increase vt become clinically relevant . we observed an increase of nearly 10 % in vt after applying three sequences of the pse maneuver . in the clinical practice , however , physical therapists , when using the pse maneuver technique , perform a greater number of maneuvers , basing the number of repetitions on the improvement in pulmonary auscultation . thus , it is unlikely that the actual increase of vt determined by the pse maneuver technique in the daily practice be much more expressive than the one found in our study . rrs in our study was maintained after the application of the pse maneuver , in disagreement with studies in patients on mechanical ventilation . this finding can be explained by evaluating patients breathing spontaneously , without hypersecretion and therefore without change in the rrs at the beginning of the protocol . it is described that techniques with intense mechanical vibrations in the chest , such as \" tapotement \" ( percussive tapping ) and vibration , can aggravate bronchospasm , evidenced by the reduction in fev1 and pef . there is no description of the unconventional techniques of physiotherapy favoring bronchospasm , due to the fact that these techniques cause no abrupt mechanical vibrations in the chest . in our study , we observed no change in either rrs or pef , confirming that pse maneuver did not induce bronchospasm in this group of wheezing infants , and we consider it a safe technique to perform even in individuals prone to bronchospasm . a group of authors , when evaluating unconventional techniques of respiratory therapy similar to that applied in this study , observed no significant changes in pef . the maintenance of the values of crs in this study can be justified due to fact that the initial values were within normal limits , and to the lack of pulmonary hypersecretion . authors who observed that variation in respiratory function after physical therapy in mechanically ventilated patients described the secretion clearance as the main reason . our study was limited by the fact that patients are not in exacerbation or presented hypersecretion . individuals with hypersecretion were not selected , due to the fact that , in addition to the interference of this condition in the variables analyzed , the secretion could also compromise the safety of the infant , since the sedation associated with hypersecretion aggravates airway obstruction in patients breathing spontaneously . the short application time of pse maneuver ( three sequences ) and functional revaluation soon after its completion are other limitations to our study . this , however , could hardly be altered due to the short time of sedation induced by chloral hydrate . even with a small evaluation time , we observed significant changes in vt and we can speculate that the performance of a greater number of sequences of the pse maneuver could increase the differences found . we conclude that the application of pse maneuver in wheezing infants is able to induce changes in pulmonary function with increased vt and reduced rr . the maintenance of the airway resistance values demonstrates that the pse maneuver technique is safe for application in infants with propensity to bronchospasm .\noutput:\n" }, { "from": "agent", "value": "objective : to evaluate changes in respiratory mechanics and tidal volume ( vt ) in wheezing infants in spontaneous ventilation after performing the technique known as the prolonged , slow expiratory ( pse ) maneuver . methods : we included infants with a history of recurrent wheezing and who had had no exacerbations in the previous 15 days . for the assessment of the pulmonary function , the infants were sedated and placed in the supine position , and a face mask was used and connected to a pneumotachograph . the variables of tidal breathing ( vt and rr ) as well as those of respiratory mechanics - respiratory system compliance ( crs ) , respiratory system resistance ( rrs ) , and the respiratory system time constant ( prs ) - were measured before and after three consecutive pse maneuvers . results : we evaluated 18 infants . the mean age was 32 11 weeks . after pse , there was a significant increase in vt ( 79.3 15.6 ml vs. 85.7 17.2 ml ; p = 0.009 ) and a significant decrease in rr ( 40.6 6.9 breaths / min vs. 38.8 0,9 breaths / min ; p = 0.042 ) . however , no significant differences were found in the variables of respiratory mechanics ( crs : 11.0 3.1 ml / cmh2o vs. 11.3 2.7 ml / cmh2o ; rrs : 29.9 6.2 cmh2o ml1 s1 vs. 30.8 7.1 cmh2o ml1 s1 ; and prs : 0.32 0.11 s vs. 0.34 0.12 s ; p > 0.05 for all ) . conclusions : this respiratory therapy technique is able to induce significant changes in vt and rr in infants with recurrent wheezing , even in the absence of exacerbations . the fact that the variables related to respiratory mechanics remained unchanged indicates that the technique is safe to apply in this group of patients . studies involving symptomatic infants are needed in order to quantify the functional effects of the technique ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: they are a congenital disturbance of the position of the eyelashes , which are usually on the lateral quadrant of the upper eyelid or conjunctival surface of the eyelid . the origin of these abnormally placed cilia is not clear , but a previous theory of meibomian gland substitution has been refuted and an embryologic origin suggested .1,2 in most cases , it causes no apparent medical morbidity and there is no positive family history . here we report a case of a patient with ectopic cilia and hypochromic patches on the right arm . a 6 - year - old girl was referred for evaluation of a congenital lateral upper eyelid ectopic cilia cluster ( figure 1 ) . on physical examination , she had hypochromic lesions on the right arm , diagnosed by the dermatology service as hypochromic nevi ( figure 1 ) . the specimen comprised a circular 106 mm portion of skin and contained a centrally placed tuft of strong and pigmented hairs . longitudinal sections and histologic analysis showed dermal and subcutaneous pilosebaceous follicles ( figure 1a and 1b ) , packed in a dense fibrous tissue core ( figure 1b ) extending through the eyelid from the subcutaneous area , scarcely represented in the specimen . well developed sebaceous lobules ( figure 1c ) , bulbs of pilous follicles ( figure 1d ) , and apocrine - lined epithelial ducts consistent with glands of moll ( figure 1e ) and associated with pilous follicles were observed . occasional striated orbicularis muscle fibers were present in the depths of the specimen ( figure 1f ) , with the lowest hair bulbs ( figure 1f ) superficial to them . they have been observed to protrude from the anterior surface of the eyelid skin and the posterior aspect of the tarsal plate . there are 15 cases located on the anterior surface of the eyelids .1,2 histologic examination has demonstrated the presence of apocrine and pilosebaceous glands , and there is evidence that ectopic cilia in the palpebral conjunctiva are acquired aberrant cilia , in contrast with anterior ectopic cilia , which are congenital .3 in this case , histopathologic examination of the specimen revealed the typical characteristics of ectopic cilia described in the rare cases reported in the literature . we found strong and pigmented hairs in a dense fibrous stroma associated with sebaceous and apocrine glands located in the dermis and subcutis and superficial to the orbicular muscle fibers . importantly , ectopic cilia must be differentiated from abnormally placed hairs . as in our present case , the diagnosis of ectopic cilia is confirmed histologically by identification of sweat glands of the apocrine type attached to the follicles .4 recent reports also underscore the importance of morphologic observation of ectopic cilia in association with lobules of sebaceous glands and apocrine glands .5 in the present case , the cilia arose from the anterior surface of the tarsal plate , being classified as anterior - type ectopic cilia , which are congenital , in contrast with posterior ectopic cilia that arise in the palpebral conjunctiva and are acquired aberrant cilia .3 although previous reports have not correlated ectopic cilia with other skin hypopigmentation disorders , it is important to note that congenital hypochromic patches ( hypochromic nevi ) were observed in this case .\noutput:\n" }, { "from": "agent", "value": "ectopic cilia are rare in humans . we report a 6 - year - old girl with typical characteristics of ectopic cilia as described in the rare cases reported in the literature , in association with cutaneous lesions that appeared to be hypochromic nevi . this framework could be a different clinical presentation of ectopic cilia ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: over the last few years , dental implants have shown satisfactory success rates in several clinical situations . for favorable prognosis , some requirements are needed such as the absence of mobility of the implant during surgical procedure , which is defined as primary stability . this property is essential for the maintenance of the peri - implant hard and soft tissues and , for this reason , it is a determining factor for complete osseointegration . good primary stability allows balanced distribution of masticatory effort and functional occlusal loads soon after the implant is inserted . this stability may decrease over time due to peri - implant bone remodeling . for long - term success in implant dentistry , the following factors related to the patient must be taken into consideration : bone quality and volume , peri - implant clinical parameters , implant stability , factors related to the surgical technique , and the selection of implants . these previously assessed factors provide predictable osseointegration and if load can be applied or not . some methods for assessing primary stability have already been proposed , as insertion torque and resonance frequency , but no methods show completely precise results . medical orthopedics proposes a method to simulate this analysis , the pullout test , which despite the need for specific devices for each type of implant , it is established in this medical specialty . moreover , it is necessary to select materials to be used as a substrate for these tests in view of the disadvantages found in selecting similar substrates to the human bone as well as the difficult access to good in vivo quality bone , which is a prerequisite for the initial fixation . the variety of cadaver bones and variables that influence quality , such as fenestrations , which are frequent and unknown in these bones , may influence reliability and validity of the measurements , making it difficult to conduct the study due to the need for large samples to obtain significant results . furthermore , the use of human bones presents difficulties with regard to availability , preparation , and preservation . these conditions have led science to seek for substitutes for the human bone , which led to the development of synthetic bones that allow the standardization of mechanical testing and increased availability . the use of polyurethane models began with uta for analysis of the femur . over the years , anisotropy and heterogeneity , which are characteristics belonging to the human bone , have improved and composite models have been proposed . at present , the most complete validation of these models has been described by cristofolini et al . , who compared synthetic bone with the human bone , emphasizing the mechanical properties such as viscoelastic behavior , main deflection and strain distribution under axial loading , bending , and torsion for the orthopedics area . in addition to the polyurethane , wood araucaria augustifolia , basic density from 0.42 to 0.48 g / cm , similar to the averages of the bones of the mandible and maxilla , is also suggested as a material for the analysis of implant fixation to be anisotropic and resembles human bone sensation perceived in the drilling and installation . based on these concepts , the aim of this study was to propose the evaluation of the mechanical behavior of dental implants inserted in different substrates , in order to determine an experimental model of dental implants using pullout tests . four types of materials used as substitutes for human bone were selected for this study . the samples were divided into three groups ( n = 8 ) according to the type of substrate of the test specimen : pig rib bone , polyurethane synbone ( synbone ag , malans , switzerland ) ; polyurethane nacional ( nacional ossos , ja , brazil ) ; and wood of the species of araucaria angustifolia . the cylindrical implants of the type master porous of the brand conexo ( conexo sistemas de prtese , aruj , brazil ) measuring 11.5 mm in height and 3.75 mm in diameter with an external hexagon and porous surface treatment were used . the implants were inserted in pig rib bone segments with 20 mm long , approximately the same thickness of cortical and spongy bone , and included in pvc cylinder ( 20 mm diameter and 15 mm height ) , filled with acrylic resin , such that 5 mm of bone stay outside of the cylinder , not included by the material . samples were kept under freezing ( 215c ) to maintain their physical properties and , previously to surgical procedures and measurements of implants , remained at ambient temperature for 2 hours to reach thermal equilibrium and not change biomechanical properties . others implants were inserted in a rectangular polyurethane block nacional with a density of 40 pcf and measuring 4.2 mm in height , 17.8 mm wide , and 13 mm in length . an artificial bone specimen similar to the human femur in shape and density of the brand synboneeight wood cylindrical test specimens measuring 30 mm in diameter and 13 mm in length were fabricated in the precision workshop of the school of medicine of ribeiro preto in order to facilitate mechanical testing and prevent future damages to the screws and test specimens . the test specimens of a specific group were perforated and the implants were inserted by a single operator with the aid of a counter - angle , a surgical electric motor mc 101 omega adjusted to 45 n and 1861 rpm , both of the brand dentscler ( dentscler indstria de aparelhos odontolgicos ltda . , ribeiro preto , brazil ) , and a set of cutters and accessories from the connect master kit ( conexo sistemas de prtese , aruj , brazil ) , following the sequence of steps recommended by the manufacturer . each implant was inserted in the test specimens with the exact distance of 5 mm from the other implant in order to prevent possible alterations in the material after performing the test causing interference in the analysis of adjacent implant . group 1 received the implants in the central portion of the block in order to avoid interference that the press on the sides of the material might cause to the results . group 2 had the implants placed in the upper portion of the femoral head that had a strip of cortical bone with an average thickness of 2 mm and a medullary portion with an average thickness of 15 mm . in group 3 , the implants were inserted in the central part of the diameter of each cylindrical test specimen . after the implants were inserted and tested in the specific group , they were removed with the aid of the torque meter connection applying the reverse torque and then the test specimens were inserted in the other group to test the pullout strength . insertion torque analysis was made in digital torquimeter kratos ( kratos industrial equipment inc . , cotia , sp , brazil ) coupled to devices or implants mounts , adapted to the respective implants shapes ( figure 1 ( a ) ) . value was measured at each turn screw , being considered the maximum value obtained , which was converted to ncm by the formula : y = 0,0449 x 0.7907 , where y is the value ncm , and x is the value read . to verify the pullout strength , the mount implants of the porous master implant of the brand conexo were used , which were coupled to a piece adapted to a load cell of 200 kg of a universal testing machine emic brand model dl10000 ( emic equipamentos e sistemas de ensaios ltda , so jos dos pinhais , brazil ) ( figure 1 ( a ) ) . the pullout test was performed using an axial traction force in the direction of the long axis of the implant for 2 min / mm , obtaining maximum pullout force and the relative rigidity of the material ( figures 1 ( a ) and 1 ( b ) ) . data were analyzed with regard to their distribution and homogeneity , and since they were normal ( kolmogorov - smirnov test ) and homogeneous ( levene test ) , the one - way analysis of variance was used ( one - way anova : material ) . to differentiate the means , the bonferroni test was used at a level of significance of 5 % . after statistical analysis of insertion torque , it was found that there was the highest average when the implant was inserted into the polyurethane national 40 pcf ( 31.157.53 ) and in the wood ( 20.702.77 ) , with significant difference with all other substrates ( p 0.05 ) ( figure 2 ) . the results of maximum pullout force showed that there was a difference between the groups studied ( p 0.05 ) . the implants inserted in the polyurethane national 40 pcf ( 603.10190.33 n ) and wood ( 740.06268.13 n ) showed higher pullout strength values with a statistically significant difference when compared with synbone and natural bone ( p 0.05 ) , as in insertion torque analysis . implants inserted in bone possessed the lowest mean strength ( 44.7413.36 n ) ( figure 3 ) . however , it is of great importance that more studies determine primary stability for it is an indicator of greater significance to guarantee of osseointegration . the methods for measuring clinical primary stability , although feasible and useful , have limitations , and a method that correlates the different types of implants with its initial fixation is needed , similar to what occurs to the human bone with the use of a similar material for laboratory mechanical testing . the present study assessed four materials that could be indicated as substitutes for the human bone to perform the mechanical tests of dental implants with the purpose of developing a new experimental model for the analysis of primary stability . due to the difficulty in obtaining of human bone models with a homogeneous sample , the american society for testing materials has shown that polyurethane blocks have mechanical properties that mimic the human bone and thissome authors have used polyurethane blocks for analyzing primary stability of dental implants using methods such as resonance frequency analysis and insertion torque . thus , the selection of polyurethane materials used in this study derived from the analysis of similar studies to assess the insertion torque and pullout or tensile strength of dental implants since they showed similar results when compared with the human cadaver bone . the choice of wood was due to its similar characteristics to the bone , which were perceived through tactile sensitivity during perforation of the substrate , and its intrinsic anisotropic properties , homogeneity and uniformity . this quality may explain the results presented in this study , which showed that wood presented high mean insertion torque and pullout strength when compared with the other materials , as synbone and wood . periotest ( siemens ag , germany , bensheim ) is an instrument that has been proposed to measure primary stability , but it was not considered an ideal tool for this evaluation due to its inability to respond to minor changes at the bone - implant interface . several studies have reported that resonance frequency analysis is a useful tool to analyze primary stability after implantation , as well as the degree of stability after osseointegration . however , the interpretation of the values of the implant stability quotient ( isq ) still lacks scientific knowledge and there is no consensus of a presupposed value for high or sufficient primary stability for immediate loading . furthermore , the isq values of different implant systems can not be compared . another widely used method described by friberg to measure primary stability is insertion torque . our study used this method as standard analysis of primary stability , that it can be used to assess more accurately bone quality and support , which are measured at the time of final seating of the implant in the receptor bed . determining insertion torque is one of the most reliable methods to obtain information about bone quality . although insertion torque is proposed by many scholars , comparability among different implant systems is still unclear , and the minimum level of primary stability needed for immediate loading has not been defined . thus , besides the insertion torque , widely used for analysis of primary stability of dental implants , the method pullout test was used , which is widely used in orthopedic implants for the analysis of mechanical resistance , using natural and synthetic bones or substrates that satisfy the reproduction of the human bone tissue to measure resistance of the screw . although the physiological cyclic forces on the implants in a mandible or maxilla are not only limited to the axial forces shown in the test , this method allows the parameters studied to be assessed through maximum pullout force as well as comparing the different implants and types of implantation . studies have reported that screws have the capacity to resist to pullout strength , mechanical property related to the geometry and size of the screw , bone quality and quantity , insertion torque , and pilot orifice preparation . furthermore , the surface of the screw in contact with the bone tissue and the number of threads per unit length of the screw is proportional . the correlation of stability with design and surface treatment of implants allows different screws to be idealized in order to optimize osseointegration , help indication of implants , and reduce the indication of bone grafts to facilitate the surgical technique , although little has been done to apply these assumptions in the development of new projects for screws . despite the paucity of studies in the literature on the subject proposed , the experimental model showed that the pullout test can provide important data , such as initial stability through maximum pullout force , since the measurement method is still controversial . it may also provide information about the substrate behavior obtained from the results such as relative rigidity and deformation . thus , the pullout test associated with the use of a substrate that mimics the real conditions of bone enables conducting laboratory studies that correlate mechanical properties with the shape and surface treatment of the implant , allowing great industrial advance , since these results may lead to the proposal of new models of screws . the analysis of the mechanical behavior of different implants inserted in substrates of human bone substitutes showed the polyurethane nacional 40 pcf and wood with the highest values for insertion torque and maximum pullout strength . therefore , bone density influenced this analysis , seen by the highest torque and resistance pullout in materials compared to bone type d2 , and the lowest values in bones less dense because they have a density similar to bones d4 , based on some studies that show that bones type d2 and d3 , reveal no statistical difference between implants analyzed only between bones d2 and d4 , and d3 and d4 . furthermore , the low density of the rib bone is evidenced by the fact they can not be compared to bone cortical bone , which influences the density of the substrate .\noutput:\n" }, { "from": "agent", "value": "the aim of the study was to evaluate mechanical behavior of implants inserted in three substrates , by measuring the pullout strength and the relative stiffness . 32 implants ( master porous - conexao , cylindrical , external hexagon , and surface treatment ) were divided into 4 groups ( n = 8 ) : pig rib bone , polyurethane synbone , polyurethane nacional 40 pcf , and pinus wood . implants were installed with the exact distance of 5 mm of another implant . the insertion torque ( ncm ) was quantified using the digital kratos torque meter and the pullout test ( n ) was performed by an axial traction force toward the long axis of the implant ( 2 min / mm ) through mount implant devices attached to a piece adapted to a load cell of 200 kg of a universal testing machine ( emic dl10000 ) . data of insertion torque and maximum pullout force were submitted to one - way anova and bonferroni tests ( = 0.05 ) . polyurethane nacional 40 pcf and pinus wood showed the highest values of insertion torque and pullout force , with significant statistical difference ( p < 0.05 ) with other groups . the analysis showed stiffness materials with the highest values for primary stability ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: undifferentiated embryonal sarcoma of the liver ( uesl ) has also been called undifferentiated sarcoma of the liver or malignant mesenchymoma of the liver . as the disease name and synonyms imply , uesl chiefly occurs in pediatric patients and is composed of poorly differentiated cells of undetermined cellular lineage other than mesenchymal differentiation . primary malignant mesenchymal tumors in the liver are relatively rare compared with carcinomas originating from hepatocytes or cholangiocytes . although there are some sarcomas that can primarily occur in the liver , such as angiosarcoma , rhabdomyosarcoma , leiomyosarcoma , and synovial sarcoma , their histologic features and diagnostic criteria are similar to those of soft tissue tumors . uesl is a unique primary sarcoma in liver that has specific histologic and clinical characteristics and has no similar entities among soft tissue tumors . uesl is the third most common malignant tumor in older children , following hepatoblastoma and hepatocellular carcinoma , and 75 % of cases have been diagnosed in children aged 615 years . herei report a undifferentiated embryonal sarcoma case that occurred in an adult patient and review the relevant literature . a 51 - year - old man was admitted for abdominal pain that developed 2 days ago . abdominal magnetic resonance imaging ( mri ) showed a 15 cm lobulated cystic mass with thin enhancing septa in the right lobe of the liver with fluid levels suggesting internal hemorrhage . serum levels of tumor markers ( carcinoembryonic antigen , ca - 19 - 9 , alpha - fetoprotein , and prostate specific antigen ) were all within normal limits and he was negative for hepatic viral markers ( hbsag and anti - hcv ) . he had regular follow - up for cardiac valve disease and no history of a previously diagnosed malignancy . on gross examination , a 14.010.05.5 cm multilocular cystic lesion was identified in non - cirrhotic hepatic parenchyma the cystic contents were bloody and the cyst wall was covered with dark red bloody material . the thick cystic wall showed a mixed yellow and white , glistening , myxoid fish - flesh - like cut surface with hemorrhage ( fig . the thick cystic wall was a hypercellular solid lesion bordered by non - neoplastic hepatic parenchyma with a thin fibrous capsule ( fig . the cells were plump ovoid or spindle cells that showed a diffuse sheet - like pattern without an organoid pattern ( fig .2 a ) the tumor stroma was loose edematous myxoid or fibrous in the periphery of the lesion . the tumor cells had a moderate amount of cytoplasm and hyperchromatic nuclei with severe pleomorphism . pinkish hyaline globules or clusters of eosinophilic granules were frequently found in the extracellular area or in the intracellular cytoplasm reminiscent of hemophagocytic cells ( fig . mitosis were frequently found , up to 12/10 high power field ( hpf ; 400 ) ( fig . the thin cystic wall had similar histologic features to the solid lesion but the cyst wall had no lining cells . immunohistochemical staining revealed that the tumor cells were diffusely reactive for vimentin , and focally positive for desmin , smooth muscle actin , and cytokeratin , but not positive for s - 100 , cd117 , myogenin , cd34 , or ets - related gene ( erg ) ( fig. 2f - h ) . uesl is a rare primary mesenchymal tumor that usually occurs in older children , but some cases have been reported in adults . a solid mass with extensive cystic or necrotic changes is a notable manifestation of uesl . this frequent cystic change in uesl and the rarity of uesl in adults often leads to a misdiagnosis during preoperative evaluation . commonly reported differential diagnoses are hepatic abscess , hydatid cyst , hemorrhage cystic tumor , and klatskin tumor [ 3 - 7 ] . in pediatric patients , the main differential diagnosis of uesl before treatment is mesenchymal hamartoma , which is the second most common benign liver tumor after infantile hemangioendothelioma . generally , serum tumor markers are within the normal range , but one case of erythropoietin - secreting uesl has been reported . histologically , tumor cells have high pleomorphism , hyperchromasia , and abundant mitoses , representing an undifferentiated and highly proliferative phenotype . multiple intracellular or extracellular eosinophilic globules that are positive for periodic acid - schiff ( pas ) stain and resistant to diastase pas are characteristic histologic features of uesl . ultrastructurally , these globules are electron - dense lysosomes with dense precipitates and dilated rough endoplasmic reticulum with scanty actin filaments in the cytoplasm , suggesting fibroblastic , fibrohistiocytic , and undifferentiated cells as a cellular lineage . immunohistochemically , vimentin is consistently expressed in the tumor cells but desmin , keratin , - smooth muscle actin , -1-antichymotrypsin , cd10 , cd68 , and calponin show variable expression [ 11 - 13 ] . glypican 3 , a fetal oncoprotein that is normally expressed during embryogenic development , has been reported to be expressed in uesl , suggesting that uesl has an immature phenotype . alterations of tp53 ; allelic imbalances of 1p , 80 , and 20q ; and loss of heterozygosity of 7p , 11p , 17p , and 22q have been reported in uesdl . however , beta - catenin activation , a commonly - altered pathway in pediatric tumors , has not been identified . a few cases of uesl arising in mesenchymal hamartomas have been reported in pediatric patients and they showed common cytogenetic alterations , t ( 11 ; 19 ) ( q13 ; q13 .4 ) , suggesting a common pathogenic pathway of the two lesions . the malat1 gene was the break - apart site at 11q13 , and it has been reported in a subset of renal tumors . the other breakpoint at 19q13 .4 was the mhlb1 locus that does not contain a known gene . pathologic diagnosis of uesl is an exclusive diagnosis because of the lack of specific diagnostic markers and its primitive histology . among the malignant pediatric tumors in the liver , embryonal rhabdomyosarcoma and malignant rhabdoid tumor have to be preferentially excluded , since they share histologic features with uesl . co - expression of desmin , myogenin , and myoglobin suggests rhabdomyosarcoma and loss of expression of ini1 suggests a malignant rhabdoid tumor . in adult patients , differential points are somewhat different from those of pediatric patients . because primary sarcoma of liver is rare in adult , metastatic sarcomashould first be excluded and then sarcomatoid carcinoma should be excluded . because the primary carcinomas in the liver or peritoneum , such as hepatocellular carcinoma , cholangiocarcinoma , and mesothelioma , can be transformed to have both mesenchymal and epithelial differentiation , epithelial differentiation of tumor cells and the co - existence of carcinoma should be excluded to confirm uesl . because this case also had entrapped bile ducts in the peripheral portion and showed cystic changes , multiple tumor sections were obtained to examine for evidence of concomitant epithelial neoplasms , including adenocarcinoma or dysplasia . the prognosis of uesl has been poor until recently , but some improvements in survival have been achieved in both pediatric and adult patients by combined modality treatments . repeated complete resection , neoadjuvant or adjuvant chemotherapy , and liver transplantation have been applied as multimodal treatment . the patient in this case received adjuvant chemotherapy after complete resection and has no evidence of disease recurrence to date . this case presented as a cystic lesion in the liver and had typical histological features of uesl . it is a rare case of a malignant pediatric tumor occurring in an adult patient .