Datasets:

clinicalnlplab

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PubmedSumm_train

like 0

[ { "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: parkinson 's disease ( pd ) is one of the most common neurodegenerative movement disorders . it affects more than 0.1 % of the population older than 40 years of age . a number of patients also suffer from anxiety , depression , autonomic disturbances and dementia . although there are effective symptomatic therapies , there are no proven neuroprotective or neurorestorative therapies . the major clinical symptoms of pd is loss of dopamine ( da ) neurons in the substantia nigra pars compacta ( snc ) , but there is wide - spread neuropathology and the snc only becomes involved toward the middle stages of the disease . lewy bodies and dystrophic neurites ( lewy neurites ) are a pathologic hallmark of pd and classically are round eosinophilic inclusions composed of a halo of radiating fibrils and a less defined core . however , the other disorder like depression is the main confounding factor that impacts quality - of - life in pd and prevalence of depression in pd varies from 20 % to 50 % and is frequently associated with greater disability , rapid progression of motor symptoms and increased mortality . granulocyte - colony stimulating factor ( g - csf ) , a hematopoietic growth factor has a potential role in mobilizing peripheral blood progenitor cells and form new myeloid cells with potential neuroprotective effect in several studies . experimental evidencehave shown that neuroprotective effect of g - csf is due to inhibitory activity of the production or activity of the main inflammatory mediators interleukin - 1 , tumor necrosis factor - alpha and interferon gamma . hence , present study was designed to evaluate the effect of g - csf on experimentally induced pd and co - morbid depression in rats because it is very difficult to target multiple contributing factors by a drug . adult wistar male rats weighing about 180 - 250 g were obtained from the central animal house of the institute . the animals were housed in standard laboratory conditions in groups of three at 252c , humidity of 602 % and 12 h light : dark cycle . all experiments were conducted daily between 09:00 am and 03.00 pm h. the protocol was approved from institutional animal ethics committee and the animal housing , care and handling was followed as per committee for the purpose of control and supervision on experiments on animals guidelines for animal care and use . the experiment was carried out in eight groups namely , control group ( n = 5 ) : in this group , healthy normal rats were taken and the vehicle ( phosphate buffered saline , ph 7.4 with 0.01 % ascorbic acid ) was given from 1 to 14 days intraperitoneally ; sham operated group ( n = 5 ) : rats were exposed to stereotaxis / intracerebroventricular injection , but were not treated with any drug preparation , then sutured back and was analyzed on day 15 . vehicle group ( n = 5 ) : rats were exposed to stereotaxis / intracerebroventricular injection on day 0 in the fixed coordinates and 6 - hydroxydopamine ( 6 - ohda ) at the concentration of 12 g in 4 l in 0.01 % ascorbic acid was inserted and treatment with the vehicle for 14 days ; g - csf group ( 70 g / kg , s.c . ) ( n = 5 ) : rats were exposed to stereotaxis / intracerebroventricular injection on day 0 in the fixed coordinates and 6 - ohda at the concentration of 12 g in 4 l in 0.01 % ascorbic acid was inserted and g - csf ( 70 g / kg , s.c . ) treatment was given for 1 - 6 days and followed for 14 days . l - dopa group ( 30 mg / kg ) ( n = 5 ) : rats were exposed to stereotaxis / intracerebroventricular injection on day 0 in the fixed coordinates and 6 - ohda at the concentration of 12 g in 4 l in 0.01 % of ascorbic acid was introduced and treated with l - dopa / carbidopa ( 30 mg / 7.5 mg ; 4:1 ) for 1 - 14 days . + xylazine ( 10 mg / kg , i.p . ) and placed in a stereotaxic frame . the coordinates of the substantia nigra was located at anterior - posterior ( ap ) : 3.0 mm and middle lateral ( ml ) : + 2.5 mm ( relative to bregma ) , dorsal ventral ( dv ) : 7.6 mm ( relative to dura ) . next , 4 l ( 12 g ) of 6 - ohda hydrochloride in 0.1 % of ascorbic acid / saline solution was drawn into a 10 l hamilton syringe and infused into the substantia nigra at a rate of 1 l / min followed by a 5 - min equilibration time . infusions were made during which the needle remained in place and was then slowly retracted . after surgery , the wound of rats were wiped with 70 % of ethanol and iodine solution . then , treated with neosporin power before sifting to their home cage and were treated with parenteral analgesics daily for 5 days . small adhesive stimuli ( 10 mm round ) were placed on the snout of the rat and the time to make contact and remove the stimulus was recorded . to remove the stimulus , animals would raise both forelimbs toward their face and swipe off the stimulus with both forepaws . in general , rats make contact and remove the stimulus within 10 s. each animal received two trials and the trials were alternated and hencethat each rat has an intertribal interval of at least 2 min . all the testing was performed in the animal 's home cage and cage mates were temporarily removed during testing because they can interfere with stimulus removal . if the animals not able to remove the stimulus within 60 s , the experimenter removed it . stimulus contact time , removal time and removal contact time was calculated for each animal .1977 was slightly modified and followed briefly , each rat was placed individually in a glass cylinder ( diameter 22.5 cm , height 30 cm ) that was filled to the 25 cm mark with water . the rat was forced to swim for 15 min on the 1 day of experiment ( pre - test day ) . rats were then allowed to return to their home cage . on day 1 , 7 and 15 , rat was immobile , when its front and hind paws were no longer moving and the rat was in floating position without struggle , whereas climbing was defined when rats were tried to move its front paws on the cylinder wall and try to climb . the rat was considered to be immobile when it stopped struggling and passively moved to remain floating and keep its head above water . water was changed between the experiment to make rats clear and visible and the temperature was maintained at 222c throughout the experiment . the immobility time was recorded manually by an observer who was blind to the drug treatment . briefly , nissl - stained neurons were analyzed in ( light microscopy ; 400 ) . watson planes ( 4.2 , 3.8 , 3.2 , 2.97 ; interaural ) were examined by scanning the mounted sides . observations were recorded and arranged on a microsoft excel spreadsheet ( microsoft , seattle , wa , usa ) . the data was imported into statistical package of social science ( spss version 16.0 ; ibm corp . armonk , ny ) and behavioral measurements were analyzed using the one - way anova post - hoc tukey 's test . + xylazine ( 10 mg / kg , i.p . ) and placed in a stereotaxic frame . the coordinates of the substantia nigra was located at anterior - posterior ( ap ) : 3.0 mm and middle lateral ( ml ) : + 2.5 mm ( relative to bregma ) , dorsal ventral ( dv ) : 7.6 mm ( relative to dura ) . next , 4 l ( 12 g ) of 6 - ohda hydrochloride in 0.1 % of ascorbic acid / saline solution was drawn into a 10 l hamilton syringe and infused into the substantia nigra at a rate of 1 l / min followed by a 5 - min equilibration time . infusions were made during which the needle remained in place and was then slowly retracted . after surgery , the wound of rats were wiped with 70 % of ethanol and iodine solution . then , treated with neosporin power before sifting to their home cage and were treated with parenteral analgesics daily for 5 days . small adhesive stimuli ( 10 mm round ) were placed on the snout of the rat and the time to make contact and remove the stimulus was recorded . to remove the stimulus , animals would raise both forelimbs toward their face and swipe off the stimulus with both forepaws . in general , rats make contact and remove the stimulus within 10 s. each animal received two trials and the trials were alternated and hencethat each rat has an intertribal interval of at least 2 min . all the testing was performed in the animal 's home cage and cage mates were temporarily removed during testing because they can interfere with stimulus removal . if the animals not able to remove the stimulus within 60 s , the experimenter removed it . stimulus contact time , removal time and removal contact time was calculated for each animal .1977 was slightly modified and followed briefly , each rat was placed individually in a glass cylinder ( diameter 22.5 cm , height 30 cm ) that was filled to the 25 cm mark with water . the rat was forced to swim for 15 min on the 1 day of experiment ( pre - test day ) . rats were then allowed to return to their home cage . on day 1 , 7 and 15 , rat was immobile , when its front and hind paws were no longer moving and the rat was in floating position without struggle , whereas climbing was defined when rats were tried to move its front paws on the cylinder wall and try to climb . the rat was considered to be immobile when it stopped struggling and passively moved to remain floating and keep its head above water . water was changed between the experiment to make rats clear and visible and the temperature was maintained at 222c throughout the experiment . the immobility time was recorded manually by an observer who was blind to the drug treatment . briefly , nissl - stained neurons were analyzed in ( light microscopy ; 400 ) . at least two sections representative of each of four paxinos watson planes ( 4.2 , 3.8 , 3.2 , 2.97 ; interaural ) were examined by scanning the mounted sides . observations were recorded and arranged on a microsoft excel spreadsheet ( microsoft , seattle , wa , usa ) . the data was imported into statistical package of social science ( spss version 16.0 ; ibm corp . armonk , ny ) and behavioral measurements were analyzed using the one - way anova post - hoc tukey 's test . + xylazine ( 10 mg / kg , i.p . ) and placed in a stereotaxic frame . the coordinates of the substantia nigra was located at anterior - posterior ( ap ) : 3.0 mm and middle lateral ( ml ) : + 2.5 mm ( relative to bregma ) , dorsal ventral ( dv ) : 7.6 mm ( relative to dura ) . next , 4 l ( 12 g ) of 6 - ohda hydrochloride in 0.1 % of ascorbic acid / saline solution was drawn into a 10 l hamilton syringe and infused into the substantia nigra at a rate of 1 l / min followed by a 5 - min equilibration time . infusions were made during which the needle remained in place and was then slowly retracted . after surgery , the wound of rats were wiped with 70 % of ethanol and iodine solution . then , treated with neosporin power before sifting to their home cage and were treated with parenteral analgesics daily for 5 days . small adhesive stimuli ( 10 mm round ) were placed on the snout of the rat and the time to make contact and remove the stimulus was recorded . to remove the stimulus , animals would raise both forelimbs toward their face and swipe off the stimulus with both forepaws . in general , rats make contact and remove the stimulus within 10 s. each animal received two trials and the trials were alternated and hencethat each rat has an intertribal interval of at least 2 min . all the testing was performed in the animal 's home cage and cage mates were temporarily removed during testing because they can interfere with stimulus removal . if the animals not able to remove the stimulus within 60 s , the experimenter removed it . stimulus contact time , removal time and removal contact time was calculated for each animal .1977 was slightly modified and followed briefly , each rat was placed individually in a glass cylinder ( diameter 22.5 cm , height 30 cm ) that was filled to the 25 cm mark with water . the rat was forced to swim for 15 min on the 1 day of experiment ( pre - test day ) . rats were then allowed to return to their home cage . on day 1 , 7 and 15 , rat was immobile , when its front and hind paws were no longer moving and the rat was in floating position without struggle , whereas climbing was defined when rats were tried to move its front paws on the cylinder wall and try to climb . the rat was considered to be immobile when it stopped struggling and passively moved to remain floating and keep its head above water . water was changed between the experiment to make rats clear and visible and the temperature was maintained at 222c throughout the experiment . the immobility time was recorded manually by an observer who was blind to the drug treatment . briefly , nissl - stained neurons were analyzed in ( light microscopy ; 400 ) . at least two sections representative of each of four paxinos watson planes ( 4.2 , 3.8 , 3.2 , 2.97 ; interaural ) were examined by scanning the mounted sides . observations were recorded and arranged on a microsoft excel spreadsheet ( microsoft , seattle , wa , usa ) . the data was imported into statistical package of social science ( spss version 16.0 ; ibm corp . armonk , ny ) and behavioral measurements were analyzed using the one - way anova post - hoc tukey 's test . the surgical procedure was conducted after proper anesthesia and all animals tolerated well the surgical operations and found there was no mortality due to treatments . however , we observed there is weight loss in some rodents , but found not significantly different from one another ( data not shown ) . on day 1 , reaction time to remove the adhesive from their snout was very less , however , on day 7 and 14 reaction time was significantly increased in vehicle treated group when compared to control and sham operated group ( p 0.001 ; 15.82.26 vs. 2.00.32 vs. 1.60.24 ) . treatment with g - csf 70was found to significantly reduced the reaction time as compared to vehicle treated as well as standard drug l - dopa ( p 0.05 ; 4.81.07 vs. 24.84.18 vs. 12.41.50 ) [ figure 1 ] . adhesive removal test , effect of granulocyte - colony stimulating factor on adhesive removal test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats : * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidopa rats were exposed to the fst on day 13 of experiment and immobility behavior was assessed on day 14 . in the vehicle group , immobility timewas significantly increased when compared with control and sham operated group ( p 0.001 ; 76.65.56 s vs. 11.82.05 vs. 13.81.65 ) treatment with g - csf 70 was significantly reduced the immobility time on day 14 when compared with vehicle treated group ( p 0.005 ; 17.03.03 s vs. 76.65.56 s ) and l - dopa + carbidopa group ( p 0.05 ; 17.03.03 s vs. 39.41.72 ) [ figure 2 ] . immobility test , effect of granulocyte - colony stimulating factor on fst test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats , * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidopa nissl staining for the snc neuron showed significantly loss in vehicle treated group as compared to control and sham operated group . however , g - csf 70 showed significantly increased neuronal density in snc region of rat brain when compared with the vehicle as well as l - dopa + carbidopa group [ figure 3 ] . nissl staining , effect of granulocyte - colony stimulating factor ( g - csf ) on neuronal density in substantia nigra pars compacta in 6 - hydroxydopamine induced parkinson 's disease model of rats , ( a ) control group , ( b ) sham operated group , ( c ) vehicle treated group ( d ) g - csf 70 and ( e ) l - dopa + carbidopaon day 1 , reaction time to remove the adhesive from their snout was very less , however , on day 7 and 14 reaction time was significantly increased in vehicle treated group when compared to control and sham operated group ( p 0.001 ; 15.82.26 vs. 2.00.32 vs. 1.60.24 ) . treatment with g - csf 70 was found to significantly reduced the reaction time as compared to vehicle treated as well as standard drug l - dopa ( p 0.05 ; 4.81.07 vs. 24.84.18 vs. 12.41.50 ) [ figure 1 ] . adhesive removal test , effect of granulocyte - colony stimulating factor on adhesive removal test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats : * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidopa rats were exposed to the fst on day 13 of experiment and immobility behavior was assessed on day 14 . in the vehicle group , immobility timewas significantly increased when compared with control and sham operated group ( p 0.001 ; 76.65.56 s vs. 11.82.05 vs. 13.81.65 ) treatment with g - csf 70 was significantly reduced the immobility time on day 14 when compared with vehicle treated group ( p 0.005 ; 17.03.03 s vs. 76.65.56 s ) and l - dopa + carbidopa group ( p 0.05 ; 17.03.03 s vs. 39.41.72 ) [ figure 2 ] . immobility test , effect of granulocyte - colony stimulating factor on fst test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats , * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidopa nissl staining for the snc neuron showed significantly loss in vehicle treated group as compared to control and sham operated group . however , g - csf 70 showed significantly increased neuronal density in snc region of rat brain when compared with the vehicle as well as l - dopa + carbidopa group [ figure 3 ] . nissl staining , effect of granulocyte - colony stimulating factor ( g - csf ) on neuronal density in substantia nigra pars compacta in 6 - hydroxydopamine induced parkinson 's disease model of rats , ( a ) control group , ( b ) sham operated group , ( c ) vehicle treated group ( d ) g - csf 70 and ( e ) l - dopa + carbidopaon day 1 , reaction time to remove the adhesive from their snout was very less , however , on day 7 and 14 reaction time was significantly increased in vehicle treated group when compared to control and sham operated group ( p 0.001 ; 15.82.26 vs. 2.00.32 vs. 1.60.24 ) . treatment with g - csf 70 was found to significantly reduced the reaction time as compared to vehicle treated as well as standard drug l - dopa ( p 0.05 ; 4.81.07 vs. 24.84.18 vs. 12.41.50 ) [ figure 1 ] . adhesive removal test , effect of granulocyte - colony stimulating factor on adhesive removal test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats : * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidoparats were exposed to the fst on day 13 of experiment and immobility behavior was assessed on day 14 . in the vehicle group , immobility time was significantly increased when compared with control and sham operated group ( p 0.001 ; 76.65.56 s vs. 11.82.05 vs. 13.81.65 ) treatment with g - csf 70 was significantly reduced the immobility time on day 14 when compared with vehicle treated group ( p 0.005 ; 17.03.03 s vs. 76.65.56 s ) and l - dopa + carbidopa group ( p 0.05 ; 17.03.03 s vs. 39.41.72 ) [ figure 2 ] . immobility test , effect of granulocyte - colony stimulating factor on fst test in 6 - hydroxydopamine ( 6 - ohda ) induced parkinson 's disease model of rats , * p 0.05 , as compared to control ; p 0.05 , as compared to sham ; p 0.05 , as compared to 6 - ohda + vehicle group , p 0.05 , as compared to l - dopa / carbidopanissl staining for the snc neuron showed significantly loss in vehicle treated group as compared to control and sham operated group . however , g - csf 70 showed significantly increased neuronal density in snc region of rat brain when compared with the vehicle as well as l - dopa + carbidopa group [ figure 3 ] . nissl staining , effect of granulocyte - colony stimulating factor ( g - csf ) on neuronal density in substantia nigra pars compacta in 6 - hydroxydopamine induced parkinson 's disease model of rats , ( a ) control group , ( b ) sham operated group , ( c ) vehicle treated group ( d ) g - csf 70 and ( e ) l - dopa + carbidopathe present study is a preliminary one , aimed to show the neuroprotective effect of g - csf in pd rat model . this is the first study , which implicated the effect of g - csf on pd associated with depression . present study showed that g - csf significantly reduced the adhesive removal time and immobility time in fst test . neuronal density was also found to increase highly in snc region of the brain . among the model of pd , unilateral 6 - ohda modelis frequently used in rats and has the advantage of presenting side - biased motor impairments and produced symptoms like pd . as the finding of the present study rats 6 - ohda2009 showed that adhesive removal test is of have high sensitivity , because it showed coordination behavior of paw and mouth . hence , this test gives correct outcome of sensitivity such as time to contact paw and mouth and correct dexterity , i.e. , time to remove . cummings , 1992 reported that depression occurs in approximately 40 % of patients with pd and it is distinguished from other depressive disorders by greater anxiety and less self - punitive ideation . fst showed significantly increased immobility time in vehicle treated rats , whereas g - csf treatment significantly reduced the immobility time . the neuroprotective activity of g - csf is significantly supported by the increased neuronal density in snc . similarly , song et al . 2011 , reported that g - csf enhances recovery of da nigro - striatal function from mptp toxicity in part by modulating the microglial response to injury . however , other studies reported that neuroprotective effects of g - csf have been attributed to activation of several anti - apoptotic pathways . g - csf prevented neuronal death triggered by methyl - phenylpyridinium in cell cultures of primary midbrain neurons and pc12 cells by increasing expression of the anti - apoptotic protein bcl - 2 while decreasing the pro - apoptotic bax . activation of the pi3k / akt pathway by g - csf in cultured rat cortical neurons was reported to be another anti - apoptotic pathway responsible for neuroprotection . the present study showed that g - csf have a potential role in the treatment of pd associated with depression . however , this is a preliminary part of study and has required more molecular assessment to conclude the finding of the present study .\noutput:\n" }, { "from": "agent", "value": "introduction : the present study was designed to evaluate the effect of granulocyte - colony stimulating factor ( g - csf ) in the treatment of parkinson 's disease ( pd ) , the second most common neurodegenerative disease characterized by muscle and movement disorder , often associated with depression . pd is very difficult to treat . hence , the present study was aimed to evaluate the effect of g - csf in pd associated with depression.materials and methods : adult wistar male rats weighing about 180 - 250 g were selected and divided into five groups in parallel designed method namely ; control group ( n = 5 ) ; sham operated group ( n = 5 ) ; vehicle group ( n = 5 ) ; g - csf group ( 70 g / kg , s.c . ) ( n = 5 ) and l - dopa group ( n = 5 ) . the rats were treated with 6 - hydroxydopamine ( 6 - ohda ) on day 0 and then treatment was continued for 14 day of l - dopa / carbidopa , whereas g - csf ( 70 g / kg , s.c . ) was given from day 1 to 6 . thereafter , adhesive removal and forced swim tests were conducted to evaluate the behavioral outcome of g - csf treatment . the finding was correlated and analyzed with nissl staining findings for the final conclusion.results : the behavioral parameters were assessed and found to be ameliorate the symptoms of parkinson 's and reduced the depression like behavior in pd . the histological findings were supported the behavioral findings and showed pathological improvement.conclusion : as a preliminary work , the present study first time suggested that g - csf have a potential role in pd and associated 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: erythropoiesis is optimized in chronic kidney disease by treatment with iron and erythropoiesis - stimulating agents ( esas ) . for end - stagerenal disease patients on hemodialysis , intravenous ( iv ) iron is more efficacious than oral iron . potential advantages of iv iron include direct iron delivery to bone marrow and tissue stores , large - dose delivery , and elimination of frequent gastrointestinal side effects associated with oral iron treatment . among iv iron formulations , iron isomaltoside , ferric carboxymaltose , and the iron dextrans ( ids ) can be administered in total dose infusion ( tdi ) . both ferric gluconate and iron sucrose can be safely administered as a bolus or short infusion at doses up to 250 mg and 300 mg , respectively . higher doses of either drug as a bolus or short infusion have been associated with unpleasant vasoactive and gastrointestinal symptoms . however , accelerated regimens of high - dose iv iron sucrose ( 500 mg over 3 hours ) have been demonstrated to be safe in several studies . the safety and efficacy of i d in nondialysis chronic kidney disease ( nd - ckd ) is less well reported , especially for the low molecular weight iron dextran ( lmwid ) infed . imferon , dexferrum , and infed are the ids that have been used in the usa . the first two are high molecular weight iron dextrans ( hmwids ) ; the last is an lmwids . imferon is no longer available ; it was withdrawn by the original manufacturer , fisons , based on economic decisions . these preparations are erroneously classified by some as a single class of product with similar side - effect profile . however , recently published literature revealed that lmwid has a different safety profile than hmwid . several studies have shown that hmwid is associated with more adverse drug events ( ades ) than other iron preparations in the market . the level and methods of ade reporting vary between different studies . some reportthe ade rate per episode of i d administered , others per unit i d infusion or per patients treated . moreover , there is no uniform definition of what constitutes a serious adverse event . after recent concerns about the safety of esas and the current economic realities , the need for more effective anemia management strategies is of paramount importance . incorporation of iv iron into the anemia treatment paradigm is needed to achieve the lowest effective esa dose . at the henry ford hospitalchronic kidney disease clinic , lmwid in conjunction with esa is used for nd - ckd anemia management using a computerized algorithm for dosing ( see section 2 ) . i d is infused in accelerated fashion ( 1.52 hours ) and in amounts considered to be tdi . this study reports the 2 - month outcomes of hemoglobin ( hb ) , ferritin , and transferrin saturation ( tsat ) in both iv and oral treatment groups from baseline . the cumulative incidence of ades related to i d in a cohort of 935 patients followed in nd - ckd is also reported . , a retrospective chart review was done of all nd - ckd patients who received iron dextran ( infed ) between january 2001 and november 2005 in the outpatient ckd clinic at henry ford hospital , detroit , michigan . the 936 nd - ckd subjects identified in the database each received either 0.5 or 1.0 g infusion by peripheral vein over 1.52.0 hours . the dosing of infed during this study period was at the discretion of the treating physician . all ade presumed to be related to lmwid were also reported to the food and drug administration ( fda ) medwatch . moderate ades were categorized as dyspnea , severe urticaria , chest discomfort , or neck / back spasms . mild ades were classified as headache , dizziness , tachycardia , and hypertension in which the infusion was stopped but the patient subsequently completed the infusion . the efficacy outcomes were obtained from analysis of the data of patients enrolled in the clinic 's computerized anemia management program ( camp ) between december 2005 and january 2007 . camp is designed to treat anemia of ckd using darbepoetin