\noutput:\n" }, { "from": "agent", "value": "undifferentiated embryonal sarcoma of the liver ( uesl ) is rare primary hepatic sarcoma and is known to occur in pediatric patients . this case is the uesl occurred in a 51 - year old male patient . multilocular cystic lesion was composed of primitive spindle cells without specific differentiation . this rare case would help to review differential diagnosis of primary sarcoma in liver and cystic neoplasm of the liver ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: periodontal inflamed surface area ( pisa ) quantifies the amount of inflamed periodontal tissue and is supposed to quantify the inflammatory and infectious burden resulting from periodontitis . periodontitis may cause an inflammatory burden through the production of local inflammatory mediators entering the systemic circulation . this inflammatory burden is evidenced by increased serum c - reactive protein ( crp ) levels found in patients suffering from periodontitis . periodontitis may also cause an infectious burden through bacteria and their products entering the systemic circulation . this burden may endanger overall health by for example causing atherosclerosis and cardiovascular diseases . circulating oral bacteria and lipopolysacharides are also able to stimulate hepatocytes to secrete crp . thus , increased levels of crp associated with periodontitis may be considered as a common pathway for both the inflammatory and infectious burden resulting from periodontitis . the high levels of crp accompanying periodontitis , may lead to insulin resistance and thereby to poor control of blood glucose in type 2 diabetes mellitus ( dm2 ) and healthy subjects resulting in increased levels of glycated hemoglobin ( hba1c ) . accordingly , high levels of crp are correlated with increased hba1c levels in dm2 patients . increased crp levels have also been associated with an increased risk of cardiovascular disease ( cvd ) in dm2 patients , the major cause of the increased mortality in dm2 patients . given the importance of blood glucose control in preventing cvd in dm2 patients , relatively few studies assessed whether the specific combination of periodontitis and crp as a reflection of inflammatory burden , predict hba1c levels . furthermore , no study has investigated this issue in indonesia while this country is in the top ten of countries with the highest prevalence of dm ( at 5.7 % ) in the world in 2005 . it has been estimated that by the year 2030 , the prevalence of dm in indonesia will be about 10 % , corresponding with 20 million dm patients . in addition to a high dm prevalence , a high prevalence of periodontitis has been reported in indonesia . finally , depending on the definition used , our previous study showed that indonesian dm2 patients have a prevalence of periodontitis at 72 % to 93 % and an increased severity of periodontitis . therefore , the aim of this study was to assess whether periodontitis severity , as measured with the pisa method and crp predict hba1c levels in healthy indonesians and indonesian treated for dm2 patients . the participants in this study were recruited from three different sites , namely ( 1 ) the internal medicine department dr . soedomo dental hospital , faculty of dentistry , gadjah mada university , yogjakarta , and 3 ) diabetes center of jogjakarta international hospital , yogjakarta , indonesia . all participants had to be aged 18 years and had to have 8 remaining teeth . the latter inclusion criteria was proposed prior to commencing the study since current inflammatory burden posed by periodontitis requires the presence of at least a minimum number of teeth affected by periodontitis . this study was approved by the ethical committee for research of the medical faculty of gadjah mada university , yogjakarta , indonesia . all participants completed a validated general health assessment questionnaire to check for other medical conditions that might be a risk factor for periodontitis . information on age , gender , height and weight ( for body mass index ( bmi ) calculation ) , education , and smoking were obtained from each participant . all participants underwent a periodontal examination including periodontal probing pocket depth ( pd ) , gingival recession , plaque score , and bleeding on probing ( bop ) measurements by trained and calibrated examiners ( hs , yhr , and eh ) . all measurements were performed on all teeth , on six sites per tooth using a manual periodontal color - coded standard probe ( dentsply , london , uk ) . clinical attachment loss ( al ) was defined as the distance from the cementoenamel junction to the bottom of the pocket / sulcus and calculated as the mathematical sum of the pd and gingival recession measurements . bop was recorded as either present or absent within 30 s of probing at six sites per tooth . plaque score was defined as being present or absent at six points on each tooth . periodontitis extent and severity were operationalized using a variety of methods , all of which are currently used in literature studying the association between periodontitis and other diseases . all measurements were calculated using conventional clinical measurements obtained during the full - mouth periodontal examination ( hs and wn ) . the number of sites with probing pd of 4 , 5 , and 6 mm , the numbers of sites with clinical al of 3 , 4 , 5 , and 6 mm , mean pd , mean al , and the percentage of sites with bop were calculated . additionally , a recently introduced measure of periodontitis severity , the pisa was calculated , pisa quantifies the amount of inflamed periodontal tissue , and it is suggested that pisa thereby quantifies the inflammatory burden exerted by periodontitis . finally , all participants underwent a venapuncture to obtain a blood sample . both blood glucose ( fasting blood glucose ) , determined by glucose oxidase enzymatic method , and glycosilated / glycated hemoglobin ( hba1c ) values , determined using low pressure cation ion exchange chromatography ( diastat , bio - rad , usa ) , were determined for all participants . additionally , crp , determined by a high - sensitivity chemiluminescent immunometris assay ( immulite 2000 , diagnostic products corp . differences in periodontitis severity between dm2 and healthy subjects were analyzed first using univariate analyses ( independent sample t test , mann whitney u test , or chi - square test as appropriate ) . likewise , differences in potential predictors of periodontitis ( age , gender , bmi , education , smoking , plaque score , number of teeth , ethnicity , and other medical conditions ) between dm2 patients and healthy subjects were tested for significance using univariate analyses . since periodontitis severity was operationalized in 12 different ways , significance level of 0.05 was corrected for multiple comparisons according to the bonferroni holm method . to assess periodontitis and crp as potential predictors of hba1c in subjects with and without dm2 , as independent variables , i.e. , predictors of hba1c : age , sex , bmi , pack years , education , crp , and all measures of periodontitis severity . differences in periodontitis severity between dm2 and healthy subjects were analyzed first using univariate analyses ( independent sample t test , mann whitney u test , or chi - square test as appropriate ) . likewise , differences in potential predictors of periodontitis ( age , gender , bmi , education , smoking , plaque score , number of teeth , ethnicity , and other medical conditions ) between dm2 patients and healthy subjects were tested for significance using univariate analyses . since periodontitis severity was operationalized in 12 different ways , significance level of 0.05 was corrected for multiple comparisons according to the bonferroni holm method . to assess periodontitis and crp as potential predictors of hba1c in subjects with and without dm2 , as independent variables , i.e. , predictors of hba1c : age , sex , bmi , pack years , education , crp , and all measures of periodontitis severity . in a total of 101 participants , 40 men and 61 women , with a mean age of 54 years treated for dm2 , diagnosed according to world health organization criteria were included ( table 1 ) . the mean bmi in this group was 25.5 , labeling them as being overweight according to the world health organization classification ( overweight bmi , 2327.5 ) . the dm2 patients had an average of 24 teeth with a mean plaque score of 91 % ( table 2 ) . in addition , a total of 132 healthy controls was enrolled , 34 men and 98 women , with a mean age of 48 years . again , the healthy subjects were mainly of javanese origin ( 90 % ) and were on average ranked as being overweight according to the bmi index for asian populations ( bmi , 24.4 ) . the healthy subjects had an average of 26 teeth and a mean plaque score of 93 % . the average hba1c level of this group was 5.5 % ( below 6.5 % classified as healthy / non diabetic ) . table 1characteristics of the participantsvariablesdm2 ( n = 101 ) healthy controls ( n = 132 ) p valuedemographyage ( years ) mean ( sd ) 54.4 ( 10.7 ) 47.9 ( 10.1 ) 0.001 smoking ( pack year ) median ( iqr ) 0.0 ( 0.00.0 ) 0.0 ( 0.00.0 ) 0.109 bmi ( kg / m ) mean ( sd ) 25.5 ( 4.2 ) 24.4 ( 3.8 ) 0.054 java origin ( n ( % ) ) 94 ( 93 % ) 119 ( 90 % ) 0.431 gender ( n ( % ) ) 0.05 male40 ( 40 % ) 34 ( 26 % ) female60 ( 60 % ) 98 ( 74 % ) education ( n ( % ) ) 2.18 ( 0.79 ) 2.13 ( 0.77 ) 0.662 low ( 69 years ) 32 ( 24 % ) 24 ( 23 % ) middle ( 912 years ) 51 ( 39 % ) 34 ( 34 % ) high ( 1217 years ) 49 ( 37 % ) 43 ( 43 % ) hypertension ( yes ) ( n ( % ) ) 26 ( 26 % ) 24 ( 18 % ) 0.164 medication ( n ( % ) ) sulfonylurea55 ( 54 % ) nana insulin41 ( 41 % ) na metformin37 ( 37 % ) na acarbose33 ( 33 % ) nalaboratory serum markershba1c ( % ) mean ( sd ) 8.9 ( 2.4 ) 5.5 ( 0.4 ) 0.001 crp ( mg / l ) median ( iqr ) 2.8 ( 1.67.0 ) 1.1 ( 0.62.3 ) 0.001 p values were bonferroni holm corrected . a p value of 0.05 was considered statistically significantp probability , bmi body mass index , crp c - reactive protein , dm2 diabetes mellitus type 2 , hba1c glycated hemoglobin , iqr interquartile range , n number of participants , na not applicable , sd standard deviation , low , elementary and junior school ( education ) , middle high school ( education ) , high university ( education ) result of chi - square testresult of mann whitney u test ; other results are the results of the independent samples t testtable 2periodontal status of healthy controls and dm2variableshealthy controls ( n = 132 ) dm2 ( n = 101 ) p valueperiodontal prevalence ( n ( % ) ) pd ( 4 mm ) and al ( 3 mm ) 89 ( 67 % ) 89 ( 88 % ) 0.001 pd ( 5 mm ) al ( 2 mm ) 43 ( 33 % ) 67 ( 66 % ) 0.001 periodontal severity ( median ( iqr ) ) pisa ( mm ) 83.9 ( 35.2206.4 ) 170.4 ( 91.5392.6 ) 0.017 al ( mm ) 1.8 ( 1.72.3 ) 2.4 ( 2.03.4 ) 0.001 pd ( mm ) 1.7 ( 1.61.9 ) 1.9 ( 1.72.4 ) 0.001 number of sites ( median ( iqr ) ) al ( 3 mm ) 30.0 ( 17.047.0 ) 54.0 ( 32.5074.50 ) 0.001 al ( 4 mm ) 5.0 ( 1.015.8 ) 25.0 ( 9.048.0 ) 0.001 al ( 5 mm ) 1.0 ( 0.04.8 ) 13.0 ( 2.031.50 ) 0.001 al ( 6 mm ) 0.0 ( 0.01.0 ) 4.0 ( 0.019.5 ) 0.001 pd ( 4 mm ) 2.0 ( 0.04.0 ) 6.0 ( 2.018.0 ) 0.001 pd ( 5 mm ) 0.0 ( 0.01.0 ) 2.0 ( 0.08.0 ) 0.001 pd ( 6 mm ) 0.0 ( 0.00.0 ) 1.0 ( 0.03.0 ) 0.001 bop ( n ( % ) ) 9.0 ( 4.020.0 ) 18.0 ( 10.031.5 ) 0.001 mean ( sd ) plaque score ( % ) 93 % ( 8.5 ) 91 % ( 7.9 ) 0.059 number of teeth25 .7 ( 4.7 ) 23.6 ( 6.2 ) 0.005 p values were bonferroniholm corrected . a p value of 0.05 was considered statistically significantp probability , bop bleeding on probing , al clinical attachment loss , dm2 diabetes mellitus type 2 , iqr interquartile range , n number of participants , pisa periodontal inflamed surface area , pd probing pocket depth , sd standard deviationresult of chi - square testresult of mann whitney u test ; other results are the results of the independent samples t test characteristics of the participants p values were bonferroni holm corrected . a p value of 0.05 was considered statistically significant p probability , bmi body mass index , crp c - reactive protein , dm2 diabetes mellitus type 2 , hba1c glycated hemoglobin , iqr interquartile range , n number of participants , na not applicable , sd standard deviation , low , elementary and junior school ( education ) , middle high school ( education ) , high university ( education ) result of chi - square test result of mann whitney u test ; other results are the results of the independent samples t test periodontal status of healthy controls and dm2 p values were bonferroni holm corrected . a p value of 0.05 was considered statistically significant p probability , bop bleeding on probing , al clinical attachment loss , dm2 diabetes mellitus type 2 , iqr interquartile range , n number of participants , pisa periodontal inflamed surface area , pd probing pocket depth , sd standard deviation result of chi - square test result of mann whitney u test ; other results are the results of the independent samples t test the severity of periodontitis was significantly higher in participants with dm2 when compared to controls , again independent of the method used to operationalize periodontitis severity ( table 2 ) . in the dm2 patients , none of the measures of periodontitis severity predicted hba1c . only ses ( = 0.752 ; 95 % ci = 1.345 to 0.158 ) was a predictor of hba1c , ( r of 6.0 % ; data not shown ) . by contrast , in healthy indonesians , pisa ( = 0.0004 ; 95 % ci = 0.00004 - 0.00076 ) was a predictor of hba1c together with age , sex , smoking and crp , ( r = 21 % ) in the model ( table 3 ) . table 3results of the multiple linear regression analysis healthy control groupmodel predictorsp value of r95 % confidence interval of model0 .21 pisa ( mm ) 0.00040.050.00004 to 0.00076 age ( year ) 0.01050.0010.00431 to 0.01674 male / female ( 1/0 ) 0.13780.080.29170 to 0.01595 smoking ( pack year ) 0.00860.070.00074 to 0.01805 crp ( mg / l ) 0.02120.060.00093 to 0.04343 constant4 .95910.0014.62706 to 5.29121 a p value of 0.05 was considered statistically significant . hba1c ; independent variables : pisa , age , sex , and smoking / pack years . constantp probability , unstandardized coefficient , hba1c glycated hemoglobin , periodontal inflamed surface area , crp c - reactive proteinother measures of periodontitis severity were not predictors of hba1c results of the multiple linear regression analysis healthy control group a p value of 0.05 was considered statistically significant . hba1c ; independent variables : pisa , age , sex , and smoking / pack years . constant p probability , unstandardized coefficient , hba1c glycated hemoglobin , periodontal inflamed surface area , crp c - reactive protein other measures of periodontitis severity were not predictors of hba1cthis study showed that pisa is a predictor of hba1c , in conjunction with crp , age , sex , and smoking , in healthy indonesians . it is thought that periodontitis exerts an inflammatory and infectious burden as evidenced by increased levels of crp which may increase hba1c levels . it is striking that out of the various methods to operationalize periodontitis severity , only the pisa emerged as a predictor of hba1c . the other methods for determining the severity and extent of periodontitis did not contribute significantly to a model that predicts hba1c . it may be that the pisa is a predictor of hba1c because it reflects the amount of inflamed periodontal tissue , thereby predicting both infectious and inflammatory burden more accurately than other methods used to operationalize periodontitis . in indonesian dm2 patients , first , almost all dm2 patients used a combination of medication to control blood sugar , drugs that healthy indonesians obviously did not take . use such medication may mask an effect of periodontitis on the hba1c level in dm2 patients . second , dm2 patients may have dietary restrictions , e.g. , avoiding sugar rich foods . such a diet may impact blood sugar and may mask an affect of periodontitis on hba1c level . response relationship was observed between pisa and hba1c in dm2 patients from the caribbean island , curacao . additionally , an increased hba1c was observed to be associated with increased severity of periodontitis . moreover , it has been reported that periodontal treatment leads to improvement of glycemic control in dm2 patients . these findings appear to be in sharp contrast with the findings in this study , i.e. , pisa is not a predictor of hba1c in a group of indonesian dm2 patients . the difference between the current study and the study in curacao could be explained by differences in populations . first , substantial differences were observed in the frequency of antidiabetics used between dm2 from indonesia and curacao . acarbose ( 33 % vs. 5 % ) , insulin ( 41 % vs. 21 % ) , and sulfonylurea ( 54 % vs. 35 % ) were used more often in dm2 patients from indonesia , while metformin 37 vs. 67 % was used more often in dm2 patients from curacao . additionally , 16 % of dm2 patients from curacao used tolbutamide , while none of indonesian dm2 patients used it . differences in the frequency of antidiabetics used , may also explain the differences in results . as reported by teeuw et al . and simpson et al . , hba1c levels might be affected by the treatment dm2 patients receive , i.e. , both the drugs they use and the periodontal treatment the patients have received . thus , a drug - related reduction in hba1c levels in patients not yet adequately periodontally treated might be responsible for the failure of pisa to predict hba1c levels in our indonesian dm2 . second , the average bmi of dm2 patients from curacao was 31 while the average bmi of indonesian dm2 patients was substantially lower , namely 25 . bmi may be an effect modifier , i.e. , a higher bmi may increase the potential insulin resistance inducing effect of periodontitis in dm2 patients . third , there is clear difference in ethnicity between the two groups , i.e. , one from indonesia of javanese origin and the other from curacao of african - american origin . possible differences in ( health promoting ) behavior , diet , and genes , related to the differences in ethnicity , may be another explanation for the differences in results . pisa was shown to be a predictor of hba1c in healthy indonesians in conjunction with crp , age , sex , and smoking . this implies that periodontitis might contribute to insulin resistance through the inflammatory and infectious burden leading to dm2 . in indonesian patients ,\noutput:\n" }, { "from": "agent", "value": "periodontitis may exert an infectious and inflammatory burden , evidenced by increased c - reactive protein ( crp ) . this burden may impair blood glucose control ( hba1c ) . the aim of our study was to analyze whether periodontitis severity as measured with the periodontal inflamed surface area ( pisa ) and crp predict hba1c levels in a group of healthy indonesians and a group of indonesians treated for type 2 diabetes mellitus ( dm2 ) . a full - mouth periodontal examination , including probing pocket depth , gingival recession , clinical attachment loss , plaque index and bleeding on probing , was performed in 132 healthy indonesians and 101 indonesians treated for dm2 . using these data , pisa was calculated . in addition , hba1c and crp were analyzed . a validated questionnaire was used to assess smoking , body mass index ( bmi ) , education and medical conditions . in regression analyses , it was assessed whether periodontitis severity and crp predict hba1c , controlling for confounding and effect modification ( i.e. , age , sex , bmi , pack years , and education ) . in healthy indonesians , pisa and crp predicted hba1c as did age , sex , and smoking . in indonesians treated for dm2 , pisa did not predict hba1c . periodontitis may impair blood glucose regulation in healthy indonesians in conjunction with elevated crp levels . the potential effect of periodontitis on glucose control in dm2 patients may be masked by dm2 treatment . clinical relevance : periodontitis may impair blood glucose control through exerting an inflammatory and infectious burden evidenced by increased levels of crp ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: written , informed consent was obtained from 12 patients with type 1 diabetes and 12 patients with insulin - treated type 2 diabetes . participants were recruited from the outpatient diabetes clinic of the radboud university nijmegen medical centre and by advertisement in a local newspaper . all patients were at least 18 years of age and had a bmi 32 kg / m and hba1c 9 % . patients were excluded if they had experienced a major vascular event ( e.g. , myocardial infarction , stroke , symptomatic peripheral artery disease , coronary artery bypass surgery , or percutaneous coronary or peripheral artery angioplasty ) in the previous 6 months ; used immunosuppressant agents , nonsteroidal anti - inflammatory drugs , anticoagulant therapy , or oral antidiabetic drugs other than metformin for type 2 diabetic patients ; or had symptomatic diabetic neuropathy . the study was approved by the institutional review board of the radboud university nijmegen medical centre . patients were requested to reduce the evening dose of insulin or the basal rate of insulin pump administration by 1020 % to avoid nocturnal hypoglycemia and were instructed to consume a low glycemic index meal on the evenings before the experimental days . on each experimental day , participants were admitted to the research unit at 0730 h in fasting condition and having abstained from smoking , alcohol use , and caffeine use for at least 24 h. patients with subcutaneous insulin pumps were asked to stop the pump . the experiments were performed with the patients in supine position in a temperature - controlled room ( 2224c ) . one catheter was inserted in retrograde fashion in a dorsal hand vein for blood sampling , with the vein kept patent by placing the hand in a heated box at 55c ( 11 ) . the other catheter was placed in an antecubital vein of the contralateral arm for insulin and glucose administration . after baseline variables were obtained , low - dose insulin was infused to achieve normoglycemia , after which insulin infusion was either terminated or , for patients treated with insulin pumps , continued at a rate corresponding to the basal rate of the patient s insulin pump . thirty minutes after achievement of stable normoglycemia , patients received insulin ( aspart ; novo nordisk , bagsvaerd , denmark ) either by jet injection ( insujet ; european pharma group bv , schiphol - rijk , the netherlands ) or by conventional insulin pen ( novopen iii ; novo nordisk ) and a comparable volume of placebo solution ( test medium penfill ; novo nordisk ) by the alternate device in a double - blind fashion , both administered subcutaneously in the abdomen . on the other occasion , thus all participants received both insulin and placebo on the two experimental days ( double dummy ) . the dose of insulin was individualized to the patient s usual prandial insulin requirements and averaged 17.63.9 units ( 840 units , 16.33.9 units for patients with type 1 diabetes and 18.911.1 units for patients with type 2 diabetes ; p = 0.44 ) . two - by - two block randomization was used to randomize the sequence by which the two devices were used for insulin and placebo injections . to ensure blinding , both pen devices were prepared by a nurse who was not otherwise involved in conducting the experiments . insulin administration with both devices was performed by trained staff only , as described in detail previously ( 10 ) . one minute after insulin administration , the participant consumed a standardized meal consisting of three white - bread sandwiches with marmalade and honey and a glass of orange juice ( total energy 538 kcal , 108 g carbohydrates , 7 g fat , 11 g protein ) in 1015 min . plasma glucose measurements were measured at 5 - min intervals during the first 3 h of the study and at 10 - min intervals for another 3 h. blood for plasma insulin levels was sampled every 5 min during the first hour , every 15 min for the second hour , and every 30 min thereafter . when plasma glucose values dropped below 4.8 mmol / l , 20 % dextrose in water was administered intravenously to maintain normoglycemia . on the second experimental day , patients were asked to rate the amounts of discomfort or pain experienced with the two administration methods on a visual analog scale from 0 to 10 cm and to indicate which device they would prefer should they have a choice . all pharmacologic parameters were derived from the plasma glucose and insulin levels . with respect to the pharmacokinetics , we calculated the time to maximal insulin concentration ( t - insmax ) , the maximal insulin concentration ( c - insmax ) , the area under the insulin concentration curve ( c - insauc ) , and the time until 50 % of insulin absorption ( t - insauc50 % ) . we also calculated the times until reaching 50 % of the c - insmax as insulin levels rose and until reaching the same value as insulin levels declined . the pharmacodynamic parameters consisted of the area under the baseline - subtracted plasma glucose concentration time curve during the first hour ( bg - auc1h ) and first 2 h ( bg - auc2h ) after insulin injection , representing the initial glycemic load , the maximal glucose excursion ( bgmax ) , the area under the total baseline - subtracted plasma glucose concentration time - curve ( bg - auc6h ) , and the time until plasma glucose had returned to baseline . safety parameters included the number of patients requiring exogenous glucose infusion to prevent postprandial hypoglycemia , the amount of exogenous glucose required , and the duration that exogenous glucose was required . plasma glucose was measured with the glucose enzymatic - amperometric method ( biosen c - line gp + ; ekf - diagnostic gmbh , barleben , germany ) during the experiments . blood sampled for determination of plasma insulin levels was collected in lithium - heparin tubes . mean outcomes for all study end points and most safety end points were tested with paired t tests . a test was used to compare the numbers of patients requiring exogenous glucose with the two injection devices . continuous data were tested for normal distribution ( shapiro - wilk test and kolmogorov - smirnov test ) and subsequently analyzed with repeated measures anova ( wilks test ) , with the device as between - subjects factor . all statistical analyses were performed with spss software ( statistical package for the social sciences , version 18.0 ; ibm corporation , armonk , ny ) . mean outcomes for all study end points and most safety end points were tested with paired t tests . a test was used to compare the numbers of patients requiring exogenous glucose with the two injection devices . continuous data were tested for normal distribution ( shapiro - wilk test and kolmogorov - smirnov test ) and subsequently analyzed with repeated measures anova ( wilks test ) , with the device as between - subjects factor . all statistical analyses were performed with spss software ( statistical package for the social sciences , version 18.0 ; ibm corporation , armonk , ny ) . in one instance , the insulin dose administered was erroneously calculated too low , and in the other , the spring of the jet injector released prematurely , so that it could not be assessed how much insulin ( or placebo ) , if any , had actually crossed the skin . that jet injector was subsequently returned to the manufacturer and replaced . baseline characteristics plasma insulin levels at initiation of insulin injections were slightly higher for the experiments where the conventional pen was used than those for the jet injector ( 22.82.5 vs. 19.42.4 mu / l ; p = 0.037 ) . thereafter , plasma insulin levels increased faster when insulin was injected with the jet injector than when injected by conventional pen ( table 2 ) . the time until peak plasma insulin concentrations was advanced from 91.910.2 min with the conventional pen to 51.36.4 min with the jet injector ( p = 0.003 ) , a difference of 40.612.3 min ( fig . 1a , table 2 ) . in addition , t - insauc50 % and the time for insulin levels to decline after reaching peak values were significantly shorter when insulin was administered by jet injection rather than by conventional pen ( table 2 ) . in contrast , the total amount of insulin absorbed during the entire 6 - h period , as reflected by the c - insauc , did not differ between the two devices . pharmacokinetic and pharmacodynamic parameters for insulin administration with the jet injector and the conventional insulin pen changes from baseline during the standardized meal test . a : changes in plasma insulin levels after insulin administration by jet injector ( ) and conventional pen ( ) . b : changes in plasma glucose levels after insulin administration by jet injector ( ) and conventional pen ( ) . there were no differences in plasma glucose values between the two experimental conditions , either at baseline ( 10.50.6 vs. 10.80.7 mmol / l ; p = 0.65 ) or directly before the experiments ( 5.610.13 vs. 5.450.18 mmol / l ; p = 0.49 ) . the time - action curves for the plasma glucose level after meal ingestion were significantly different between the two devices ( p = 0.018 by anova ) . in line with the faster insulin pharmacokinetics , the hyperglycemic burden during the first hour , as reflected by the area under the glucose concentration curve ( bg - auc1h ) was significantly reduced when insulin was administered with the jet injector rather than by conventional pen ( fig . this benefit favoring the jet injector relative to the conventional insulin pen was no longer apparent after 2 h ( table 2 ) . although glucose values tended to be lower in the late postprandial phase after conventional pen administration , there were no significant differences between the two devices with regard to the maximal glucose value , maximal glucose increment , or area under the 6 - h glucose concentration curve ( table 2 ) . there were no differences between the jet injector and conventional pen with respect to number of patients requiring exogenous glucose to prevent hypoglycemia ( 17 vs. 18 ; p = 0.75 ) , the timing of initiation of glucose administration ( 180 vs. 194 min ; p = 0.79 ) , or the amount of glucose administered ( 21.05.5 g vs. 23.75.7 g ; p = 0.61 ) . both injection methods were well tolerated and elicited similar experiences of pain or discomfort ( visual analog scale 1.96 vs. 1.40 ; p = 0.14 ) . of the total of 24 patients , 13 preferred the conventional pen to the jet injector , 4 preferred the jet injector , and 6 remained indifferent . the pharmacodynamic benefits of insulin administration by jet injection tended to be numerically higher in patients with type 2 diabetes ; however , the difference was not statistically different between patients with type 1 and type 2 diabetes . for type 1 diabetes , bg - auc2h after jet injection was 478117 vs. 50098 mmol min l after conventional administration ( p = 0.87 ) ; values for type 2 diabetes were 47182 vs. 66296 mmol min l ( p = 0.09 ) ( fig .2 ) . there were no differences in subgroups defined by age , sex , or bmi ( data not shown ) . the 2 - h bg - auc values for the jet injector ( white bars ) and conventional pen ( black bars ) in subgroups according to type of diabetes . plasma insulin levels at initiation of insulin injections were slightly higher for the experiments where the conventional pen was used than those for the jet injector ( 22.82.5 vs. 19.42.4 mu / l ; p = 0.037 ) . thereafter , plasma insulin levels increased faster when insulin was injected with the jet injector than when injected by conventional pen ( table 2 ) . the time until peak plasma insulin concentrations was advanced from 91.910.2 min with the conventional pen to 51.36.4 min with the jet injector ( p = 0.003 ) , a difference of 40.612.3 min ( fig . 1a , table 2 ) . in addition , t - insauc50 % and the time for insulin levels to decline after reaching peak values were significantly shorter when insulin was administered by jet injection rather than by conventional pen ( table 2 ) . in contrast , the total amount of insulin absorbed during the entire 6 - h period , as reflected by the c - insauc , did not differ between the two devices . pharmacokinetic and pharmacodynamic parameters for insulin administration with the jet injector and the conventional insulin pen changes from baseline during the standardized meal test . a : changes in plasma insulin levels after insulin administration by jet injector ( ) and conventional pen ( ) . b : changes in plasma glucose levels after insulin administration by jet injector ( ) and conventional pen ( ) . there were no differences in plasma glucose values between the two experimental conditions , either at baseline ( 10.50.6 vs. 10.80.7 mmol / l ; p = 0.65 ) or directly before the experiments ( 5.610.13 vs. 5.450.18 mmol / l ; p = 0.49 ) . the time - action curves for the plasma glucose level after meal ingestion were significantly different between the two devices ( p = 0.018 by anova ) . in line with the faster insulin pharmacokinetics , the hyperglycemic burden during the first hour , as reflected by the area under the glucose concentration curve ( bg - auc1h ) was significantly reduced when insulin was administered with the jet injector rather than by conventional pen ( fig . this benefit favoring the jet injector relative to the conventional insulin pen was no longer apparent after 2 h ( table 2 ) . although glucose values tended to be lower in the late postprandial phase after conventional pen administration , there were no significant differences between the two devices with regard to the maximal glucose value , maximal glucose increment , or area under the 6 - h glucose concentration curve ( table 2 ) . there were no differences between the jet injector and conventional pen with respect to number of patients requiring exogenous glucose to prevent hypoglycemia ( 17 vs. 18 ; p = 0.75 ) , the timing of initiation of glucose administration ( 180 vs. 194 min ; p = 0.79 ) , or the amount of glucose administered ( 21.05.5 g vs. 23.75.7 g ; p = 0.61 ) . both injection methods were well tolerated and elicited similar experiences of pain or discomfort ( visual analog scale 1.96 vs. 1.40 ; p = 0.14 ) . of the total of 24 patients , 13 preferred the conventional pen to the jet injector , 4 preferred the jet injector , and 6 remained indifferent . the pharmacodynamic benefits of insulin administration by jet injection tended to be numerically higher in patients with type 2 diabetes ; however , the difference was not statistically different between patients with type 1 and type 2 diabetes . for type 1 diabetes , bg - auc2h after jet injection was 478117 vs. 50098 mmol minl after conventional administration ( p = 0.87 ) ; values for type 2 diabetes were 47182 vs. 66296 mmol min l ( p = 0.09 ) ( fig .2 ) . there were no differences in subgroups defined by age , sex , or bmi ( data not shown ) . the 2 - h bg - auc values for the jet injector ( white bars ) and conventional pen ( black bars ) in subgroups according to type of diabetes . previously , we showed in young , healthy volunteers that absorption and action of aspart insulin occurred twice as fast when administered by jet injection as by conventional pen ( 10 ) . the current study confirms a more rapid absorption of insulin aspart when administered by the current jet injector compared with a conventional pen in patients with type 1 and type 2 diabetes . these pharmacokinetic properties translated into a significant , albeit modest , decrease in early ( first 60 min ) postprandial hyperglycemia after a standardized meal rich in carbohydrates . beyond 1 h , the benefit of jet injection on postprandial glycemic burden was no longer statistically significant . considering the substantial enhancement of insulin action by jet injection in our clamp study ( 10 ) and the current improvement of insulin absorption , we anticipated a sizeable pharmacodynamic benefit of insulin administration by jet injection in the current study . although the lower early postprandial glucose levels and tendency toward lower glucose levels in the later postprandial phase confirmed the results of the clamp study under conditions more like an actual clinical situation , the effects were rather modest . this partial discrepancy may be explained first by the relatively large variation , both inter - and intraindividually , in glucose excursions after the meal test . glucose levels at admission at the research unit were similarly variable , although all patients had consumed a low glycemic index supper on the evening before the experiments . factors contributing to this large variation may include the heterogeneity of the participants , the suboptimal glycemic control , and use of insulin by all participants , including those with type 2 diabetes . a second explanation concerns the finding that insulin absorption was much slower in the patients than we had previously observed in healthy volunteers ( 10 ) . although jet injection advanced insulin absorption to roughly similar extents in both groups , insulin levels peaked substantially later in diabetic subjects with than in those without diabetes ( 51.3 vs. 30.6 min ; p = 0.012 ) . because the standardized meal consisted mainly of high glycemic index carbohydrates , insulin absorption may have been too slow to sufficiently counteract the fast glucose load absorption . whether jet injection would have performed better for a more usual mixed meal with slower food absorptionparenthetically , most patients in our study claimed never to consume high glycemic index carbohydrates in such large quantities , to avoid extreme glucose excursions . why rapid - acting insulin absorption is slower in patients with diabetes than in subjects without diabetes is unknown . we previously showed a strong association between bmi and rate of insulin absorption in healthy subjects , arguing a role for greater subcutaneous tissue thickness ( 13 ) . in the current patient group , however , insulin absorption was unrelated to the bmi or any other measure of body composition . the presence of insulin antibodies , commonly found in patients on long - term insulin therapy , has been suggested to attenuate the absorption of subcutaneous insulin ( 14 ) ; however , insulin antibodies were not measured in our study . alternatively , subcutaneous adipose tissue blood flow ( atbf ) may also affect the absorption of insulin ( 15 ) . reduced subcutaneous atbf has been reported in overweight nondiabetic subjects ( 16 ) , as well as in patients with type 1 ( 17,18 ) and type 2 diabetes ( 19 ) . in addition , atbf may fail to increase in response to dietary stimuli in overweight subjects ( 16 ) and in patients with type 2 diabetes ( 19 ) . although the pharmacodynamic benefit of jet injection appears small , it is of potential clinical relevance for patients with early postprandial glucose excursions not sufficiently covered by conventional insulin injections . administration of rapid - acting insulin by this jet injector may represent an especially valuable alternative for patients with type 2 diabetes , in whom the postprandial glycemic benefit of jet injection tended to be more pronounced than in those with type 1 diabetes . parenthetically , a device that performs at least as well as , and potentially better than , conventional pens may be a good option for any patient who does not tolerate insulin injections by needle or regards these as otherwise uncomfortable . a recent survey showed that 28.6 % of patients with type 2 diabetes perceive insulin injections as painful ( 20 ) , putting such patients at high risk of skipping at least occasional injections ( 7 ) . when questioned , most patients still preferred the conventional pen to the jet injector ; however , these patients were unselected , generally tolerated conventional injections without discomfort , consequently feeling no need to change the mode of administration , and did not handle the jet injector ( or the conventional pen ) themselves under study conditions . future research will need to reveal tolerability of the jet injector after personal experience with the device in daily practice for a longer period . it requires sufficient training in air - free filling of the chamber with insulin and correct placement of the injector on the skin to ensure that the entire volume of insulin reaches the subcutaneous compartment . inadequate contact between injector and the skin has been reported to result in bruises and wet injections , leading to discomfort and unpredictable insulin absorption profiles ( 21 ) . importantly , the current device has a built - in lock - release system that only releases insulin when proper skin contact has been made and sufficient pressure has been applied to the nozzle of the injector . other factors that determine optimal insulin delivery relate to jet velocity and nozzle diameter ( 2224 ) . our data are therefore in part specific to the jet injector used and can not be extrapolated to other jet injectors . these strategies include local skin heating to stimulate tissue perfusion ( 25 ) , coadministration with hyaluronidase to break the solidity of the extracellular matrix ( 26 ) , and destabilizing insulin hexamer formation by addition of edta and citric acid ( 27 ) . the pharmacokinetic and pharmacodynamic benefits of these interventions are more or less comparable to those of jet injection and range from 10 to 60 % advancement of peak insulin levels and maximal glucose - lowering effect ( 2527 ) . a difference between jet injection and other developments to enhance insulin absorption is that the former is already available for clinical application , whereas the latter are in still in various stages of development and have not yet been marketed . in the current study , we found that jet injection accelerated the absorption of insulin aspart in patients with type 1 and insulin - treated type 2 diabetes . this better pharmacokinetic profile was initially followed by a congruent reduction in glucose excursions after a high - glycemic index meal , in particular during but not beyond the first hour . jet injection may therefore be a good needle - free alternative to conventional insulin pens of at least equivalent pharmacological efficacy for the administration of insulin in patients with diabetes . future research is needed to determine whether the better pharmacologic properties of insulin jet injection translate into beneficial long - term effects on glycemic control and risk of hypoglycemia in patients with diabetes .\noutput:\n" }, { "from": "agent", "value": "objectiveclamp studies have shown that the absorption and action of rapid - acting insulin are faster with injection by a jet injector than with administration by conventional pen . to determine whether these pharmacokinetic changes also exist in patients with diabetes and benefit postprandial glucose control , we compared the pharmacologic profiles of insulin administration by jet injection versus conventional insulin pen after a standardized meal in patients with type 1 or type 2 diabetes.research design and methodsin a randomized , double - blind , double - dummy crossover study , 12 patients with type 1 diabetes and 12 patients with type 2 diabetes received insulin aspart either by jet injection or by conventional pen , in both cases followed by a standardized meal . blood was sampled for 6 h for determination of glucose and insulin levels to calculate pharmacologic profiles.resultsinsulin administration by jet injection resulted in shorter time until peak plasma insulin level ( 51.3 6.4 vs. 91.9 10.2 min ; p = 0.003 ) and reduced hyperglycemic burden during the first hour ( 154.3 20.8 vs. 196.3 18.4 mmol min l1 ; p = 0.041 ) compared with conventional administration . jet injection did not , however , significantly reduce the hyperglycemic burden during the 5 - h period thereafter . there was no indication that the jet injector performed differently in patients with type 1 and type 2 diabetes.conclusionsthe considerably more rapid insulin absorption after administration by jet injector translated to a significant if modest decrease in postprandial hyperglycemia in patients with type 1 and type 2 diabetes . the improved early postprandial glucose control may specifically benefit patients who have difficulty in limiting postprandial glucose excursions ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: despite considerable development of technology and techniques used in dentistry throughout the last few decades , tooth loss is still a common problem . as practitioners gained experience in the implantology field , they became exposed to various complications arising as a result of the surgical procedure . one of the most common and serious complications faced by the clinician and the patient following implant placement in the mandible is injury to the inferior alveolar nerve ( ian ) . it ranges from 0 % to 40 % of implant - related ian injuries [ 1 - 4 ] . they may be directly related to the depth of preparation or implant length or width and may result from local anaesthetic application as well . , nerve injuries are divided into 3 types based upon the severity of tissue injury , prognosis , and time for recovery - neurapraxia , axonotmesis , and neurotmesis . neurapraxia is the mildest form , with the best prognosis , while neurotmesis is the most severe . sensory disturbances resulting from the injury will provide an unpleasant experience for both the doctor and the patient . effective management of those cases is based on providing treatment - conservative or surgical , immediately upon diagnosis of damage . renton and coworkers state that peripheral sensory nerve injuries are more likely to be persistent when there is an increased duration between injury and reviewing of the patient . the problem is that occasionally the diagnosis is delayed , which may have a crucial effect on treatment results . its underlying pathophysiology is ascribed to an increased pressure on peripheral nerves , which leads to impaired neural microcirculation followed by focal demyelination . for example , an unnoticeable , minor ian injury may develop due to haematoma , and the practitioner may not diagnose it on time because of its mildness . this is due to the fact that the ian is bounded within the limits of the mandibular canal ( mc ) . mc width depends on the patient s age and gender - females and elderly patients thus are at higher risk to develop tunnel syndrome - related nerve degeneration . using long - acting local anaesthetics and the difficulty of evaluating the extent of the damage are some of the factors preventing early disclosure of the complication . literature regarding this topic suggests diagnostic methods such as neurosensory testing , including objective and subjective methods , but those tests can be performed only after fading of the local anaesthetic effect . the presence of continuous anaesthesia , dysaesthesia , or spontaneous pain indicates poor prospects for recovery , even with surgical intervention . overall , 25 % of patients with iatrogenic paraesthesia suffer permanent effects . to make it easier for readers , we presented the following important aspects regarding ian injury separately : risk factors , diagnostic methods , adequate time for diagnosis , and treatment outcome as a function of diagnosis time . diagnosis of ian injury according to early signs and symptoms reported by patients signs and symptoms , any sensation described by the patient , should be taken into consideration since radiography is not always helpful . there are cases were the implant does not seem to damage the nerve , but in fact , it does . one of the most important things the practitioner should check after the operation is completed is whether the patient experienced a return of normal sensation . six hours after operation ( after the local anaesthesia effect wears off ) , the patient should be contacted . in cases of the patient reporting persistent numbness or anaesthesia , it would be the first sign for the surgeon that something went wrong and nerve damage probably occurred . numbness usually will be felt on the side of implant placement , including the lower lip and chin . another symptom that may indicate nerve damage is the feeling of tingling , tickling , or burning skin in other words , paraesthesia . in some cases , numbness may not appear immediately but later on . the patient does feel improvement in sensation in the beginning , although some discomfort is present , and later numbness appears . a case study of 4 females , which recorded their sensations following implant - associated ian damage , concluded that all patients suffered from numbness of the affected inferior alveolar dermatome . . found , in 2012 , in their study regarding post - implant neuropathy of the trigeminal nerve , that over 50 % of patients suffered constant pain and / or discomfort . paraesthesia was the main feature for 47 % of cases . however , there are various alterations of sensation patients can report , such as dysaesthesia , allodynia , hypoaesthesia , hyperaesthesia , and more . diagnosis of ian injury based on subjective sensory tests a study in the year 2009 by poort et al . reveals an interesting fact - subjective evaluation has been found to be the most commonly used method ( 64 % of all methods used ) to detect implant - associated ian injury . every alteration in sensation reported by the patientthat is because the patient s own feeling is the best evaluation for change in sensation , as sometimes the alteration may be not big enough to be detected by any diagnostic tools , which are less sensitive than the human him / herself . electric - shock - type sensation during administration of local anaesthetic , which can give a hint about further nerve injury , but it is not a definitive sign since injuries can occur without any intraoperative demonstration . after the fading of the local anaesthetic effect , the doctor should ascertain with the patient if any changes occurred and if some suspicion for neuropathy is present . basically , subjective sensory tests are divided into 2 major categories : mechanoceptive and nociceptive . first is static light touch ( slt ) detection , in which the patient closes his eyes and says yes whenever he feels a light touch with cotton to the face . the second one is brush directional discrimination ( brush stroke direction [ bsd ] ) in which the patient tells if any sensation is detected and in which direction the filament or brush moved . the third is two - point discrimination ( tpd ) , in which the patient closes his eyes , and the clinician , using an object having two sharp edges , touches the face in different areas . the distance between the sharp edges should be changed in order to define the minimal distance in which the patient is still able to discriminate two points . the average value of this test is about 5 mm , but it is very individual and varies considerably . generally , it depends on the size of receptive fields in the tested area and on the density of the fields . some investigators found that the tpd test is unreliable because it has great variability between measurements even on the control side and does not add information to the slt test . another method is sharp / blunt discrimination ( sbd ) , in which a sharp right - angle dental probe is applied to the area , with indentation but with no breach of the mucosa / skin . the patient is then asked to compare this sensation to that produced by a blunt region of the probe . the test is considered positive if the patient recognises 3 out of 5 of each stimulus correctly . the former compares the pain threshold of affected and unaffected areas and allows defining the response as hyperaesthesia , anaesthesia , or hypoaesthesia . the aim is to establish the sensation threshold for the unaffected side and compare it to the affected side . this type of test checks whether the patient feels normal cold or heat sensation by applying ethyl chloride and a mirror handle warmed to 43 c to affected and unaffected areas . diagnosis of ian injury based on objective sensory tests a study conducted in june 2011 by biasiotta et al . states that the masseter inhibitory reflex ( mir ) test is the most used neurophysiological tool for the functional assessment of the trigeminal mandibular division . it consists of a reflex inhibition of the jaw - closing muscles elicited by peri - or intraoral electrical stimulations . their study revealed that mir testing shows an almost absolute specificity ( 99 % ) and reliably demonstrates nerve damage beyond doubt , whereas the relatively low sensitivity ( 51 % ) makes the finding of a normal mir by no means sufficient to exclude nerve damage . in other words , this test principle is that abnormality does prove nerve damage , and normality does not disprove it . it is important to remark that in that study , all patients ( 160 ) were examined at least 2 months after injury , so its efficiency as an early diagnostic method can not yet be discussed . the recording of somatosensory evoked potentials ( seps ) is a noninvasive , routine clinical testing procedure in neurology . the idea is to stimulate the peripheral nerves and then record the electric potential occurring in the brain through the scalp . electrodes are applied to the skin of the area to be tested as well as on the scalp . for trigeminal nerve stimulation , in addition , this technique has a lot of disadvantages : the reliability of the recorded signals has been questioned because , rather than reflecting genuine brain activity , they probably result from volume - conducted muscle signals , as they disappear in the curarized subject . thus , more researches should be conducted in order to establish some general guidelines for using this method . orthodromic sensory nerve action potential is another method used to record the function of ian . however , it was not used by the clinicians to evaluate ian function after implant - related injury . recently , the international federation of clinical neurophysiology has recommended investigating the trigeminal function with reflex rather than evoked potential studies . unlike the above techniques , the blink reflex after mental or lingual stimulation seems a promising alternative to the mir . blink reflex proved to be a sensitive test in detecting ian lesions within 2 to 3 months from injury . diagnosis of ian injury using alternative methods several researches have proposed that early implant removal may lead to better healing with the return of sensation . however , in most cases , by the time diagnosis is made , it may lose its efficiency . the problem in making an immediate diagnosis is that usually , by the end of the surgery , the patient is still found under the effect of local anaesthetics . that occurs especially when surgeons use long - acting anaesthetics in order to delay the pain as much as possible . phentolamine mesylate ( pm ) is an anti - hypertensive reversal agent of local anaesthesia . a study conducted by froum et al . in 2010 checked the possibility of its utilisation immediately after implant placement . without using pm , the local anaesthetic effect fades away in the range of 3 to 5 hours after injection . thus , using a reversing agent will significantly increase the chances of full recovery , as its application permits making the earliest detection of nerve damage currently available . the purpose of the present article is to identify the time interval of inferior alveolar nerve injury diagnosis after dental implant placement operation and compare between outcomes of early and delayed diagnosis and treatment given after inferior alveolar nerve injury based on case series recorded throughout the years . protocol and registration the review is registered in an international prospective register of systematic reviews , prospero . registration number : crd42014014724 . the review included studies on humans published in english . inferior alveolar nerve injury ( ian ) definition ian injury includes damage or severance of nervous tissue as a result of trauma transaction , cutting ( laceration ) , compression , shearing , or crushing , which results in sensory disturbances . literature search strategy according to the prisma guidelines , we conducted an electronic search using medline ( pubmed ) database to locate articles concerning ian injury following implant placement . the keywords used to find related articles were inferior alveolar nerve injury associated with implant surgery , inferior alveolar nerve injury implant , inferior alveolar nerve injury diagnosis , andthe search was restricted to english language articles published during the last 10 years , from december 2004 to march 2014 . however , most of the articles were excluded due to irrelevancy of their titles or abstracts . we assessed 32 full text articles , of which 5 articles were found suitable to be included in the review . we also performed a manual search in dental journals , and 1 article was added . inclusion and exclusion criteria inclusion criteria for the selection were the following : studies performed on humans only ; articles associated with implant surgery ( ian injury as a result of implant placement in posterior mandible ) ; articles that specify the diagnostic method that had been used ; subjects with neurosensory deficit as a result of implant placement and who were