alpha ( da ) and iron treatment algorithms . after manual data input , the iron dosing algorithm prescribes no iron , oral iron , or 1 g of infed over 1.52 hours based on hb , tsat , and ferritin levels . at all times , ironsufficiency is to be achieved / maintained with oral or parenteral i d per the algorithm ( figure 1 ) . esa dosing is based on three separate protocols for first , second , and maintenance da doses with a target to achieve and maintain hb in the range of 10.012.0 g / dl . the second dose is based on the initial da dose , initial hb and current hb . maintenance da doses are based on trend analysis of the most recent hb , the last two da doses and any increase or decrease in the last two doses . all subjects were 18 years old , nd - ckd with an estimated glomerular filtration rate ( gfr ) of 60 ml / min , and fulfilled criteria for iron deficiency anemia per the camp protocol . for the 26 - month period , 166 subjects were found in the database of camp who received and completed iv or oral iron treatment as prescribed by camp . sixteen patients were excluded because either their second evaluation day period exceeded 37 days from baseline or the third evaluation day exceeded 37 days from second evaluation day . among the remaining 150 patients , 50 received lmwid and 100 received oral iron because their parameters never fulfilled the criteria to receive iv iron per camp . each tablet contained 200 mg of ferrous fumarate ( 33 % elemental iron ) , 40 mg of ascorbic acid , 1 mg folate , 75 mg of sodium docusate , and all b vitamins . priorto being enrolled in camp , 32 of 50 patients assigned to iv iron had received da in the past three months . in the oral iron group , 75 of 100 patients had received da . only 2 of 50 patients assigned to iv iron group needed a second dose of lmwid on second evaluation . secondary endpoints were iron indices ( tsat , ferritin ) at 30 and 60 days in each group as well as esa dose requirements . since the two groups by protocol design were assigned to different iron and esa dosing , and dosingwas adjusted to reach or maintain a target goal ; we only compared mean differences between the two groups at the third clinic visit ( 60 days ) . comparisons of baseline characteristics between oral and iv iron groups were tested using two - sample t - tests for continuous variables , and chi - square and fisher 's exact tests for categorical variables . intra - individual changes between time points for hb , ferritin , tsat , and da were tested using student 's paired t - test . statistical analysis was performed using sas software version 9.2 ( sas institute , inc . , cary , nc ) and graphs were produced using stata software version 10 ( statacorp lp , college station , tx ) . for the 150 patients represented in the efficacy analysis , baseline characteristics of both oral and iv iron groups are listed in table 1 . there was no statistical difference in age , race , or gender between frequencies of coronary artery disease , diabetes , and hypertension . however , the patients who received iv iron had a higher frequency of congestive heart failure . baseline hb , tsat , and ferritin were lower in the iv group , as expected based on camp . for the 935 patients represented in the safety analysis , the mean age was 63.915.0 years ; 60 % were women ; 64 % were african american , 32 % white , and 4 % either asian or hispanic . over the 6 - year study period ,935 nd - ckd patients ( 488 stage 3 ckd and 447 stage 4 ckd ) were treated with i d . a total of 1699 infusions ( 141 gram and 16850.5 gram doses ) were administered over the study period ( 17130.5 g equivalents ) . the overall ade event rate was 0.175 % per 0.5 gram dose equivalents and 0.177 % per episode of iv iron infusion . all three ades occurred in women ( mean age 70.3 years [ range , 5085 years ] ) . all ades occurred with the first dose and within 30 minutes of i d administration . in these patients , a test dose did not predict the occurrence of a subsequent ade . of the three patients with ades , one experienced a severe reaction requiring 1 mg of epinephrine to reverse hypotension and bradycardia ; one experienced a moderate reaction with dyspnea and responded to diphenhydramine ; the third experienced a moderate reaction with a rash that responded to diphenhydramine and dexamethasone treatment . there were no fatalities noted from i d administration during the 6 - year study period . figures 2 , 3 , 4 , and 5 show the mean hb , tsat , ferritin , and da levels , respectively , over time by treatment group . tables 2 and 3 display pairwise comparison of these parameters at three evaluation days in the iron dextran group ( idg ) and oral group ( og ) , respectively . the idg showed significant improvement in the mean hb compared to baseline at days 30 ( 10.7 versus 9.4 g / dl ; p 0.0001 ) and 60 ( 11.3 versus 9.4 g / dl ; p 0.0001 ) . in the og , mean hb also increased at 30 days ( 11.1 versus 10.9 g / dl ; p = 0.0258 ) and 60 days ( 11.3 versus 10.9 g / dl ; p = 0.0003 ) . tsat in idg improved significantly by day 30 ( 23.4 versus 12.9 ; p 0.0001 ) . the effect of 1 gram i d on tsat was maintained through day 60 ( 24.0 versus 12.9 ; p 0.0001 ) . the mean tsat was maintained by oral iron and increased slightly from baseline ( 25.0 versus 23.2 ; p = 0.0401 ) . a robust increase in ferritin from baseline was observed in the idg at day 30 ( 359.0 versus 134.7 ; p 0.001 ) . the iron stores as reflected by ferritin remained higher than baseline at day 60 ( 294.0 versus 134.7 ; p 0.001 ) . no statistically significant change in ferritin was seen in the og by 60 days ( 220.2 versus 216.7 ; p = 0.8339 ) . da use , as prescribed by the algorithm , was greater in idg than og at all evaluation days ( p 0.001 ) as shown in figure 5 . by day 60 , hb , tsat , and ferritin were not statistically different between the idg and og ( hb : 11.31.1 versus 11.31.2 ; tsat : 24.09.9 versus 25.08.4 ; ferritin : 294.0254.6 versus 220.2213.5 ; all p values 0.20 ) . four main iron preparations are used in the usa : two iron dextrans ( lmwid , infed ; hmwid , dexferrum ) , sodium ferric gluconate ( ferrlecit ) , iron sucrose ( venofer ) , and ferumoxytol ( feraheme ) . both infed and dexferrumare fda approved for patients with documented iron deficiency in whom oral administration was unsatisfactory or not possible . in addition to hemodialysis patients , the efficacy of iron dextran has been demonstrated in different patient populations with documented iron deficiency , such as patients with pregnancy - related anemia , cancer patients , surgical patients who refuse transfusions , and patients on ambulatory peritoneal dialysis . among the iron preparations used in the usa , the iron dextrans can be administered as tdi . the accelerated tdi of iron dextran was also recently reported safe by auerbach et al . . slow infusion of high - dose i d ( 0.51.0 g ) is frequently termed tdi because it provides enough iron to produce the desired hb increase as well as to replete tissue and reticuloendothelial stores . tdi is deemed appropriate by the national kidney foundation 's kidney disease outcomes quality initiative guidelines in ckd patients who despite oral iron supplementation have persistent evidence of iron deficiency . however , tdi is not fda approved because of high incidence of delayed arthralgias and myalgias . these symptoms usually occur about 24 hours later , abate without therapy , and should not be considered ades . both the hmwid and lmwid carry a black box warning regarding the risk of anaphylactoid reactions . although anaphylaxis has been reported with lmwid , its incidence is rare ( 1 : 200000 ) . acute chest and back pain at times are mistakenly described as anaphylaxis attributable to lmwid . these symptoms when not accompanied by hypotension , tachypnea , tachycardia , wheezing , stridor , or orbital edema are harmless , abate in few minutes , and do not automatically qualify for treatment by diphenhydramine or epinephrine . further premedication with diphenhydramine can cause tachycardia , sweating , somnolence , supraventricular tachycardia , and hypotension , all of which are attributed to the iv iron . prior to initiating iv iron dextran therapy , the package insert states administer a test infed dose prior to the first therapeutic dose . if no signs or symptoms of anaphylactic - type reactions follow the test dose , administer the full therapeutic infed dose . criticism and controversy surrounding iron dextran 's side effect profile surfaced in its postmarketing phase . although us sales for iron preparations have soared since the late 1990s , there has been a noticeable decline in i d use . this decline was likely secondary to the market 's introduction of newer iv formulations and at least partially due to the adverse events reported in several studies . however , none of these observational studies could establish whether other iron formulations possess a superior adverse effect profile than lmwid . moreover , in 2010 , the fda issued a warning letter to luitpold pharmaceuticals to stop claiming a safety advantage over iron dextrans in the absence of comparative clinical trials ( pers comm , m safarik , department of health and human services , fda ) . three life - threatening , immediate anaphylactoid and eight severe , delayed reactions were observed . compared ades among three iron preparations ( iron dextran , ferrlecit , and venofer ) using data from the freedom of information surveillance database from january 1997 to september 2002 . the all - event reporting rates for iron dextran , sodium ferric gluconate , and iron sucrose were 29.2 , 10.5 , and 4.2 reports per million 100 mg dose equivalents , while the all - fatal - event reporting rates were 1.4 , 0.6 , and 0.0 reports per million 100 mg dose equivalents . this paper did not distinguish between hmwid and lmwid formulations , nor did it characterize the population being studied . faich and strobos reviewed the spontaneous adverse reaction reporting of iron dextran in the usa and sodium ferric gluconate in germany and italy from 1976 to 1996 . data was gathered from the world health organization , pharmaceutical manufacturers , and the german health bureau . the 21 - year period had 74 reports of suspected allergic or anaphylactoid reactions for sodium ferric gluconate complex and 196 comparable reports for iron dextran in the us . the comparison was made based on the assumption that the extent of drug exposure to both iv preparations was similar during that time period . data for iron dextrans was combined because reporting databases did not distinguish between the different iron dextran formulations . fishbane conducted a retrospective chart review of 573 hemodialysis patients treated with iv iron dextran ( infed ) over a 2 - year period . although the ade rate appears high in this study , the unit of evaluation was neither the dose nor the episode of iv iron dextran administration but the patient . chertow and colleagues examined ades among three iron formulations ( hmwid , lmwid , and sodium ferric gluconate ) using data from the fda during 19982000 . the total number of reported parenteral iron - related ades was 1981 among approximately 21060000 doses . the total major ade rates were significantly higher among recipients of hmwid and sodium ferric gluconate complex than among recipients of lmwid . in 2006 , chertow et al . examined ades among four iron formulations ( hmwid , lmwid , sodium ferric gluconate complex , and iron sucrose ) using fda medwatch data from 2001 to 2003 . the rates of both total and life - threatening ades were significantly higher among recipientsof hmwid than lmwid or other iron formulations . the total ade reporting rates for dexferrum , infed , sodium ferric gluconate , and iron sucrose were 129 , 40.2 , 19.4 , and 19.8 reports per million / 100 mg equivalents , respectively , whereas the absolute rates of life - threatening events were 11.3 , 3.3 , 0.6 , and 0.9 per million . the investigators point out that several life - threatening ades did not specify the iron dextran formulation but were attributed to lmwid , without definitive data . however , when hmwid was avoided , the other formulations were safe with an estimated serious adverse event rate of 1 : 200,000 . in 2001 , fletes et al . reported on iron dextran - related ades using data from fresenius medical care north america ( fmcna ) clinical variance reports . among 841252 iv iron dextran administrations from october 1998 through march 1999 in patients with end - stage renal disease , there were 165 reported suspected ades , corresponding to an overall rate of 0.000196 % , or approximately 20 per 100000 doses . patients with ades had a mean age of 61.7 years ; almost 50 % of ades occurred in women ; 66 % occurred on initial dosing and with a median time of 5 minutes into dosing . in our study , all ades occurred in older women ( mean age 70.3 years ) , on initial dosing , and within 30 minutes of dosing . none of our patients required emergency evaluation , was hospitalized , or had fatal outcomes . while the retrospective nature of this study would likely underestimate minor reactions , it likely offers a reasonable estimation of major adverse events . our major ade rate per 100 mg dose would translate to 12 per 100,000 . however , we strongly feel that ades reported per episode of iv iron administered better reflect the true event rate . the study also shows that slow infusion of high - dose infed is well tolerated in nd - ckd patients . unlike the nondextran iv formulations where repeated iv infusions are required to achieve iron repletion , it can be conveniently administered in a single clinic visit . efficacy studies of iv iron undertaken in predialysis chronic renal failure have yielded contradictory results . some randomized controlled trials have shown that iv iron is superior to oral iron in raising hb in nd - ckd patients whereas other trials failed to demonstrate the same . randomized 40 patients to either oral ferrous sulfate , 200 mg three times a day ( tid ) , or iron dextran , 100 mg iv ( imferon ) twice a month , and followed for up to 3 months . iv iron dextran was more effective than oral iron sulfate in increasing hb and in improving iron parameters . van wyck et al . randomized 188 esa - treated and non - esa - treated patients to either oral ferrous sulfate , 325 mg for 56 days , or iron sucrose , 1 g iv in divided doses over a 2 - week period . iv iron sucrose was more effective than oral ferrous sulfate in improving iron indices and in increasing hb levels by at least 1 g / dl at any time point during the study . randomized 304 esa - treated and non - esa - treated patients to either two 510 mg of ferumoxytol or 200 mg of elemental iron for 21 days . at day 35 , randomized 96 patients to either oral iron for 29 days or iron sucrose 200 mg iv once a week for 5 doses and followed patients for 43 days . no significant difference was found between the two groups in hb levels , but serum ferritin levels improved more in the iv iron sucrose group . randomized 45 patients to either oral ferrous sulfate , 200 mg tid , or iron sucrose , 300 mg iv once a month , and followed them for an average of 5.2 months . all patients were simultaneously started on esa , and the dose was adjusted according to a preestablished protocol . although serum ferritin improved more in the iv group , iron sucrose was not superior to ferrous sulfate in improving hb or decreasing the esa doses . . showed that ferrous sulfate , 325 mg three times a day 42 days , and sodium ferric gluconate , 250 mg iv weekly 4 , similarly increase hb in anemic iron - depleted nd - ckd patients not receiving esas . the aim of our study was to demonstrate the efficacy of the computerized anemia management protocol . i d allows for high - dose infusions , giving it a practical advantage over other iv formulations . these tend to be more costly in terms of iv tubing , monitoring , iv access , nursing , and allotted time . in theory , at least , repeated injury to the venous system poses potential problems with future venous access . in our protocol , in the group assigned to lmwid + esa , hb increased by 1.31 g / dl and 1.91 g / dl at days 30 and 60 , respectively . despite the robust rise in hb in the idg and the incorporation of transferrin bound iron to erythroid precursors , tsat increased considerably at days 30 ( 23.4 versus 12.9 ; p 0.0001 ) and 60 ( 24.0 versus 12.9 ; p 0.0001 ) . iron stores as reflected by ferritin increased significantly from baseline at day 30 and remained higher than baseline at day 60 . by 60 days , mean hb , tsat , and ferritin in idg all increased to levels dictating transition to oral iron replacement per protocol ( figure 1 ) . our results support that lmwid when combined with esa is efficacious in raising hb and replenishing iron stores in as early as 30 days in nd - ckd patients . it also supports that high - dose lmwid should be considered in nd - ckd patients who fail or can not tolerate oral iron . the limitation of this study is its retrospective design which is subject to reporting bias . a predominant fraction of the patients in both groups had already been managed in the ckd clinic and had received da in the three months prior to being enrolled in camp . table 4 represents the average selling price ( asp ) for different iron formulations based on centers for medicare and medicaid services for the fourth quarter of 2012 . in the usa , each of the currently available parenteral iron preparations has safety or convenience limitations in patients not on dialysis . the nondextran formulations available in the usa are not recommended for tdi , and multiple administrations must be scheduled . in europe , two other formulations are approved for tdi in 15 minutes : ferric carboxymaltose ( 1000 mg ) and iron isomaltoside ( 20 mg / kg ) . ferumoxytol is approved in the usa , and there might be emerging data that it could be given in tdi ( abstract , am soc hematol 54th annual meeting , 2012 ) . however , the characteristics of the ade make it difficult to conduct comparative safety studies between the different formulations with sufficient methodological consistency and statistical power . moreover , adequately powered prospective comparative trials between two iron formulations will likely never be done due to the large sample sizes needed . for example , at 90 % power , to detect a difference between iron dextran with our reported serious ade rate ( 1/1699 ) and an iv formulation with half as common serious ades , about 114,000 patients are required in each group . it is safe and effective in the treatment of iron deficiency in nd - ckd . because fatal anaphylactic reactions have been reported after administration of iron dextran injection , the drug should be given only when resuscitation techniques and treatment of anaphylactic and anaphylactoid shock are readily available . our study did not show that higher doses of i d were associated with worse ade rates . if other potential formulations are used , ade profile , potential benefits , and relative costs should be established .\noutput:\n" }, { "from": "agent", "value": "objective . we aimed to demonstrate safety and efficacy of intravenous ( iv ) low molecular weight iron dextran ( lmwid ) during treatment of anemic stage 3 and 4 chronic kidney disease ( ckd ) patients . methods . efficacy data was obtained by retrospective chart review of 150 consecutively enrolled patients . patients were assigned per protocol to oral or iv iron , with iv iron given to those with lower iron stores and / or hemoglobin . iron and darbepoetin were administered to achieve and maintain hemoglobin at 1012 g / dl . efficacy endpoints were mean hemoglobin and change in iron indices approximately 30 and 60 days after enrollment . safety data was obtained by retrospective review of reported adverse drug events ( ades ) following 1699 infusions of lmwid ( 0.51.0 g ) . results . mean hemoglobin , iron saturation , and ferritin increased significantly from baseline to 60 days in patients assigned to lmwid ( hemoglobin : 11.3 versus 9.4 g / dl ; iron saturation : 24 % versus 12.9 % ; ferritin : 294.7 versus 134.7 ng / ml ; all p values < 0.0001 ) . iron stores and hemoglobin were maintained in the group assigned to oral iron . of 1699 iron dextran infusions , three ades occurred . conclusions . treatment of anemia in ckd stages 3 and 4 with lmwid and darbepoetin is efficacious . the serious ade rate was 0.06 % per infusion ." } ]

[ { "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 5 - year prospective observational cohort study was performed in a primary care setting to investigate the potential probability of reduction in albuminuria , i.e. , remission from macroalbuminuria to microalbuminuria and a decrease in albuminuria 50 % , to explore the factors associated with the reduction and to assess the effect of reduction on renal prognosis . subjects were recruited consecutively from japanese patients with t2 dm who were new patients at an outpatient clinic of jiyugaoka internal medicine from 2002 to 2008 ( n = 2,500 ) and met the following criteria at the first visit : macroalbuminuria ( urinary albumin - to - creatinine ratio [ acr ] 300 mg / g creatinine ( cr ) in a random spot urine ) and estimated glomerular filtration rate ( egfr ) 30 ml / min / 1.73 m. those included had not been treated for diabetes or had not received adequate intensive diabetes treatment . namely , patients visited the clinic with or without referral letters and with or without prior treatment histories . the medical team , composed of medical doctors , nurses , and dietitians in the clinic , assessed patients ' diabetic condition and immediately started adequate diabetes care for them according to the clinical practice recommendations for diabetes treatment . thereafter , patients attended the clinic every month and received appropriate diabetes care and education , which was intended to maintain glycosylated hemoglobin a1c ( hba1c ) values 7.0 % ( 53 mmol / mol ) , blood pressure ( bp ) 130/80 mmhg , serum concentrations of total cholesterol 5.2 mmol / l ( 200 mg / dl ) , triglycerides 1.7 mmol / l ( 150 mg / dl ) , hdl cholesterol 1.0 mmol / l ( 40 mg / dl ) , and bmi 2024 kg / m , as recommended by the japan diabetes society ( jds ) guidelines . in this study , patients who continuously received diabetes care at the clinic for 1 year were included . the study was approved by the local ethics committee and was carried out in accordance with the declaration of helsinki ii . bp was measured in the sitting position after taking a rest of 5 min . hba1c was measured by high - performance liquid chromatography , which was certified by the american national glycohemoglobin standardization program . serum and urinary concentrations of cr were measured by an enzymatic method with an isotope - dilution mass spectrometry traceable calibrator ( n - assay l creatinine kit ; nittoubo medical co. , tokyo , japan ) . the egfr was calculated using the following equation proposed by the japanese society of nephrology : egfr ( ml / min / 1.73 m ) = 194 ( age [ years ] ) ( serum cr [ mg / dl ] ) 0.739 ( if female ) ( 9 ) . the new japanese equation is reasonably accurate in estimating gfr for japanese populations and is more accurate than the modified modification of diet in renal disease equation refitted for japanese by overcoming the underestimation of gfr at high values up to 110 ml / min / 1.73 m ( 9 ) . neuropathy was diagnosed in patients with two or more of three components : the presence of symptoms , the absence of ankle tendon reflexes , and abnormal scores of the vibration perception threshold using a c128 tuning fork , where bilateral spontaneous pain , hypoesthesia , or paresthesia of the legs was considered a neuropathic symptom . the history of cardiovascular disease ( cvd ) included ischemic heart disease , ischemic cerebrovascular stroke , and peripheral artery disease . the urinary albumin excretion was assessed by using acr in random spot urine samples when the subject did not have any urinary tract infections and menstruation . urinary albumin was measured by a turbidimetric immunoassay . to determine the baseline acr , a single measurement before starting diabetes treatmenthowever , this was difficult to achieve , since treatments for blood glucose and bp were started immediately based on the patient s intentions , and the inconvenience to patients of repeatedly bringing urine samples should be avoided to enhance the adherence to treatments . after 1 year of treatment , acr was measured three times a year . at each yearbased on the three samples , the stage of nephropathy was defined as normoalbuminuria , microalbuminuria , or macroalbuminuria , corresponding to acr 30 mg / g cr , 30 acr 300 mg / g cr , or acr 300 mg / g cr , respectively , in at least two of three samples . the geometric mean from three samples was used as a continuous variable . remission was defined as stage of albuminuria , determined each year , improved from macroalbuminuria to micro / normoalbuminuria at least once . the main evaluation of this study was to estimate the rate of remission of macroalbuminuria to acr 300 mg / g cr and the reduction in acr of 50 % from the baseline . the second evaluation was to investigate the association between reduction in albuminuria and development of renal events , i.e. , doubling of serum cr or onset of esrd . the decline in renal function estimated by the gfr slope was also compared between those with and without remission and reduction in albuminuria . this study was also designed to explore the effect of intensive diabetes treatment on the subsequent reduction in acr . the levels of blood glucose control , bp control , and lipid profiles at the 1 - year time point after starting intensified diabetes treatment were used because these variables almost persisted throughout the whole follow - up period . data are expressed as mean sd or median ( interquartile range [ iqr ] ) . for comparisons between two groups , the unpaired student t test was used for normally distributed variables and the mann - whitney u test for variables with skewed distribution . statistical significance of the differences for categorical variables between the groups was determined by test . for each subject , a linear regression model of time on gfr ( least - squares method ) was created , and the slope of the regression line was used to estimate the subject s change in gfr over time . then , the gfr slope was expressed as percent per year by dividing the slope by the baseline gfr value . cumulative incidence of remission to acr 300 mg / g cr and to acr 30 mg / g cr was calculated using life - table analysis . logistic regression analysis was used to compute odds ratio ( or ) and 95 % ci to assess the effect of blood glucose and bp controls on remission of macroalbuminuria . since remission of macroalbuminuria is a categorical analysis , we concomitantly used changes in acr from the baseline to follow - up as a continuous analysis to compensate for the inherent problem associated with the categorical analysis . cox proportional hazards analysis was used to compute the hazard ratio and 95 % ci to assess the effect of obtaining remission and / or the reduction in acr of 50 % at the 1 - year study time point on the renal events of doubling serum cr or onset of esrd after adjustment for baseline considerable variables . age , sex , smoking , bmi , systolic bp , hba1c , hdl cholesterol , triglycerides , albuminuria , egfr , retinopathy , and prevalent cvd were included in the multivariate model as baseline clinical variables . all analyses were performed with the statistical software package spss ( spss japan , tokyo , japan ) . this 5 - year prospective observational cohort study was performed in a primary care setting to investigate the potential probability of reduction in albuminuria , i.e. , remission from macroalbuminuria to microalbuminuria and a decrease in albuminuria 50 % , to explore the factors associated with the reduction and to assess the effect of reduction on renal prognosis . subjects were recruited consecutively from japanese patients with t2 dm who were new patients at an outpatient clinic of jiyugaoka internal medicine from 2002 to 2008 ( n = 2,500 ) and met the following criteria at the first visit : macroalbuminuria ( urinary albumin - to - creatinine ratio [ acr ] 300 mg / g creatinine ( cr ) in a random spot urine ) and estimated glomerular filtration rate ( egfr ) 30 ml / min / 1.73 m. those included had not been treated for diabetes or had not received adequate intensive diabetes treatment . namely , patients visited the clinic with or without referral letters and with or without prior treatment histories . the medical team , composed of medical doctors , nurses , and dietitians in the clinic , assessed patients ' diabetic condition and immediately started adequate diabetes care for them according to the clinical practice recommendations for diabetes treatment . thereafter , patients attended the clinic every month and received appropriate diabetes care and education , which was intended to maintain glycosylated hemoglobin a1c ( hba1c ) values 7.0 % ( 53 mmol / mol ) , blood pressure ( bp ) 130/80 mmhg , serum concentrations of total cholesterol 5.2 mmol / l ( 200 mg / dl ) , triglycerides 1.7 mmol / l ( 150 mg / dl ) , hdl cholesterol 1.0 mmol / l ( 40 mg / dl ) , and bmi 2024 kg / m , as recommended by the japan diabetes society ( jds ) guidelines . in this study , patients who continuously received diabetes care at the clinic for 1 year were included . the study was approved by the local ethics committee and was carried out in accordance with the declaration of helsinki ii . bp was measured in the sitting position after taking a rest of 5 min . hba1c was measured by high - performance liquid chromatography , which was certified by the american national glycohemoglobin standardization program . serum and urinary concentrations of cr were measured by an enzymatic method with an isotope - dilution mass spectrometry traceable calibrator ( n - assay l creatinine kit ; nittoubo medical co. , tokyo , japan ) . the egfr was calculated using the following equation proposed by the japanese society of nephrology : egfr ( ml / min / 1.73 m ) = 194 ( age [ years ] ) ( serum cr [ mg / dl ] ) 0.739 ( if female ) ( 9 ) . the new japanese equation is reasonably accurate in estimating gfr for japanese populations and is more accurate than the modified modification of diet in renal disease equation refitted for japanese by overcoming the underestimation of gfr at high values up to 110 ml / min / 1.73 m ( 9 ) . neuropathy was diagnosed in patients with two or more of three components : the presence of symptoms , the absence of ankle tendon reflexes , and abnormal scores of the vibration perception threshold using a c128 tuning fork , where bilateral spontaneous pain , hypoesthesia , or paresthesia of the legs was considered a neuropathic symptom . the history of cardiovascular disease ( cvd ) included ischemic heart disease , ischemic cerebrovascular stroke , and peripheral artery disease . the urinary albumin excretion was assessed by using acr in random spot urine samples when the subject did not have any urinary tract infections and menstruation . urinary albumin was measured by a turbidimetric immunoassay . to determine the baseline acr , a single measurement before starting diabetes treatmenthowever , this was difficult to achieve , since treatments for blood glucose and bp were started immediately based on the patient s intentions , and the inconvenience to patients of repeatedly bringing urine samples should be avoided to enhance the adherence to treatments . after 1 year of treatment , acr was measured three times a year . at each yearbased on the three samples , the stage of nephropathy was defined as normoalbuminuria , microalbuminuria , or macroalbuminuria , corresponding to acr 30 mg / g cr , 30 acr 300 mg / g cr , or acr 300 mg / g cr , respectively , in at least two of three samples . the geometric mean from three samplesremission was defined as stage of albuminuria , determined each year , improved from macroalbuminuria to micro / normoalbuminuria at least once . the main evaluation of this study was to estimate the rate of remission of macroalbuminuria to acr 300 mg / g cr and the reduction in acr of 50 % from the baseline . the second evaluation was to investigate the association between reduction in albuminuria and development of renal events , i.e. , doubling of serum cr or onset of esrd . the decline in renal function estimated by the gfr slope was also compared between those with and without remission and reduction in albuminuria . this study was also designed to explore the effect of intensive diabetes treatment on the subsequent reduction in acr . the levels of blood glucose control , bp control , and lipid profiles at the 1 - year time point after starting intensified diabetes treatment were used because these variables almost persisted throughout the whole follow - up period . remission was defined as stage of albuminuria , determined each year , improved from macroalbuminuria to micro / normoalbuminuria at least once . the main evaluation of this study was to estimate the rate of remission of macroalbuminuria to acr 300 mg / g cr and the reduction in acr of 50 % from the baseline . the second evaluation was to investigate the association between reduction in albuminuria and development of renal events , i.e. , doubling of serum cr or onset of esrd . the decline in renal function estimated by the gfr slope was also compared between those with and without remission and reduction in albuminuria . this study was also designed to explore the effect of intensive diabetes treatment on the subsequent reduction in acr . the levels of blood glucose control , bp control , and lipid profiles at the 1 - year time point after starting intensified diabetes treatment were used because these variables almost persisted throughout the whole follow - up period . data are expressed as mean sd or median ( interquartile range [ iqr ] ) . for comparisons between two groups , the unpaired student t test was used for normally distributed variables and the mann - whitney u test for variables with skewed distribution . statistical significance of the differences for categorical variables between the groups was determined by test . for each subject , a linear regression model of time on gfr ( least - squares method ) was created , and the slope of the regression line was used to estimate the subject s change in gfr over time . then , the gfr slope was expressed as percent per year by dividing the slope by the baseline gfr value . cumulative incidence of remission to acr 300 mg / g cr and to acr 30 mg / g cr was calculated using life - table analysis . logistic regression analysis was used to compute odds ratio ( or ) and 95 % ci to assess the effect of blood glucose and bp controls on remission of macroalbuminuria . since remission of macroalbuminuria is a categorical analysis , we concomitantly used changes in acr from the baseline to follow - up as a continuous analysis to compensate for the inherent problem associated with the categorical analysis . cox proportional hazards analysis was used to compute the hazard ratio and 95 % ci to assess the effect of obtaining remission and / or the reduction in acr of 50 % at the 1 - year study time point on the renal events of doubling serum cr or onset of esrd after adjustment for baseline considerable variables . age , sex , smoking , bmi , systolic bp , hba1c , hdl cholesterol , triglycerides , albuminuria , egfr , retinopathy , and prevalent cvd were included in the multivariate model as baseline clinical variables . a p value 5 % ( two tailed ) was considered significant . all analyses were performed with the statistical software package spss ( spss japan , tokyo , japan ) . about half of the subjects had previously been treated with antidiabetic and / or antihypertensive drugs , but their blood glucose and bp control were insufficient . diabetic retinopathy and / or neuropathy were present in 165 ( 78 % ) patients . during a mean of 4.5 years follow - up ( median 4.2 years [ iqr 2.45.8 ] ) after the initiation of intensive diabetes treatment , 116 patients ( 55 % ) obtained remission to acr 300 mg / g cr , including 28 patients ( 13 % ) with acr 30 mg / g cr ( table 2 ) . most of the cases obtained the remission to acr 300 mg / g cr at the 1 - year study time point after starting the intensive treatment . the 5 - year cumulative incidences of remission to acr 300 mg / g cr and 30 mg / g cr were 58.3 and 18.5 % , respectively . baseline characteristics of t2 dm subjects with acr 300 mg / g cr and egfr 30 ml / min / 1.73 m number of patients who obtained remission to acr 300 mg / g cr or 30 mg / g cr and the cumulative incidence at each 1 - year study time point the clinical characteristics of the study groups stratified by remission of macroalbuminuria ( categorical analysis ) or of those stratified by a reduction in acr of 50 % ( continuous analysis ) are shown in table 3 . both comparisons indicated significantly higher proportions of female sex and nonsmoking in the albuminuria reduction groups . baseline values of acr were not different between the two study groups in continuous analysis , whereas these were significantly lower in the albuminuria reduction groups in categorical analysis . otherwise , no major differences were found with respect to baseline characteristics among the groups . at 1 year , patients with remission or albuminuria reduction of 50 % had lower hba1c and systolic bp levels and a higher proportion taking lipid - lowering drugs . both categorical and continuous analyses in the whole period of follow - up indicated a clearly beneficial effect of albuminuria reduction on gfr decline and the onset of doubling serum cr or esrd . the overall incidence of esrd ( per 1,000 person - years ) was 13.6 ( 95 % ci 7.323.2 ) , and it was high in subjects with persistent macroalbuminuria ( 25.1 [ 13.442.5 ] ) and in subjects with albuminuria reduction of 50 % ( 35.4 [ 20.356.7 ] ) . clinical data at baseline , at 1 year , and in the whole period of follow - up , which were compared among groups with or without remission to microalbuminuria and normoalbuminuria ( categorical analysis ) and between those with albuminuria reduction of 50 % from the baseline and those without ( continuous analysis ) among 116 subjects with remission to acr 300 mg / g cr , 67 ( 57.8 % ) patients remained in remission until the end of follow - up , with a follow - up time of 4.12.2 years and a duration of remission of 3.52.0 years , and 49 ( 42.2 % ) patients relapsed from remission , with a follow - up time of 5.82.1 years and duration of remission of 3.42.0 years . no differences were found with respect to clinical characteristics , including renal events between patients without and with relapse , except for the final acr , with the median being significantly higher in patients with relapse ( 323.9 [ iqr 111.3574.6 ] ) than in those without ( 102.0 [ 49.8174.5 ] , p 0.0001 ) . the combined effects of systolic bp and hba1c on remission to acr 300 mg / g cr are presented in table 4 . patients were stratified according to predefined target levels of systolic bp and hba1c at 1 year . the achievement of the systolic bp therapeutic target significantly increased the remission rate whether the hba1c target was achieved or not , and bp and blood glucose control increased the remission rate significantly . of interest , similar significant ors were obtained when the analysis was confined to subjects with higher acr or lower acr divided by the median acr ( data not shown ) , and rates of remission were apparently lower in subjects with higher acr than those with lower acr ( 34.9 vs. 75.2 % , p 0.0001 ) . furthermore , the rates of patients obtaining remission to acr 300 mg / g cr according to quartiles of systolic bp at 1 year ( 142 , 141132 , 131124 , and 124 mmhg ) were 36 , 46 , 68 , and 74 % , respectively . according to quartiles of hba1c at 1 year ( 8.0 , 7.97.3 , 7.26.7 , and 6.7 % ) , the rates were 44 , 50 , 70 , and 56 % , respectively . if continuous data were used , the or ( 95 % ci ) for remission to acr 300 mg / g cr associated with a 10 - mmhg decline in systolic bp at 1 year was 2.23 ( 1.483.36 ) ( p 0.0001 ) and with a reduction of 1 % in hba1c was 1.41 ( 1.041.92 ) ( p = 0.03 ) after adjustment for the baseline clinical covariates . rates and adjusted ors for remission to acr 300 mg / g cr in subjects stratified by achievement of target levels of systolic bp and hba1c at 1 year after starting intensive diabetes treatment finally , the association of the combined effect of remission of macroalbuminuria and reduction of 50 % in albuminuria at the 1 - year study time point with renal events ( onset of doubling serum cr and esrd ) was investigated . percentages of the events ( number of events / total number of patients ) were 9.2 ( 8/87 ) , 22.2 ( 2/9 ) , 27.3 ( 6/22 ) , and 29.0 ( 27/93 ) in groups with remission + / reduction + , remission + / reduction , remission / reduction + , and remission / reduction , respectively . as compared with those with no remission and no reduction , hazard ratios ( 95 % ci ) adjusted for baseline clinical covariates ( table 4 , model 2 ) were 0.30 ( 0.120.76 ) with obtaining both remission and reduction and 0.79 ( 0.341.82 ) with obtaining either remission or reduction . we found in this study that 1 ) more than half of patients with macroalbuminuria obtained remission to microalbuminuria after the intensive diabetes treatment in a primary care setting , 2 ) the rate of remission increased according to the achievement of therapeutic targets for bp and blood glucose , and 3 ) the reduction in macroalbuminuria at the 1 - year study time point after starting the intensive diabetes treatment was associated with the preservation of renal function . these results suggest that the progressive decline in renal function of t2 dm with macroalbuminuria can be prevented by adequate diabetes treatment in a primary care setting . in particular , whether or not the reduction in macroalbuminuria can be achieved soon after starting the intensive diabetes treatment is quite important with respect to renal prognosis . given that the risk for esrd is directly and strongly related to the level of albuminuria ( 6 ) , and that reductions in albuminuria are associated with reductions in the risk for esrd ( 7 ) , the beneficial effects of the results on such outcomes obtained in the primary care setting can be anticipated in the longer term . this study showed that the 5 - year cumulative incidence rates of remission from macroalbuminuria to microalbuminuria or normoalbuminuria were 58.3 or 18.5 % . to date , a few clinical studies have reported the rate of remission from macroalbuminuria to microalbuminuria or normoalbuminuria in t2 dm . the action in diabetes and vascular disease : preterax and diamicron mr controlled evaluation ( advance ) study reported that 229 ( 57.1 % ) of 401 t2 dm subjects with macroalbuminuria obtained remission to microalbuminuria ( n = 131 ) or normoalbuminuria ( n = 98 ) in 4.3 years ( 2 ) . the action to control cardiovascular risk in diabetes ( accord ) study also indicated that 101 ( 42.6 % ) of 237 patients with macroalbuminuria obtained remission over 4.7 years of observation ( 3 ) . the jddm study also reported that 39 ( 22.3 % ) of 136 patients obtained remission over 3.8 years of observation ( 10 ) . overall , these results clearly indicate that remission of macroalbuminuria in patients with t2 dm is not rare and can be frequently achieved by the adequate diabetes treatment . notably , remission occurred at the 1 - year study time point after starting the intensive treatment in 96 ( 82.8 % ) of 116 patients who obtained remission , and the reduction in albuminuria in response to the initial intensive treatment was valuable in terms of predicting renal prognosis . the high remission rate seen in the early course of treatment may be attributable to insufficient prior controls , or may reflect the preserved renal function at that time . on the other hand , a considerable number of patients did not show a reduction in macroalbuminuria . male sex and smoking were also associated with unresponsiveness , which is consistent with previous studies indicating that these were risk factors for albuminuria progression and renal function loss in subjects with nephropathy ( 4,5,11 ) . the unresponsiveness to the intensive treatment may be explained by the existence of irreversible structural alterations in the kidneys or genetic differences , which may be responsible for the variability in responses to treatment . in terms of the effect on remissionit was interesting that the or for obtaining remission was similar between those with higher and lower albuminuria . this may indicate that there is no threshold of albuminuria that discriminates the response to the intensive diabetes treatment . the remission rate of 34.9 % seen in subjects with higher albuminuria ( 815.8 mg / g cr ) , together with a report indicating that 26 % ( 32/122 ) of patients showed a reduction in nephrotic range albuminuria after aggressive lowering of bp in type 1 diabetes ( 4 ) , may support the commencing of intensive treatment , although the remission rate itself is low due to the severity of existing glomerular damage as reflected by high albuminuria . in addition , the higher proportion of lipid modification treatment observed in subjects with a reduction in albuminuria may indicate the pleiotropic effect of lipid - lowering drugs on albuminuria reduction ( 12 ) , although differences in lipid profiles were not prominent between the groups . otherwise , no differences were found between the two . as reported in type 1 diabetes , 46 % of subjects who obtained remission of macroalbuminuria experienced relapse ( 5 ) , so this phenomenon of relapse is common . the implications of relapse should be considered carefully , and longer follow - up is required on this issue . we should acknowledge that the single measurement of acr at the baseline may have included patients with microalbuminuria because of the physiological variation in albuminuria , leading to an overestimation of remission rate from macroalbuminuria . however , data on albuminuria in each year after starting the intensive treatment were collected from multiple urine samples , and changes in albuminuria from the baseline level were analyzed in two ways : improvement in stage of diabetic nephropathy and percent albuminuria change from the baseline . a serious problem inherent in an observational cohort study is the reason for censoring . some censored cases were due to the end of the observation period , but in 30 % of the subjects in our study , they were due to loss of follow - up . loss of follow - up was likely due to moving to other cities / hospitals or discontinuation of treatment . those due to nonattendance are likely to develop events , since medication noncompliance and clinic nonattendance are closely associated with development of complications ( 13 ) . this survival effect may have yielded an overestimation of remission in this study . we believe that the present prospective observational cohort simply reflected real - world practice and is valuable and important . in conclusion , this study showed that a reduction in macroalbuminuria of t2 dm subjects frequently occurred and was associated with the preservation of renal function . this result expands the concept regarding the effect of remission of microalbuminuria to normoalbuminuria on the improvement of renal prognosis in patients with t2 dm ( 14,15 ) . taken together , these results strongly suggest the importance of adequate initial intervention aimed at reducing albuminuria to improve renal prognosis in t2 dm patients in primary care practice .\noutput:\n" }, { "from": "agent", "value": "objectivestudies on the rate of remission of macroalbuminuria in patients with type 2 diabetes mellitus ( t2 dm ) and the effects of reduction in albuminuria on renal prognosis in a primary care setting are absolutely lacking.research design and methodsa total of 211 t2 dm patients with albuminuria 300 mg / g were enrolled in a prospective observational study ( mean of 4.5 years ) . the incidence of patients with remission of macroalbuminuria at every 1 - year study time point after starting intensified diabetes treatment and the factors associated with remission were evaluated . the association of reduction in albuminuria with renal events ( doubling of serum creatinine and end - stage renal disease ) was also investigated.resultsduring the 5 - year study period , remission to microalbuminuria occurred in 116 patients and the 5 - year cumulative incidence was 58.3 % . notably , most cases ( 82.8 % ) obtained remission at the 1 - year study time point . the remission rate increased with achieving therapeutic targets for blood pressure and blood glucose . remission and reduction in albuminuria of 50 % were associated with preservation of renal function . in particular , patients who obtained both remission and 50 % reduction at the 1 - year study time point exhibited a significantly reduced risk for renal events as compared with those with no remission and no reduction ( adjusted hazard ratio 0.30 [ 95 % ci 0.120.76 ] ) . conclusionsremission of macroalbuminuria occurs frequently and is associated with the preservation of renal function in t2 dm patients . the initial adequate diabetes treatment aimed at reducing albuminuria may lead to improved renal prognosis in the primary care setting ." } ]

[ { "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: addiction is a biological , mental and social illness viewed as one of the four prominent social damages interlinking poverty , unemployment and divorce ( 1 ) . because of its progressive nature through all aspects of life , addiction endangers people s health , and its adverse effects on mental , physical , social , emotional , spiritual and cognitive health are clear ( 2 ) . addiction is based on an uncontrolled desire to enjoy and reduce stress in a person with personality and behavior disorders ( 3 , 4 ) . it seems that personality traits have significant effects on individuals behaviors ; addiction is no exception to this rule . askari believes that personality traits and predisposition are related addiction ( 5 ) . around three quarters of patients who sought treatment for drug abuse had a history of psychiatric disorders and two - thirds suffered from psychiatric disorders along with their drug abuse ( 6 ) , and , about 90 % of them also suffered from a psychiatric or personality disorder , simultaneously ( 7 ) . from a psychological perspective , nearly 30 % 60 % of drug addicts meet the diagnostic criteria for antisocial personality disorder , while this is 2 % 3 % in the normal population ( 9 ) . the most prevalent psychiatric diagnoses include major depressive disorder , alcohol - related disorders , antisocial personality disorders , and anxiety disorder ( 7 , 10 ) . ( 7 ) studied opium and heroin addicts , demonstrating that the most frequent psychological characteristics in these addicts were hysteria and depression . there was a significant correlation between abnormal personal characteristics and educational level ( 11 ) . there was a significant difference between the case and control groups in terms of hypochondria and hysteria ( 12 ) . identification and understanding of behavioral factors are therefore necessary to prevent these problems . in thisregard , understanding personality traits of drug addicts is one of the important factors ( 15 , 16 ) ; a better understanding of drug addicts personality disorders allows for more comprehensive planning to treat these patients according to their dominant personality , and provides policymakers in the health and drug control sectors with opportunities to develop more efficient preventive programs in the society . regarding the importance of the problem of addiction , one approach to reduce the demand for drugs includes the three areas of prevention , treatment , and harm reduction . drug rehabilitation centers are considered as one of the important tools of performing these macro policies ( 17 ) . the establishment of drug rehabilitation centers in the society provides addicts with the possibility to access the services more easily . addicts enjoy the social and clinical support by visiting these centers to undergo treatment for addiction . also , such centers help to minimize the possibility of return to addiction . in fact , in these centers , addicts enjoy the advantages of the existence of social capital which has an important and effective influence on their self - esteem ( 18 ) . therefore , in order to help achieve this aim , this paper investigated the personality traits of drug addicts in a drug rehabilitation center in the city of isfahan . it sought the following objectives : 1 . determining the demographic characteristics of the sample , 2 . determining addicts psychological profiles as divided by the type of drug , and personal and social characteristics , and 3 . determining the relationship of psychological profiles to type of drug as well as personal and social characteristics . in this analytical cross - sectional study performed in 2012 , the population consisted of all addicts who had referred to shefa drug rehabilitation center , isfahan , iran . to perform this studypersonal information of participants that completed the questionnaires , remains confidential and only the required data was analyzed . participants completed questionnaires by the consent and knowledge and the ethics committee approved this study . two questionnaires were used to collect data ; the first questionnaire examined family , social , and economic demographic characteristics of the subjects and the second one was minnesota multi - phasic personality inventory ( mmpi ) . the 71 - item mmpi short form was developed by kincannon ( 19 ) and it is used widely in iranian studies ( 3 , 7 , 1113 ) , so its validity is proved ( 20 ) . besides , the reliability of this questionnaire has been examined and verified ( 21 ) . this test consists of 11 standard scales , 3 of which are related to validity scales and the other 8 scales are related to clinical or personality scales . clinical scales are hypochondrias ( hs ) , depression ( d ) , hysteria ( hy ) , psychopathic deviation ( pd ) , paranoia ( pa ) , psychasthenia ( pt ) , schizophrenia ( sc ) , and mania or hypomania ( ma ) ( 11 ) . these characteristics are explained as follows : l scale ( 5 items , this validity scale is used to detect attempts by individuals to present themselves in a favorable light . ) f scale ( 15 items , it measures exceptional and deviant responses provided by individuals . high scores on this test can be considered as a general pathological index . ) k scale ( 16 items , it is developed to detect individuals who attempt to present themselves in the best possible way . ) hs scale ( 14 items , hypochondria is a psychological disorder which refers to individuals excessive preoccupation for their health . the patient suffers from painful emotional perceptions , and tends to attribute them to nonexistent bodily disorders and to ask for help . ) d scale ( 20 items , it is characterized by low activity , fatigue and low energy , substantially decreased interest in enjoyable activities , sadness , stress , lack of mental focus , hopelessness and desperateness , loss of confidence , insomnia or constant sleeping , weight loss or gain , slowness of thought , feeling of guilt , and thoughts of suicide . ) hy scale ( 25 items , it is characterized by preliminary social behaviors , need to be loved and helped out by others , childish reactions to failures , physical and psychological disorders without bodily origin . ) pd scale ( 19 items , it includes characteristics such as lack of responsibility , lack of moral perception , inattention to others , uncontrolled behaviors and actions , lack of feeling of guilt , impulsiveness and immediate satisfaction of needs , and inability to show sympathy or loyalty . ) pa scale ( 13 items , it includes characteristics such as chronic suspicion , lack of trust in others and ascribing one s own undesirable tendencies to others , irritability , and rigidity in morals and logic . ) pt scale ( 16 items , it is related to stress , anxiety , and irrational and unfounded apprehension . ) sc scale ( 20 items , it is characterized by odd behaviors and actions , isolation , misanthropy , sense of difference from others , feeling of not being understood by people , loneliness , and dissatisfaction with family status . ) ma scale ( 12 items , it is characterized by high activity , intense emotional states , interruption in the train of thought , pleasure accompanied by self - confidence , indifference , and mobility and restlessness . ) l scale ( 5 items , this validity scale is used to detect attempts by individuals to present themselves in a favorable light . ) f scale ( 15 items , it measures exceptional and deviant responses provided by individuals . k scale ( 16 items , it is developed to detect individuals who attempt to present themselves in the best possible way . ) hs scale ( 14 items , hypochondria is a psychological disorder which refers to individuals excessive preoccupation for their health . the patient suffers from painful emotional perceptions , and tends to attribute them to nonexistent bodily disorders and to ask for help . ) d scale ( 20 items , it is characterized by low activity , fatigue and low energy , substantially decreased interest in enjoyable activities , sadness , stress , lack of mental focus , hopelessness and desperateness , loss of confidence , insomnia or constant sleeping , weight loss or gain , slowness of thought , feeling of guilt , and thoughts of suicide . ) hy scale ( 25 items , it is characterized by preliminary social behaviors , need to be loved and helped out by others , childish reactions to failures , physical and psychological disorders without bodily origin . ) pd scale ( 19 items , it includes characteristics such as lack of responsibility , lack of moral perception , inattention to others , uncontrolled behaviors and actions , lack of feeling of guilt , impulsiveness and immediate satisfaction of needs , and inability to show sympathy or loyalty . ) pa scale ( 13 items , it includes characteristics such as chronic suspicion , lack of trust in others and ascribing one s own undesirable tendencies to others , irritability , and rigidity in morals and logic . ) pt scale ( 16 items , it is related to stress , anxiety , and irrational and unfounded apprehension . ) sc scale ( 20 items , it is characterized by odd behaviors and actions , isolation , misanthropy , sense of difference from others , feeling of not being understood by people , loneliness , and dissatisfaction with family status . ) ma scale ( 12 items , it is characterized by high activity , intense emotional states , interruption in the train of thought , pleasure accompanied by self - confidence , indifference , and mobility and restlessness . ) ( 3 ) . the inclusion criteria included addicts who visited this center for treating addiction and receiving health care and who were willing to fill both questionnaires . in addition , another inclusion criterion was those who had at least 6 months of experience in addiction . this study was conducted under the aegis of daman sanat sepahan company of isfahan , iran . considering its vision of promoting applied knowledge and contributing to evidence - based decision - making , this company laid the foundation for conducting research , and , finally , after confirmation by its research and development unit , the findings were finalized . when questionnaires were completed and gathered , data were drawn and compared by considering their keys on the profile , and then they were analyzed individually . for data analysis , various methods of descriptive statistics such as frequency distribution , mean , standard deviation , percentage , and of inferential statistics such as chi - square , fisher s , and kruskal - wallis test as well as spss20 software ( chicago , il , usa ) were used . in this analytical cross - sectional study performed in 2012 , the population consisted of all addicts who had referred to shefa drug rehabilitation center , isfahan , iran . to perform this studypersonal information of participants that completed the questionnaires , remains confidential and only the required data was analyzed . participants completed questionnaires by the consent and knowledge and the ethics committee approved this study . two questionnaires were used to collect data ; the first questionnaire examined family , social , and economic demographic characteristics of the subjects and the second one was minnesota multi - phasic personality inventory ( mmpi ) . the 71 - item mmpi short form was developed by kincannon ( 19 ) and it is used widely in iranian studies ( 3 , 7 , 1113 ) , so its validity is proved ( 20 ) . besides , the reliability of this questionnaire has been examined and verified ( 21 ) . this test consists of 11 standard scales , 3 of which are related to validity scales and the other 8 scales are related to clinical or personality scales . clinical scales are hypochondrias ( hs ) , depression ( d ) , hysteria ( hy ) , psychopathic deviation ( pd ) , paranoia ( pa ) , psychasthenia ( pt ) , schizophrenia ( sc ) , and mania or hypomania ( ma ) ( 11 ) . these characteristics are explained as follows : l scale ( 5 items , this validity scale is used to detect attempts by individuals to present themselves in a favorable light . ) f scale ( 15 items , it measures exceptional and deviant responses provided by individuals . high scores on this test can be considered as a general pathological index . ) k scale ( 16 items , it is developed to detect individuals who attempt to present themselves in the best possible way . ) hs scale ( 14 items , hypochondria is a psychological disorder which refers to individuals excessive preoccupation for their health . the patient suffers from painful emotional perceptions , and tends to attribute them to nonexistent bodily disorders and to ask for help . ) d scale ( 20 items , it is characterized by low activity , fatigue and low energy , substantially decreased interest in enjoyable activities , sadness , stress , lack of mental focus , hopelessness and desperateness , loss of confidence , insomnia or constant sleeping , weight loss or gain , slowness of thought , feeling of guilt , and thoughts of suicide . ) hy scale ( 25 items , it is characterized by preliminary social behaviors , need to be loved and helped out by others , childish reactions to failures , physical and psychological disorders without bodily origin . ) pd scale ( 19 items , it includes characteristics such as lack of responsibility , lack of moral perception , inattention to others , uncontrolled behaviors and actions , lack of feeling of guilt , impulsiveness and immediate satisfaction of needs , and inability to show sympathy or loyalty . ) pa scale ( 13 items , it includes characteristics such as chronic suspicion , lack of trust in others and ascribing one s own undesirable tendencies to others , irritability , and rigidity in morals and logic . ) pt scale ( 16 items , it is related to stress , anxiety , and irrational and unfounded apprehension . ) sc scale ( 20 items , it is characterized by odd behaviors and actions , isolation , misanthropy , sense of difference from others , feeling of not being understood by people , loneliness , and dissatisfaction with family status . ) ma scale ( 12 items , it is characterized by high activity , intense emotional states , interruption in the train of thought , pleasure accompanied by self - confidence , indifference , and mobility and restlessness . ) ( 3 ) . l scale ( 5 items , this validity scale is used to detect attempts by individuals to present themselves in a favorable light . ) f scale ( 15 items , it measures exceptional and deviant responses provided by individuals . k scale ( 16 items , it is developed to detect individuals who attempt to present themselves in the best possible way . ) hs scale ( 14 items , hypochondria is a psychological disorder which refers to individuals excessive preoccupation for their health . the patient suffers from painful emotional perceptions , and tends to attribute them to nonexistent bodily disorders and to ask for help . ) d scale ( 20 items , it is characterized by low activity , fatigue and low energy , substantially decreased interest in enjoyable activities , sadness , stress , lack of mental focus , hopelessness and desperateness , loss of confidence , insomnia or constant sleeping , weight loss or gain , slowness of thought , feeling of guilt , and thoughts of suicide . ) hy scale ( 25 items , it is characterized by preliminary social behaviors , need to be loved and helped out by others , childish reactions to failures , physical and psychological disorders without bodily origin . ) pd scale ( 19 items , it includes characteristics such as lack of responsibility , lack of moral perception , inattention to others , uncontrolled behaviors and actions , lack of feeling of guilt , impulsiveness and immediate satisfaction of needs , and inability to show sympathy or loyalty . ) pa scale ( 13 items , it includes characteristics such as chronic suspicion , lack of trust in others and ascribing one s own undesirable tendencies to others , irritability , and rigidity in morals and logic . ) pt scale ( 16 items , it is related to stress , anxiety , and irrational and unfounded apprehension . ) sc scale ( 20 items , it is characterized by odd behaviors and actions , isolation , misanthropy , sense of difference from others , feeling of not being understood by people , loneliness , and dissatisfaction with family status . ) ma scale ( 12 items , it is characterized by high activity , intense emotional states , interruption in the train of thought , pleasure accompanied by self - confidence , indifference , and mobility and restlessness . ) ( 3 ) . the inclusion criteria included addicts who visited this center for treating addiction and receiving health care and who were willing to fill both questionnaires . in addition , another inclusion criterion was those who had at least 6 months of experience in addiction . this study was conducted under the aegis of daman sanat sepahan company of isfahan , iran . considering its vision of promoting applied knowledge and contributing to evidence - based decision - making , this company laid the foundation for conducting research , and , finally , after confirmation by its research and development unit , the findings were finalized . when questionnaires were completed and gathered , data were drawn and compared by considering their keys on the profile , and then they were analyzed individually . for data analysis , various methods of descriptive statistics such as frequency distribution , mean , standard deviation , percentage , and of inferential statistics such as chi - square , fisher s , and kruskal - wallis test as well as spss20 software ( chicago , il , usa ) were used . eighty five percent ( 85 % ) of the participants had a high school diploma or a lower degree , and 15 % of them had academic education . forty six percent of the participants owned their houses and 54 % lived in rented houses . table 1 indicates that , among different groups , cigarette was used more than other types of drugs . frequency distribution of drug type divided by demographic characteristics the average age of participants was 37 , the oldest was 67 and the youngest was 20 . the average age of drug abusers was 21 , the youngest person was 11 and the oldest was 47 . eighty percent of the participants started drug abuse with cigarette , 62 % with opium , 15 % with hashish , 15 % with other drugs , and 23.6 % had also experienced drug injection . at the time of completing the questionnaires , 89.4 % of participants smoked cigarette and 20.7 % smoked hashish , 19 % used methamphetamine , and 29.1 % of participants drank alcohol . as illustrated by table 2 , among individuals with abnormal or high risk psychological profiles , l scale and k scale had respectively the highest and lowest percentages among validity scales respectively . among the clinical scales , depression and hypomania were the most and least prevalent scales , respectively . a comparison of low risk , at risk , and high risk sections reveals that in all scales , except k scale , at risk individuals have high scores . table 3 indicates that , among validity scales , l and f were mostly relevant to men and women , respectively . among the clinical scales , depression was highly related to men , and women s share was higher in schizophrenia scale . psychological profiles divided by addicts range of risk frequency distribution of personality traits as divided by demographic characteristics individuals with different marital , education and home status have scored higher on l and depression scales . as regards occupation , psychopathic deviation and schizophrenia scales are mainly related to unemployed addicts . the employed had a greater percentage in terms of depression and hypochondrias scales , and self - employed individuals suffered from depression more than other scales . table 4 suggests that , among cigarette smokers , l and depression scales had the highest frequency . among hashish addictsf and depression scales were the most frequent , while l and schizophrenia scales were mainly related to methamphetamine abusers . f , depression , and schizophrenia scales were the most frequent ones among alcoholics . frequency distribution of personality traits as divided by drug type chi - square , fisher s , annova , and kruskal - wallis tests were then used to investigate the relationships between personality traits and factors such as gender , marital status , occupation , education , home status , drug abuse , drug injection , type of drug abuse , history of excessive drug abuse , history of aggression , delirium , and hallucination , history of hospitalization in psychiatric centers , history of psychiatric medications , history of withdrawal and treatment , major problematic narcotics ( opium , heroin , crack , norgesic , methamphetamine , hashish , alcohol , cocaine , sedatives and hypnotics , and other drug combinations ) , income , beginning age of drug abuse , beginning age of addiction , duration of drug abuse , the longest withdrawal time , and number of imprisonment times . these are presented bellow as divided by the results relevant to each personality trait : according to chi - square and fisher s exact tests ; d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc scale was significantly related to the norgesic use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . f and d scales was significantly related to marital status ( p 0.05 ) . hy scale was significantly related to occupation ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . according to kruskal - wallis test ; l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l scale was significantly related to duration of cigarette use ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . according to chi - square and fisher s exact tests ; d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc scale was significantly related to the norgesic use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . f and d scales was significantly related to marital status ( p 0.05 ) . hy scale was significantly related to occupation ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . according to kruskal - wallis test ; l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l scale was significantly related to duration of cigarette use ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . eighty five percent ( 85 % ) of the participants had a high school diploma or a lower degree , and 15 % of them had academic education . forty six percent of the participants owned their houses and 54 % lived in rented houses . table 1 indicates that , among different groups , cigarette was used more than other types of drugs . frequency distribution of drug type divided by demographic characteristics the average age of participants was 37 , the oldest was 67 and the youngest was 20 . the average age of drug abusers was 21 , the youngest person was 11 and the oldest was 47 . eighty percent of the participants started drug abuse with cigarette , 62 % with opium , 15 % with hashish , 15 % with other drugs , and 23.6 % had also experienced drug injection . at the time of completing the questionnaires , 89.4 % of participants smoked cigarette and 20.7 % smoked hashish , 19 % used methamphetamine , and 29.1 % of participants drank alcohol . as illustrated by table 2 , among individuals with abnormal or high risk psychological profiles , l scale and k scale had respectively the highest and lowest percentages among validity scales respectively . among the clinical scales , a comparison of low risk , at risk , and high risk sections reveals that in all scales , except k scale , at risk individuals have high scores . table 3 indicates that , among validity scales , l and f were mostly relevant to men and women , respectively . among the clinical scales , depression was highly related to men , and women s share was higher in schizophrenia scale . psychological profiles divided by addicts range of risk frequency distribution of personality traits as divided by demographic characteristics individuals with different marital , education and home status have scored higher on l and depression scales . as regards occupation , psychopathic deviation and schizophrenia scales are mainly related to unemployed addicts . the employed had a greater percentage in terms of depression and hypochondrias scales , and self - employed individuals suffered from depression more than other scales . table 4 suggests that , among cigarette smokers , l and depression scales had the highest frequency . among hashish addictsf and depression scales were the most frequent , while l and schizophrenia scales were mainly related to methamphetamine abusers . f , depression , and schizophrenia scales were the most frequent ones among alcoholics . frequency distribution of personality traits as divided by drug type chi - square , fisher s , annova , and kruskal - wallis tests were then used to investigate the relationships between personality traits and factors such as gender , marital status , occupation , education , home status , drug abuse , drug injection , type of drug abuse , history of excessive drug abuse , history of aggression , delirium , and hallucination , history of hospitalization in psychiatric centers , history of psychiatric medications , history of withdrawal and treatment , major problematic narcotics ( opium , heroin , crack , norgesic , methamphetamine , hashish , alcohol , cocaine , sedatives and hypnotics , and other drug combinations ) , income , beginning age of drug abuse , beginning age of addiction , duration of drug abuse , the longest withdrawal time , and number of imprisonment times . these are presented bellow as divided by the results relevant to each personality trait : according to chi - square and fisher s exact tests ; d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc scale was significantly related to the norgesic use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . f and d scales was significantly related to marital status ( p 0.05 ) . hy scale was significantly related to occupation ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . according to kruskal - wallis test ; l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l scale was significantly related to duration of cigarette use ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . according to chi - square and fisher s exact tests ; d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc scale was significantly related to the norgesic use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . f and d scales was significantly related to marital status ( p 0.05 ) . hy scale was significantly related to occupation ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . d scale was significantly related to the use of cigarette and cocaine use ( p 0.05 ) . l , f , sc , hy , ma , pd and pa scales was significantly related to the use of alcohol ( p 0.05 ) . l , sc , d , ps , ma , hy , pd and hs scales was significantly related to the use of hashish ( p 0.05 ) . sc , ps , ma , pd and hs scales was significantly related to the methamphetamine abuse ( p 0.05 ) . l , sc , d , ps and pd scales was significantly related to the heroin use ( p 0.05 ) . l and ma scales was significantly related to the crack use ( p 0.05 ) . sc , pd and pa scales was significantly related to the opium use ( p 0.05 ) . ps and hy scales was significantly related to the sedatives and hypnotics medications ( p 0.05 ) . l , f , sc , ps , pd and ps scales was significantly related to the psychiatric medications ( p 0.05 ) . sc , ps , pd and pa scales was significantly related to the history of drug injection ( p 0.05 ) . l , k , sc and pd scales was significantly related to the history of addiction withdrawal and treatment ( p 0.05 ) f , sc , d , ps pd and pa scales was significantly related to the history of aggression , delirium and hallucination ( p 0.05 ) . f and pd scales was significantly related to the history of hospitalization in psychiatric centers ( p 0.05 ) . pa scale was significantly related to education , and major ( p 0.05 ) . according to kruskal - wallis test ; l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l scale was significantly related to duration of cigarette use ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . l , sc , d , pd and hs scales was significantly related to age ( p 0.05 ) . l , sc , ps and pd scales was significantly related to beginning age of addiction ( p 0.05 ) . l and f scales was significantly related to duration of methamphetamine abuse ( p 0.05 ) . l , sc , ps , pd and pa scales was significantly related to number of imprisonment periods ( p 0.05 ) . sc , d , ps , pd and hs scales was significantly related to the duration of hashish use ( p 0.05 ) . the results of this research indicated that addiction was highly prevalent among men , married individuals , and individuals with education below high school diploma ; this is in line with findings made by previous studies ( 12 , 13 , 22 ) . in the present study , hashish abuse had the third rank , and , in motozaker s study conducted in the drug rehabilitation ward of a hospital , heroin abuse had the first rank ( 23 ) . in the present research , 23.6 % of the participants had a history of drug injection ; this was 14.8 % in the study by sahebolzamani et al . findings revealed that the average age of drug abuse was 21 and the average age of addiction was 24 . thirty six percent of addicts began using drugs when they were under 20 ( 7 ) . in the study conducted in drug rehabilitation centers , the beginning age of drug abuse was obtained at 21 years old ( 24 ) . previous studies found that 38 % of visitors to california mental health center reported the use of at least one or more drugs ; 21 % also reported use of at least three ( or more ) types of illegal drugs ( 25 ) . in the present research , among individuals with abnormal or high risk psychological profiles , depression and hypomania were respectively the most and the least prevalent clinical scales . also , depression had a significant role in killen s study ( 26 ) . in their investigation of addicts in drug rehabilitation centers , shargh et al . concluded that the feelings of loneliness and isolation were among the causes of return to addiction ( 27 ) . with respect to the existence of psychiatric disorders in addicts , the findings are consistent with previous studies ( 2830 ) . the rate of depression was 24.4 % in the present study and 26.4 % in miller s ( 28 ) . in a research on addicts ,44 % of addicts suffered from psychopathic deviation disorder and 24 % had depression ( 31 ) . fifty percent of addicts suffered from mental and social problems ( 33 ) . having addicted friends who have made no effort to treat it , serves as a motive for addiction , and raises its severity ( 34 ) . therefore , drug rehabilitation centers are helpful and can introduce motivated individuals to one another and provide appropriate social support for addicts . among individuals with abnormal or high risk psychological profiles , l scale and k scales of validity had the highest and lowest percentage , respectively . participants scored low on these scales ( 3 ) , which was interpreted as absence of psychological defense mechanism in the individuals . among validity scales , l was mostly related to men and f to women . among clinical scales , the depression scale was highly related to men , and women s proportion was higher in the schizophrenia scale . individuals with different marital , education , and housing status scored higher on l and depression scales , which is in line with another study ( 3 ) . as regards occupation , psychopathic deviation and schizophrenia scales were mainly related to unemployed addicts . employees had a greater percentage in terms of depression and hypochondriasis scales , and self - employed individuals suffered from depression more than other scales . in their study conducted in drug rehabilitation centers , investigated the factors contributing to return to addiction , concluding that unemployment was an important factor in the return to drug abuse ( 35 ) . among cigarette smokers , l and depression scales had the highest frequency . among hashish addicts , f and depression scales were the most frequent , while l and schizophrenia scales were mainly related to methamphetamine users . various studies about simultaneous outbreak of drug abuse and psychological disorders indicate that the amount of alcohol and drug abuse is significantly higher among individuals who seek help from mental health centers than ordinary people ( 36 ) . compared to ordinary people , the risk of addiction to alcohol and drugs is 21 times as high in individuals with psychopathic personality disorders , 6 times as high in people with hypomania , 4 times as high in schizophrenics and twice as high in individuals with panic disorders ( 37 , 38 ) . drake found that 37 % of alcohol abusers and 53 % of drug abusers suffered at least from one serious mental illness ( 39 ) . in this research , l scale was significantly related to the use of hashish , alcohol , major problematic narcotics including heroin and crack , psychiatric medications , history of withdrawal and treatment , age , beginning age of addiction , duration of use of cigarettes and methamphetamine , and number of imprisonment periods . however , l scale was significantly related to housing status and education and k scale was significantly related to housing , education and marital status ( 3 ) . depression scale in the present study was significantly related to marital status ; use of cigarettes and hashish ; major problematic narcotics including heroin and cocaine ; history of aggression , delirium and hallucination ; and age and duration of hashish use . hypomania scale , on the other hand , according to fisher s exact test , was significantly related only to major problematic narcotics including crack , methamphetamine , hashish , and alcohol . this study suggested that personality disorders were prevalent among drug addicts ; therefore those therapies which lack pre - assessment of addiction - predisposing factors and are not defined according to personal characteristics of patients lose the chance of offering complete treatment . it is then necessary to include psychological therapies in treatment programs for addicts in order to identify the gaps in their personalities and define the treatment period according to each person s mental needs . the paper also showed that different drugs had different effects on personality disorders and could highlight or marginalize a particular scale . findings also revealed that demographic backgrounds affect personality disorders in addicts which can be investigated more widely for sociological planning and prevention of social abnormalities . therefore , for treatment of drug addicts it is essential to therapists to consider a triangle of demographic characteristics , type of drug , and personality disorders in their analysis of patients . considering the fact that depression was the most common personality disorder among the addicts participating in this study , it is recommended that this disorder be given priority in investigations in the treatment programs of these patients . in addition , the scales of disorder , schizophrenia , mental infirmity , mental deviation , and paranoia had a significant relationship to aggression , delirium and hallucination , which must be taken into consideration in the treatment of such patients . ethical issues ( including plagiarism , informed consent , misconduct , data fabrication and / or falsification , double publication and / or submission , redundancy , etc . ) have been completely observed by the authors\noutput:\n" }, { "from": "agent", "value": "background : addiction is one of the most serious social damages and due to its progressive nature in all aspects , adversely affects people s physical and psychological health . hence , this paper investigates the characteristics of drug addicts in a drug rehabilitation center in the city of isfahan.methods : in this cross - sectional study conducted in 2012 , the population consisted of all addicts that referred to shefa drug rehabilitation center . a sample of 201 individuals was selected randomly . two questionnaires were drawn up to collect data ; the first questionnaire examined demographic characteristics and the second was the 71 - item minnesota multiphase personality inventory short form . chi - square test , fisher s exact test and kruskal - wallis test were used in spss20 to analyze the data.results : overall , 98 % of participants were men , 65.7 % were married , and 13.3 % were unemployed . depression and hypomania were respectively the most and the least prevalent disorders among individuals with high - risk psychological profiles of clinical scales respectively . psychopathic deviation and schizophrenia were seen among the unemployed more than the employed ones.conclusion : considering the fact that depression was the most common personality disorder among the addicts participating , it is recommended that this disorder be given priority in investigations in the treatment programs of these patients . in addition , the scales of disorder , schizophrenia , mental infirmity , mental deviation , and paranoia had a significant relationship to aggression , delirium and hallucination , which must be taken into consideration in the treatment of such 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: trigeminal neuralgia ( tn ) is a sudden , unilateral , brief , stabbing , recurrent pain , localized to one or more divisions of the fifth cranial nerve . it is classified into primary ( idiopathic or classic ) and secondary or symptomatic tn . the precise etiology of primary tn is unknown , although vascular compression is often accepted as the origin of pain . however , symptomatic tn is thought to have a manifested cause such as tumors , infarct , or multiple sclerosis . although most tn cases have long been called idiopathic , neuropathy of the trigeminal nerve ( fifth cranial nerve ) can involve its full course , from its nuclei in the brain stem to its peripheral branches . therefore , imaging is needed to visualize the entire course of the trigeminal nerve to exclude the possibility of a structural lesion . if the imaging results are normal , laboratory tests should be considered to exclude neuralgia caused by infectious agents or connective tissue diseases and vasculitis . although paraneoplastic neurologic syndrome ( pns ) is infrequent , rare cases of facial sensory neuropathy have been diagnosed as pns . here , we report a case of classic tn with positive onconeural antibodies ( anti - hu ) , followed by limbic encephalitis ( le ) , which called for rapid detection and removal of an ovarian intestinal - type mucinous borderline tumor , resulting in the rapid recovery of the patient . on june 5 , 2012 , a 76 - year - old female patient was transported to the intensive care unit of mehr general hospital ( tehran , iran ) via ambulance . she had a 3 - week history of progressive somnolence , confusion , agitation , symptoms of depersonalization , and visual hallucinations . her disorder began 12 weeks prior to her current admission , with daily and repeated short , sharp , lancinating , electric shock - like pain involving the left lower division of the fifth cranial nerve . she was taken to a local hospital in another city , where she underwent neurological evaluation by magnetic resonance imaging ( mri ) and electroencephalography ( eeg ) , with normal results . the patient was instructed to take 200 mg carbamazepine 3 times a day , which partially relieved her pain episodes . eight weeks later , and following attacks of nocturnal hallucinations , a neurologist prescribed 5 mg olanzapine to be taken each night . however , her mental and psychiatric state deteriorated , and she was transferred to mehr general hospital . on physical examination , scars from a coronary artery bypass surgery performed in 2008 were present on her anterior chest wall . neurological evaluation revealed an awake , agitated , confused woman with garbled and incoherent speech . cranial nerves were grossly normal , and no sensory or motor abnormalities were detected in the fifth cranial nerve . her motor power was 5/5 in all 4 extremities , her deep tendon reflexes were 2/4 in the arms and 1/4 in the legs , she had normal flexor plantar responses , and no abnormalities were seen in gait or coordination .1 ) . a lumbar puncture was performed , and the results of the cerebrospinal fluid analysis are shown in table 1 . to avoid any possible treatable diagnosis , intravenous phenytoin and acyclovir were started , but acyclovir was stopped 5 days later when the final diagnosis was achieved . blood tests showed an elevated erythrocyte sedimentation rate ( 40 mm after 1 h ; normal : 20 mm ) with normal complete blood count , and low hemoglobin ( 10.6 mg / dl ; normal : 1216 mg / dl ) . immunologic tests showed negative anti - ro , anti - nuclear , and anti - neutrophil cytoplasmic antibodies . broad serological screening assays for infectious conditions , including hiv , herpes simplex virus 1 and 2 , hepatitis , lyme disease , syphilis , and tuberculosis using the intermediate - strength purified protein derivative skin test , were negative . tumor markers , including carbohydrate antigen ( ca ) - 125 , ca - 19.9 , ca - 15.3 , ca - 242 , carcinoembryonic antigen , serum alpha - fetoprotein , and anti - ri and anti - yo antibodies were not detected , but anti - hu antibodies were present in the serum , as visualized by dot blot and indirect immunofluorescence techniques . to localize the suspected malignancy , the patient underwent computed tomography scans of the chest and abdomen , which disclosed a large mass in the left ovary ( fig . she underwent surgery , and a 20 - cm ovarian intestinal - type mucinous tumor ( fig .4 ) . two months after the operation , the patient was pain - free , and her carbamazepine and phenytoin were gradually discontinued . at herlast follow - up visit in march 2013 , the patient was well and free of symptoms . pns is a rare , cancer - associated disorder that is detected before cancer diagnosis in 80 % of cases . pns results from immune cross - reactivity between tumor cells and components of the nervous system . in response to the developing tumor , a patient produces tumor - directed antibodies known as onconeural antibodies ( onas ) . due to antigenic similarity , these onas and associated ona antigen - specific t lymphocytes inadvertently attack components of the nervous system . here , we present a case of classic tn , followed by le due to an underlying ovarian intestinal - type mucinous borderline tumor . cranial nerve involvement including tn is one manifestation of anti - hu - associated brainstem encephalitis , which is associated with small - cell lung carcinoma in most patients . the frequency of trigeminal involvement in patients with anti - hu antibodies is unknown . in a report by dalmau et al . , facial numbness was described in 2 of 23 patients with brainstem encephalitis , and demarquay et al . reported signs of fifth cranial nerve neuropathy as the first manifestation of anti - hu - positive pns . although tn is a well - known symptom in patients with anti - hu - associated pns , there are few reports of tn in the literature in this regard . in fact , of the 33 cases of facial pain as the first manifestation of lung cancer reported in the literature in 2003 , only 2 patients had a previous diagnosis of tn . in our study , le appeared after tn , with a subacute onset of short - term memory loss , confusion , and psychiatric symptoms , in addition to elevated cells and protein in the patient 's cerebrospinal fluid and positive oligoclonal bands in the serum . le is a neurological condition associated with various tumors , such as small - cell lung cancer , testicular germ cell neoplasms , breast cancer , and 34 % of ovarian teratomas , which are usually associated with anti - n - methyl - d - aspartate receptor antibodies . anti - hu antibodies are uncommonly reported in association with gynecological cancer ( 2.5 % ) , and le has not been reported in association with ovarian mucinous borderline tumors . ten percent of ovarian epithelial tumors consist of mucinous tumors . a vast majority ( 75 % ) of these tumorshistologically , ovarian intestinal - type mucinous borderline tumors are composed of multiple cysts and glands of various sizes that are lined with a mixture of cell types , including endocervical , gastric , and neuroendocrine cells . these neuroendocrine cells may have been the source of ona secretion in the serum of our patient . to the best of our knowledge , this study is the first reported case of pns produced by an ovarian intestinal - type mucinous borderline tumor with anti - hu antibodies and clinical presentation of idiopathic tn followed by le . we propose that pns be considered during the management of tn when brain imaging is normal , as it is followed by other central and / or peripheral neurological manifestations and the presence of systemic symptoms , such as anemia , fatigability , loss of appetite , or weight loss .\noutput:\n" }, { "from": "agent", "value": "paraneoplastic neurologic syndrome ( pns ) is an uncommon manifestation of cancer that is not caused by the tumor or metastasis . trigeminal neuralgia ( tn ) is an initial symptom of this disease , but it has rarely been reported in the literature . here , we report the case of a 76 - year - old woman who presented with classic tn , followed by limbic encephalitis due to an underlying ovarian intestinal - type mucinous borderline tumor , with the presence of anti - hu antibodies . she recovered quickly after removal of the tumor and was essentially free of symptoms 2 weeks after surgery . because pns precedes the tumor in approximately 60 % of cases , its rapid detection and treatment are crucial . therefore , we propose that pns be considered during the management of tn when brain imaging is normal , as it is followed by other central and / or peripheral neurological manifestations as well as the presence of systemic symptoms such as anemia , fatigability , loss of appetite , or weight loss ." } ]

[ { "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 well known that alcoholism can lead , in the long - term , to deficits in neurocognitive functions that involve memory , learning , visual - spatial orientation , psychometricity , and information processing , among other skills .1,2 in addition , previous authors have highlighted pronounced impairments in the recognition of affective and / or emotional information . such impairments promote deficits in social cognition and , consequently , in the adaptation and interaction of alcohol abusers with their social environment .36 these deficits occur because social cognition is one of the key aspects of emotional adaptive functioning . it is also an important nonverbal social skill that conveys messages about individuals emotional states at the moment of interaction , thus providing clues that aid the interpretation of behaviors .7 these deficits , together with the development of interpersonal problems , could become risk factors for the maintenance of an individual s cycle of alcohol abuse and / or dependence . they may induce relapses to drinking and hinder the processes of withdrawal , treatment , and recovery .810 given this situation , the majority of studies in the area that have aimed to verify and / or measure the presence of such deficits have employed tasks that involve recognition of basic facial expressions , such as anger , disgust , fear , and sadness ( negative emotions ) , and happiness and surprise ( positive emotions ) . these studies have primarily assessed one or more of the following three key variables : accuracy , latency time , and emotional intensity , pointing to some specific changes . in addition , smaller and more recent studies in this field have monitored brain electrical activity during the performance of cognitive tasks through the use of electroencephalogram instrumentation . these studies have shown that alcoholics exhibit lower brain activation in regions that mediate visual , auditory , and visual - motor processes and deficits in processing anger .1114 other studies have investigated the recognition of facial expressions during neuroimaging tests performed via functional magnetic resonance imaging techniques . these studies have indicated , for example , that alcoholics show lower brain activity in the cingulate , orbitofrontal , and insular cortex ( regions that mediate emotional processing ) during recognition of facial expressions of fear15 and disgust .6 in addition , marinkovic et al16 showed that alcoholic individuals have lower activation in the right amygdala and hippocampus upon negative and positive stimuli compared with nonalcoholics . these studies suggest that this deficient activation may underlie impaired processing of emotional faces in alcoholic individuals . considering the field of knowledge in question and the nonsystematization of findings , the present study consists of a systematic literature review of facial expression recognition by individuals with a history of alcohol abuse and dependence . this aim was achieved by reviewing clinical studies that included accuracy , latency time , and emotional intensity . this review was conducted in accordance with the preferred reporting items for systematic reviews and meta - analyses ( prisma ) statement17 and followed the instructions in the cochrane handbook for systematic reviews of interventions .18 a systematic search was performed in the psycinfo , pubmed , and scielo electronic databases using the following keywords : ( alcohol or alcoholism or alcoholics ) and ( faces or facial ) and ( recognition or expression or emotional ) . the cut - off date for the search was february 6 , 2014 . the main aspects of the article inclusion and exclusion process are shown in figure 1 . as observed in figure 1 , a total of 1,145 articles were found . applying the inclusion and exclusion criteria , two researchers selected 26 articles for analysis in the current review .3,4,6,7,915,1933 in general , most of the studies were conducted in belgium ( 57.7 % , n = 15 ) , beginning in the early 2000s ( 96 % ) . only one study had a descriptive methodological design ,30 with the remaining studies being of case - control design . the data are presented in table 1 , which also shows the main sociodemographic and clinical characteristics of the samples . the majority of the clinical subjects were alcohol - abstinent individuals who were undergoing treatment . of these individuals , 80.8 % were inpatients ( n = 21 ) ,3,4,7,9,1115,1926,28,3133 and 7.7 % were outpatients ( n = 2 ) .10,29 the samples ranged from eight to 52 subjects ( mean 22.9 and median 24 ) , with mean ages between 35.7 and 60.8 years ( median 44.7 years ) and varying education levels . prior consumption of alcohol ranged from 12.8 to 39.1 ( mean 19 ) drinks per day . periods without alcohol consumption generally ranged from 18 ( median 3 ) weeks . in two of the studies , this variability was greater , reaching up to 21 years .19,27 in terms of the control group , 88.5 % of the studies ( n = 23 ) selected healthy subjects with no history of alcohol use from the general population . social drinkers were used as the control group in only two studies , and their alcohol consumption was 3.313 drinks per week .4,7 the control group sample sizes ranged from ten to 47 subjects ( mean 23 and median 24 ) , with ages ranging from 33.7 to 45.5 years ( median 43.8 years ) and variable education levels . most studies diagnosed alcohol abuse and / or dependence according to the diagnostic and statistical manual of mental disorders ( dsm - iv ; n = 25 ) , with the exception of one study that used the dsm - iii - r. 9 all subjects abstained from alcohol . furthermore , only one study utilized the structured clinical interview for dsm - iv axis i disorder .32 the controls were primarily healthy subjects from the general population without a prior history of alcohol dependence ( n = 23 ) . exclusion criteria for both groups were as follows : presence of comorbidity with any axis i psychiatric disorder ( n = 17 ) ; 3,4,912,14,20,22,2528,3033 presence of comorbidity with any axis ii psychiatric disorder ( n = 1 ) ; 33 visual or hearing impairment ( n = 8 ) ; 4,1114,2426 epilepsy ( n = 9 ) ; 1114,2427,32 health problems in general ( n = 8 ) ; 4,7,12,14,24,25,27,32 intellectual impairment ( n = 4 ) ; 3,9,20,27 wernicke - korsakoff syndrome ( n = 2 ) ; 26,27 and use of medications ( n = 2 ) .21,32 five studies did not present their exclusion criteria .6,15,23,28,29 the main aspects related to types of stimuli and the procedures that the studies used to perform facial expression recognition tasks ( fert ) are summarized in table 2 , which shows that the studies used a wide variety of stimuli and procedures . however , this diversity does not seem to have influenced the outcomes , as discussed below . the main results according to the outcome variables analyzed in the studies are listed in table 3 . of the 23 studies that analyzed accuracy , 17 ( 73.9 % ) found at least some difference between the groups , indicating impairment in alcoholic individuals with regard to correctly identifying disgust ( 26 % ) and sadness ( 26 % ) . however , 16 studies found no differences between the groups , indicating no impairment in alcoholic individuals with regard to identifying emotions , especially anger ( 43.7 % ) . in addition , ten studies ( 43.5 % ) that evaluated accuracy found differing results for the same sample group . of the eight studies that evaluated the emotional intensity needed for emotion recognition , at least six found a difference in specific emotions . the group of alcoholics required higher intensities for emotion recognition , particularly for fear ( 50 % ) and anger ( 37.5 % ) . however , in seven of these studies this difference was not observed , especially with regard to happiness ( 75 % ) . finally , ofthe eleven studies that evaluated latency time , five ( 45.5 % ) found that alcoholics required more time for emotion recognition . all of the results presented were also analyzed while taking into account the different variables associated with the stimuli and procedures used in fert , ie , the methods chosen for data collection . despite the great diversity of employed methodologies , none of them seemed to have clearly interfered with the results . in other words , no particular result was associated with any specific stimulus and / or procedure . the influence of sociodemographic features , particularly the influence of male / female sex on fert performance , was also evaluated . of the four studies that analyzed this variable ,9,10,23,27 only the study of frigerio et al10 found significant differences . this study indicated that women needed less emotional intensity than men to recognize facial expressions , regardless of whether they had a history of alcoholism . only the study by kornreich et al19 evaluated the influence of duration of alcohol abstinence on fert performance . this study found that alcoholics who abstained from alcohol for a longer period of time required a lower intensity to judge the emotion compared with recently detoxified alcoholics ; however , there was no improvement in accuracy . in addition , only the study by foisy et al23 evaluated the difference between a group of abstinent subjects undergoing treatment and a group of subjects who discontinued alcohol detoxification due to relapses . this study showed that the latter had lower accuracy , but no difference was observed in the emotional intensity required for recognition . in general , most of the studies were conducted in belgium ( 57.7 % , n = 15 ) , beginning in the early 2000s ( 96 % ) . only one study had a descriptive methodological design ,30 with the remaining studies being of case - control design . the data are presented in table 1 , which also shows the main sociodemographic and clinical characteristics of the samples . the majority of the clinical subjects were alcohol - abstinent individuals who were undergoing treatment . of these individuals , 80.8 % were inpatients ( n = 21 ) ,3,4,7,9,1115,1926,28,3133 and 7.7 % were outpatients ( n = 2 ) .10,29 the samples ranged from eight to 52 subjects ( mean 22.9 and median 24 ) , with mean ages between 35.7 and 60.8 years ( median 44.7 years ) and varying education levels . prior consumption of alcohol ranged from 12.8 to 39.1 ( mean 19 ) drinks per day . periods without alcohol consumption generally ranged from 18 ( median 3 ) weeks . in two of the studies , this variability was greater , reaching up to 21 years .19,27 in terms of the control group , 88.5 % of the studies ( n = 23 ) selected healthy subjects with no history of alcohol use from the general population . social drinkers were used as the control group in only two studies , and their alcohol consumption was 3.313 drinks per week .4,7 the control group sample sizes ranged from ten to 47 subjects ( mean 23 and median 24 ) , with ages ranging from 33.7 to 45.5 years ( median 43.8 years ) and variable education levels . most studies diagnosed alcohol abuse and / or dependence according to the diagnostic and statistical manual of mental disorders ( dsm - iv ; n = 25 ) , with the exception of one study that used the dsm - iii - r. 9 all subjects abstained from alcohol . furthermore , only one study utilized the structured clinical interview for dsm - iv axis i disorder .32 the controls were primarily healthy subjects from the general population without a prior history of alcohol dependence ( n = 23 ) . exclusion criteria for both groups were as follows : presence of comorbidity with any axis i psychiatric disorder ( n = 17 ) ; 3,4,912,14,20,22,2528,3033 presence of comorbidity with any axis ii psychiatric disorder ( n = 1 ) ; 33 visual or hearing impairment ( n = 8 ) ; 4,1114,2426 epilepsy ( n = 9 ) ; 1114,2427,32 health problems in general ( n = 8 ) ; 4,7,12,14,24,25,27,32 intellectual impairment ( n = 4 ) ; 3,9,20,27 wernicke - korsakoff syndrome ( n = 2 ) ; 26,27 and use of medications ( n = 2 ) .21,32 five studies did not present their exclusion criteria .6,15,23,28,29 the main aspects related to types of stimuli and the procedures that the studies used to perform facial expression recognition tasks ( fert ) are summarized in table 2 , which shows that the studies used a wide variety of stimuli and procedures . however , this diversity does not seem to have influenced the outcomes , as discussed below . the main results according to the outcome variables analyzed in the studies are listed in table 3 . the results concerning accuracy were highly divergent . of the 23 studies that analyzed accuracy , 17 ( 73.9 % ) found at least some difference between the groups , indicating impairment in alcoholic individuals with regard to correctly identifying disgust ( 26 % ) and sadness ( 26 % ) . however , 16 studies found no differences between the groups , indicating no impairment in alcoholic individuals with regard to identifying emotions , especially anger ( 43.7 % ) . in addition , ten studies ( 43.5 % ) that evaluated accuracy found differing results for the same sample group . of the eight studies that evaluated the emotional intensity needed for emotion recognition , at least six found a difference in specific emotions . the group of alcoholics required higher intensities for emotion recognition , particularly for fear ( 50 % ) and anger ( 37.5 % ) . however , in seven of these studies this difference was not observed , especially with regard to happiness ( 75 % ) . finally , ofthe eleven studies that evaluated latency time , five ( 45.5 % ) found that alcoholics required more time for emotion recognition . all of the results presented were also analyzed while taking into account the different variables associated with the stimuli and procedures used in fert , ie , the methods chosen for data collection . despite the great diversity of employed methodologies , none of them seemed to have clearly interfered with the results . in other words , the influence of sociodemographic features , particularly the influence of male / female sex on fert performance , was also evaluated . of the four studies that analyzed this variable ,9,10,23,27 only the study of frigerio et al10 found significant differences . this study indicated that women needed less emotional intensity than men to recognize facial expressions , regardless of whether they had a history of alcoholism . only the study by kornreich et al19 evaluated the influence of duration of alcohol abstinence on fert performance . this study found that alcoholics who abstained from alcohol for a longer period of time required a lower intensity to judge the emotion compared with recently detoxified alcoholics ; however , there was no improvement in accuracy . in addition , only the study by foisy et al23 evaluated the difference between a group of abstinent subjects undergoing treatment and a group of subjects who discontinued alcohol detoxification due to relapses . this study showed that the latter had lower accuracy , but no difference was observed in the emotional