neurologically healthy before surgery . exclusion criteria for the selection were the following : articles associated with ian injury but not as a result of implant placement ; studies performed on animals ; studies of cases where implants were placed in anterior mandible . article review and data extraction the search delivered 734 search results , of which 700 abstracts were screened . the reasons for article exclusion were as follows : literature reviews ( n = 7 ) ; studies performed on animals ( n = 4 ) ; studies did not mention diagnostic method ( n = 3 ) ; neurosensory deficit occurred not as a result of implant ( n = 4 ) ; articles not describing diagnostic procedures ( n = 7 ) ; no ian injury occurred ( n = 2 ) ; the data was included on 157 patients . risk of bias across studies we assessed the risk of bias ( for example , operation was not performed by authors themselves , missing information regarding exact time of diagnosis , postoperative neurosensory examination performed by single examiner , sex scission , and low objectives number ) that could affect the cumulative evidence across the studies . a total of 6 studies were included in this review : one study was related to diagnostic methods that can be used , two studies were discussing treatment outcomes of different techniques , two studies described clinical presentation of patients with ian injury , and one study was related to risk factors and management of ian injuries ( table 1 ) . study characteristics the studies that have been included in this review discussed different aspects related to ian injury as a result of implant placement . all studies were performed on humans and published in english between december 2004 and march 2014 . studies were generally divided into 2 types : studies where the authors themselves performed the operation and studies in which the authors were the specialists to whom patients with injury were referred ( did not perform the operation themselves ) . the studies discussed the cause of injury , time of diagnosis , and post - injury diagnostic methods that were used . data regarding given treatment ( timing , type , and outcome ) were presented in all studies except one . that study solely assessed the diagnostic aspect of injuries ( it checked the efficiency of mir as a diagnostic method for ian injury detection ) . reliability of studies we evaluated the reliability of the selected studies by the following factors : the number of patients treated ( figure 2 ) , the neurosensory evaluation methods used ( table 2 ) , the method used for data analysis ( table 3 ) , and the bias within studies ( table 4 ) . neurosensory methods used lt = light touch ; sbd = sharp blunt discrimination ; tpd = two point discrimination ; mvp = moving point discrimination ; ppt = pin prick test ; bsd = brush stroke direction ; ptd = pain threshold detection ; mir = masseter inhibitory reflex . methods used for data analysis assesment of the risks of bias risk of bias within studies all studies included exhibited at least 1 bias . we grouped the risks of bias that were indicated within other studies and presented as a lack of information value as follows : operation was not performed by the authors , exact time of diagnosis was not indicated for each patient , postoperative neurosensory examination performed by single examiner , low number of patients , and sex scission ( table 4 ) . risk factors associated with ian injury risk factors may be classified into general , intraoperative , and postoperative , as described by juodzbalys et al . . possible risk factors associated with ian injury following implant placement ian = inferior alveolar nerve . diagnosis of ian injury diagnosis of ian injury should be done based on the patient s complaints and clinical symptoms , in combination with different techniques . nerve injury can lead to anaesthesias , paraesthesias , and dysaesthesias . as has been already mentioned , moreover , khawaja and renton made a conclusion based on 4 case studies : early removal of implants associated with ian injury ( less than 36 hours post - injury ) may assist in minimising or even resolving ian neuropathy , while delayed diagnosis and removal may result in no improvement at all . time interval between nerve injury and its diagnosis and treatment kim et al . found in their study regarding clinical outcomes of conservative treatment in cases of ian injury that patients who visited the hospital within 9 months after injury exhibited greater improvement in their symptoms than those visiting after 9 months . these results reinforce the already proven fact that early treatment is important in cases of nerve damage . for treatment to be as early as possible , timely diagnosis should be done . case series were reviewed and the time interval between the time of injury and the diagnosis and treatment was recorded . in some of the articlesthus , we based our determination of diagnosis time upon the assumption that the practitioner realised the injury was present when it was revealed that the subject continued to feel numbness after the effect of local anaesthetic wore off , since it s the first postoperative alarming sign . in addition , it is important to mention that we divided the studies mainly into 2 types . the first type of articles described operations performed by the authors themselves . however , the second type of articles described reports by specialists to whom patients were referred after nerve injury for consultation ( surgical implant placement was not performed by them ) . time of diagnosis and associated outcome for different patients groups first type articles . the diagram above ( figure 3 ) is based on data extracted from articles and presented in table 6 . the first is that in 47 % of the cases , doctors performed the diagnosis early . the other fact , which is more surprising , is that in 43 % of the cases , the diagnosis was established very late . this finding is controversial because in some of the cases , it was mentioned that patients were referred for specialist consultation , so it is not clear when the first diagnostic evaluation was performed . thus , it is not enough evidence to define for sure that diagnosis was not performed on time . in addition , we can observe that in 8 % of the cases , timely diagnosis was done , which is quite consoling because the first 36 hours are the most critical . in addition , we analysed the following information regarding treatment : time of treatment , type of treatment , and outcome . as for the treatment outcomes ( table 7 ) , in all the cases that were treated before 48 hours post - injury , full recovery was observed , except 6 patients who suffered an injury of severe degree , and for them , no recovery was observed . reported in their studies in the years 2003 and 2005 , respectively , that the incidence of temporary ian injury despite careful planning ranges from 0 % to 24 % , while persistent injury has been found in 11 % of cases . these days wide ranges of diagnostic methods are available for detecting such injuries and defining their extent , severity , and more . as has been previously mentioned , nerve injuries are classified according their severity into neurapraxia , axonotmesis , and neurotmesis . practitioners should be familiar with these types of nerve injuries and by undertaking basic examination procedures should be able to determine which injury they are facing . this is an essential step for selecting adequate treatment steps , knowing possible outcomes of the situation , and deciding whether referral to a specialist is needed . the main diagnostic methods that were used in the studies reviewed for this paper can not be used immediately after injury occurs but only when the effect of the anaesthetic is gone , especially the subjective methods since they are based on the patient s evaluation of his / her own sensation . one exceptional method that is not widely accepted or used is the utilisation of pm , which acts to reverse the effect of local anaesthetic and thus permit an earlier return to sensation and as a result earlier examination of the patient for neurosensory deficiency . in 2009 , renton and khawaja evaluated the neurosensory function of the ian by first mapping the area of neuropathy extra - and intraorally . then they used lt , sbd , tpd and mpd , which are all subjective methods . evaluated the extent of injury by performing sensographic examinations - tactile and pain thresholds were recorded . later on , in 2012 , renton , together with other scientists , again used the same strategy - mapping the area together with subjective evaluation . however , 2 additional methods were added to the process this time : a pin prick test and brush stroke direction testit is clearly seen that most of the practitioners chose to deal with ian injury using subjective methods of examination . statement that the masseter muscle inhibitory reflex ( objective method ) is the most used neurophysiologic tool for the functional assessment of the trigeminal mandibular division . surprisingly , not even 1 clinician from the reviewed studies has used this method or any other objective test . the muscle inhibitory reflex method has been proven to be very accurate , and maybe its efficiency is somehow underestimated in general practice . as the importance of early diagnosis for better treatment outcomesis well documented in previous studies , the objective was to find how prevalent early diagnosis is among practitioners . it is important to mention that treatment outcome is influenced not just by time of diagnosis but by several other factors , for example , severity of injury - in some cases , the damage extent is so wide that the timing plays a minor role in recovery , if any . thus , we can see that occasionally , although patients are diagnosed within a period of 48 hours , which is considered early , they experience persistent neurosensory deficit because the injury was severe . however , when the damage has a better prognosis , time is a crucial factor , and satisfactory treatment results are achieved . in case of ian injury , early implant removal is suggested for resolution of neuropathy if there is radiographic evidence of contact between the mc and implant . sometimes , it does not seem like injury has occurred because the implant is not intruded into the mc , but in fact there is injury to the ian as a result of improper implant bed preparation ( injury by implant drill ) . the implant is placed in the proper position , but the depth of preparation is inadequate ( too deep ) - it is reaching the mc , as can be seen in figure 4 ( 2 descending straight lines , which contact the upper and lower borders of the mc ) . no implant intrusion to mc . one of the drawbacks of this review is that the quantity of cases analysed is relatively limited . additionally , another obstacle we faced during data organisation is that not all cases mentioned the exact time of diagnosis . some articles reported cases of patients referral to a specialist for consultation . the specialist him / herself did not perform the surgery ; thus , he / she probably was not the first person to diagnose the injury . various diagnostic methods , as well as treatment strategies , have been developed throughout the years for dealing with one quite prevalent complication in the implantology field - inferior alveolar nerve injury . basically , it is recommended to establish diagnosis within the first 36 hours . according to the results of our data analysis , a relatively high percentage of the practitioners successfully accomplished this target and achieved good treatment outcomes .\noutput:\n" }, { "from": "agent", "value": "abstractobjectivesthe purpose of this article is to systematically review diagnostic procedures and risk factors associated with inferior alveolar nerve injury following implant placement , to identify the time interval between inferior alveolar nerve injury and its diagnosis after surgical dental implant placement and compare between outcomes of early and delayed diagnosis and treatment given based on case series recorded throughout a period of 10 years.material and methodswe performed literature investigation through medline ( pubmed ) electronic database and manual search through dental journals to find articles concerning inferior alveolar nerve injury following implant placement . the search was restricted to english language articles published during the last 10 years , from december 2004 to march 2014 . resultsin total , we found 33 articles related to the topic , of which 27 were excluded due to incompatibility with established inclusion criteria . six articles were eventually chosen to be suitable . the studies presented diagnostic methods of inferior alveolar nerve sensory deficit , and we carried out an assessment of the proportion of patients diagnosed within different time intervals from the time the injury occurred.conclusionsvarious diagnostic methods have been developed throughout the years for dealing with 1 quite frequent complication in the implantology field - inferior alveolar nerve injury . concurrently , the importance of early diagnosis and treatment was proved repeatedly . according to the results of the data analysis , a relatively high percentage of the practitioners successfully accomplished this target and achieved good treatment outcomes ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: large - cell neuroendocrine carcinoma of the lung ( lcnec ) was first proposed by travis and colleagues1 in 1991 as a separate fourth category of pulmonary neuroendocrine tumors , in addition to typical carcinoid tumor , atypical carcinoid tumor and small - cell lung cancer . the incidence of lcnec is very low , and appears to be between 2.1 % and 3.5 % .2 the clinical outcome of lcnec is reported to be poorer than that of stage - comparable conventional non - small - cell lung cancer .3,4 lcnec belongs , together with small - cell lung cancer , to a group of high - grade malignancies , and the prognosis of patients with lcnec falls between that of patients with atypical carcinoid tumor and those with small - cell lung cancer .1 little information on chemotherapy for advanced lcnec exists , and a standard treatment strategy for advanced lcnec is far from being established .58 here , we report a patient with stage iv lcnec who achieved a complete response after undergoing whole brain irradiation followed by a combination of amrubicin and irinotecan chemotherapy . in february 2007 , a 66 - year - old male patient was transferred to the kitasato university hospital after an annual check - up chest x - ray revealed a nodule in the right lower field of his lung . the results of routine laboratory studies , including a complete blood count , platelet , and blood chemistry screening , were normal , including the tumor marker levels ( carcinoembrionic antigen , neuron - specific enolase , and pro - gastrin - releasing peptide ) . a computed tomography ( ct ) of the lung confirmed a nodule in the right lower lobe with no signs of mediastinal lymphadenopathy ( figure 1a ) . soon after his first visit , he started to complain of rapidly developing dysarthria , right hemiparesis , and gait disturbance . a solitary metastasis with a midline shift ( 2.6 cm in diameter ) was identified on a brain ct examination ( figure 2a ) . since we could not rule out the diagnosis of small cell lung cancer which has a high propensity for early micrometastases , whole - brain irradiation was first given in march 2007 , with a total dose of 50 gy delivered in 25 fractions ; this treatment resulted in a marked symptomatic and a good radiological partial response ( figure 2b ) . histologically , tumor cells were arranged in nests or trabeculae , and infiltrated in the fibrous stroma . immunohistochemistry showed positive staining for cd 56 , protein - gene product 9.5 ( pgp 9.5 ) and neuron - specific enolase ( nse ) ( figure 3b ) . additional examinations , including bone scanning and an upper abdominal ct , showed no signs of abnormalities . after whole - brain irradiation , the patient was treated at three - week intervals with 25 mg / m of amrubicin ( 5 - min intravenous injection on days 13 ) plus 60 mg / m of cpt - 11 ( 90 - min intravenous infusion on days 1 and 8 ) starting in may 2007 . the selection of this regimen was based on our previous phase i trial .9 out of 11 patients entered onto the trial , five partial responses were obtained . one good partial response was observed only in a patient with neuroendocrine properties who had huge liver metastases . he received four cycles of this chemotherapy , ending in mid - august 2007 , and a chest x - ray showed that the primary lesion had rapidly decreased in size from 2.5 cm 2.6 cm to 1.4 cm 0.7 cm within two weeks . a further follow - up ct examination showed the complete resolution of both the primary lesion and the brain metastasis , and the patient s quality of life was improved ( figures 1b , 2c ) . as of march 1 , 2009 , he has been progression - free from disease for a total of 24 months . because of the difficulty in making an immunohistochemical diagnosis using small specimens , lcnec is often difficult to diagnose correctly using small specimens obtained by bronchoscopy or fine needle biopsy .10 although lcnec is categorized as a variant of large - cell carcinoma ,11 lcnec exhibits features of a high - grade neuroendocrine tumor , and the biological behavior of lcnec tumors resembles that of small cell lung carcinomas . lcnec has a worse prognosis than stage - equivalent nsclc .2 specimens obtained using fiber - optic bronchoscopy or percutaneous fine needle aspiration should be carefully examined because the accurate differentiation of lcnec from the more common large cell lung cancer is important for identifying patients with a dismal prognosis . rossi and colleagues7 reported that platinum - doublet chemotherapy regimens that are generally recommended for nsclc , including cisplatin plus gemcitabine , were relatively ineffective and that the use of standard chemotherapy regimens for sclc seemed to be the most important survival - related variable . iyoda and colleagues12 described a survival benefit in patients with surgically resected stage i lcnec who underwent a standard adjuvant chemotherapy regimen typically used for sclc patients . kozuki and colleagues6 also stated in their study of 12 lcnec patients that combination therapy of cisplatin plus etoposide was useful for improving outcome . in a retrospective analysis , yamazaki and colleagues8fujiwara and colleagues5 suggested that a regimen comprised of a platinum - doublet combined with irinotecan ( cpt - 11 ) or paclitaxel might be active against lcnec . all these authors recommended that lcnecs should be treated in a manner similar to that used for small cell lung cancer , given their similarity in chemosensitivity and aggressive characteristics , even though lcnecs are classified as non - small cell lung cancer . amrubicin is a totally synthetic anthracycline anticancer agent that acts as a potent topoisomerase ii inhibitor . amrubicin is converted to an active metabolite , amrubicinol .13 the response rates to amrubicin in patients with non - small cell lung cancer and small cell lung cancer were 25 % and 52 % 79 % , respectively .1416 cpt - 11 is a water - soluble camptothecin derivative that inhibits topoisomerase i. cpt - 11 has shown a significant antitumor activity against various human malignancies including non - small cell lung cancer and small cell lung cancer .1720 dna topoisomerase i and ii are functionally related and are known to act in concert . since the combined use of topoisomerase i and ii inhibitors is theoretically attractive because of the complementary functions of their targets ,21 we previously conducted a phase i study of amrubicin combined with cpt - 11 for the treatment of advanced non - small cell lung cancer .9 during this trial , one good pr was obtained in a patient with lcnec . similar to this previous experience , the present case also showed a marked response to the nonplatinum doublet of amrubicin and cpt - 11 , with a progression - free survival period of 24 months . to our knowledge , this is the first report describing the use of a nonplatinum doublet for advanced lcnec . since the combination of cisplatin andetoposide has been used extensively for the treatment of this disease , our case report adds to the medical literature on the use of amrubicin and cpt - 11 regimens for the treatment of this increasingly recognized malignancy , which has a dismal prognosis and a high and early propensity to metastasize . however , rossi and colleagues7 reported the median diameter of their lcnec tumors was 40 mm . the small tumor volume may have good influence on the response to the combination regimen of amrubicin and cpt - 11 . however , it is difficult to make valid conclusions about the ultimate clinical activity of this combination regimen on the basis of this case report . therefore , phase ii / iii trials are needed to allow a precise estimate of the degree of activity of this regimen against advanced lcnec . in conclusion , the combination of amrubicin and cpt - 11 is a promising and well - tolerated regimen based on its unique mechanisms of action and may be a novel therapeutic approach capable of improving the survival rates of patients with lcnec , a very rare but aggressive neuroendocrine tumor .\noutput:\n" }, { "from": "agent", "value": "large - cell neuroendocrine carcinoma ( lcnec ) is a relatively uncommon variant of non - small cell lung cancer . since the biological characteristics of lcnec are similar to those of small cell lung cancer , lcnec is usually treated with chemotherapy regimens used for small cell lung cancer . however , the outcomes are usually dismal . here , we report a patient with lcnec ( a metastasis to the brain ) . after whole brain irradiation , he received a combination of amrubicin and irinotecan chemotherapy , and has been relapse - free for two years . this treatment regimen may be beneficial for patients with advanced lcnec ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: pseudorabies virus ( prv ) is a member of the family herpesviridae , subfamily alphaherpesvirinae and the causative agent of pseudorabies ( pr ) or aujezsky 's disease . infections with prv result in nervous disorders , respiratory distress , weight loss , young piglet death , and abortion . the virus has a double - stranded linear dna genome 1.4310 kb in length and contains a unique long region ( ul ) , a unique short region ( us ) , a terminal repeat sequence ( trs ) , and internal repeat sequences ( irs ) . to date , at least 11 different glycoproteins of prv ( gb , gc , gd , ge , gg , gh , gi , gk , gl , gm , or gn ) have been identified and the genes that encode these proteins have been sequenced . the essential glycoproteins of prv include gb gd , gh , gl , and gk ; the others are considered nonessential . there are several nonstructural proteins of prv such as thymus kinase ( tk ) and protein kinase ( pk ) , which are associated with virulence ; however , this subset of genes can be replaced by heterologous genes without affecting infectivity or virus propagation provided the essential genes remain intact . a schematic drawing regarding common sites for gene insertion in the prv genome is shown in figure 1 . the efficacy of multivalent prv vaccines has been investigated . herein , we review research progress using attenuated recombinant prvs ( rprvs ) as vaccine candidates with application for advancing the development of rprv vector vaccines . recombinant viruses represent a particularly promising avenue of vaccine research both for improving existing vaccines and for developing new ones . in principle , the design of prv vector vaccines is predicated upon the genome of live prv being used to insert and express genes encoding protective antigens from other pathogens including viruses , bacteria , and parasites . the existence of numerous nonessential genes in the large prv genome permits the simultaneous insertion of multiple foreign genes in the hope of vaccinating against several diseases at the same time . it is an attenuated prv which has been passaged repeatedly in pig kidney cells , chicken eggs , and chicken embryo cells . in this strain , the complete ge and part of gi genesnonetheless , this construct has met with good success in developing multivalent vaccines to control various infectious diseases . the common strategy for using rprv involves constructing a transfer vector harboring a portion of the prv genome . this vector is transfected into susceptible cells along with the native prv , and then the cells are screened for the presence of the recombinant . in addition to a portion of the prv genome , the transfer vector also contains a promoter , the foreign genes of interest , and a reporter gene . prv sequences should appear at the start and end of the vector to permit homologous recombination between the arms of the vector and virus genomes . one study demonstrated that the human cytomegalovirus ( cmv ) promoter is more efficient than the prv promotor in directing viral gene synthesis . as such , the immediate early gene promoter of cmv has become the most common promoter used in these constructs . in addition to conventional approaches to generating recombinants , viral genomes can be cloned into bacterial artificial chromosome ( bac ) vectors . the use of herpesvirus bacs for generating site - directed and transposon mutagenic recombinants has been reviewed . to date , most of the foreign genes that have been inserted into the prv genome encode key antigens derived from animal viruses . a summary of constructs developed to date is provided in table 1 which includes parental prv strains , foreign genes , and insertion sites . the examples which follow provide a more in - depth discussion of successes using this technology . porcine reproductive and respiratory syndrome virus ( prrsv ) is an enveloped , positive strand rna virus which is a member of the familyarteriviridae . it causes tremendous economic losses worldwide and is among the most important diseases in countries where swine are intensively raised . the genome of prrsv is 15 kb in length and contains nine open reading frames ( orfs ) designated orf1a , orf1b , orf2a , orf2b , orf3 , orf4 , orf5 , orf6 , and orf7 . a decade ago , an attenuated rprv , rprv - gp5 , was developed that expresses the gp5 envelope protein of prrsv ; the gp5 protein is encoded by orf5 . the rprv - gp5 was able to confer significant protection against clinical symptoms and reduce pathogenic lesions caused by prrsv challenge in vaccinated pigs . pigs immunized either with rprv or with prrsv inactivated vaccine remained clinically healthy before and after challenge . following immunization , only a short period ( 3 days ) of mild fever ( 41c ) , gradually improving lung and kidney lesions , and short - term viremia ( 2 and 3 weeks , resp . ) resulted ; however , no anti - prrsv antibody was detected before challenge . in order to improve the protective efficacy of rprv - gp5 , a modified gp5 gene ( gp5 m ) was synthesized wherein a pan dr t - helper cell epitope ( padre ) sequence was inserted between the n - terminus and the neutralizing gp5 epitope . the new rprv - gp5 m elicited a higher level of prrsv - specific neutralizing antibodies and cellular immune responses than the rprv - gp5 . recently , this group generated another construct named rprv - gp5 m - m that expresses two major membrane - associated proteins ( gp5 and m ) of prrsv within the same vector . mice immunized with rprv - gp5 m - m developed prv - specific humoral immune responses and provided complete protection against a lethal prv challenge . at the same time , high levels of prrsv - specific neutralizing antibodies and lymphocyte proliferation responses were observed in the immunized mice . once proof of principle was demonstrated in mice , studies advanced to piglets . when compared to the commercially available prrsv killed vaccine , rprv - gp5 m - m immunized animals generated higher prrsv - specific neutralizing antibodies and higher lymphocyte proliferation responses resulting in better protection against prrsv . these data indicate that prv is an excellent vector for developing virus - based vaccines against prv and prrsv . porcine circovirus type 2 ( pcv2 ) is the primary cause of postweaning multisystemic wasting syndrome ( pmws ) , which is a worldwide disease that debilitates pigs with lymphadenopathy and interstitial pneumonia . pcv2 is a single - stranded circular dna virus and a member of the family circoviridae . pcv2 has three major orfs ; orf1 encodes two replication - related proteins , rep and rep ' , which are essential for viral dna replication ; orf2 encodes the major capsid protein of pcv2 ; and orf3 encodes the nonstructural orf3 protein . a rprv expressing a fusion protein of orf1 and 2 was constructed and its immunogenicity tested in mice and pigs . the rprv - pcv2 elicited strong anti - prv and anti - pcv2 antibodies in balb / c mice wherein rprv - pcv2 protected mice against a lethal challenge with a virulent prv . in pigs , a second rprv was constructed expressing only the orf2 gene that was also used to immunize piglets . results showed that the rprv - orf2 elicited significant humoral immune responses to both prv and pcv2 wherein pcv2 - specific lymphocyte proliferation responses could be detected by 49 days after immunization . the rprv - orf2 was better at eliciting protective immune responses in piglets than rprv expressing both orf1 and 2 . these findings demonstrate that rprv - pcv2 may be a suitable bivalent vaccine against prv and pcv2 and that multiplicity is not always the optimal approach to vaccine development . foot - and - mouth disease virus ( fmdv ) is highly contagious and affects all cloven - hoofed domestic animals including cattle , sheep , goats , pigs , and buffalo . it is a positive single - stranded rna virus approximately 8.5 kb in length and belongs to the