intensity required for recognition . the present study aimed to systematize the literature on recognition of basic facial expressions by alcoholic subjects in terms of the following outcome variables : accuracy , emotional intensity , and latency time . one noteworthy finding is that these studies were conducted recently and were primarily developed by european researchers , with a group of researchers from belgium being responsible for 57.7 % of the studies ( n = 15 ) . homogeneity in the group of researchers who have studied the topic and the significantly diverse methodologies used across studies could have considerably influenced the results . however , despite the great variability of stimuli and procedures in the reviewed studies , a qualitative initial analysis indicated that these variables did not have a direct influence on the studied outcomes . specifically , different results did not display a direct relationship with any of these variables . none of the studies included subjects in the clinical groups who were consuming alcohol at the time of measurement . it is also noteworthy that a small number of subjects were examined in both the clinical groups ( 852 ) and the control groups ( 1047 ) . namely , the following variables stand out : male / female sex of the respondent , given that women recognize both positive and negative emotions more accurately and more rapidly than men ; 34 age of the respondent , given that adults above the age of 45 years tend to wrongly identify facial stimuli more often than do younger subjects ; 35 education level of the respondent , as individuals with lower education levels identify facial expressions of fear and disgust less accurately than individuals with higher education levels ; 36 and type of task used , because dynamic tasks have greater ecological validity than do static tasks , given that the former involve movement and are thus more similar to the actual stimuli .3739 only four studies used an intelligence test to screen the sample , and just one study considered the presence of comorbidity with axis ii personality disorders when assessing exclusion criteria . this observation warrants attention because the literature indicates that the presence of both cognitive deficits and a specific personality disorder can negatively impact fert performance .4045 these variables are particularly important when considering alcoholics , because cognitive deficits may be associated with degeneration of specific brain areas due to chronic and excessive alcohol use .40,41,46 the same approach is valid for personality disorders , as comorbidity rates ( especially with antisocial and borderline personality disorders ) are considerable , reaching levels greater than 50 % .4345 some studies indicated alcoholics greater impairment in fert , while others did not differentiate between their clinical and control groups . for sadness3 ,9,10,28,30 and disgust ,3,9,13,20,30,33 which are considered negative emotions , there was a slight tendency towards impairment in the group of alcoholics . the same result was observed for emotional intensity , as some studies found that alcoholics were less sensitive in fert3 ,9 and required greater emotional intensity to judge anger7 ,9,23 and fear .7,9,26,31 the justification given for such positive findings was that the chronic use of alcohol caused changes in the brain structures involved in processing visual - spatial information and the perception of , for example , nonverbal signals ,9,20 especially with regard to negative and / or aversive emotions .19,28,30 in addition , it has been found that alcoholics show dysfunction in the right cerebral hemisphere , which is responsible for processing negative emotions .19,47 thus , some authors support the hypothesis that impairments in social cognition are consequences of deficits in the central nervous system and that they even become a reason for maintaining the vicious cycle of drinking .2,3,9,13,20 unlike the variables of accuracy and emotional intensity , studies have shown greater homogeneity for latency time . specifically , alcoholics require more time to judge emotions as a whole .11,30,31,3335,41 this difference suggests that chronic use of alcohol may impair cognitive functions , such as the speed of processing of emotional information and attention level while performing a task . thus , alcoholics needed more time to focus on the task and complete it .4,12,14,27,29 overall , most justifications for the presence of impairments are related to neurocognitive function .1,2 in contrast , the hypothesis used to explain the lack of differences in the three outcome variables ( accuracy , intensity , and latency time ) between the groups in terms of fert is associated with the different methodological procedures used . according to fein et al27 some paradigms may be more sensitive than others in detecting differences between groups . studies that used simpler tasks , such as those in which the subject was offered the possibility of classifying emotions as high ( 70 % ) or low ( 30 % ) intensity or in which the subject answered yes or no as rapidly as possible after recognizing the emotion displayed ,15,23 found no differences between groups . conversely , studies that used more complex tasks , such as requesting the subject to classify the intensity of an emotion using a seven - point likert scale or to choose one of four options of available emotions ,10,19 found differences between groups . more complex tasks that require more effort from the subjects are able to demonstrate impairment , whereas simpler tasks can level all individuals and thus underestimate the possible deficits . in addition , other hypotheses underpinning the lack of differences between groups suggest that impairments in the ability to recognize emotions may be independent of alcohol abuse . such impairments may be associated with other factors , such as primary impairment , which is due to altered emotional intelligence21 or the genetic history of the individual . further , this genetic history is capable of potentially leading to an increased predisposition to the development of abnormalities in the brain regions involved in emotional processing .9 as an example , in the study reported by schandler et al48 preschool children from families with alcoholic individuals exhibited deficits in processing visual - spatial information . despite the inconclusive results , it is important to consider the judgment deficits mentioned because they may have a negative impact on the social life of the individual who abuses or is dependent on alcoholthis potential impact becomes even more relevant because the impairments related to social cognition are not restricted to the variables that were analyzed in the current study . it is also known that alcoholics have a tendency to overestimate emotions7 and show response biases toward negative emotions .11,12,22,23 considering this set of impairments , alcoholics are more vulnerable to displaying inappropriate reactions in social situations . thus , they may experience difficulties in interpersonal relationships and social isolation , and even become involved in fights and / or aggression , which can reduce their quality of life and reinforce their continued alcohol use .8,20 the presented data demonstrate divergent results across the relevant studies . therefore , rather than reaching definite conclusions , only trends can be identified . the current study showed that this line of research is recent and restricted to small groups of researchers who do not use standard methodology . these inconsistencies further complicate direct comparison between studies because , as previously noted , the number of variations between the stimuli and procedures adopted is high . most of the studies were performed in european countries , limiting potential generalizations of the findings to other sociocultural contexts . however , context is an important variable in the etiology of alcoholism .49,50 attention must be paid to other critical points in the studies , such as : adoption of intellectual screening tests ; ascertainment of comorbidity , particularly with personality disorders ; the lack of samples arising from different sociocultural contexts ; and the lack of samples comprising subjects who are currently consuming alcohol . future research can still delineate this field of knowledge , providing more accurate evidence on whether alcoholism influences social cognition . nevertheless , some of the findings herein regarding the negative effect of alcohol use on the recognition of emotions have clinical implications . such implications should be considered in both the treatment of alcoholism and the prevention of relapse , with the aim of minimizing the negative impacts of the distorted interpretation of feelings and / or emotions .19,27\noutput:\n" }, { "from": "agent", "value": "backgroundalcohol abuse and dependence can cause a wide variety of cognitive , psychomotor , and visual - spatial deficits . it is questionable whether this condition is associated with impairments in the recognition of affective and / or emotional information . such impairments may promote deficits in social cognition and , consequently , in the adaptation and interaction of alcohol abusers with their social environment . the aim of this systematic review was to systematize the literature on alcoholics recognition of basic facial expressions in terms of the following outcome variables : accuracy , emotional intensity , and latency time.methodsa systematic literature search in the psycinfo , pubmed , and scielo electronic databases , with no restrictions regarding publication year , was employed as the study methodology.resultsthe findings of some studies indicate that alcoholics have greater impairment in facial expression recognition tasks , while others could not differentiate the clinical group from controls . however , there was a trend toward greater deficits in alcoholics . alcoholics displayed less accuracy in recognition of sadness and disgust and required greater emotional intensity to judge facial expressions corresponding to fear and anger.conclusionthe current study was only able to identify trends in the chosen outcome variables . future studies that aim to provide more precise evidence for the potential influence of alcohol on social cognition are needed ." } ]

[ { "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: urethral calculi are already an uncommon entity and giant calculi in the urethra are extremely rare . we present a case of giant urethral calculus secondary to a urethral stricture in a man . a 55 year male was admitted to our institution with complaints of pain and swelling in perineal region for 6 days and purulent discharge from the swelling for 2 days . patient was apparently quite well 4 months prior when he noticed a progressive thinning of urinary stream along with dysuria and burning on micturition . three months later the patient had an episode of retention of urine for which patient attended our outpatient department . a trocar suprapubic catheterisation ( spc ) was performed and a 16 fr foley s catheter was passed into the bladder . patient was asymptomatic for 1 month followed by reappearance of the swelling and pain in the perineal region . on local examination there was a swelling 2 x 2 cms in size in the left perineal region with purulent discharge . patient was subjected to retrograde urethography ( figure 1 ) and micturiting cystourethography ( figure 2 ) . patient was diagnosed as a case of urethral calculus with urethral stricture and was posted for urethral calculus removal with urethroplasty . the calculus of 30 mm x 20 mm x15 mm ( figure 3 ) was extracted successfully and end to end urethroplasty was performed . urethral stones are classified as ( a ) native or autochthonous and ( b ) migrant or secondary depending upon their site of origin . ( 1,2 ) migrant stones are much more common and are ones which have migrated from higher up in the urinary tract . native stones are struvite , calcium phosphate or calcium carbonate in composition , have no nucleus and are of uniform structure . they are formed in the urethra proximal to strictures , in congenital and acquired diverticula , with chronic infection with especially urea splitting organisms or with foreign bodies . . may present with a mass on the undersurface of penis , urethral discharge , dyspareunia , irritative voiding symptoms and haematuria migrant stones are calcium oxalate and phosphate in composition . they often cause acute symptoms causing retention , frequency , dysuria , poor stream or dribbling . urethral calculi are preponderantly found in the prostatic urethra , the bulb , the proximal penile urethra , the fossa navicularis and external meatus . treatment is contingent on the size and location of calculus and condition of the urethra . meatotomy may be used if stone is in fossa navicularis or external meatus small stones can be gently massaged with intraurethral instillation of xylocaine . calculi in posterior urethra can be pushed back into bladder in cases of urethral diverticulum , diverticulectomy and repair should be done .\noutput:\n" }, { "from": "agent", "value": "primary urethral calculus is rarely seen and is usually encountered in men with urethral stricture or diverticulum . we present a case of giant urethral calculus secondary to a urethral stricture in a man . the patient was treated with calculus extraction with end to end urethroplasty ." } ]

[ { "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 first approach of using lipid microparticles was described by eldem et al . , reporting the production by high - speed stirring of a melted lipid phase in a hot surfactant solution obtaining an emulsion . solid microparticles are formed when this emulsion is cooled to room temperature , and the lipid recrystallizes . the obtained products were called lipid nanopellets , and they have been developed for oral administration . lipospheres were described by domb applying a sonication process . to overcome the drawbacks associated to the traditional colloidal systems , such as emulsions , liposomes , and polymeric nanoparticles , solid lipid nanoparticles ( sln ) sln are biocompatible and biodegradable and have been used for controlled drug delivery and specific targeting . these colloidal carriers consist of a lipid matrix that should be solid at both room and body temperatures , having a mean particle size between 50 nm and 1000 nm . a clear advantage of the use of lipid particles as drug - carrier systems is the fact that the matrix is composed of physiological components , that is , excipients with generally recognized as safe ( gras ) status for oral and topical administration , which decreases the cytotoxicity . sln have been already tested as site - specific carriers particularly for drugs that have a relatively fast metabolism and are quickly eliminated from the blood , that is , peptides and proteins . the cytotoxicity of sln can be attributed to nonionic emulsifiers and preservative compounds which are used in the production of these systems . sln prepared up to concentrations of 2.5 % lipid do not exhibit any cytotoxic effects in vitro . even concentrations higher than 10 % of lipid have been shown a viability of 80 % in culture of human granulocytes . in addition , a high loading capacity for a broad range of drugs can be achieved , especially if they have lipophilic properties . due to their physiological and biodegradable properties , sln have been tested for several administration routes , including the oral and peroral routes . sln can be obtained by exchanging the liquid lipid ( oil ) of the o / w nanoemulsions by a solid lipid . in general , a solid core offers many advantages in comparison to a liquid core . emulsions and liposomes usually show lack of protection of encapsulated drugs , and drug release as a burst ( emulsions ) or noncontrolled ( from liposomes ) . in addition , sln are of low cost , the excipients and production lines are relatively cheap , and the production costs are not much higher than those established for the production of parenteral emulsions . at the turn of the millennium , modifications of sln , the so - called nanostructured lipid carriers ( nlcs ) , have been introduced to the literature , and these nlc represent nowadays the second generation of lipid nanoparticles . the main difference between sln and nlc is the fact that the concept of these latter is performed by nanostructuring the lipid matrix , in order to increase the drug loading and to prevent its leakage , giving more flexibility for modulation of drug release . this approach is achieved by mixing solid lipids with liquid lipids in nlc instead of highly purified lipids with relatively similar molecules in sln . the result is a less - ordered lipid matrix with many imperfections , which can accommodate a higher amount of drug . a limiting factor for in vivo performance of poorly water - soluble drugs for oral administration is their resistance of being wetted and dissolved into the fluid in the git ( apart from potential drug degradation in the gut ) . thus , the increase in the dissolution rate of poorly water - soluble drugs is relevant for optimizing bioavailability . over the last 10 years , the features of lipid nanoparticles for oral and peroral delivery are related with their adhesive properties . once adhered to the git wall , these particles are able to release the drug exactly where it should be absorbed . in addition , the lipids are known to have absorption - promoting properties not only for lipophilic drugs , such as vitamin e , repaglinide , and puerarin . hydrophilic drugs can also be incorporated in sln ; nevertheless , the affinity between the drug and the lipid needs to be analysed . therefore , loading hydrophilic drugs in sln is a challenge due to the tendency of partitioning the encapsulated molecules in the water during the production process of nanoparticles . there are even differences in the lipid absorption enhancement depending on the structure of the lipids . for example , medium - chain triglycerides ( mct ) lipids are more effective than long - chain triglycerides ( lct ) . basically , the body is taking up the lipid and the solubilized drug at the same time . it can be considered as a kind of trojan horse effect . oral administration of sln is possible as aqueous dispersion or alternatively transformed into a traditional dosage forms such as tablets , pellets , capsules , or powders in sachets . for this routein addition , all compounds of gras status or accepted gras status can be employed as well as from the food industry . since the stomach acidic environment and high ionic strength favour the particle aggregation , aqueous dispersions of lipid nanoparticles might not be suitable to be administered as dosage form . in addition , the presence of food will also have a high impact on their performance . the packing of sln in a sachet for redispersion in water or juice prior to administration will allow an individual dosing by volume of the reconstituted sln . for the production of tablets , the aqueous sln dispersions can be used instead of a granulation fluid in the granulation process . alternatively , sln can be transferred to a powder ( by spray - drying or lyophilization ) and added to the tabletting powder mixture . in both cases , it is beneficial to have a higher solid content to avoid the need of having to remove too much water . for cost reasons , spray drying might be the preferred method for transforming sln dispersions into powders , with the previous addition of a protectant . for the production of pellets , alternatively , sln can be produced directly in liquid peg 600 and put into soft gelatine capsules . advantages of the use of sln for oral and peroral administration are the possibility of drug protection from hydrolysis , as well as the possible increase of drug bioavailability . prolonged plasma levels has also been postulated due to a controlled , optimized released in combination with general adhesive properties of small particles . the advantage of colloidal drug carriers described above is that they are generally linked to their size in the submicron range . therefore , the preservation of particle size of colloidal carrier systems after peroral administration is a crucial point . the gastric environment ( ionic strength , low ph ) may destabilize the sln and potentially lead to aggregation . however , it is possible to produce stable sln dispersions by optimizing the surfactant / mixture for each lipid in vitro . the drug release from sln in the git is also dependent on the lipase / colipase activity for the git digestion of the lipid matrix . the lipase / colipase complex leads to a degradation of food lipids as a prestep of the absorption . in vitro degradation assay based on pancreas lipase / colipase complexhave been developed to obtain basic information about the degradation velocity of sln as a function of lipid and surfactant used in the production process . lipid nanoparticles show great promise to enhance oral bioavailability of some of the most poorly soluble drugs . the physical / chemical characteristics of lipid particulate systems are highly complex due to the existence of a variety of lipid assembly morphologies , the morphology - dependent solubility of drug , the interconversion of assembly morphology as a function of time and chemical structure , and the simultaneous lipid digestion . their main characteristic is the fact that they are prepared with physiologically well - tolerated lipids . during the last ten years , different substances have been entrapped into lipid nanoparticles ( table 1 ) , ranging from lipophilic and hydrophilic molecules , including labile compounds , such as proteins and peptides . the term lipid is used here in a broader sense and includes triglycerides , partial glycerides , fatty acids , steroids , and waxes . however , it is required that matrix maintains the solid state at room temperature , and for this purpose , the selection of lipids is based on the evaluation of their polymorphic , crystallinity , miscibility , and physicochemical structure . furthermore , the use of mono - and diglycerides as lipid matrix composition might increase drug solubility compared to highly pure lipids , such as monoacid triglycerides . naturally occurring oils and fats comprise mixtures of mono - , di - , and triglycerides , containing fatty acids of varying chain length and degree of unsaturation . the melting point of these lipids increases with the length of the fatty acid chain and decreases with the degree of unsaturation . the chemical nature of the lipid is also important , because lipids which form highly crystalline particles with a perfect lattice ( e.g. , monoacid triglycerides ) lead to drug expulsion during storage time . physicochemically stable lipid nanoparticles will be obtained only when the right surfactant and adjusted concentration have been employed . the choice of the ideal surfactant for a particular lipid matrix is based on the surfactant properties such as charge , molecular weight , chemical structure , and respective hydrophile - lipophile balance ( hlb ) . the hlb of an emulsifier is given by the balance between the size and strength of the hydrophilic and the lipophilic groups . griffin defined the lipophilic emulsifiers as low hlb values ( below 9 ) , and hydrophilic emulsifiers as high hlb values ( above 11 ) . the hlb system is a useful method to choose the ideal emulsifier or blend of emulsifiers for the system , that is , if its required an oil - in - water ( o / w ) , water - in - oil ( w / o ) , or a double ( w / o / w ) emulsion . matching the hlb value of the surfactant with the lipid will provide a suitable in vitro performance . determined the hlb value for stearic acid and stearic acid capric / caprylic triglycerides to reach the best combination of surfactants ( trioleate sorbitan and polysorbate 80 ) to obtain a stable lipid nanoparticles emulsion . the hlb value obtained for stearic acid was 15 and for stearic acid capric / caprylic triglycerides was 13.8 . sorbitan trioleate has an hlb value of 1.8 and polysorbate 80 of 15 , when used in the ratio 10 : 90 , respectively . polysorbate 80 is often used in combination with sorbitan trioleate due to their appropriate compatibility attributed to the similar chemical structure ( same hydrocarbon chain length ) for the production of stable emulsions . pharmacokinetic behaviour of drugs loaded in lipid nanoparticles need to differentiate if the drug is present as the released free form or as the associated form with lipid nanoparticles . however , the poor aqueous solubility of some drugs turns difficult the design of pharmaceutical formulations and leads to variable bioavailability . xie et al . reported a significant increase in the bioavailability and extended the systemic circulation of ofloxacin formulated in sln , which could be attributed to a large surface area of the particles , improving the dissolution rate and level of ofloxacin in the presence of git fluids , leading to shorter tmax and higher peak plasma concentration . in addition , lipid nanoparticles may adhere to the git wall or enter the intervillar spaces due to their small particle size , increasing their residence time . moreover , nanoparticles could protect the drug from chemical and enzymatic degradation and gradually release drug from the lipid matrix into blood , resulting in a several - fold increase mean residence time compared with native drug . han et al . demonstrated that 5 oral doses of tilmicosin loaded in lipid nanoparticles administered every 10 days provided an equivalent therapeutic benefit to 46 daily doses of oral free drugs . in vitro release profile demonstrated that tilmicosin loaded in lipid nanoparticles followed a sustained release profile , and in vivo results showed that nanoparticles remained effective for a longer period of time , which was attributed to sustained release of the drug and also to enhanced antibacterial activity by the sln . developed paclitaxel loaded in sln with the aim at improving the oral bioavailability of this antineoplastic drug . in vitro studies of sln formulation exhibited an initial low burst effect within 24 h followed by a slow and sustained release . statistical analysis of in vivo experiments concluded that the oral bioavailability of paclitaxel loaded in sln was significantly higher than the control group . produced stearic acid - sln with a fluorescence marked for evaluation of in vivo pathway by oral administration . about 30 % of sln transport was efficient , where particles were absorbed following linear mechanism in the git . the release profile in plasma increased with the increasing of dosage depicting two concentration peaks . the first peak of sln in blood took place during 1 - 2 h , attributed to the fast uptake of sln from the git into systematic circulation . drug concentration began to decrease attributed to the uptake by and the distribution of sln among particular organs . the second peak occurred at about 68 h , and the maximum concentrations were lower than that of the first peak . lipid nanoparticles are well tolerated in living systems , since they are made from physiological compounds leading to the metabolic pathways . for this purpose , however , such effects often occur first at rather in high concentrations and the subtler effects that arise at lower concentrations , without necessarily causing cell death , also need to be considered . one the most important effect is dna damage , since an increased genetic instability is associated with cancer development . the interaction with proteins and cells are an essential