family picornaviridae . the fmdv capsid precursor p1 - 2a is cleaved and released from the polyprotein by l protease and processed by viral protease 3c to form four structural proteins , vp1 , vp2 , vp3 , and vp4 . fmdv has seven serotypes , a , o , c , asia1 , sat1 , sat2 , and sat3 , each of which contains multiple subtypes . using prv as a vector , the vp1 gene was fused to the prv genome . the immunogenicity of the recombinant product was tested in 15 fmdv seronegative white pigs . although the antibody levels were lower than those induced by commercially available fmdv vaccines and protection against virulent fmdv was not observed , the rprv - vp1 construct still alleviated clinical symptoms in infected pigs . to improve the immune response , another rprv was generated that expresses p1 - 2a of fmdv ; its protective effects were evaluated in white pigs . in contrast to the earlier version , these pigs exhibited high levels of neutralizing antibodies to both fmdv and prv and further showed strong ctl responses against fmdv antigen activation . following challenge , replication of fmdv was significantly lower in pigs vaccinated with the new rprv construct when compared to the commercially available vaccine . recently , another rprv which coexpresses p1 - 2a and the viral protease 3c was developed and tested in piglets . these results showed that rprv - p12a3c induced a high level of neutralizing antibodies and fmdv - specific lymphocyte proliferative responses . relative to the inactivated fmdv vaccine which provided 100 % protection , the rprv - p12a3c induced only 60 % protection in challenged piglets but was able to reduce pathogenic lesions . these findings suggest that rprv - p12a3c was better at protecting piglets than the previous constructs and support further development of vaccines against both fmdv and prv . work must now focus on targeting other serotypes of fmdv with the hope of finding one vaccine with good efficacy against all or most serotypes . it is characterized by fetal death , mummification , stillbirth , and prolonged farrowing intervals . ppv is a single - strand dna virus , which is a member of the familyparvoviridae . its genome is 5 kb is size and contains two large orfs ; the left orf encodes the nonstructural protein ns1 and the right orf encodes three capsid proteins . one of the three capsid proteins , vp2 , can self - assemble into virus - like particles ( vlps ) that are immunologically indistinguishable from inactivated whole - virus vaccines . piglets vaccinated with rprv - vp2 elicited prv - and ppv - specific humoral immune responses and generated complete protection against a lethal dose of prv . this finding lends further support to the development of bivalent vaccines and in particular , against prv and ppv . a rprv coexpressing p1 - 2a of fmdv and vp2 of ppv was constructed and used to vaccinate balb / c mice . both total antibody and neutralizing antibody levels to prvprotection to fmdv or ppv was 60 % when compared to inactivated vaccines . neutralizing antibody titers induced by the rprvconstruct against fmdv or ppv were 50 % of the level induced by their respective inactivated vaccines . unlike previous constructs , this vaccine candidate demonstrated the feasibility of using rprv to develop trivalent vaccines , in particular against prv , fmdv , and ppv . future work should be performed in swine to test the utility of such vaccine in the natural host for these viruses . classical swine fever virus ( csfv ) is a significant impediment to global trade in swine products and results in considerable financial loss . csfv is an enveloped , positive , single - stranded rna virus which belongs to the genus pestivirus of the family flaviviridiae . its genome , which is 12.3 kb long , encodes a single glycoprotein , glycoprotein el ( later called e2 ) , which is highly immunogenic and capable of inducing protective immune responses . a bivalent rprv was synthesized that was gd / ge negative and that expressed glycoprotein e2 . vaccination of piglets exhibited strong protection against both aujeszky 's disease and csfv supporting the use of rprv - based bivalent vaccines against csfv . swine influenza virus ( siv ) is a type a virus , which is enveloped and consists of negative single - stranded rna . rna segment 4 contains the gene encoding the large hemagglutinin ( ha ) glycoprotein which is the major surface glycoprotein . it is also a major immunogen which induces subtype - specific protective cellular and humoral immune responses in animals . segment 5 encodes the nucleoprotein ( np ) gene a rprv expressing the ha gene of serotype h3n2 subtype siv ( a / swine / inner mongolia / 547/2001 ) was constructed and its immunogenicity was tested in mice . upon challenge , no virus could be isolated from the vaccinated mice ; however , mild pathological lesions were observed in the lungs . at the same time , the rprv - ha construct protected mice from challenge using a heterologous virulent siv ( a / swine / heilongjiang / 74/2000 ) as well . recently , klingbeil et al . used bac technology to generate a ha - based vaccine derived from the swine h1n1 virus cloned into prv . pigs given a single injection of the vaccine produced high levels of antibody directed at the h1n1 - derived ha protein and were protected from clinical signs of infection when challenged . prv has a wide range of hosts including swine , sheep , cattle , and dogs . as such , the prv vector has been used to develop recombinant vaccines in other hosts and in systems unrelated to viral protection , that is , protozoan parasites . the sag1 protein domain belongs to a group of glycosylphosphatidylinositol ( gpi ) - linked proteins with sag1 related sequences that can be found on the surface of the parasite . the protective character of the rprv - sag1 construct was tested in balb / c mice . all mice vaccinated with the rprv - sag1 developed high levels of specific antibodies against t. gondii lysate antigen ( tla ) and neutralizing antibodies . in addition , they observed an increase in the splenocyte proliferative response , ifn - and il - 2 and strong cytotoxic t lymphocyte responses . when the mice were challenged with the highly virulent rh strain of t. gondii , the rprv - sag1 construct induced partial protection ( 60 % ) . this is likely related to the significantly complex life cycle of protozoan parasites and the stage specificity of sag1 expression . in order to improve the protective response , two additional rprvs expressing sag1 or the micronemal protein mic3 ( rprv - mic3 ) were developed and used to immunize balb / c mice separately and simultaneously . all mice vaccinated with the rprvs induced high levels of antibodies to t. gondii lysate antigen , splenocyte proliferation , ifn - , and il - 2 . the vaccinated mice survived a lethal challenge with t. gondii rh strain ; however , protection was not complete . these results support previous studies showing the utility of expressing t. gondii protective antigens in prv as a novel approach for developing vaccine candidates against pseudorabies and toxoplasmosis ; however additional research is needed to increase the survivability of host animals to parasite challenge . one approach is to make a multivalent vaccine that targets more than one stage of infection or to test other parasite antigens . unlike viruses , parasites are far more complex both biologically and genetically which complicates the approach to recombinant vaccine development . three rprvs expressing s. japonicum glutathione s - transferase ( sj26gst ) , fatty acid binding protein ( sjfabp ) , or both were constructed and named rprv / sj26gst , rprv / sjfabp , and rprv / sj26gst - sjfabp , respectively . the results showed that all rprvs induced specific antibody responses against total worm extracts , increased splenocyte proliferation , and elevated ifn - and il - 2 levels in the immunized mice . however , better immune stimulation was observed in animals given rprv / sj26gst - sjfabp than in those given either rprv / sj26gst or rprv / sjfabp . further , in all immunized sheep , the treatment was deemed safe and the worm and egg burdens were demonstrably reduced following challenge . these results indicated that the multivalent rprv - based vaccines for s. japonicum can produce significant protection and are capable of preventing infection from protozoan parasites . less than 100 % protection , which is very common among putative parasite vaccines , has hindered acceptance and further development . a rprv expressing the ns1 protein of japanese encephalitis virus ( jev ) was constructed . a test using 10 pfu , in mice , piglets , and pregnant sows indicated a good safety profile for the rprv . animals given the rprv - ns1 virus developed jev - specific humoral and cellular immune responses and protected the animals from a lethal challenge with the virulent prv ea strain . these experiments provided evidence that the rprv may serve as a candidate for generating a novel vaccine that can be used for controlling pseudorabies and japanese encephalitis . this recombinant virus was deemed safe for dogs by oral and intramuscular inoculation routes and induced protective immune responses against both rabies and pseudorabies . neutralizing antibody titers against rabies and pseudorabieswere demonstrably elevated by 5 weeks after vaccination and remained as such for at least 6 months . this experiment indicates that constructs designed herein survived well in the host such that the immune profile of vaccinated animals was long - lived . clearly , there are other viral genomes that can serve as vaccine vectors such as adenovirus , poxvirus , and baculovirus . these have all been tested as delivery vehicles for exogenous antigens that had been previously expressed in prv vectors . , they have a high capacity for the insertion of foreign genes ( 536 kb ) , are able to transduce a broad range of cell types , and are commercially available in kit form for subsequent genetic modification . they have been extensively used as expression vectors for vaccination , expression of large foreign genes , and induction of cellular and humoral immune responses . among the more common poxvirusesare modified vaccinia virus ankara ( mva ) , fowlpox virus , and orf virus . mva has been a smallpox vaccine for many years and more recently it has been used as a viral vector for preventing both cancer and infectious diseases . other examples include the use of a canarypox - based recombinant containing the prm and e genes of the west nile virus ( wnv ) to induce protection in cats and dogs . this study resulted in the expression of the wnv genes and the induction of protective immunity . the orf virus has been used to generate protective immunity against csv using the e2 gene and pseudorabies in pigs . inasmuch as the orf virus rarely causes system infections and has a narrow infection host range ; it is a logical choice for developing multivalent viral vaccines . its host specificity was originally thought to be restricted to cells derived from arthropods ; however , recent studies have shown that baculoviruses carrying mammalian cell - active promoters are capable of transferring and expressing foreign genes in a variety of mammalian cell types as well as in animal models . baculovirus systems have been very popular because like adenoviruses , they also are available commercially and in kit form for easy genetic modification . above - mentioned viruses have also been used to develop recombinant live viruses bearing components of prrsv , pcv2 , fmdv , csfv , and siv . a comparison of key immunological efficacies among these many virus vectors is shown in table 2 . past successes of rprv as a vector for expressing exogenous antigens has resulted in new rprvs being constructed that are less pathogenic . first , live attenuated prv has a large genome wherein half of the genome is considered nonessential thus permitting modification without affecting key characters such as infectivity . although some of these genes are associated with virulence , their deletion and replacement by foreign genes has no adverse effects on the propagation of prv . the benefits of viral vectors are that they not only express their own protective antigens , but any inserted exogenous genes as well . inasmuch as they use host machinery to replicate and express proteins , the resultant exogenous gene products have a higher probability of being correctly modified or folded posttranslationally , something which is lacking in bacterial systems . as such , products derived from rprvs are more likely to mimic native immunogens and correctly induce humoral and / or cellular responses in immunized animals . as shown above , one can target multiple diseases within a single vector construct . prv vaccine strains have been used for decades and exhibit high safety and efficacy profiles in vivo . third , prv has a broad host range including pigs , cattle , goats , and dogs among others . this makes it possible to target animal diseases in multiple hosts without resorting to multiple vector constructs to express the antigens . therefore , rprvs can be maintained for long periods in a given host thereby providing constant stimulation of the protective immune responses . finally , prv can be propagated in various cell lines including spf chicken embryo fibroblast cells . other points to consider when developing prv - based vector vaccines are that this vector system requires a strong promoter to maintain high and stable expression levels . also , selection of nonessential genes in the prv genome to be replaced with the foreign genes of interest can affect optimizing the immune response . given competing interests between vector - derived and exogenous protein - derived immune responses , recombinant constructs should be characterized with respect to optimal inoculation dosage . for development of effective rprv vaccines , the pathogenic features , protective mechanisms , and the epidemiology of diseases must be taken into account in all future work . many of the rprv vaccine candidates that have been reported here either have not been further pursued or are not yet commercially available . first , optimizing viral infection and replication are required to produce efficient and safe vaccines suitable for release into the environment . to this end , identifying more appropriate nonessential regions within the virus is needed to enhance expression of exogenous genes particularly when multivalent rprvs are being developed . this is not a trivial task in view of the large genome size of prv and the interplay between essential regions and exogenous genes that can affect viral virulence and replication . second , modifications to the parent prv in generating a rprv are often required to eliminate or replace existing marker genes or important regulatory elements to make the construct more suitable for clinical application . third , plans are needed to transition between available vaccinations and those derived from rprvs . concurrent or overlapping vaccinations of the two will have a significant and deleterious impact on the efficacy and propagation of subsequent rprv - based immunizations . finally , many of the studies using rprvs have not been advanced to the natural host , that is , swine . problems with the high cost of clinical trials , manufacturing sufficient amounts to advance these studies and releasing biologicals into the environment are often limiting factors . yet these studies are necessary to get a more comprehensive picture of the immunogenicity of the expressed genes , the persistence of the viral infection , and longevity of the stimulation in the natural host and to study the potential for tumorigenesis when using uniquely modified rprv - based vectors .\noutput:\n" }, { "from": "agent", "value": "pseudorabies virus ( prv ) is a double - stranded , dna - based swine virus with a genome approximating 150 kb in size . prv has many nonessential genes which can be replaced with genes encoding heterologous antigens but without deleterious effects on virus propagation . recombinant prvs expressing both native and foreign antigens are able to stimulate immune responses . in this paper , we review the current status of live attenuated recombinant prvs and live prv - based vector vaccines with potential for controlling viral infections in animals ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: the normally quasi - fractal three - dimensional ( 3d ) growth mechanism of aunp / cb [ n ] networks is redirected into a quasi one - dimensional growth of chains of alternating aunp and cb [ n ] building blocks . this is achieved by the electrokinetic control of the aunp / cb [ n ] interaction across a nanoporous polycarbonate ( pc ) membrane , separating two compartments containing the aunp suspension ( aunp : diameter d = 16.5 nm ) and the cb solution , respectively , as shown in figure 1c . ( c ) electrophoresis cell , where a nanoporous pc membrane separates two compartments containing the aunp ( aunp : d = 16.5 nm ) and cb building blocks , respectively . the application of a small potential difference between two feeder electrodes ( e 2 v ) , with the negative pole in the aunp chamber , triggers the formation of chain - type objects in the aunp compartment , as demonstrated by tem ( see figure 2 ) . within the membrane , as well as in the cb chamber , only very few individual aunp or small aunp aggregates ( dimers / trimers ) were observed by tem . this indicates that only the cb molecules are able to pass through the pores of the membrane , whereas the aunps remain in their compartment . after transfer of the objects to a tem grid , the interparticle distances ( lgap ) were analyzed from tem images . figure 2 reveals that the chains exhibit a fixed interparticle distance , which was evaluated as being lgap = 9.13 ( 0.41 ) , resulting from an analysis of 100 interparticle distances . this value is in good agreement with the value of 9.1 ( see figure 1b ) , which is theoretically expected for cb - bridging and seen in previous optical experiments . this strongly suggests , together with the sers signal generated by the cbs present in the gap , that the generated aunp chains actually contain cb nanojunctions and consist of alternating aunp and cb building blocks . the chain formation is believed to occur at the membrane / solution interface in the aunp compartment , according to the mechanism proposed in figure 3 , where the movements of aunp and cb [ n ] in opposite directions favor the interaction of these two chain building blocks . the application of an electric field induces an electroosmotic flow ( eof ) of positive charge carriers present along the negatively charged surface of the nanopores ( membrane thickness / depth of nanopores = 6 m ) toward the negative electrode , which transports the neutral cb molecules along the flow direction through the membrane into the aunp compartment . in contrast , an oppositely directed electrophoretic motion of aunp , which are stabilized by a negatively charged citrate layer , is induced in direction of the positive electrode . this directs the aunp toward the membrane , however the opposed electroosmotic flow does not allow aunp transfer through the nanopores of the membrane . these two electrokinetic phenomena are proportional to the applied electric field and lead to an encounter of the two chain building blocks at the membrane interface in the aunp compartment , resulting in the formation of anisotropic aunp / cb chains . the electrophoresis of aunp toward the membrane interface allows a continuous particle supply for chain prolongation . schematic of one nanopore of the pc membrane to illustrate the synergy between electroosmotic and electrophoretic motion leading to chain formation ( vem , supply rate of the aunps by electromigration ; veof , supply rate of cb by electroosmotic flow ; vr , reaction rate of the cb / aunp assembly ; vdiff , evacuation rate of the formed chains ) . the dependence of the aunp / cb chain assembly on the applied voltage , the reaction time t , the cb / aunp ratio ( r ) , as well as the temperature is studied by tem in order to investigate the possibility of tuning the chain geometry . figure 4a shows that an increase in the applied dc voltage ( at constant t = 30 min , r = 4500:1 , and t = 20 c ) first causes an increase in the chain length l with a maximum chain length ( l 48 np ) around 1 v , followed by a significant decrease in chain length . moreover , the increase in chain length is accompanied by a decrease in chain linearity , until the formation of complex 2d networks with interconnected aunp chains , as shown in the tem image in figure 5c and statistically analyzed in figure s5 in the supporting information . this continuous transition between ideal nonbranched aunp chains , branched chains , and complex two - dimensional ( 2d ) networks are categorized in figure 5 into five structural regimes . ideal nonbranched 1np chains were observed at small ( regime b , 0.5 v e 0.75 v ) as well as higher voltages ( regime d , 1.25 v e 2.0 v ) , whereas a voltage in an intermediate regime c ( 0.75 v e 1.25 v ) favors branching with the extreme case of 2d networks of interconnected chains ( figure 5 , regime c ) . statistical analysis of the length of aunp / cb aggregate chains ( based on an analysis of three tem grids for each set of parameters and two independent sets of experiments ) , prepared with the setup shown in figure 1c for ( a ) different applied dc potentials between 0.25 and 2 v at constant t = 30 min , r = 4500:1 and t = 20 c ; ( b ) different reaction times t 75 min at constant e = 0.85 v , r = 4500:1 and t = 20 c . an increase in reaction time ( at constant e = 0.85 v , r = 4500:1 , t = 20 c ) in contrast provokes a clear increase in the chain length ( figure 4b ) , whereas the chain linearity remains rather constant . an increase in temperature to 50 c under conditions which lead to the branched networks of regime c of figure 5 ( e = 1 v , r = 4500 , t = 30 min ) increases the chain linearity , whereas a decrease to 4 c increases aggregation . a decrease of r from 4500:1 to 1:1 under regime c conditions ( at constant e = 1 v , t = 30 min , t = 20 c ) results in a suppression of the branching and the predominance of 1d chains , corresponding to a shift of the structure spectrum shown in figure 5 toward the left . a further decrease of r to 0.1:1 leads to shorter chains resembling those of regime a. aggregation regimes during chain formation . the growth regime can be controlled by both the applied voltage and the ratio r of cb / aunp ( tem images : t = 30 min and r = 4500 , varying voltages ; the scale bar denotes 50 nm ) . the degree of branching of the formed structures between the regimes a e shown in figure 5 can be tuned by the applied dc potential , the cb / aunp ratio r as well as the temperature , whereas an increase in reaction time only provokes an increase in chain length . the influence of the applied voltage or of r on the formation of the different structural regimes shown in figure 5 can be explained based on the mechanism depicted in figure 3 . aunp and cb building blocks reach the membrane interface in the aunp compartment with an electrophoretic mobility vem for aunps and an electroosmotic flow rate veof for cb . the affinity of cbs for gold surfaces suggests that the reaction rate vr should not be a determining kinetic step . however the evacuation rate of the formed chains vdiff , which is composed of an electrophoretic and a diffusional component , has to be considered . this diffusional rate will become smaller with growing chain length . for successful chain formation in the ideal regime b of figure 5 , the cb supply rate at the nanopore needs to be faster than the rate of aunp supply due to the need of several cb molecules to be adsorbed for the formation of a successful junction between two gold particles . furthermore , the supply of aunps toward the nanopore should be as fast as the movement of the formed chains away from the nanopore . an excess supply of cb molecules leads on average to more than one junction per aunp and thus to chain branching , as seen in regime c. a further increase of the local cb concentration can lead to the saturation regimes d and e , where with an increasing cb supply the branched structures of regime c are first cut into individual chains ( regime d ) in analogy to the dynamics known for 3d aunp / cb aggregation under an excess of cb , which then decrease in length with increasing cb concentration ( regime e ) . a deficiency of cb at the nanopore leads to chain termination and thus shortening of the chain lengths according to regime a. these basic considerations can furthermore explain the impact of the duration of the experiment , as well as the applied temperature on chain formation . since time does not influence the kinetics of chain assembly , an increase in chain length and no change in the aggregation state is observed when prolonging the experiment . the observed increase in chain linearity at elevated temperatures might be because under these conditions initial alignment errors can be corrected . individual particles can overcome more easily the activation barrier for disconnection from the aggregate and can then easily rebind at a different position , still under the influence of the electric field . furthermore the viscosity of the medium is decreasing , allowing faster diffusion and position correction . optical excitation of the chain plasmons facilitates an analysis of the chain structure via extinction spectroscopy . the evolution of a longitudinal surface plasmon resonance ( lspr ) mode at longer wavelengths than the plasmon resonance of individual nanoparticles indicates the formation of nanoparticle chains , as it results from the excitation of electron oscillations parallel to the long axis of a nanoparticle chain . thus , the chain growth can be observed in real time by extinction spectroscopy ( = 400800 nm ) based on this chain plasmon mode . the extinction measurements were performed in a cell comparable to the one used for the synthesis of the chains for the tem measurements but in addition a collimated light beam is focused close to the membrane in the aunp - containing compartment . figure 6 shows the extinction spectra detected over a time of 2 h when applying parameters optimized to yield regime b - type linear chains . real - time extinction spectroscopy during the chain growth process ( r = 1800 , e = 1.5 v ) . figure 6 reveals that over a reaction time of 2 h the lspr mode grows significantly , as seen by the emergence of the mode at wavelengths 600 nm , next to the transverse surface plasmon resonance ( tspr ) mode of the gold nanoparticles at = 530 nm . this correlates very well with the observation of an expanding front of gray / blue color in the red aunp suspension at the membrane interface ( see figure 7 ) . photo of the nanoparticle compartment at the membrane / solution interface , revealing the development of the aunp / cb chains as a growing blue front ( r = 18720 , t = 60 min , e = 1.5 v , d = 16.5 nm ) . figure 8a presents the corresponding analysis of the wavelength of the extinction maximum agg of the lspr mode and its peak intensity aagg after subtraction of the extinction spectrum of individual aunps . it shows that aagg increases over 2 h in a nucleation growth process that follows a sigmoidal profile ( sigmoidal fit : r = 0.9978 ) and agg increases to values of up to 650 nm during the first 60 min . the increase in aagg relates to the chain formation , which occurs first with an increasing local chain concentration and stagnates at t 120 min , when the local chain concentration remains constant as soon as the formation of new chains and the chain transport along the capillary proceed with the same speed . the redshift of agg can be related to the increase in chain length during the growth process . full electromagnetic simulations by aizpurua et al . for linear chains of alternating aunp and cb building blocksfacilitate the assignment to the extinction spectra of an effective chain length from the peak of the chain plasmon wavelength agg . thus , the spectra in figure 6 can be assigned to a chain length l = 7 nps at t = 15 min , which increases to a length of 16 nps for t 60 min . the chain plasmon mode supports nanoparticle coupling over aunp chain - lengths less than 16 np , so that no further wavelength shifts are detected even though longer chains can form . the small concentration of chains in the beginning of the chain growth ( t 15 min ) also shows that only chains shorter than 7 nps are seen during the initial phase of chain growth . the spatial distribution of the chain concentration profile in the aunp chamber after 2 h of chain growth was analyzed by extinction spectroscopy in order to gain further insight into the chain growth mechanism and the subsequent chain diffusion . to accomplish this , the cell is scanned by changing the position of the light beam along the long axis of the cell by a distance dm from the membrane . figure 8b shows the analysis of aagg and agg of the chain mode recorded at increasing dm at intervals of 0.5 mm . it reveals that both aagg , as well as agg , decrease with increasing dm , indicating that with increasing distance from the membrane the chain concentration decreases and furthermore the predominating chain length gets smaller . according to the theoretical calculations , the longest chains with a length of 16 nps can be found at the membrane interface , while shorter chains with a length of 10 nps are dominant when moving away from the membrane , on account of their faster diffusion . this profile underscores the proposed mechanism of chain formation at the membrane interface in the aunp compartment and the subsequent diffusion of the formed chains into the bulk solution , as depicted in figure 1c and figure 3 . analysis of the extinction spectra showing peak intensity aagg and peak wavelength agg of the lspr mode in the extinction spectra . ( a ) peak wavelength and amplitude recorded during chain growth over t = 2 h ( regime b : r = 1800 , e = 1.5 v , d ( aunp ) = 16.5 nm ) . ( b ) peak wavelength and amplitude recorded after t = 2 h at increasing distances dm from the membrane with dm = 0.3 mm being the beam position during the experiment in panel a. ( c ) extinction difference spectra of regime b - type chains ( black line ; r = 1800 , t = 30 min , e = 1.5 v , d = 16.5 nm ) and regime d - type chains ( red line ; r = 18720 , t = 30 min , e = 1.5 v , d = 16.5 nm ) . ( d ) extinction difference spectra of 1d chains ( red line ) and 3d aggregates ( black line ; d = 19.5 nm ) . extinction spectroscopy provides additional insight into differences in the formation of the two types of 1d chains in regimes b and d ( figure 8c ) . the spectral analysis of the chain formation under conditions yielding linear chains in regime d ( e = 1.5 v , aunp / cb = 18720 ) reveals that this process is significantly faster than the regime b - type chain growth , most likely due to the higher cb concentration . at a fixed analysis time of t = 30 min ( as in the tem pictures shown in figure 5 ) the faster regime d - type chain growth already yields chains with the maximal detectable length of 16 nps , whereas the regime b - type chains have only reached a length of 12 nps , which explains the tem detection of longer regime d - type chains . however , after a reaction time of 2 h , both processes yield lspr modes related to the maximal detectable chain length of 16 nps . extinction spectroscopy in solution is unable to distinguish 3d fractal aggregates from 1d near - linear chains , because the anisotropy in optical response is washed out by the rotational diffusion of the chains within the optical interrogation volume . however , after both 3d aggregates and 1d chains have been allowed to form over 18 h ( by mixing the aunp and cb in the bulk , or in the electrochemical cell ) , a different response is clearly observed ( figure 8d ) . the shorter wavelength peak observed from the 3d aggregates is evidence for less linear , more branched and compact aunp clusters . the spatial structure of the formed aunp / cb chains is studied and visualized by cryo - tem . this excludes possible misinterpretations about the formed nanoparticle assemblies based on standard tem measurements . standard tem requires the adsorption of the chain assemblies onto the membrane of the tem grid , which forces the formed 3d structures into adsorbed 2d objects , potentially leading to distortion or destruction of the initially formed structures , as well as the condensation of several objects into new aggregates . cryo - tem measurements completely conserve the 3d conformations of the electrokinetically formed nanoparticle assemblies and prevent any interactions between nanoparticle assemblies and the support . the obtained cryo - tem images reveal one - dimensional linear chains ( regimes b and d ) as well as branched structures ( regime c ) similar to what is observed in standard tem ( figure 9 ) . this confirms the formation and existence of these assemblies in solution , and excludes their accidental formation upon adsorption onto the tem grid . furthermore , it can be concluded that the cb - connected nanoparticle chains are sufficiently stable to allow a reliable analysis with standard tem . however based on cryo - tem , also full 3d images of the topology of the nanoparticle assemblies can be obtained , which allows further examination of the chain growth mechanism . these images reveal that the detected linear chains , as well as the branched structures , extend mostly in two dimensions and not in three , as would be expected for a random statistical assembly of isotropic particles in solution . this indicates that the chain growth occurs within a two - dimensional plane , which is in agreement with the chain growth mechanism depicted in figure 3 . although the cryo - tem images reveal in principle the same structures as the ones observed in standard tem , they occasionally exhibit aunp aunp distances which are significantly larger than the expected lgap = 9.1 of a cb [ n ] - nanojunction and which are never observed in standard tem measurements . in addition there is also a constant systematic overestimation of the interparticle distances with respect to the 9.1 obtained by normal tem . both observations can be explained by the fact that cryo - tem images are obtained and analyzed by an automatic measurement procedure based on noise - reduced and thresholded images ( see supporting information ) , whereas normal tem images are analyzed manually . the 3d - images of aunp / cb chains ( orange spheres ) of a near - ideal 1d chain ( a ) and a branched structure ( b ) calculated from cryo - tem images , which were recorded at three different tilt angles = 15 , 0 , and + 15 and are shown in the background ( method described in the supporting information ) . the strategy presented in this work allows the synthesis of gold nanoparticle chains with fixed sub - nm gap molecular junctions . the normal spontaneous 3d aggregation of aunp and cb is redirected into one - dimensional chain growth by the electrokinetic control of the interactions between the aunp and cb building blocks at the interface of a nanoporous membrane , separating aunp and cb containing compartments . the nanoparticle assembly can be tuned to yield structures ranging from ideal 1d chains to near - 2d networks of interconnected linear chains by adjusting the rate with which the cb molecules enter the aunp compartment . tem , cryo - tem , and spectroscopic analysis of the impact of different experimental parameters on the final aggregate structure allow studying the chain formation mechanism . this synthesis strategy holds promising potential for the controlled assembly of chains of electrostatically interacting building blocks , under the influence of moderate electric fields . no restrictions to conductive , magnetic , or prefunctionalized particles are inherent , which makes this method in principle attractive for generating a large variety of nanoparticle chain systems .\noutput:\n" }, { "from": "agent", "value": "one - dimensional ( 1d ) nanoparticle chains with defined nanojunctions are of strong interest due to their plasmonic and electronic properties . a strategy is presented for the assembly of 1d gold - nanoparticle chains with fixed and rigid cucurbit [ n ] uril - nanojunctions of 9 . the process is electrokinetically accomplished using a nanoporous polycarbonate membrane and controlled by the applied voltage , the nanoparticle / cb [ n ] concentration ratio , time and temperature . the spatial structure and time - resolved analysis of chain plasmonics confirm a growth mechanism at the membrane nanopores ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: drospirenone ( drs ) , chemically ( 6r ,7 r ,8 r ,9 s ,10 r ,13 s ,14 s ,15 s ,16 s ,17 s ) 1,3,4,6,6a,7,8,9,10,11,12,13,14,15,15a,16 - hexadecahydro - 10 , 13 - dimethylspiro - [ 17h - dicyclopropa [ 6,7:15,16 ] cyclopenta [ a ] phenanthrene - 17 , 2 ( 5h ) - furan ] - 3,5 ( 2h ) - dione ( figure 1 ) , is used in contraception and hormone replacement therapy after menopause . 17 - estradiol ( esr ) , chemically ( 17 ) - estra - 1,3,5 ( 10 ) - triene -3,17-diol ( figure 1 ) , is the most potent form in mammalian estrogenic steroids . the combination of drospirenone and 17 -- estradiol is used to treat menopause symptoms . so far , some high performance liquid chromatograph ( hplc ) techniques coupled with ultraviolet ( uv ) , radioimmunoassay ( ria ) , and tandem mass spectrometry ( ms / ms ) methods have been published for quantification and pharmacokinetic studies of drospirenone alone and in combination with drugs in pharmaceutical formulations and biological fluids . a number of efficient analytical techniques and procedures have been developed for the determination and pharmacokinetic studies of esr individually as well as in combination with other drugs in pharmaceutical formulations , biological matrices , nutrients , and in water from different sources . for the determination of esr , hplc coupled with tandem mass spectrometry ( ms / ms ) methods has been widely used since they are highly sensitive and efficient methods , particularly in biological matrices . however , the hplc - ms / ms method is expensive to analyze and time consuming and requires complicated procedures . some hplc with fluorescence ( fl ) detection methods and gas chromatography coupled to ms methods have also been applied for the determination of esr . various hplc - uv detection techniques , which are used commonly for the separation of comparatively high concentrations of drugs , have been reported for the determination of esr in combination with different related estrogenic compounds in pharmaceutical dosage forms , biological matrices , nutrients , and waters . to the best of our knowledge , the simultaneous determination of esr and drs with the hplc - uv method and spectrophotometric method has not yet been reported in the literature . the purpose of this study was to develop and validate an easy , precise , and selective rp - hplc and derivative spectrophotometric method for the simultaneous determination of drugs in bulk and in tablets . analysis was performed on the following operating conditions : 1 - cm path length quartz cells , high scan speed , scan range 200400 nm , 2 nm of slits width , and derivatives interval ( ) of 1 nm . hplc measurements were performed on the thermo separation system ( san jose , ca ) with the following parts : controller sn 4000 , pump p 4000 and auto sampler as 3000 , fitted with 20 l sample loop , and photodiode array detector uv ( uv - dad ) 6000 lp . separation on a waters symmetry c18 column ( 4.6 mm 250 mm , in diameter 5 m ) was performed . the mobile phase of acetonitrile and water ( 70 : 30 ) was used with an isocratic mode at ambient temperature , 1 ml / min flow rate . the mobile phase was filtered through a 0.45 m hv filter with a millipore vacuum filter system . the pure water was obtained by an aquamaxtm - ultra water purification device ( young - lin instrument , south korea ) . stock solutions of the studied drugs at 1.0 mgml were prepared separately in methanol . the preparations of working standard solutions were made by appropriate dilutions from stock solution in methanol for the spectrophotometric methods and with acetonitrile - water ( 70 : 30 , v / v ) for the hplc method . aliquots of standard solution of esr and drs ( each 0.1 mgml ) in mixture were transferred into 10 ml volumetric flasks to obtain the final concentrations of 0.58 g ml for esr and 0.532 gml for drs in methanol . the zero order and first order derivative absorption spectra of standard solutions in the range of 200400 nm were recorded against a blank solvent . firstly , the zero order spectra were recorded and then they transformed into their first derivative order form . zero - crossing amplitudes in the first order derivative spectra were measured at 208 and 282 nm for esr and drs , respectively . each concentration level was performed using 6 independent assays . to determine the calibration curves , the first order derivative amplitude values of each compound were plotted against the concentrations and the corresponding regression equationsthe standard solutions of esr and drs in the mixture at six different concentration levels were transferred into 10 ml volumetric flasks to achieve final concentrations of 0.237.5 gml for esr and 0.082.5 gml for drs in the mobile phase and injected into the hplc system . the peak areas plotted against the concentration of the compounds under the optimized conditions to obtain calibration curves and the corresponding regression equations were obtained . the powder equivalent to an average tablet was weighed and then transferred to a 50 ml volumetric flask with 30 ml methanol and sonicated at room temperature for 1 h. the volume was completed with methanol and filtered . tablet solution was appropriately diluted with methanol for the derivative spectrophotometric method and with acetonitrile : water ( 70 : 30 , v / v ) for the hplc method . corresponding amounts of the drugs in the tablets were analyzed by related regression equations of the calibration curves . direct uv - absorption method was found to be inappropriate for the simultaneous determination of esr and drs due to some spectral interference . in addition , the wavelength of absorbance of esr was lower than 205 nm and gave absorption bonds that were not sharp enough especially at low concentrations ( figure 2 ) . however , derivative spectrophotometry which is based on mathematical transformation has the advantages of reducing background absorbance and increasing the resolution of overlapping spectral bands and allows for the simultaneous analysis of organic compounds in the mixtures . other important advantages of derivative spectroscopy are suppressing broad bands relatively to sharp bands and developing spectral details . for the reasons described hereinabove , the derivative spectra of esr and drs solutions from first up to fourth were recorded separately and their spectra were compared in a row by memory of the device . the 1st order derivative ( 1d ) spectroscopy was chosen for simultaneous determination due to the obtained zero crossing points for both compounds . the optimum wavelength without interferences for est and drs was 208 and 282 nm , respectively ( figure 3 ) . for the derivative uv spectrophotometric method , methanol and acetonitrile alone and with mixtures of 50 % water were tested as the solvent and methanol was found to be the most suitable solvent by considering the sensitivity , noise level , and resolution . an rp - hplc method has also been developed for the simultaneous determination of esr and drs . in order to improve the resolution of the drugs , methanol - water and acetonitrile - water in different portions were tested as the mobile phase . the best results in terms of obtaining sharp peaks , resolution , and analysis time were obtained using acetonitrile : water ( 70 : 30 , v / v ) . a phenomenex c18 - column , venusil xbp c18 ( agela ) , and a waters symmetry c18 - column were tried to obtain the best separation . the optimized detection wavelengths and flow rate were 279 nm and 1 ml / min , respectively , at room temperature . the average retention time of the esr and drs was approximately 3.54 and 4.55 min , respectively . rsd % of the retention times for both drugs was approximately 2.18 % for 9 independent analyses . a typical chromatogram of drugs in mixture in selected conditions is shown in figure 4 . the linearity range of esr and drs was found as 0.58.0 gml and 0.532 gml , respectively . for the hplc method , the linearity range of esr and drs was found as 0.237.5 gml and 0.082.5 gml , respectively . in both cases , correlation coefficients ( r ) were greater than 0.9967 , indicating good linearity ( table 1 ) . limit of detection ( lod ) and quantification ( loq ) of drugs for proposed methods was calculated with the following equation : lod = 3.3 sa / b and loq = 10 sa / b , where sa is the standard deviation of the intercept and b is the slope of calibration curve . lod and loq values were 0.14 and 0.42 gml for esr , 0.10 , and 0.29 gml for drs , respectively , for first derivative spectrometry method . the lod and loq values were 0.05 and 0.15 gml for esr , 0.02 , and 0.05 gml for drs , respectively , for the hplc method ( table 1 ) . intraday and interday accuracy and precision were validated by solutions of drugs at three different concentrations for both proposed methods . determinations were performed at five replicates within the same day for intraday and on five separate days for interday precision . for intraday and interday precision , the percent relative standard deviation ( rsd % ) values of esr ranged from 0.01 to 0.32 % and 0.45 to 1.07 % , respectively , for the derivative spectroscopy method ( table 2 ) and 0.02 to 1.18 % and 0.08 to 1.03 % , respectively , for the hplc method ( table 2 ) . rsd % values of drs ranged from 1.04 to 1.94 % and 1.17 to 2.84 % , respectively , for spectrometry and 0.69 to 1.90 % and 0.15 to 2.67 % , respectively , for the hplc method . recovery studies were conducted by spiking known amounts of pure compounds solutions at three different concentrations to a known amount of tablet solutions . the results given in table 3 revealed that the percent recovery for esr by derivative spectrophotometry and hplc methods was in the range of 91.75104.62 % and 98.75106.57 % , respectively . the recovery values for drs were 96.40100.00 % and 93.3396.50 % for the derivative spectrophotometric and hplc methods , respectively . the recovery results offer that the method is not affected by the presence of the excipients in the formulation and confirms the high accuracy . the rsd % values of both drugs for both methods were less than 7.72 % ( table 3 ) . to examine the stability of the esr and drs solutions , the compounds in the mixture stored in the refrigerator at + 4c for a month and in the dark for 4 days at room temperature andthe analyses results of these samples were compared with the results of freshly prepared drug solutions and found to be stable under these conditions . the proposed methods were administered for the analysis of the drugs studied in their tablet form , namely , angeliq , which contains 1 mg esr and 2 mg drs per tablet . for the first derivative spectrophotometric method , the mean recovery values were 101 % ( rsd % = 0.79 ) and 99 % ( rsd % = 0.03 ) for esr and drs , respectively ( table 4 ) . for the hplc method , the mean recovery values were 97 % ( rsd % = 0.21 ) and 98 % ( rsd % = 0.36 ) for esr and drs , respectively ( table 4 ) . in this study , a simple , rapid , accurate , and sensitive first derivative spectrophotometric and an rp - hplc method were developed and validated for the simultaneous determination of esr and drs in their tablets for the first time . both methods are cost effective compared to the lc - ms methods . considering the linearity values and lod values of drs , the both proposed methods were more sensitive than reported rp - hplc methods for the assay of the drug alone and in combination with ethynyl estradiol in pharmaceutical preparations . the proposed methods for the determination of esr were found to be more sensitive than some of the published hplc - uv methods . in addition , the lod value of esr for the proposed rp - hplc method was found to be more sensitive than the other reported hplc methods and a spectrophotometric method that has been published very recently . the methods developed can be successfully used in the laboratories of quality control for the routine analysis of both compounds in pure form and pharmaceutical forms without preseparation .\noutput:\n" }, { "from": "agent", "value": "simple , rapid spectrophotometric , and reverse - phase high performance liquid chromatographic methods were developed for the concurrent analysis of 17 - beta - estradiol ( esr ) and drospirenone ( drs ) . the spectrophotometric method was based on the determination of first derivative spectra and determined esr and drs using the zero - crossing technique at 208 and 282 nm , respectively , in methanol . the linear range was 0.532.0 gml1 for drs and 0.58.0 gml1 for est . the limit of detection ( lod ) values were 0.14 gml1 and 0.10 gml1 and limit of quantification ( loq ) values were 0.42 gml1 and 0.29 gml1 for esr and drs , respectively . the chromatographic method was based on the separation of both analytes on a c18 column with a mobile phase containing acetonitrile and water ( 70 : 30 , v / v ) . detection was performed with a uv - photodiode array detector at 279 nm . the linear range was 0.082.5 gml1 for drs and 0.237.5 gml1 for est . lod values were 0.05 gml1 and 0.02 gml1 and loq values were 0.15 gml1 and 0.05 gml1 for esr and drs , respectively . these recommended methods have been applied for the simultaneous determination of esr and drs in their tablets ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: this ca cycle is the result of the coordinated actions of channels in the sarcoplasmic reticulum ( sr ) membrane , which release ca into the cytoplasm during contraction , and the sr calcium pump ( serca ) , which transports ca ions back into the sr to allow muscle relaxation . in the heart , disordered serca expression , function , and regulationare linked to cardiac disease , motivating investigation of serca structure / function mechanisms as a path to new therapeutic interventions . one important aspect of serca function is the large amplitude conformational changes that occur during the transport cycle . in particular , the role of domain dynamics in ion transport has been vividly illustrated by x - ray crystallography of serca . several x - ray structures obtained for different catalytic substates are provided in figure 1a , which shows the serca transmembrane domain ( tm , gray ) and the three cytoplasmic domains : nucleotide - binding ( n , yellow ) , phosphorylation ( p , black ) and actuator ( a , blue ) . these and other structure solutions reveal that translations and rotations of these cytoplasmic domains accompany the transport of ions from the cytoplasmic side to the lumenal side of the sarcoplasmic reticulum membrane . even though many such high - resolution structures are available , there are also likely to be undiscovered states that will continue to resist crystallization because they are short - lived intermediate conformations or because they are structurally dynamic . for example , while there are many crystal structures showing a closed , compact headpiece , there is a paucity of structural information for serca in the open state . it has been suggested that this is because open structures only occur in the ( nonphysiological ) absence of nucleotide . however , our previous fret studies indicate significant population of open headpiece conformations in vitro and in live cardiac muscle cells . thus , we consider it likely that there are other open structures , unsuitable for crystallization , which may be discovered with alternative approaches . investigation of novel states and the structural mechanisms driving transitions between different states has benefitted from computational modeling . molecular dynamics ( md ) studies have revealed possible transition pathways for a large - scale open - to - closed conformational change and predicted novel intermediate states including an e12k conformation that has a very open headpiece architecture . other studies used coarse - grained molecular dynamics ( cgmd ) to investigate e2 to e1 and e1p to e2p transitions , revealing how mutations may alter transition kinetics . for example , cgmd provided a structural mechanism that explained previous biochemistry experiments in which insertions in the m3 linker decreased the rate of the e1p to e2p transition . this observation could be attributed to accumulation of water around the insertion region , increasing the stability of the e1 state . together , the results underscore the value of md simulations for discovering new structures and for investigating the motions of those structures . in many of these studies , attention has justifiably centered on the tm domain where the active sites for ion binding are located . however , tm domain active sites are structurally and functionally coupled to the cytoplasmic domains , so there is also great interest in understanding how the a - , n - , and p - domains move and interact during transport . in the present study , we characterize the dynamics of serca in different structural substates using md simulations starting from x - ray crystal structures determined for serca enzymatic substates e1 - ca ( 1su4 ) , e2 - p ( 1wpg ) , and e1p - adp ( 2zbd ) ( figure 1a ) . these structures were chosen to represent the extremes of the range of serca headpiece conformations from open ( 1su4 ) to closed ( 1wpg , 2zbd ) . the goal of these experiments is to test the hypothesis that serca conformational fluctuations vary according to the catalytic substates of the pump and identify structural mechanisms for the differential dynamics of enzymatic substates . the results of md simulations are compared with our previous study in which we used intramolecular fret between the n - and a - domains as an index of headpiece conformation . those experiments revealed four discrete structural substates of serca expressed in cardiac muscle cells , including several conformations not yet accounted for by published high - resolution structural data . the present md experiments reveal structural ensembles compatible with those fluorescent measurements and provide insight into the structural details of serca domain dynamics . specifically , we report a structural mechanism that could account for our previous observation that serca dynamic disorder decreased with decreasing domain domain separation distance . crystal structures of the serca were obtained from the rcsb protein data bank ( pdb entries 1su4 ,1 wpg and 2zbd ( 11 ) ) ( figure 1 ) . serca structures labeled with fluorescent protein tags were generated using fpmod and were kindly provided by david d. thomas and bengt svensson , university of minnesota . molecular dynamics simulations were performed with the gromacs software package using martini coarse grained force field and domelnedin setup , which allows cytoplasmic domains move freely . the crystal structures were energy minimized in vacuum to eliminate unfavorable interactions , then two - color serca was placed into a palmitoyl - oleoyl - phosphatidyl - choline ( popc ) lipid bilayer . nonbonded interactions were calculated with a cutoff of 12 , on which a shift function was applied , starting at 9 for the lennard - jones potential and at 0 for the electrostatic potential . simulations were run in the npt ensemble with pressure 1 bar and temperature 300 k using berendsen thermostat and barostat . all - atom md ( aamd ) simulations were carried out using the gromacs software package with the charmm 27 force field and tip3p water model . energy minimization was performed on the crystal structures using the steepest descent method for 1000 steps , then each model was embedded into a popc lipid bilayer and solvated in a rectangular water box size with dimensions 130130160 . na and cl ions were added to the solution to neutralize the charge of the system and to produce an ion concentration of 150 mm . the particle mesh ewald method was used to calculate the long - range electrostatic interactions and cutoff of 12 was used for the short - range . van der waals interactions were reduced to zero by switch truncation applied from 8 to 12 . simulations were carried out with an integration time step of 2 fs . to heat the system from 0 k to the target temperature ( 300 k ) andreach the target pressure ( 1 bar ) , the berendesen method was used with relaxation times of 0.1 ps . after 1 ns equilibration , the production run was performed in the npt ensemble using the noseeach independent production run was started with a different set of assigned velocities corresponding to 300 k. the atoms coordinates of the trajectories were saved every 1 ps . we used principal component analysis ( pca ) to extract the essential motions sampled by the md trajectory . the set of principal components is the solution to the eigenvalue problem ( eq 1 ) , in which the second - moment matrix , a , contains the mass - weighted internal atomic displacements . the elements of the matrix , aij , are given by1where mi are the masses . the diagonalization of a yields the eigenvectors , wk , that is , the principal components , and their associated eigenvalues , k . to estimate disorder dynamics of serca domains we performed correlation analysis of the domain orientation . we quantified the orientation of the vector ( where x is n , p , or a ) , which connects the domain hinge point and middle of the domain . we computed the domain disorder function x ( t ) defined as2 in fact , x ( t ) describes how orientation of domain changed relative to initial one . table 1 provides a summary of the type , duration , and starting conditions for the molecular dynamics simulations . to study the differential dynamics of open and closed conformations of the serca cytoplasmic headpiece we performed three or four independent 400 ns all - atom molecular dynamics ( aamd ) simulations of serca for each of three crystal structures , 1su4 , 1wpg , and 2zbd . figure 1b shows root - mean square deviations ( rmsd ) of simulations of open and closed / compact structures of the serca as a function of time . three repeated simulations starting from the open conformation ( 1su4 , three black traces ) showed evidence of structural disorder compared to three repeated simulations of each of the closed / compact structures ( 1wpg , red , and 2zbd , blue ) . residue - by - residue analysis of structural fluctuations showed that the difference in dynamics of open and closed conformational substates of serca was due primarily to high root - mean - square fluctuations ( rmsf ) of the 1su4 n - domain ( figure 1c ) . for all structures , we observed large rmsf values for the cytoplasmic domains a , n , and p and solvent exposed tm bundle loops compared to tm - domain residues , which is in agreement with previous molecular dynamics simulations studies . another group s previous studies quantified serca domain disorder by measuring the wobble cone of a phosphorescent probe . this parameter describes the angles sampled by the probe on a submicrosecond to microsecond time scale , integrating motions that include domain motions and the independent mobility of the phosphorescent probe . here , we obtained analogous information for the nanosecond time scale by way of a correlation analysis of the vectors that connect the hinge point of the domains ( a - domain , residue 128 ; n - domain , residue 360 ; p - domain , residue 328 ) with the domain center of mass . we quantified the disorder of domains over a range of time scales , calculating a