focus in assessing and understanding compatibility and toxicity . cell and nanoparticle reactions of interest include cellular uptake and processing of nanoparticle in various routes , effects on cell signalling , membrane perturbations , influence on the cellular electron transfer cascades , production of cytokines , chemokines , and reactive oxygen species ( ros ) , transcytosis and intercellular transport , gene regulation overt toxic reactivity , no observable toxicity , and cell necrosis or apoptosis . in vitro culture of cell lines or primary cells on plastic platesare employed in a wide varieties of assays and reflect the variety of possible physiologic responses to nanoparticles in vivo and all possible cell processing routes and natural reactions . silva et al . studied the toxicity of sln and risperidone loaded sln with caco - 2 cells by ( 4,5 - dimthylthiazol -2-yl ) 2,5 - diphenyl - tetrazolium bromide ( mtt ) assay . the results suggest that all formulations evaluated are biocompatible with caco - 2 cells and well tolerated by the git . this test evaluates the mitochondrial function as a measurement of cell viability , which allows the detection of dead cells before they lose their integrity and shape . the amount of viable cells after sln exposure was performed by the mtt assay with caco - 2 cell models , which are a well - established in vitro model that mimics the intestinal barrier and is often used to assess the permeability and transport of oral drugs . other authors have also reported that sln show biocompatibility , which increase their attractiveness for drug - delivery applications . since early nineties , researchers turned their attention to lipid nanoparticles because of their nontoxicity and cost / effectiveness relationship . in spite of the advantages , formulating with lipid nanoparticles has been suffering some drawbacks . because of the git conditions , most of promising drugs do not reach clinical trials . the stability of particles must be comprehensively tested due to ph changes and ionic strength as well as the drug release upon enzymatic degradation . lipid nanoparticles absorption through git occurs via transcellular ( through m cells or enterocytes ) or paracellular ( diffusion between cells ) . if the major drug uptake occurs through m cells , the portal vein to the liver is bypassed , resulting in higher drug concentrations to the lymph rather than to plasma . despite the low number of lipid nanoparticles formulations on the market for drug delivery , mucosolvan retard capsules ( boehringer - ingelheim ) is a story of success . it was produced by high - speed stirring of a melted lipid phase in a hot surfactant solution obtaining an emulsion . this emulsion was then cooled down to room temperature obtaining the so - called lipid nanopellets for oral administration . successful in vivo studies also include rifampicin , isoniazid , and pyrazinamide that are used in tuberculosis treatment . the methodology employed for production is acceptable by the regulatory agencies and has been addressed by various papers and patents . poor water - soluble drugs , as camptothecin , vinpocetine , and fenofibrate , can have their solubilization improved if incorporated into sln . injections are often painful and must be administered daily , which result in low patient compliance . unfortunately , oral administration of insulin , produced by solvent emulsification - evaporation method based on a w / o / w double emulsion , has limitations such as low bioavailability due to degradation in the stomach , inactivation and degradation by proteolytic enzymes , and low permeability across the intestinal epithelium because of lack of lipophilicity and high molecular weight . the main advantages of incorporate insulin into sln would be the enhancement of transmucosal transport and protection from the degradation in the git . lipids and lipid nanoparticles are promising for oral and peroral administration route for drugs , proteins , and peptides . theses matrices are able to promoting controlled release of drugs in git and reducing absorption variability . in addition , these matrices can be absorption as food lipids together with drugs improving the bioavailability . these systems present several advantages , including drug protection and excipients of gras status , which decreases the danger of acute and chronic toxicity . in addition , the oral administration of lipids nanoparticles is possible as aqueous dispersion or alternatively transformed into a traditional dosage forms such as tablets , pellets , capsules , or powders in sachets .\noutput:\n" }, { "from": "agent", "value": "lipids and lipid nanoparticles are extensively employed as oral - delivery systems for drugs and other active ingredients . these have been exploited for many features in the field of pharmaceutical technology . lipids usually enhance drug absorption in the gastrointestinal tract ( git ) , and when formulated as nanoparticles , these molecules improve mucosal adhesion due to small particle size and increasing their git residence time . in addition , lipid nanoparticles may also protect the loaded drugs from chemical and enzymatic degradation and gradually release drug molecules from the lipid matrix into blood , resulting in improved therapeutic profiles compared to free drug . therefore , due to their physiological and biodegradable properties , lipid molecules may decrease adverse side effects and chronic toxicity of the drug - delivery systems when compared to other of polymeric nature . this paper highlights the importance of lipid nanoparticles to modify the release profile and the pharmacokinetic parameters of drugs when administrated through oral route ." } ]

[ { "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 significant number of ades are preventable in nature , and therefore this represents an avoidable burden on health care .2 ades are monitored in a clinical setup using a number of methods like case reports , spontaneous reporting systems , intensive event recording , case - control studies , case - cohort studies , prospective cohort studies , incident reports , retrospective or concurrent chart reviews and observational studies .35 each methodology has its own advantages and disadvantages .6 an indicator is a clue that helps a health care organization to identify adverse events and assess the overall harm that occurs from medical care within that organization .7 this methodology is based on identifying and addressing errors that are highly associated with negative outcomes .8,9 indicators offer an approach to standardizing error identification that may provide more consistent and accurate information than traditional error reporting systems .10 this system was also used for identification of adverse events along with traditional chart audits , incident reporting , or voluntary reporting . there are a number of reports on implementing electronic triggers to screen hospital records for the occurrence of ades .11,12 india is a developing country which is a member of the world health organization - run pharmacovigilance program . the pharmacovigilance in this country is still in its infancy .13 ade monitoring is carried out sporadically , and studies have reported that under - reporting is common in many of the study sites .1416 this study was carried out in a tertiary care teaching hospital in south india . the ade monitoring program was initiated in the current setup around a decade ago , but the level of participation of clinicians in this program is low .17 it was planned to use indicators to identify ades in the current setup . for this purposethe present work was aimed to develop an indicator list based on available literature and modify it suitably with the help of a delphi panel review and review of adverse event case reports . an initial list of ade indicators was prepared based on published literature .7,1823 these indicators were reviewed by a panel of three experts ( two clinical pharmacists and a clinician ) . the indicators relevant to general medical practice were kept in the list , whereas the indicators related to other specialties like psychiatry , intensive care unit ( icu ) , and surgery , were deleted . the review team collectively decided on whether to keep or delete a particular indicator from the list . this exercise was carried out to condense the list , so that the delphi panel could work on it for the development of a final set of indicators . the panel members rated each item on the list on a likert scale which represented a score from 1 to 5 . during thisreview panel members were asked to suggest any additional indicators which could be added to the list . at the end of the first review , the scores were summarized and this was presented to the panel members along with their own scores . in the second review , panel members were encouraged to reassess their opinion in light of scores given by other members . the mean score of 3 and above , out of 5 , was considered as criteria for inclusion into the list . for the newly added indicators , one more review was conducted and mean scores were calculated . the final comprehensive list was divided into four categories , namely : ( 1 ) abnormal changes in clinical condition , ( 2 ) changes in patient care process , ( 3 ) drug - related alterations , ( 4 ) changes in lab investigations . ( tables 14 ) after the preparation of a comprehensive list of indicators , they were used to screen previously identified and documented ade case reports . a set of 100 previously documented ade reports were randomly picked from the documented database . these adverse events were identified by clinical pharmacists from medicine wards during their rounds with clinicians . these reports contain complete details of the case which included medical history , diagnosis , lab investigations , therapy and ade . the following four factors were then assessed : mean number of indicators per case report , commonly identified indicators , total number of identified indicators , and indicators that were not identified in any of the case reports . an initial list of ade indicators was prepared based on published literature .7,1823 these indicators were reviewed by a panel of three experts ( two clinical pharmacists and a clinician ) . the indicators relevant to general medical practice were kept in the list , whereas the indicators related to other specialties like psychiatry , intensive care unit ( icu ) , and surgery , were deleted . the review team collectively decided on whether to keep or delete a particular indicator from the list . this exercise was carried out to condense the list , so that the delphi panel could work on it for the development of a final set of indicators . the panel members rated each item on the list on a likert scale which represented a score from 1 to 5 . during this review panel memberswere asked to suggest any additional indicators which could be added to the list . at the end of the first review , the scores were summarized and this was presented to the panel members along with their own scores . in the second review , panel members were encouraged to reassess their opinion in light of scores given by other members . the mean score of 3 and above , out of 5 , was considered as criteria for inclusion into the list . for the newly added indicators , one more review was conducted and mean scores were calculated . the final comprehensive list was divided into four categories , namely : ( 1 ) abnormal changes in clinical condition , ( 2 ) changes in patient care process , ( 3 ) drug - related alterations , ( 4 ) changes in lab investigations . ( tables 14 ) after the preparation of a comprehensive list of indicators , they were used to screen previously identified and documented ade case reports . a set of 100 previously documented ade reports were randomly picked from the documented database . these adverse events were identified by clinical pharmacists from medicine wards during their rounds with clinicians . these reports contain complete details of the case which included medical history , diagnosis , lab investigations , therapy and ade . the following four factors were then assessed : mean number of indicators per case report , commonly identified indicators , total number of identified indicators , and indicators that were not identified in any of the case reports . items were added to the list based on the relevance of indicators for the internal medicine department and the utility of specific indicators . indicators like hospital visit due to depression or other psychiatric illness due to drug treatment or lack of monitoring was removed since such cases are usually presented to the psychiatry department and do not come under the general medicine department . specific indicators like theophylline toxicity were removed because the use of theophylline is less common and its monitoring is not carried out . indicators like toxicity of individual antiepileptic drugs such as phenytoin , carbamazepine , and sodium valproate were combined asdrug toxicity . an indicator on long term use of codeine and acetaminophen for pain relief resulting in broken bones was removed since such a practice of using codeine for pain relief is not common in this setup . indicators on gastritis and upper intestinal bleeding due to many different drugs and factors were reduced to two indicators . many indicators were recommended to be deleted since their prevalence was thought to be low for this setup . some indicators were combined with others since they were similar . at the end of the review , five reviewers independently reviewed the list and rated them on a scale of 1 to 5 . at the end of the first review ,22 out of 63 items in the list were rated less than 3 points and were subsequently eliminated . eight new indicators were suggested by the members of delphi panel . in the second reviewthe panel members were asked to rate all of the items . at the end of the second review , the results were again presented to the panel members with their scores against the scores of other team members for the third review . the third review did not alter the scores , 49 were rated above 3 points , and were included in the list . indicators which were most frequently identified from the reports were studied ( table 5 ) . abrupt drug withdrawal was the most common indicator identified in the reports , followed by repeat requests for laboratory tests , and use of antihistamine / steroids for the management of drug allergies . drug induced pyrexia , edema , raised serum creatinine , and tremors were among the least identified indicators in reviewed reports . items were added to the list based on the relevance of indicators for the internal medicine department and the utility of specific indicators . indicators like hospital visit due to depression or other psychiatric illness due to drug treatment or lack of monitoring was removed since such cases are usually presented to the psychiatry department and do not come under the general medicine department . specific indicators like theophylline toxicity were removed because the use of theophylline is less common and its monitoring is not carried out . indicators like toxicity of individual antiepileptic drugs such as phenytoin , carbamazepine , and sodium valproate were combined asdrug toxicity . an indicator on long term use of codeine and acetaminophen for pain relief resulting in broken bones was removed since such a practice of using codeine for pain relief is not common in this setup . indicators on gastritis and upper intestinal bleeding due to many different drugs and factors were reduced to two indicators . many indicators were recommended to be deleted since their prevalence was thought to be low for this setup . some indicators were combined with others since they were similar . at the end of the review , five reviewers independently reviewed the list and rated them on a scale of 1 to 5 . at the end of the first review ,22 out of 63 items in the list were rated less than 3 points and were subsequently eliminated . eight new indicators were suggested by the members of delphi panel . in the second reviewthe panel members were asked to rate all of the items . at the end of the second review , the results were again presented to the panel members with their scores against the scores of other team members for the third review . the third review did not alter the scores , 49 were rated above 3 points , and were included in the list . indicators which were most frequently identified from the reports were studied ( table 5 ) . abrupt drug withdrawal was the most common indicator identified in the reports , followed by repeat requests for laboratory tests , and use of antihistamine / steroids for the management of drug allergies . drug induced pyrexia , edema , raised serum creatinine , and tremors were among the least identified indicators in reviewed reports . this study used a team of clinicians and pharmacists to review the developed ade indicators . the delphi technique , which has been used in a number of previous studies , was used as a method of assessing the developed indicator list . an initial list of 71 indicators selected from the literature was considered unmanageable , and after the delphi panel review , the number of indicators was reduced to 49 . in a study by matlow et al on the development of trigger tools for pediatrics , they reported that 94 indicators were initially selected by a review committee . this list was considered as not practical for routine use , and was subsequently reduced to a manageable list of 40 indicators .19 an indicator list containing a reasonably limited number of items is preferable since it reduces the burden on case record reviewers . abrupt withdrawal of drugs was identified most frequently as an indicator in the records . since this is the first step in management of any drug - related adverse event , it could be found in many of the previously documented adverse event reports . repeat requests for a particular investigation signifies a certain level of complication in the management of the patient s condition , and might be associated with drug - related adverse events . the indicator list was classified under four major categories : abnormal clinical changes , change in patient care , laboratory investigation - related , and drug / antidote - related . among these four classes of indicatorsthis showed the preference of reviewers for the indicators which can identify adverse events based on the data available from patient progress charts and follow - up . changes in patient care and lab investigations were the other important group of indicators considered for identifying ades ( 10 each ) . in contrast to a study published by handler et al in which the medication concentration signals were considered as important , abnormal clinical changes were considered as important indicators in this study .24 in this study , even when toxicity was suspected for a drug , estimation of drug levels was not carried out routinely because of economic considerations , and clinicians mostly rely on clinical signs and symptoms to assess toxicity . morris and cantril validated drug - related morbidity indicators developed in the united states and united kingdom , and studied differences between the two setups . they attributed this to the difference in clinical practice and philosophical view points of professional practice . but they concluded that if suitable validation processes can be developed , indicators from one setup can act as a starting point for another setup .22 the current work used indicators reported from various studies and attempted to validate such indicators for the study setup . this exercise gave insight into the viewpoints of health care professionals in the study center . the methodology of using specific triggers or indicators offers flexibility in using this system for a variety of health care systems . the indicators can be modified suitably according to individual setup .7 several institutions have used this approach in their setup and have reduced harm up to 50 % . even though this method itself may not result in improvement in prevention of adverse events concerned , it provides a good platform for any organization which attempts to reduce adverse events . record review using indicators might provide a better chance of detecting ades compared with many other commonly used methods like voluntary reporting , intensive monitoring , and reporting of summary data . even though indicators developed for one setup could be adopted for another setup , indicators adopted from a predominantly western setup may not have relevance in the indian setting . unless the indicators are assessed by using them in the record reviewfurther validation is needed for this indicator list by actually using it for adverse event screening from the medical records . the current work resulted in the development of an indicator list for identification of adverse events in the current setup . the relevance of this indicator list was demonstrated by the presence of these indicators in the previously documented ade case reports . this is the first study from india to report on the development of indicators , and this might provide an alternative method to detect ades in the studied health care setting .\noutput:\n" }, { "from": "agent", "value": "objective : adverse drug events ( ades ) are drug - related events which continue to pose serious challenges to the safety of patients . there are a number of ways to monitor ades , and the use of indictors to screen them provides an alternative method for detecting them . this method helps to assess the safety of drugs by the manual record review technique . the aim of this work was to develop a list of indicators to use in medical units of the study hospital to identify ades.setting : tertiary care teaching hospital in india.method : an initial list of ade indicators based on published literature was developed by a panel of three experts . the list of indicators was subjected to review by a delphi panel of five members . the delphi panel reviewed the list of valid indicators and also suggested an addition of new indicators . the final list of indicators was used to review 100 previously documented ade case reports . the case reports were screened for the presence of any of the indicators from the list . parameters studied included number of indicators per case report and the most used indicators.results : from the literature , a 72 item indicator list was initially prepared which was further narrowed down to a list of 63 items . the delphi panel conducted a review with these 63 items . at the end of review , and after addition and deletion of indicators , a 49 item indicator list was finalized . when this list of indicators was used for the review of ade case reports , 42 indicators were identified . on average , three indicators were present in the reviewed case reports.conclusion : an indicator list was developed for identification of ades in the study setup . the relevance of this indicator list was demonstrated by the presence of these indicators in the previously documented ade reports . this is the first study from india to report on the development of ade indicators , which might provide an alternative method to detecting ades in the setup of future studies ." } ]

[ { "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 first step in the prevention of stress - induced diseases could be to quantify anxieties that individuals have , although quantification per se may not prevent the diseases . while a variety of written self - report anxiety measures provide valid and reliable measures of anxiety , these indices tend to be time consuming to acquire . for medical patients , completing a written report can be burdensome if they are weak , in pain , or in acute anxiety states . thus , simple and fast non - invasive methods for assessing stress response from neurophysiological data are essential . in , we used a near - infrared spectroscopy ( nirs ) device to investigate neurophysiological mechanisms of stress responses . one of our findings was that the prefrontal cortex ( pfc ) plays an important role in stress response as the asymmetry of pfc activity measured by nirs correlated with behavioral and somatic responses to mental stress . it has been observed that there is left / right asymmetry of oxy hemoglobin concentrations in pfc activities during tasks involving mental stress . we measured these activity patterns using a two - channel nirs device instead of fmri or eeg and found that they correlated with the systemic stress responses of the autonomic nervous system and the hypothalamic - pituitary - adrenal ( hpa ) axis system . our present study attempted to go beyond the study of such asymmetries of pfc activities in two directions : a ) the first direction was to consider the resting state of a subject instead of the subject being under a stress task . this makes task design easier because it is nontrivial and often difficult to design a stress task that is effective for every subject . it should be noted that research on the brain under resting conditions is an active study area , and it has been reported that the brain at rest consumes a significant amount of energy and much activities with distinctive patterns are reported.b ) the other direction was to make predictions about anxiety index from oxy and deoxy hemoglobin concentration changes of pfc using a two - channel portable nirs device . we achieved this by constructing a machine learning algorithm within a bayesian framework and implemented it with markov chain monte carlo ( mcmc ) . a brief overview of mcmc is given in appendix b. the first direction was to consider the resting state of a subject instead of the subject being under a stress task . this makes task design easier because it is nontrivial and often difficult to design a stress task that is effective for every subject . it should be noted that research on the brain under resting conditions is an active study area , and it has been reported that the brain at rest consumes a significant amount of energy and much activities with distinctive patterns are reported . the other direction was to make predictions about anxiety index from oxy and deoxy hemoglobin concentration changes of pfc using a two - channel portable nirs device . we achieved this by constructing a machine learning algorithm within a bayesian framework and implemented it with markov chain monte carlo ( mcmc ) . a brief overview of mcmc is given in appendix b. specifically the study proceeded in the following steps : i ) acquire the anxiety index via the state - trait anxiety inventory ( stai ) test.ii ) use a two - channel portable nirs device to measure oxy and deoxy hemoglobin concentration changes of pfc in four different groups , where two of them comprise young subjects , whereas the other two comprise elderly subjects.iii ) place each subject in a resting state in which no task is performed.iv ) build a hierarchical bayesian machine learning algorithm for anxiety index predictions by taking into account both oxy and deoxy hemoglobin concentration changes . because the amount of data was limited , the predictive capability of the algorithm was evaluated by excluding one set of data and using the remaining set for learning . following the learning phase , the set of data previously withheld was used to examine the predictive capability of the algorithm . the hierarchical bayesian algorithm does not need a validation set since it does not utilize leave - one - out cross validation.v ) evaluate the prediction capabilities of the algorithm against four different datasets from each of which one set of data was