wobble cone angle ( ) from 1 ps to 100 ns . small values of reflect static domains and high values represent mobile ( dynamic ) domains . the insert in figure 1d shows a schematic cartoon of the n - domain cone angle . for all domains , the range of angles sampled increases at longer time scales and is presumed to increase further at time scales longer than the 100 ns regime simulated here . correlation functions for the n - domain for different starting conformations revealed increased dynamic disorder of the open conformation of the pump ( 1su4 ) compared to closed structures ( 2zbd , 1wpg ) on time scales greater than 0.1 ns ( figure 1d ) . figure 1e summarizes the average value of sd at 10 ns for all three starting conformations average over three independent runs . consistent with other studies we observed high dynamics for the n - domain , which is significantly more mobile in the open conformation ( 1su4 ) versus closed structures . ( a ) starting structures for aamd simulations , showing the relative positions of three cytoplasmic domains : actuator ( a , blue ) , nucleotide - binding ( n , yellow ) , phosphorylation ( p , black ) , and the transmembrane domain ( tm , gray ) . the open conformation ( 1su4 ) showed higher rmsd values and large fluctuations in rmsd . ( c ) quantification of rmsf of c atoms revealed that the nucleotide - binding ( n ) domain was the most mobile part of serca , with relative structural dynamics 2zbd 1wpg 1su4 . ( d ) angular autocorrelation of the n - domain over a range of time scales . the inset represents angular displacement as a wobble cone originating at the hinge of the domain . ( e ) summary of serca cytoplasmic domain dynamics in the 10 ns time regime . overall , disorder is increased for the open structure ( 1su4 ) , especially in the n - domain . principal component analysis ( pca ) of aamd simulations revealed the major modes of such internal dynamics . overall , the principal components observed here are in agreement with those reported in reference , showing rotational and translational motion of n - and a - domains . figure 2a shows the three largest - contributing principal components ( pcs ) for the open and closed conformations of serca . closed conformations ( figure 2a , 1wpg , 2zbd ) were characterized by macroscopic motions of the cytoplasmic headpiece as a single unit ( pc1 , pc2 , and pc3 ) that represented 65 % of internal displacement . these components were present in the open structure ( figure 2a , 1su4 ) as well , but they were insignificant compared to large motions of the cytoplasmic domains relative to one another ( figure 2 upper left , 1su4 ) . for the open structure , pc1 and pc2 were determined to be a motion of the n - domain with respect to the p - domain , opening and closing the nucleotide - binding cleft ( 67 % of internal displacement ) . pc3 was the relative motion of the n - and a - domains ( 10 % ) . pc4 and pc5 were minor components , twisting of cytoplasmic headpiece ( 6 % ) . this analysis suggested that the fluorescent protein fusion positions selected for our previous study of two - color serca ( n - domain residue # 509 and a - domain residue # 1 ) are ideal sites for quantifying the relative motions of serca cytoplasmic domains by fret . pca analysis also provided a residue - by - residue correlation of serca motions . we compared the covariance matrices of the closed structures with the open state matrix . figure 2b , c represents large amplitude , positively correlated motion ( residues moving in the same direction ) in red . as expected , all three structures showed significant positive self - correlation of the n - domain residues ( 360600 ) due to the large collective motions of these residues . we also observed negative correlation of the n and a domains due to the contrary independent motions of these domains relative to one another . overall motion is reduced for closed conformations , evident as increased null correlation ( white ) . notably , the a - n correlation ( which was negative for the open conformation ) was positive for closed structures , especially 2zbd , indicating that upon headpiece closure these domains become coupled together and move in unison . ( a ) pca revealed large relative motions of serca cytoplasmic domains for the open structure ( 1su4 ) , while close conformations were dominated by concerted motions of the domains as a single unit . ( b ) covariance matrices revealed positively correlated ( red ) and anticorrelated ( blue ) motions of residues ( measured from c ) comparing 1su4 ( upper left ) with 1wpg ( lower right ) . ( c ) covariance analysis , comparing 1su4 ( upper left ) and 2zbd ( lower right ) . overall , 1su4 was the most dynamic , showing paradoxical ( anticorrelated ) motions of the a and n domains . to investigate how serca might undergo a conformational change from open structures ( such as 1su4 ) to compact conformations , we investigated aamd simulation results in greater detail . figure 3a shows the time dependent changes in domain domain separation distance , measured from the centers of mass of the a - and n - domains . the data comprise a total of 10 trajectories : 4 replicates starting with 1su4 ( figure 3a , 3 black and 1 gray ) , and 3 replicates each for 1wpg ( figure 3a , red ) and 2zbd ( figure 3a , blue ) . we observed larger , more variable domain separation distances for 1su4 compared to 1wpg and 2zbd . the latter two exhibited stable , ordered structures , as shown by flat trajectories with little fluctuation in the domain separation distance . thus , the simulations recapitulated previous fret measurements that suggested decreasing disorder as the cytoplasmic headpiece closes . interestingly , one of the 1su4 trajectories showed a progressive closure of the cytoplasmic headpiece over the 400 ns simulation ( figure 3a , gray ) . this trajectory was characterized by a series of plateaus ( figure 3a , # 14 ) , suggesting intermediate transition states . figure 3b shows a histogram of measured domain domain separation values , revealing the expected narrow distribution of short distances for the closed structures ( figure 3b , blue , red ) , and longer , more variable distances for the open conformation , as shown by a wide histogram ( figure 3b , black ) . the histogram of the transition trajectory showed several apparent intermediate conformations visible as multiple discrete peaks ( figure 3b , transition states ) . a detailed analysis of this trajectory revealed that the cytoplasmic headpiece underwent a progressive stepwise transition to a structure that was as tightly closed as the compact structure of 1wpg . the staircase profile of the trajectory is annotated in figure 3a to highlight the plateau phases ( # 14 ) . transitions between these apparent intermediate subconformations were rapid . early in the transition trajectory we noted an n - domain loop ( n5 - 6 ) consisting of residues 426 to 436 that sampled the space between the n - and a - domains ( figure 3c ) . this loop is near other n - domain residues that are important for interacting with mg - atp , such as glu439 . figure 3c shows that at the beginning of the simulation the headpiece was in the open 1su4 configuration , but within 1 ns , loop residues glu 429 and thr 430 ( n - domain ) stretched across the gap to form dynamic h - bonds with the a - domain arg 134 ( figure 3d ) . in addition , glu 429 repeatedly formed h - bonds with lys 135 and ser 136 in the a domain ; the n - domain n5 - 6 loop formed a bridge between the domains ( figure 3e ) . h - bond interactions began to occur in more proximal regions of the loop after 100 ns , contributing to the transition to plateau # 2 . domain contact shifted along the surface of the a - domain , drawing the two domains together and rotating the n - domain about the membrane normal axis . the structure sampled during plateau # 2 was stabilized by interactions between arg 139 and thr 430 . the conformation of plateau # 3 is shown at 235 ns ( figure 3f ) . domain interaction , such as ser 134 , ser 136 , and arg 139 ( a - domain ) with glu 466 , ser 463 , and glu 429 ( n - domain ) . by this time , the bridge loop had rotated significantly away from the cleft and was no longer the only point of interaction between the two domains . in particular , figure 3f shows that thr 430 points away from the domain domain interface . this is the most distal residue at the apex of the n5 - 6 loop and was one of the first residues to initiate domaincorresponding to the fourth plateau , the n - domain / a - domain interface was comparatively stable , and glu 435 of the n - domain bridge loop interacted with other n - domain residues asn 428 and lys 431 . the intradomain h - bonding contributed to the prevailing structure of the n5 - 6 loop . at the end of the 400 ns simulation , the n - domain a - domain interface was still partly open , and the n5 - 6 loop pointed away from the n a interface . interestingly , this final orientation could put the loop in a position to interact with phospholamban bound to the serca regulatory binding site ( figure 3 g , red ) . specifically , the acidic residues ( which were the first to interact with the a domain ) were in a good position to interact with basic residues on the cytoplasmic domain of plb . this hypothetical interaction could help complete the rotation of the n - domain and the closure of the athe plb - serca regulatory complex was recently determined , but structural dynamics prevented the cytoplasmic domain of plb from being resolved . thus , it is unknown how plb ( especially phosphorylated plb ) can induce serca to assume the highly compact serca structure that was observed by single molecule fret ( state iv ) . in live cells , this unique serca structurewas only observed in the presence of ca and phosphorylated plb , suggesting that it represents a disinhibited regulatory complex . it remains to be determined how stabilizing this putative compact intermediate could contribute to improved catalytic efficiency of ca transport.supporting information supplemental movie 1 shows the structure fluctuations of the 1su4 * trajectory that underwent an open - to - closed transition . the trajectory contrasted with the other 1su4 simulations in which the headpiece fluctuated about a broad distribution of structures without departing from the overall open configuration ( figure 3a , black traces ) . overall , saltatory closure of the headpiece was suggestive of discrete conformational substates , some of which were long - lived with 50 ns dwell times ( figure 3a , gray ) . to more clearly show the transitions between each plateau , we performed a morph between representative structures ( supporting information supplemental movie 2 ) , however we emphasize that serca did not follow a prescribed , orderly path from one static state to the next . rather , the structural transitions are highly stochastic , and the enzymatic substates are characterized by considerable structural disorder and degeneracy . a ) fluctuations in the distance between n and a domains revealed the differences in the dynamics of open and closed conformations . one 1su4 trajectory ( 1su4 * , gray ) exhibited an open - to - close conformational transition . ( b ) histograms of n and a domains separation distances show resolved peaks consistent with discrete structures and intermediate transition states . ( c ) the starting structure ( 1su4 ) with a widely open cytoplasmic headpiece . ( d ) at 1 ns , h - bonding stabilized a bridge between the n - domain loop and the a - domain . ( e ) rotation of the n - domain and partial closure of the n - a gap . ( f ) engagement of additional surfaces on the a - and n - domains stabilized a closed conformation . ( g ) after headpiece closure the n5 - 6 loop pointed toward the inhibitory binding cleft ( red ) , where it could interact with plb . the open - to - closed transition trajectory was intriguing and suggestive of a structural mechanism by which headpiece closure could be initiated . we tested the reproducibility of this apparently spontaneous conformational transition by performing repeated simulations beginning just after formation of the first h - bonds between the n - and a - domains ( figure 3d ) . of six repeated simulations with randomized velocities , four maintained the initial h - bonds that stabilized the relative position of the two domains and two spontaneously progressed toward headpiece closure within 40 ns . the results indicate that the structural transition we observed in trajectory 1su4 * is representative and reproducible . the simulations also suggest that the disorder - to - order transition is a key step for initiation of the open - to - closed conformational change . we hypothesized that key loop residues involved in initial h - bonding were important for stabilizing the relative positions of the domains and initiating headpiece closure . to test this , we mutated residues 426 , 429 , and 435 to ala to abolish h - bond interactions . this resulted in destabilization of the headpiece architecture with six simulations of mutated ( aaa ) serca showing high variability and disorder compared to wt ( figure 4a ) . without the loop residues to initiate contact , the a and n domains were separated by a water cushion ( figure 4b ) that was poorly diffusible . for the water model employed herethe diffusion coefficient was 3.20.510 in the cleft vs 4.60.210 cm / s in bulk solution . figure 4c shows how the loop residues pierced this cushion to create a hole in the water layer through which domain domain contact was initiated and expanded ( figure 4d ) . mutation of the loop residues to ala resulted in a rapid loss of domain domain contacts ( figure 4d ) . the effect of mutation of loop residues on the serca headpiece disorder - to - order transition . ( a ) wt serca h - bonds stabilize the plateau # 1 structure compared to the aaa mutant . ( d ) aaa mutation prevents normal domain interactions ( data are mean of six replicates ) . the in vivo significance of the proposed structural mechanism is suggested by a high degree of n5 - 6 loop homology among ca transporters from a range of species , including mammals , amphibians , reptiles , birds , fish , and invertebrates ( table 2 ) . the negatively charged loop residues that interacted with positive a - domain residues in our simulations are particularly well - conserved . some loop residues have already been reported in the literature to be functionally important . for example , n - domain asp426 and a - domain arg134 were previously implicated as being interacting residues from crystallography studies , and we confirmed that these residues interact at latter stages ( plateau # 3 ) of the closure transition ( figure 3a ) . interestingly , mutation of 426 and 134 to ala has been shown to decrease atpase activity by 60 and 35 % , respectively , underscoring the functional importance of interactions between the n5 - 6 loop and the a - domain . the present data suggest a key structural role for other loop residues , particularly those involved in stabilizing plateau # 1 structure ( figure 3a ) during the initiation of domain contact . one interesting residue is thr430 , an important source of early h - bond interactions with arg134 during the disorder - to - order transition of plateau # 1 for the rabbit serca1a simulated here . this polar residue is more commonly an ala in most species and isoforms ( table 2 ) , but we speculate that thr may confer a gain of function in the rabbit and dog serca1a isoforms . consistent with this , inesi and colleagues have shown that the rabbit serca1a cycles with 20 % faster kinetics compared to the chicken , which lacks thr430 . we did not observe similarities between the serca n5 - 6 loop and other p - type pumps such as pmca , nka , copper transporter , or h / k - atpases . some of the simulated conformations approximated existing serca crystal structures , as quantified by alignment of the cytoplasmic domains of these structures to conformations sampled during the simulation . while the structures of plateau # 1 still mostly closely resembled the starting structure ( 1su4 ) , after the transition to plateau # 2the conformation became more similar to e1 - mg ( 3w5b ) with a difference of 5 rmsd . for comparison , the rmsd of the trajectory versus e2 states ( e.g. , 1wpg , 1iwo ) was 15 . the similarity of the simulated structures to 3w5b was maintained at 5 through plateau # 3 . the structures of plateau # 4 were halfway between 3w5b and e1 - atp structures ( e.g. , 1t5 t , 1vfp , 2zbd ) . none of the x - ray crystal structures have captured the dynamic hydrogen bonding of the n5 - 6 loop to the a - domain that was observed in the early stages of the aamd simulation ( figure 4d , e ) . the range of structures sampled during aamd simulations is represented in ( figure 5 ) . the decrease in disorder with cytoplasmic headpiece closure was evident from a comparison of these structure families . there was tighter backbone superimposition as serca progresses from open ( left ) to closed ( right ) conformations .1 su4 showed the greatest diversity of structures ( figure 5a ) , consistent with increased disorder for this open conformation . a family of structures representing the transitional substate of plateau # 2 ( figure 3a ) is shown in figure 5b , and represents a partially closed conformation that is intermediate between open 1su4 ( figure 3a ) and closed 1wpg ( figure 3c ) . this putative transition state ( figure 3b , gray ) showed a level of disorder that was intermediate between the open ( 1su4 , black ) and closed ( 1wpg , red ) conformations . the tightly closed conformation of 2zbd ( figure 5d ) yielded an orderly array of similar compact structures . this high degree of structural order may make these conformations easier to crystallize , and most x - ray structures have a compact cytoplasmic headpiece . only one has been solved for the open conformation and intermediate structures ( figure 5b ) have not been observed yet . ( a ) a representative sample of structures assumed for the open conformation ( 1su4 ) , excluding the transition trajectory . ( e ) two - color serca , a construct that reports serca structural dynamics with fret changes . ( f ) cgmd revealed that the distance between the n - domain and gfp decreased early in the simulation ( at arrow ) , consistent with docking of the fluorescent protein to the domain to which it was attached . ( g ) there was a positive correlation between the separation of fluorescent proteins and the distance between domains . filled triangles represent cgmd simulations started from crystal structures and open squares show results from harmonically constrained simulations . horizontal lines represent discrete conformational substates previously detected as resolved populations in a fret efficiency histogram . the present observations may also be compared to our previous intramolecular fret measurements . one caveat for such an analysis is that the two techniques explore time regimes differing by 23 orders of magnitude . however , some substates were stable for the entire 400 ns simulation ( figure 3a ) and might still be represented on the s - ms time scale of the fluorescence measurements . to determine howgfp - tagrfp fret distances would be changed by structural dynamics that alter n - a distance , we performed cgmd simulations of two - color serca ( figure 5e ) . cgmd experiments recapitulated observations from aamd and fret experiments , showing increased dynamics of open structures compared to compact conformations . in addition , we analyzed the distances between centers of mass of gfp and the n - domain , tagrfp and the a - domain , the a - and n - domains , and between the fluorescent probes tagrfp and gfp ( fret distance ) . for all starting crystal structures ( 1su4 , 1wpg , and 2zbd ) , the distance between the fluorescent protein and the domain to which it was attached decreased rapidly ( figure 5f , at arrow ) as the fluorescent protein settled onto and stably interacted with the surface of the target domain . the final gfp - tagrfp separation and interdomain distances depended on the starting conformation of the serca pump . a comparison of stabilized structures revealed a positive relationship between fluorescent protein separation and domain domain distance ( figure 5 g ) . because unconstrained cgmd simulations did not fully sample the entire range of possible distances , we used the open structure ( 1su4 ) as a starting point and generated 11 new intermediate structures . these intermediate conformations were harmonically restrained to represent domain separation distances from 30 to 40 ( in 1 increments ) . cgmd simulations of these new starting structures populated the gap between open and closed serca structures in the plot of fluorescent protein separation vs domain separation ( figure 5 g , open squares ) . overall , we conclude that the fluorescent protein tags are closely associated with the target domains and fret is a good index of the overall headpiece conformation . the previously observed fret substates are represented in figure 5 g as horizontal lines ( i orange , 94 ; ii blue , 77 ; iii red , 70 ; iv green , 65 ) . the relationship of figure 5 g is useful as a guide for comparison of the present simulations with previous fret experiments . for example , we regard domain separation distances of the structures sampled by 1su4 as comparable to fret state i. specifically , the 1su4 aamd simulation ( figure 3a , black ) yielded domain domain distances of 3560 , which corresponds to fluorescent protein separation distances greater than 90 according to the relationship in figure 5 g . this prediction is compatible with the broad fret distribution and low fret efficiency observed for state i. the fluorescent protein separation distance of that state was too long to measure with the cer - yfp fret pair but changing to the gfp - tagrfp pair yielded a state i distribution center value of 5 % fret . this corresponds to a probe separation distance of 94 for state i , which compares favorably with the aamd prediction of distances greater than 90 for the open 1su4 structure . the decreased domain domain separation of 33 observed for 2zbd ( figure 3a ) would be expected to yield fluorescent protein separations of 75 according to the relationship in figure 5 g . this is in the range of distances calculated for fret states ii and iii , which were 78 and 69 for the cer - yfp pair and 77 and 70 for the gfp - tagrfp pair . figure 5 g indicates fluorescent protein separation distances of 6265 should arise from domain separation distances of less than 30 , which were not detected in aamd experiments ( figure 3a ) . this is not unexpected , as this very high fret compact state is only observed when serca is bound to phosphorylated plb , and plb was not present in the simulations . overall , the simulations complement the fret measurements and support hypotheses generated from those previous experiments . specifically , the simulations confirmed that serca structural disorder decreases as the headpiece closes , as shown by analysis of structure fluctuations ( figure 1 ) , domain separation distance ( figure 3a , b ) , principal component analysis ( figure 2 ) , and correlation analysis of domain angular disorder ( figure 1d ) . we attribute this disorder - to - order transition to interactions between acidic residues of the n - domain n5 - 6 loop and basic residues on the a - domain ( figure 3 ) . mutation of several key residues ( asp426 , glu429 , and glu435 ) to ala prevented these interactions , destabilizing the relative positions of the n - and a - domains . the simulations suggest that these h - bonds are formed early in the open - to - closed transition and help overcome the energy barrier of a poorly diffusible cushion of water to facilitate the closure of the cytoplasmic headpiece during the ca transport cycle . the high degree of conservations of residues implicated in serca headpiece closure suggests that this putative mechanism may be a general feature of the transport cycle for a wide range of ca transporters .\noutput:\n" }, { "from": "agent", "value": "to characterize the conformational dynamics of sarcoplasmic reticulum ( sr ) calcium pump ( serca ) we performed molecular dynamics simulations beginning with several different high - resolution structures . we quantified differences in structural disorder and dynamics for an open conformation of serca versus closed structures and observed that dynamic motions of serca cytoplasmic domains decreased with decreasing domain domain separation distance . the results are useful for interpretation of recent intramolecular frster resonance energy transfer ( fret ) distance measurements obtained for serca fused to fluorescent protein tags . those previous physical measurements revealed several discrete structural substates and suggested open conformations of serca are more dynamic than compact conformations . the present simulations support this hypothesis and provide additional details of serca molecular mechanisms . specifically , all - atoms simulations revealed large - scale translational and rotational motions of the serca n - domain relative to the a - and p - domains during the transition from an open to a closed headpiece conformation over the course of a 400 ns trajectory . the open - to - closed structural transition was accompanied by a disorder - to - order transition mediated by an initial interaction of an n - domain loop ( n5 - 6 , residues 426436 ) with residues 133139 of the a - domain . mutation of three negatively charged n - domain loop residues abolished the disorder - to - order transition and prevented the initial domain domain interaction and subsequent closure of the cytoplasmic headpiece . coarse - grained molecular dynamics simulations were in harmony with all - atoms simulations and physical measurements and revealed a close communication between fluorescent protein tags and the domain to which they were fused . the data indicate that previous intramolecular fret distance measurements report serca structure changes with high fidelity and suggest a structural mechanism that facilitates the closure of the serca cytoplasmic headpiece ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: racemic bupivacaine ( rbup ) can cause life - threatening cardiac complications , particularly when given intravascularly by accident . levobupivacaine ( lbup ) was developed as a long acting local anesthetic with a potentially reduced toxicity compared with rbup . lbup is considered to be safer than rbup because it has a higher cardiotoxicity threshold and lower risk of cvc ( 1 ) . however , by the direct intracoronary infusions in conscious sheep , both rbup and lbup caused similar fatal cardiotoxicity ( 2 ) . the incidence of electrical stimulation - induced ventricular tachycardia and fibrillation with lbup was similar to that with rbup ( 3 ) . a recent report showed that a relatively small amount of lbup ( approximately 1.6 mg / kg ) could lead to cvc when infused into the systemic circulation in an anesthetized human ( 4 ) . furthermore , regarding the successful resuscitation with a conventional treatment , the lbup - induced cvc failed to show significant advantage over the rbup - induced cvc ( 5 , 6 ) . the lbup - induced cvc may be different in the degree of not only cardiac depression but also vascular reactivity from the rbup - induced cvc , as cvc is caused by cardiac depression in association with vascular collapse . in spite of less cardiac depression , the vascular reactivity may be more compromised by lbup , thereby the resuscitation from the cvc caused by lbup may be as difficult as that by rbup in some studies ( 5 , 6 ) . the resuscitation from rbup - induced cvc with conventional treatment is known to be difficult , so many modalities have been applied for better results .8 ) proposed the feasibility of insulin for the resuscitation from the rbup - induced cvc . considering the channel effect ( 9 ) and cardiac supportive action of insulin ( 10 ) , it can be assumed that insulin may work on the lbup - induced cvc . we hypothesized that insulin may be effective in resuscitating the cvc by either bupivacaine , and that there may be a different pattern of recovery between the two bupivacaines . the possible difference in the cardiac depression and vasoactivity may be augmented when insulin , which has vasodilatory activity in addition to positive inotropic action ( 11 ) , is used as a resuscitative agent . this study was performed to compare the insulin - mediated recovery from the lbup - induced cvc with that from the rbup - induced cvc , and to assess the feasibility of insulin resuscitation for the lbup - induced cvc . the study was approved by the committee of animal care and use of our institute . enrolled were fourteen male mongrel dogs weighing between 19 and 32 kg . they were randomly assigned to two groups ( n = 7 for each ) ; the rbup and lbup group . anesthesia was induced using thiopental sodium ( 10 mg / kg ) and maintained by continuous sodium pentobarbital infusion ( 5 mg / kg / hr ) and vecuronium injection ( 0.2 mg / kg initially and 0.02 mg / kg at 30 - min intervals ) . additional volume support with normal saline was initiated from 2 to 8 ml / kg in response to signs of hypovolemia during the stabilization period . a fluid infusion of 2 ml / kg / hr was maintained to account for insensible losses throughout experiments . body temperature was kept at 37 - 38 and sodium bicarbonate was administered ( 2 - 4 meq / kg / hr ) to control the acid - base balance ( ph 7.35 - 7.45 ) . both femoral arterial catheters were cannulated to monitor arterial pressure continuously and to collect blood samples . a swan - ganz catheter ( opticath , p7110 - eh , abbott , u.s.a . ) was introduced via the external jugular vein to measure central venous pressure ( cvp ) and cardiac output ( co ) . after a 30 - min stabilization period , rbup or lbup infusion was started at a rate of 0.5 mg / kg / min ( 0.5 % mixture , both drugs ) until the mean arterial pressure ( map ) reached 40 mmhg , which was defined as the time of cvc as we have found that no dogs in two groups could survive spontaneously at that point in our preliminary study using three dogs in each group . at cvc , rbup or lbup infusionwas stopped and 2 u / kg of regular insulin ( novolin r , novo nordisk , denmark ) was injected via a central venous catheter followed by the infusion of d50w ( 2 ml / kg for 30 min ) and potassium ( 1 - 2 mm / kg / hr ) . the criterion for successful resuscitation was as follows ; 90 % of initial map should be achieved by 30 min following cardiovascular collapse and be maintained at that level for a minimum of 30 min . map and heart rate were continuously monitored and recorded at 1 - min intervals using a hp component monitoring system ( hewlett - packard model 54s , andover , ma ) . co was recorded as a mean of two consecutive measurements every 5 - min throughout the experiment using the thermodilution technique . systemic vascular resistance ( svr ) was calculated using the standard formula ( svr = 80 [ map - cvp ] / co ) . ecg analysis was performed every 5 - min using a resting ecg analysis system ( mac8 , marquette , u.s.a . ) . arterial blood samples were collected to determine immediate blood gas , electrolytes , and glucose levels every 10 - min through the experiment . blood samples were centrifuged at 2,500 rpm for 15 min to determine total plasma drug concentrations by high performance liquid chromatography using an ultraviolet detector operation at a wavelength of 204 nm with a limit of sensitivity of 4 ng / ml . data were expressed as meansd . the independent samples t - test and the mann - whitney u - test were used for analysis of between - group differences . recovery phase values were compared to the baseline values or to cvc values using the wilcoxon signed rank test and the sign test with dunnette or tukey post hoc testing . all statistical analyses were performed using spss software ( version 10.09 ) , and p 0.05 was considered significant . there were no differences in weight , time to cvc , drug dose required for cvc , and total plasma drug concentration at cvc between the two groups ( table 1 ) . cvp increased continuously until cvc but was not different between two groups ( 52 mmhg at baseline and 112 mmhg at cvc ) . the infusion of bupivacaines decreased co continuously with the lowest value at cvc in both groups . co was higher in the lbup group than in the rbup group at cvc ( p 0.05 ) . calculated svrs increased at cvc in both groups but the svr was significantly lower in the lbup group than in the rbup group ( p 0.05 ) ( fig . , all dogs in both groups were successfully resuscitated with restored baseline blood pressures , but time spent under 40 mmhg during resuscitation was significantly longer in the lbup group ( p 0.05 ) . map declined further in both groups for minutes and then restored 40 mmhg at 3.40.5 min after cvc in the rbup group and at 6.11.2 min in the lbup group ( table 1 ) . the co declined in the rbup group in excess of that observed in the lbup group , and the co remained lower in the rbup group at each measured time interval . the svr was higher in the rbup group from cvc for a period of 20 min , and then both groups recovered the baseline svr 40 min after insulin injection ( fig . in addition to arrhythmias , which manifested as sinus arrhythmia or 1st degree av block in the lbup group and premature ventricular complex or a supraventricular beat in the rbup group immediately prior to cvc , infusion of bupivacaines produced prolongations of pr and qrs intervals , which were less in the lbup group . the restoration of ecg parametric values during recovery was only seen in the qrs interval in both groups ( fig . blood sample analyses , which included acid - base balance ( ph 7.35 - 7.41 ) , plasma potassium ( 3.7 - 4.4 mm ) , and blood glucose ( 99 - 108 mg / dl ) , were within physiologic ranges throughout the experiment , and between - group differences were not observed . these concentrations reduced abruptly after insulin injection ( at 5 min after insulin injection , 12.21.6 mcg / ml in the lbup group , and 7.91.2 mcg / ml in the rbup group ) and continued to decrease until the end of the experiment . management of local anesthetic - induced cvc is aimed at correcting contractile dysfunction of the heart and arrhythmia . when some confounding factors such as hypoxia , hypercarbia , acidemia , and hyperkalemia were present , however , we could not determine the effect of arrhythmia on cvc in this study because arrhythmia and ecg parametric changes induced by two bupivacaines did not progress towards hemodynamic instability when eliminating confounding factors mentioned above . liu et al . noticed that ' pump failure ' was the cause of death in the rbup - treated anesthetized dogs ( 14 ) . we speculate that the primary cause of cvcs induced by two bupivacaines may be hypotension from diminished contractilities rather than arrhythmias in anesthetized dogs . most studies evaluating resuscitative modalities were performed using rbup , whereas only a few studies used lbup because lbup has been considered safer than rbup . there is indirect evidence from binding kinetics to suggest that recovery from cardiotoxicity is faster with lbup than with rbup in the guinea - pig heart ( 15 ) . moreover , following the intravenous infusion of lbup or rbup in conscious sheeps , arrhythmias due to lbup returned to sinus rhythm more readily than those due to rbup ( 16 ) . however , the parametric changes of ecg were not outstandingly different from each other , and the cvc induced by lbup was as profound as that by rbup in our study . the potential advantage of lbup over rbup was not observed in a recent study by groban et al . in anesthetized dogs ( 5 ) . after infusion of local anesthetics to the point of cvc , hypotension and arrhythmias were treated with epinephrine , open - chest massage , and advanced cardiac life support protocol , respectively . they concluded that , after rbup or lbup infusion , resuscitation is not always successful and co - administration of epinephrine may lead to severe ventricular arrhythmias . the cvc by lbup seems to require an intensive treatment such as like the cvc caused by rbup . animal studies have shown that resuscitation using sympathomimetics , particularly norepinephrine and epinephrine , improves outcome in rbup - induced asystole ( 17 ) . however , epinephrine may exacerbate arrhythmias associated with local anesthetic overdose without improving co ( 18 ) . phosphodiesterase inhibitors having both positive inotropic and vasodilatory actions are expected to improve co. however , they do not necessarily support blood pressure , and are associated with a significant incidence of ventricular arrhythmias ( 19 ) . cho et al . reported that , after the infusion of rbup in dogs , treatment with a combination of insulin and glucose facilitated recovery of blood pressure , cardiac output , and ecg parameters ( 7 ) . they supposed that intracellular k transport by insulin counteracts rbup inhibition of transient outward current improving rates of myocardial repolarization . they also proposed that insulin might have an effect on calcium homeostasis and sodium channel dynamics , and that catecholamine release might account for the benefit of insulin resuscitation . weinberg and vadeboncouer proposed the energy - related mechanism of insulin during resuscitation stating that insulin 's cardiac supportive effect is due to promoted use of fatty acid as a metabolic source by the ischemic heart ( 20 ) . we postulated that insulin might show such a favorable result in resuscitation from the lbup - induced cvc as in the rbup - induced cvc , if the same mechanism worked when the heart remained in a state of extreme depression . insulin seems to be effective for the resuscitation from the lbup - induced cvc but with substantial delays . in dogs , increases in plasma insulin levels to high physiological concentrations did not increase blood pressure because increases in cardiac output were offset by decreases in vascular resistance ( 21 ) . similarly , in humans , short - term insulin infusion failed to increase arterial pressure possibly by the same mechanism ( 22 ) . in this study , the vasodilatory effect was also seen following administration of insulin , but a discrepancy existed between two groups ; in spite of higher cardiac output , the restoration of map in the lbup group was more protracted than that in the rbup group . we infer that lbup is less cardiac depressive than rbup , but vascular reactivity to compensate the cardiac depression may be more compromised in the presence of lbup . the unfavorable results from previous reports on the resuscitation from the lbup - induced cvc might have been due to the fact that lbup has a relatively more vasodilatory property than rbup and the vasoactivity plays a role in the cvc induced by lbup . in this study , the discrepancy in immediate restoration of blood pressure seems to be due to the difference in vascular reactivity between the two bupivacaines , which was combined by the systemic vasodilatory effect of a large bolus of insulin . shaffner et al . demonstrated the importance of early institution of cardiopulmonary resuscitation because a delay beyond 6 min markedly impairs the ability to generate viable levels of cerebral blood flow in dogs ( 23 ) . furthermore , even at cerebral perfusion pressure of 35 mmhg after 6 mins of cvc , cerebral metabolic recovery is incomplete and inadequate to restore full reperfusion . the perfusion pressure and time , less than 40 mmhg for 6 min during the early resuscitation period in the lbup group , is comparable with their results , emphasizing the risk of recovery lag . insulin may be a good choice in managing the rbup - induced cvc because the severely depressed heart generally responds negatively to increased afterload and insulin may facilitate the recovery by lowering the afterload . however , based on our findings , the management strategy of the lbup - induced cvc may differ from that of the rbup - induced cvc . insulin can be effectively used for treating the lbup - induced cvc , but insulin or any inotropes with a vasodilatory activity may need adjunctive therapy to abolish the hypotensive recovery lag during the immediate resuscitation period because of lowered svr . in conclusion , a single injection of insulin can resuscitate cvcs induced by lbup or rbup in anesthetized dogs , but the innate vasodilatory property of insulin in combination with the less increased svr delays the restoration of blood pressure during the immediate resuscitation period in the lbup - induced cvc .\noutput:\n" }, { "from": "agent", "value": "although levobupivacaine ( lbup ) is less cardiotoxic than racemic bupivacaine ( rbup ) , the resuscitation from the lbup - induced cardiovascular collapse ( cvc ) has not been easy as expected . following the recent reports that proposed the resuscitative action of insulin for the rbup - induced cvc , a controlled trial was performed to assess the feasibility of insulin for the lbup - induced cvc . fourteen dogs were randomly allocated into two groups : the rbup and lbup groups . each group received continuous intravenous infusions of rbup or lbup until the mean arterial pressure ( map ) reached 40 mmhg . then , an intravenous bolus of insulin ( 2 u / kg ) was administered . both groups were successfully resuscitated . at cvc , a decrease of cardiac output and an increase of systemic vascular resistance were observed but to a lesser degree in the lbup group ( p < 0.05 ) . after insulin injection , the map further declined to under 40 mmhg for several minutes , which was more protracted in the lbup group ( p < 0.05 ) . the cvcs induced by lbup or rbup in anesthetized dogs could be successfully resuscitated by insulin . compared with rbup , however , the less degree of vasoconstriction by lbup and the innate vasodilatory property of insulin yielded a delayed increment of map during the immediate resuscitation period in the lbup - induced cvc ." } ]

[ { "from": "human", "value": "***task***\nthe task is to summarize an input biomedical literature in six sentences\n\n***input***\nthe input is a biomedical literature\n\n***output***\nthe output is the summary of an input biomedical literature in six sentences\n\n***documentation***\n\n***examples***\n\ninput: dental caries is a problem that is commonly found in the oral cavity , especially in children . the united states surgeon general 's publication in may 2000 described that dental caries is a chronic disease in childhood . based on the basic health research ( riskesdas ) in 2007 released by the ministry of health , 76 % of children in east java experienced dental caries , whereas in the department of health ( dinkes ) of surabaya , 4359 students among 61,214 students have oral cavities . even though the prevention of dental caries has been donethere are three main factors that cause dental caries , carbohydrate diet ( especially sucrose ) , streptococcus mutans infection , and specific response from the host ( innate immunity ) . innate immunity in the oral cavity is the part of immune system that serves as a front - line defense against pathogens . one of the innate immunities that has an important contribution to keep the body balance is antimicrobial peptides ( amps ) . amp that was first identified in oral cavity epithelium is beta defensins ( bds ) . these peptides have a wide range of antimicrobial activity capable of against gram - positive and gram - negative bacteria as well as against fungi and viruses . one of the caries prevention approaches that has been focused on recently is probiotics consumption . according to the who , probiotics are living microorganisms which will give benefits for health when consumed in sufficient amount . probiotics are commensal bacteria , and it is an excellent inducer for bd - 2 in oral cavity epithelial cells . the aims of this research were to determine the effects of lactobacillus reuteri probiotics induction on bd - 2 level on saliva and its expression in parotid gland epithelial cells to reduce s. mutans as the cause of dental caries . ethical clearance of this research was obtained from the commission of ethical feasibility of health research , faculty of dentistry , universitas airlangga . twenty - four male white rats ( rattus norvegicus wistar strain ) were divided into four groups : negative control group , positive control group , treatment group 1 ( t1 ) , and treatment group 2 ( t2 ) . negative control group was not induced either with s. mutans or l. reuteri and positive control group was induced with s. mutans for 14 days . t1 was induced with l. reuteri for 14 days and s. mutans for 7 days , whereas t2 was induced with s. mutans and l. reuteri simultaneously for 14 days . l. reuteri concentration that has been used as inducer was 410 colony - forming unit ( cfu ) / ml while the concentration of s. mutans was 10 cfu / ml . on the 15 day , rats ' saliva production was stimulated by the administration of 1 cc of ketamine hcl ( 100 mg / cc ) and 1 cc of diazepam ( sutezolid ) ( 5 mg / cc ) that were injected intramuscularly through the thigh . saliva was taken with micropipette after 23 of stimulation and then placed into eppendorf column for about 100 l . centrifugation was done at 6000 rpm for 10 min at 40c , and supernatants were collected with micropipette and then stored at 80c800c of temperature for elisa preparation . then , 20 l of saliva samples were added with 80 l blocking buffer ( 0.20 % triton x-100 and 5 % bsa ) , put into microplate polycarbonate previously been coated with ab capturing of anti bd - 2 rat monoclonal antibody ( santa - cruz ) , and then incubated at 4c for 24 h. after that , it was washed three times with wash solution ( 0.15 m nacl + 0.05 % triton x-100 + 0.02 g nan3 in 1 l of distilled water ) . next , it was added with ab detection ( secondary ab ) labeled with biotin and incubated at room temperature for 2 h. it was then washed three times with wash solution . afterward , each well was added with 100 l of ab detection ( anti - bd - 2 ) labeled with horseradish peroxidase and incubated at room temperature for 1 h. it was then washed three times with wash solution . next , it was added with 50 l of tetramethylbenzidine substrate , then incubated at room temperature for 40 min , and stopped by adding 1 n h2 so4 . the results of optical density were read by using microplate reader ( bio - rad model 680 ) at 450 nm wavelength . , armonk , new york , usa ) test was conducted to determine the differences between bd - 2 saliva level and bd - 2 expression in parotid gland epithelial cells among the groups . l. reuteri prodentis starter contained in tablet x ( dsm 17938 + atcc pta 5289 ) was cultured in brain heart infusion ( bhi ) broth and then incubated for 24 h at 37c anaerobically in the gas - generating kit ( oxoid ) . bacteria were then cultured into mrs medium agar ( deman - rogosa - sharpe ; merck gmbh , darmstadt , germany ) by streak method and incubated for 224 h at 37c . bacterial single - cell colony was taken and reincubated into bhi medium for 24 h at 37c to obtain od = 10 cfu / ml ( = 625 ) nm . bacterial colony was taken with inoculating loop , cultured into bhi broth , and then incubated for 24 h at 37c . the cultured bacteria were streaked into blood agar medium and incubated for 24 h at 37c . bacterial single - cell colony was taken and reincubated into bhi medium for 24 h at 37c to obtain od = 10 cfu / ml ( = 625 ) nm . observation of bd - 2 expression using immunohistochemistry and immunohistochemical staining was done based on previous research . ethical clearance of this research was obtained from the commission of ethical feasibility of health research , faculty of dentistry , universitas airlangga . twenty - four male white rats ( rattus norvegicus wistar strain ) were divided into four groups : negative control group , positive control group , treatment group 1 ( t1 ) , and treatment group 2 ( t2 ) . negative control group was not induced either with s. mutans or l. reuteri and positive control group was induced with s. mutans for 14 days . t1 was induced with l. reuteri for 14 days and s. mutans for 7 days , whereas t2 was induced with s. mutans and l. reuteri simultaneously for 14 days . l. reuteri concentration that has been used as inducer was 410 colony - forming unit ( cfu ) / ml while the concentration of s. mutans was 10 cfu / ml . on the 15 day , rats ' saliva production was stimulated by the administration of 1 cc of ketamine hcl ( 100 mg / cc ) and 1 cc of diazepam ( sutezolid ) ( 5 mg / cc ) that were injected intramuscularly through the thigh . saliva was taken with micropipette after 23 of stimulation and then placed into eppendorf column for about 100 l . centrifugation was done at 6000 rpm for 10 min at 40c , and supernatants were collected with micropipette and then stored at 80c800c of temperature for elisa preparation . then , 20 l of saliva samples were added with 80 l blocking buffer ( 0.20 % triton x-100 and 5 % bsa ) , put into microplate polycarbonate previously been coated with ab capturing of anti bd - 2 rat monoclonal antibody ( santa - cruz ) , and then incubated at 4c for 24 h. after that , it was washed three times with wash solution ( 0.15 m nacl + 0.05 % triton x-100 + 0.02 g nan3 in 1 l of distilled water ) . next , it was added with ab detection ( secondary ab ) labeled with biotin and incubated at room temperature for 2 h. it was then washed three times with wash solution . afterward , each well was added with 100 l of ab detection ( anti - bd - 2 ) labeled with horseradish peroxidase and incubated at room temperature for 1 h. it was then washed three times with wash solution . next , it was added with 50 l of tetramethylbenzidine substrate , then incubated at room temperature for 40 min , and stopped by adding 1 n h2 so4 . the results of optical density were read by using microplate reader ( bio - rad model 680 ) at 450 nm wavelength . , armonk , new york , usa ) test was conducted to determine the differences between bd - 2 saliva level and bd - 2 expression in parotid gland epithelial cells among the groups . l. reuteri prodentis starter contained in tablet x ( dsm 17938 + atcc pta 5289 ) was cultured in brain heart infusion ( bhi ) broth and then incubated for 24 h at 37c anaerobically in the gas - generating kit ( oxoid ) . bacteria were then cultured into mrs medium agar ( deman - rogosa - sharpe ; merck gmbh , darmstadt , germany ) by streak method and incubated for 224 h at 37c . bacterial single - cell colony was taken and reincubated into bhi medium for 24 h at 37c to obtain od = 10 cfu / ml ( = 625 ) nm . bacterial colony was taken with inoculating loop , cultured into bhi broth , and then incubated for 24 h at 37c . the cultured bacteria were streaked into blood agar medium and incubated for 24 h at 37c . bacterial single - cell colony was taken and reincubated into bhi medium for 24 h at 37c to obtain od = 10 cfu / ml ( = 625 ) nm . observation of bd - 2 expression using immunohistochemistry and immunohistochemical staining was done based on previous research . elisa test was conducted to determine the levels of bd - 2 in saliva after l. reuteri probiotics induction [ table 1 ] . the levels of bd - 2 in the wistar rats saliva among the treatment groups are significantly different ( p = 0.00 ) . bd - 2 level in saliva of positive control group ( induced by s. mutans ) decreased compared to negative control group ( 11.149.50 ) . otherwise , bd - 2 level in the saliva of the second group ( t2 ) ( induced with l. reuteri and s. mutans for 14 days ) increased compared to t1 ( 12.5314.96 ) [ figure 1 ] . beta defensin - 2 levels in saliva of wistar rats in each treatment group mean values and standard deviations of beta defensin - 2 levels in the saliva of wistar rats after being induced with lactobacillus reuteri probiotics in each treatment group the examination was conducted through immunohistochemistry method . the distribution of bd -2-expressing cells in parotid gland cells in each group after l. reuteri probiotics induction is shown in table 2 . beta defensin - 2 expression in parotid gland epithelial cells bd - 2 expression in parotid gland epithelial cells was significantly different among the treatment groups ( p = 0.001 ) . average bd - 2 expression of negative control group decreased compared to positive control group ( 10.005.60 ) whereas this expression in t2 increased when compared to t1 ( 24.4333.71 ) [ figure 1 ] . elisa test was conducted to determine the levels of bd - 2 in saliva after l. reuteri probiotics induction [ table 1 ] . the levels of bd - 2 in the wistar rats saliva among the treatment groups are significantly different ( p = 0.00 ) . bd - 2 level in saliva of positive control group ( induced by s. mutans ) decreased compared to negative control group ( 11.149.50 ) . otherwise , bd - 2 level in the saliva of the second group ( t2 ) ( induced with l. reuteri and s. mutans for 14 days ) increased compared to t1 ( 12.5314.96 ) [ figure 1 ] . beta defensin - 2 levels in saliva of wistar rats in each treatment group mean values and standard deviations of beta defensin - 2 levels in the saliva of wistar rats after being induced with lactobacillus reuteri probiotics in each treatment groupthe distribution of bd -2-expressing cells in parotid gland cells in each group after l. reuteri probiotics induction is shown in table 2 . beta defensin - 2 expression in parotid gland epithelial cells bd - 2 expression in parotid gland epithelial cells was significantly different among the treatment groups ( p = 0.001 ) . average bd - 2 expression of negative control group decreased compared to positive control group ( 10.005.60 ) whereas this expression in t2 increased when compared to t1 ( 24.4333.71 ) [ figure 1 ] . bds play an important role in the oral cavity ; they are the first defense against bacterial infection . they can be detected in salivary glands , gingival , tongue , and buccal mucosa . expressions of bd - 2 and bd - 3 in oral mucosal epithelial cells are influenced by the existence of bacterial components or inflammatory mediators . two main species of bacteria that cause dental caries are s. mutans and streptococcus sobrinus , which are sensitive to bd - 2 . bds expression in salivary glands is a defense mechanism in the oral cavity against infection . bd - 2 is a potent antimicrobial peptide effective against a broad spectrum of bacteria , including gram positive bacteria , gram negative bacteria and fungi . s. mutans , lactobacillus acidophilus , actinobacillus actinomycetemcomitans , and porphyromonas gingivalis are bacteria sensitive to bd - 2 and are the members of periodontal bacteria . the average concentration of defensins in epithelial cells reached 10100 g / ml . peptides ' distribution was not equal , so the local concentrations become higher . table 1 shows that the lowest concentration of bd - 2 saliva was in the positive control group . the average bd - 2 level examined with elisa of the positive control group was 9.50 g / ml . this is the lowest concentration needed for activation . this is the lowest concentration needed for activaton , because defensin will be active on 1 - 10 g / ml . almost all bds in the oral cavity are expressed by keratinocytes inside the mouth and ductal cells of salivary glands . it supports this study results as shown in table 2 and figure 2 which indicate that the highest expression of bd - 2 occurred in group 2 . the highest levels of bd - 2 also occurred in group 2 [ table 1 and figure 1 ] . the mean and standard deviations of number of cells of beta defensin - 2 expression in the epithelial parotid glands after each group is being induced by lactobacillus reuteri probiotics this study proved that l. reuteri administration can increase bd - 2 expression in epithelial parotid gland [ table 2 and figure 2 ] . parotid gland epithelial cells protect the host not only by providing a physical barrier but also through innate immune responses in the form of antimicrobial peptides . table 2 and figure 2 show that the number of bd - 2 expressions in positive control groups is the lowest compared to the other groups . it can be explained that s. mutans was not able to induce bd - 2 expression in parotid gland epithelial cells . the research conducted by schlee et al . showed that escherichia coli nissle 1917 strain can induce bd - 2 expression , while the other forty e. coli isolates can not induce it . isolation and purification results of flagellin protein in e. coli nissle 1917 were able to induce bd - 2 expressions , while flagellin - deficient mutants of these bacteria were not able to induce defensins . flagellin is an mamp - determining factor in e. coli nissle 1917 probiotic which can remarkably stimulate bd - 2 expression . the induction of l. reuteri probiotics for 14 days with a concentration of 410 cfu / ml can increase the expression of bd - 2 significantly ( p = 0.001 ) [ table 2 and figures 2 , 3 ] . it indicates that bd - 2 expression in epithelial cells of the parotid gland in group 2 ( t2 ) shows the highest bd - 2 expression compared to the other groups . this can be expected that active molecules on l. reuteri cell wall and peptidoglycan will activate nod - 2 receptors in the cytoplasm . the signaling activation through nod2 pathway involves rick adapter protein and will be activated to phosphorylate ikk complex . nuclear factor - b ( nf - b ) in inactive form will bound to iba protein inhibitor in the cytoplasm . the stimuli will induce phosphorylation , ubiquitination , and degradation of ib proteins which will lead to nf - b translocation into the nucleus cores , and then nf - b becomes active . the stimuli will induce phosphorylation , ubiquitination and degradation of ikb protein which will lead to nf - kb translocation into the nucleus cores , and then nf - kb becomes active to stimulate the target genes . results of immunohistochemical examination showing beta defensin - 2 expression in the epithelial parotid gland in each group magnified ( 1000 ) . description : ( a ) negative control , ( b ) positive control , ( c ) treatment group 1 ( p. 1 ) , ( d ) treatment group 2 ( p. 2 ) it can be concluded that the induction of l. reuteri probiotics can increase bd - 2 level in saliva and its expression in parotid gland epithelial cells .\noutput:\n" }, { "from": "agent", "value": "objective : the aim of this study was to prove that administrating l. reuteri probiotics can increase the level of bd - 2 saliva and bd - 2 expression in the epithelial parotid glands of wistar rats.materials and methods : experimental design in this study was randomized control group post test only . twenty - four white male rattus norvegicus wistar strain rats were divided into four groups . the negative control group included rats not induced by s. mutans whereas the positive control group included rats induced by s. mutans . the two treatment groups are as follows : treatment 1 ( t1 ) , the group that is induced for 14 days by l. reuteri and 7 days by s. mutans and treatment 2 ( t2 ) , the group which is induced simultaneously by s. mutans and l. reuteri for 14 days . l. reuteri culture at a concentration of 108 colony - forming unit / ml and s. mutans culture at a concentration of 1010 are induced in the oral cavity of the wistar rats . the elisa technique is used to examine the salivary level of bd - 2 , whereas the immunohistochemical technique is used to examine the bd - 2 expression in the epithelial salivary glands.results : the study shows the increasing levels of bd - 2 and bd - 2 expression in the epithelial parotid glands after the administration of l. reuteri probiotics . besides , there is a relationship between the increasing expression of bd - 2 in the epithelial parotid glands with the decreasing amount of s. mutans.conclusion : giving l. reuteri probiotic scan increases the level of saliva of bd - 2 and the expression of bd - 2 in the parotid glands ." } ]