withheld for testing . acquire the anxiety index via the state - trait anxiety inventory ( stai ) test . use a two - channel portable nirs device to measure oxy and deoxy hemoglobin concentration changes of pfc in four different groups , where two of them comprise young subjects , whereas the other two comprise elderly subjects . place each subject in a resting state in which no task is performed . build a hierarchical bayesian machine learning algorithm for anxiety index predictions by taking into account both oxy and deoxy hemoglobin concentration changes . because the amount of data was limited , the predictive capability of the algorithm was evaluated by excluding one set of data and using the remaining set for learning . following the learning phase , the set of data previously withheld was used to examine the predictive capability of the algorithm . the hierarchical bayesian algorithm does not need a validation set since it does not utilize leave - one - out cross validation . evaluate the prediction capabilities of the algorithm against four different datasets from each of which one set of data was withheld for testing . the remainder of this paper is organized as follows : section ii reviews work related to our study . section iii describes the materials and methods used as well as the experimental settings , subjects , machine learning algorithm , and feature extraction method . nirs is a relatively well established method of measuring oxy hemoglobin ( oxy - hb ) and deoxy hemoglobin ( deoxy - hb ) concentrations in cerebral vessels . changes in oxy - hb are correlated with changes in regional cerebral blood flow ( rcbf ) , whereas changes in total hemoglobin ( sum of oxy - hb and deoxy - hb ; t - hb ) reflect regional cerebral blood volume ( rcbv ) changes . the results of a number of studies indicate that correlations exist between the electrical neural activity and changes in the blood oxygenation levels measured by nirs . simultaneous recordings of nirs and visual evoked potential signals in humans during visual stimulation reveal a linear correlation between hemodynamic changes and evoked potential amplitude . further , simultaneous measurements of nirs and eeg at rest indicate that an increase in oxy - hb is associated with an increase in neuronal activity and vice versa , . a verbal evaluation method attempted in proved faster than the written method and demonstrated a high correlation with stai . in , we conclude this section by stating that this paper is a significantly improved and expanded version of in that four datasets from different age groups are analyzed here , whereas only one target dataset was used in . we acquired four datasets from different locations and on different occasions in 2010 and 2011 . i ) dataset 1population : 19 subjects ( six women ; 13 men ) , age range : 1926 years.ii ) dataset 2population : 19 subjects ( 13 women ; six men ) , age range : 2024 years.iii ) dataset 3population : 17 subjects ( 10 women ; seven men ) , age range : 6179 years.iv ) dataset 4population : 20 subjects ( 16 women ; four men ) , age range : 6079 years . population : 19 subjects ( six women ; 13 men ) , age range : 1926 years . population : 19 subjects ( 13 women ; six men ) , age range : 2024 years . population : 17 subjects ( 10 women ; seven men ) , age range : 6179 years . population : 20 subjects ( 16 women ; four men ) , age range : 6079 years . they all gave written informed consent on forms approved by the ethical committees of the nihon university school of medicine and waseda university . in our experiments , each subject was seated in a comfortable chair in a dimly lit room ( fig .1 ( a ) and we measured the oxy - and deoxy - hb concentration changes using a portable two - channel nirs system ( pnirs - 10 , hamamatsu photonics k.k . the nirs probes were set symmetrically on the forehead of each subject ; the positioning is similar to the midpoint between the electrode positions fp1 / f3 ( left ) and fp2 / f4 ( right ) of the international 10 - 20 system , as demonstrated in fig .1 ( c ) . figure 1 . ( a ) experimental setup ; ( b ) two - channel pocket nirs ; ( c ) international 1020 system red circles indicate the measurement areas . ( a ) experimental setup ; ( b ) two - channel pocket nirs ; ( c ) international 1020 system red circles indicate the measurement areas . the sensor part ( with weight approximately 100 g , resulting in only a very small burden on the subject ) communicated with a pc via bluetooth ( class 2 ) . in general , the machine learning paradigm comprises the following three ingredients : i ) preprocessingii ) feature extractioniii ) learning / prediction algorithm . the nature of nirs data is not well understood ; consequently , the procedure that needs to be followed in each step is nontrivial . this paper reports on our attempts to carry out ( ii ) and ( iii ) , with ( i ) , which is no less important , being left for future work . although the results are not included in this paper , we attempted to devise third and fifth order butterworth bandpass filters ( passband 0.011.0 hz ) and lof outlier detection / deletion on the nirs raw data for ( i ) . we will report on the effects of preprocessing in a future paper ; in this paper , our focus is on ( ii ) and ( iii ) . using all the available features is information rich ; however , less relevant features often degrade predictive performance . this is due to the fact that as the number of features increases , the number of unknown parameters also increases , such that poorly learned parameters degrade prediction capabilities . note that each channel of the target device acquires the concentration changes of oxy - and deoxy - hb so that the acquired data is a four - dimensional vector . figure 3 . typical nirs data consisting of four quantities : right / left \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy and right / left \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy . note that the measured quantities from the device used in this study are the concentration changes \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy , instead of absolute quantities . typical nirs data consisting of four quantities : right / left \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy and right / left \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy . note that the measured quantities from the device used in this study are the concentration changes \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy , instead of absolute quantities . in extracting appropriate features , we first noted that the measured quantities from the device used in the study were the concentration changes \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy , instead of absolute quantities , ( see the appendix also ) . therefore , the first order statistics , the mean values , should be avoided for prediction purposes . in the study , we used the following three pearson correlation coefficients that were reported as effective in : i ) \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( left ) ii ) \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( right ) iii ) \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( right ) across the four datasets . \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( left ) \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } oxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( right ) \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( left ) / \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ bigtriangleup \\ ) \\ end { document } deoxy ( right ) the three quantities are illustrated in fig . 4 in a schematic manner , with an arrow indicating pearson correlation coefficient between the two associated quantities . note that pearson correlation coefficients are normalized in the range [ 1 , + 1 ] . all the arguments in the ensuing section are based on these three second - order features . since the acquired nirs data was four - dimensional , there are six pearson correlation coefficients so that there were \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ sum \\ nolimits _ { n = 1 } ^ { 6 } { { } _ { 6 } c _ { n } } = 63 \\ ) \\ end { document } possibly combinations . by exhaustive searchlet \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( x ^ { ( i ) } : = ( x _ { 1 } ^ { ( i ) } , \\ ldots , x _ { k } ^ { ( i ) } ) \\ in r ^ { k } , \\ kern 1 pt \\ ; \\ kern 1 pt i \\ , =\\ ,1 , \\ ldots , n \\ ) \\ end { document } be the nirs feature vector of the \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( i \\ ) \\ end { document } - th individual . for our selected features , \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( k = 3 \\ ) \\ end { document } , as described in fig .4 . let \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( y ^ { ( i ) } , \\ kern 1 pt \\ ; \\ kern 1 pt i \\ , =\\ ,1 , \\ ldots , n \\ ) \\ end { document } be the stai state index obtained from the questionnaire , where \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( n \\ ) \\ end { document } is the number of subjects in an experiment . of the \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( n \\ ) \\ end { document } available pieces of data , we reserved one \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( ( x _ { reserved } , \\ ; y _ { reserved } ) \\ ) \\ end { document } and attempted to fit the \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( n - 1 \\ ) \\ end { document } remaining pieces of data with the following machine learning model : \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { align } p ( y ^ { ( i ) } \\ vert x ^ { ( i ) } ; \\ omega , \\ beta ) = & \\ sqrt { \\ frac { \\ beta } { 2 \\ pi } } \\ exp ( - \\ frac { \\ beta } { 2 } ( y ^ { ( i ) } - f ( x ^ { ( i ) } ; \\ omega ) ) ^ { 2 } ) \\ notag \\ \\ i = & 1 , \\ ldots , n - 1 \\ end { align } \\ end { document } where \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( f \\ ) \\ end { document } is a basis function for data fitting , and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega \\ ) \\ end { document } denotes the associated unknown parameter to be learned . \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ beta \\ ) \\ end { document } is another parameter to be learned that is often called the hyperparameter , and corresponds to the uncertainty level associated with the acquired stai value . in order to capture the potential nonlinear relationship between the nirs data and the stai , we considered the following nonlinear basis function : \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { align } f ( x ^ { ( i ) } ; \\ omega ) : = \\ sum \\ limits _ { h = 1 } ^ { h } { \\ big ( \\ omega _ { ( k +1 ) h } \\ sigma \\ big ( \\ sum \\ limits _ { k = 1 } ^ { k } { \\ omega _ { kh } x _ { k } ^ { ( i ) } + \\ omega _ { 0h } } \\ big ) \\ big ) } + \\ omega _ { 0 ( k +1 ) } \\ hspace { -1 pc } \\ notag \\ \\ \\ text { } \\ end { align } \\ end { document } where \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ sigma \\ ) \\ end { document } is a sigmoidal function . this basis function is nonlinear with respect not only to \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( x \\ ) \\ end { document } but also \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega \\ ) \\ end { document } , which makes the learning algorithm nontrivial . it is known that this basis function ( perceptron ) can approximate any nonlinear function with arbitrary precision . as in , the unknown parameter vector \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega \\ ) \\ end { document } is decomposed as \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega = \\ left \\ { { \\ { \\ omega _ { k } \\ } _ { k = 1 } ^ { k } , \\ ; \\ omega _ { ( k +1 ) , } \\ ; \\ omega _ { 0 , } \\ ; \\ omega _ { 0 ( k +1 ) } } \\ right \\ } \\ ) \\ end { document } with \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { k } : = ( \\ omega _ { k1 } , \\ ldots , \\ omega _ { kh } ) \\ in r ^ { h } \\ ) \\ end { document } , \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ vphantom { \\ sum ^ { r ^ { r ^ { r } } } } \\ omega _ { ( k +1 ) } : = ( \\ omega _ { ( k +1 ) 1 } , \\ ldots , \\ omega _ { ( k +1 ) h } ) \\ in r ^ { h } \\ ) \\ end { document } , \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { 0 } : = ( \\ omega _ { 01 } , \\ ldots , \\ omega _ { 0h } ) \\ in r ^ { h } \\ ) \\ end { document } and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { 0 ( k +1 ) } \\ in r \\ ) \\ end { document } . this decomposition amounts to the fact that each \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { k } \\ ) \\ end { document } is the first - layer weights , associated with each feature \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( x ^ { ( i ) } _ { k } , ~ k \\ , =\\ ,1 , \\ ldots , k \\ ) \\ end { document } . \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { ( k +1 ) } \\ ) the remaining two parameters \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ { { \\ omega _ { 0 , } \\ ; \\ omega _ { 0 ( k +1 ) } } \\ } \\ ) \\ end { document } were the bias parameters . the number of hidden units \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( h \\ ) \\ end { document } can be estimated within the present hierarchical bayesian framework . this endeavor , however , requires a more complicated algorithm and much more time to execute . from our own experiences , as well asthose reported by other researchers , we used eight as the choice for \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( h \\ ) \\ end { document } . our study formulated the prediction problem within a bayesian framework , where a prior distribution was assumed about the unknown parameters and that information incorporated intothe data fitting model given by ( 1 ) . the prior distribution for \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ omega _ { k } \\ ) \\ end { document } was assumed to be specified by \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { equation * } p ( { \\ omega } _ { k } | { \\ alpha } _ { k } ) = n \\ left ( 0 , \\ left ( \\ frac { 1 } { { \\ alpha } _ { k } } \\ right ) i \\ right ) \\ end { equation * } \\ end { document } which is the gaussian distribution with a zero mean vector and covariance matrix ( \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( 1 / { \\ alpha } _ { k } ) i ;{ \\ alpha } _ { k } \\ ) \\ end { document } is the hyperparameter , associated with first - layer weights \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( { \\ omega } _ { k } \\ ) \\ end { document } , and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( i \\ ) \\ end { document } denotes the identity matrix , \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( k = 1 , \\ ldots , k \\ ) \\ end { document } . this prior distribution often prevents overfitting . \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( { \\ alpha } _ { ( k +1 ) } \\ ) \\ end { document } is associated with second - layer weights \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( { \\ omega } _ { ( k +1 ) } \\ ) \\ end { document } . there were two other hyperparameters \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ { { \\ alpha _ { 0 } , \\ alpha _ { 0 ( k +1 ) } } \\ } \\ ) \\ end { document } , which were associated with the bias parameters \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ { { \\ omega _ { 0 } , \\ omega _ { 0 ( k +1 ) } } \\ } \\ ) \\ end { document } . the prior distributions for \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ beta \\ ) \\ end { document } and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ alpha \\ ) \\ end { document } were assumed to follow the gamma distribution . let \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { align } \\ alpha : = & \\ { \\ { \\ alpha _ { k } \\ } _ { k = 1 } ^ { k } , \\ alpha _ { ( k - 1 ) } , \\ alpha _ { 0 } , \\ alpha _ { 0 ( k - 1 ) } \\ } , \\ , x : =\\ { x ^ { ( i ) } \\ } _ { i = 1 } ^ { n - 1 } , \\ notag \\ \\ y : = & \\ { y ^ { ( i ) } \\ } _ { i = 1 } ^ { n - 1 } . \\ end { align } \\ end { document } the rationale behind the gamma distribution for prior is explained in appendix c. assuming the data from each individual to be independent , the bayes formula gives the posterior distribution : \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { align } & \\ hspace { -1.9 pc } p ( \\ omega , \\ alpha , \\ beta | x , y ) \\ notag \\ \\ \\ ! \\ ! =\\ ! \\ ! & \\ frac { \\ prod \\ limits _ { i = 1 } ^ { n - 1 } p ( y ^ { ( i ) } | x ^ { ( i ) } ; \\ omega , \\ beta ) p ( \\ omega | \\ alpha , \\ beta ) p ( \\ alpha , \\ beta ) } { \\ int \\ ! \\ ! \\ ! \\ int \\ ! \\ ! \\ ! \\ int \\ prod \\ limits _ { i = 1 } ^ { n - 1 } p ( y ^ { ( i ) } | x ^ { ( i ) } ; \\ omega , \\ beta ) p ( \\ omega | \\ alpha , \\ beta ) p ( \\ alpha , \\ beta ) d \\ omega d \\ alpha d \\ beta } \\ end { align } \\ end { document } prior distribution for hyperparameter \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ alpha \\ ) \\ end { document } and \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ beta \\ ) \\ end { document } are not explicitly written in ( 5 ) , for the purpose of clarity . given the reserved nirs data \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( x _ { reserved } \\ ) \\ end { document } , the prediction of the stai index associated with the reserved data \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( y _ { reserved } \\ ) \\ end { document } was performed by computing the predictive distribution : \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ begin { align } & \\ hspace { -1.3 pc } p ( y _ { reserved } \\ vert x _ { reserved } , x , y ) \\ notag \\ \\ = & \\ int \\ ! \\ ! \\ ! \\ int \\ ! \\ ! \\ ! \\ int { p ( y _ { reserved } \\ vert x _ { reserved } , \\ omega , \\ beta ) p ( \\ omega , \\ alpha , \\ beta \\ vert x , y ) d \\ omega d \\ alpha d \\ beta . } \\ notag \\ \\ \\ text { } \\ end { align } \\ end { document } as described in subsection iiid , one piece of data \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( ( x _ { reserved } , \\ ; y _ { reserved } ) \\ ) \\ end { document } out of \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( n \\ ) \\ end { document } was reserved , whereas the remaining \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( n - 1 \\ ) \\ end { document } pieces of data were used for learning the unknown parameters . after the parameters were learned , the reserved data were input to the algorithm for stai prediction . because one stai value was also reserved , we were able to compute the difference between the predicted and the reserved stai values , which can signify prediction error . since hyperparameters ( \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ alpha \\ ) \\ end { document } , \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( \\ beta ) \\ ) \\ end { document } can also be learned via ( 5 ) , the method is called the hierarchical bayesian algorithm . we performed four prediction experiments , one experiment for each of the four datasets . within each dataset , one set of data was reserved for testing while the rest were used for learning . the reserved data were not used in the learning process . it should be noted that in the stai prediction of each subject , the algorithm had never seen the data from the particular subject to be tested . it should also be noted that this is not leave - one - out cross validation . the hierarchical bayesian method used in this studyonly the state anxiety index was used in the present study , even though the trait anxiety index was available . we will attempt to make predictions of the trait anxiety index in our future project . depicts scatter plots of the actual stai values and the predicted values with the nonlinear model . figs . it should be noted that the figures are not the results of linear regression between the quantities of the horizontal and the vertical axes ( see subsection iiid ) . the blue lines signify the rmse of 10 , which is an empirical value proposed by one of the coauthors of this paper who is a clinician in neurosurgery in the sense that an rmse of 10 for stai could be tolerable in a clinical practice where the stai score is between 20 and 80 . we note that only a limited amount of data was available for stai values near 20 and 80 . as a result , the algorithm had very little chance of seeing very low / high stai scores and it was difficult to make good predictions ; however , the results appear to be reasonable , including the low / high stai values . figure 6 . scatter plots of actual stai and predicted stai values with the proposed algorithm based on the nonlinear model : ( a ) dataset 1 ; ( b ) dataset 2 ; ( c ) dataset 3 ; ( d ) dataset 4 . scatter plots of actual stai and predicted stai values with the proposed algorithm based on the nonlinear model : ( a ) dataset 1 ; ( b ) dataset 2 ; ( c ) dataset 3 ; ( d ) dataset 4 . table 1 summarizes the results with multiple evaluation indices : rmse , pearson correlation coefficients , and the p - values of two tailed t - tests between the actual stai values and the predicted stai values . note that datasets 1 and 2 were acquired from young subjects ( 1926 years and 2024 years , respectively ) whereas datasets 3 and 4 were obtained from elderly subjects ( 6179 years and 6079 years , respectively ) . the effect of aging did not appear to be critical within this prediction framework . performance indices are rmse , pearson correlation , and the associated p - value of two tailed t - test between the actual stai and the predicted values . performance indices are rmse , pearson correlation , and the associated p - value of two tailed t - test between the actual stai and the predicted values . it can be seen that the linear predictions were much less accurate than those with the proposed nonlinear predictions . table 2 . summary of the proportions of rmse for differing upper bounds with the proposed algorithm based on the nonlinear model . summary of the proportions of rmse for differing upper bounds with the proposed algorithm based on the nonlinear model . to assess the intra - subject variation of the proposed algorithm , we used the following multiple nirs measurement data . following acquisition of dataset 1 , we asked the 19 subjects to repeat three more trials subsequent on the trial described in iiiathe bayesian learning was conducted using the ( 18 out of 19 ) first set of trial data , which was in fact the same as those used in iiia and tested against the remaining data . using the parameters learned from the first set of trial data , tests were performed against the second , third , and fourth set of trial data . learning was performed with the data from the first set of trial data for 18 subjects other than subject 1 , whereas prediction capability was tested against the withheld data for subject 1 . with the same learned data , tests were performed on the second , third , and fourth sets of data from subject 1 . in 10 of the 19 subjects , the prediction error of the fourth trial was greater than that of the first trial . learning was performed with the data from the first set of trial data for 18 subjects other than subject 1 , whereas prediction capability was tested against the withheld data for subject 1 . with the same learned data , tests were performed on the second , third , and fourth sets of data from subject 1 . in 10 of the 19 subjects , the prediction error of the fourth trial was greater than that of the first trial . the prediction error for the fourth trial was greater than that for the first trial in 10 subjects out of 19 . however , in nine subjects , the prediction error for the fourth trial was less than that for the first trial .8 shows the results for subject 10 . figure 8.intra - subject variability of the prediction capability of subject 10 over four trials . learning and prediction are similar to those in fig . the prediction error for the fourth trial was less than that for the first trial . the prediction error for the fourth trial was less than that for the first trial . the overall average intra - subject prediction error was 7.638 , which is greater than those listed in table 1 . the brain at rest has been an active research area and numerous activities with distinctive patterns have been reported . our study considered the nirs data in the resting condition . the method used in the study did not need task design , which made experimentation easier . with nirs measurements for stress task , a subject s nirs data started changing when the subject was told that the task would begin in 30 s , even before the actual stress task began . in the resting condition assumed in our study , that effect was less than in the stress task ; however , we could not exclude the potential effect of the information on the subject when the subject was informed of the beginning of the measurement 30 s before the measurements began . the present study went beyond investigating the left / right asymmetry of oxy - hb concentrations in the pfc activity during tasks involving mental stresssuch that the stai index predictions were performed based on the four - dimensional nirs values instead of the mere oxy - hb concentration changes . the three - dimensional features were extracted from the oxy - and deoxy - hb concentrations changes acquired from a two - channel nirs device placed on the pfc . note that the prediction experiments were performed on four different datasets that were acquired from different individuals on different occasions . since the stai values varied between 20 and 80 , the rmse values 6.20 , 6.62 , 4.50 , and 6.38 appear reasonable . table 2 summarizes the proportions of the rmse values that were less than 10 as well as those less than five in each dataset . there are three facts that should be mentioned here : i ) the algorithm had never seen the nirs values as well as the associated stai of a particular individual before . the parameters were learned from the data of other subjects only , suggesting that the stai values of unknown subjects may be predictable once the machine learned.ii ) there were several subjects whose stai values could be predicted by the proposed algorithm with reasonable accuracy . table 2 , for instance , shows that there were 84.2100 % of the young as well as elderly subjects whose stai prediction errors were less than 10 , which appears reasonable since the stai varied between 20 and 80 . the rightmost column of table 2 gives the minimum rmse for each dataset.iii ) in machine learning prediction problems , it is often critical to choose appropriate features . the algorithm had never seen the nirs values as well as the associated stai of a particular individual before . the parameters were learned from the data of other subjects only , suggesting that the stai values of unknown subjects may be predictable once the machine learned . there were several subjects whose stai values could be predicted by the proposed algorithm with reasonable accuracy . table 2 , for instance , shows that there were 84.2100 % of the young as well as elderly subjects whose stai prediction errors were less than 10 , which appears reasonable since the stai varied between 20 and 80 .4 throughout the four datasets , irrespective of age . recall that our basis function ( 2 ) is nonlinear not only with respect to feature vector \\ documentclass [ 12 pt ] { minimal } \\ usepackage { amsmath } \\ usepackage { wasysym } \\ usepackage { amsfonts } \\ usepackage { amssymb } \\ usepackage { amsbsy } \\ usepackage { upgreek } \\ usepackage { mathrsfs } \\ setlength { \\ oddsidemargin } { - 69 pt } \\ begin { document } } { } \\ ( x \\ ) \\ end { document } , but also with respect to unknown parameters . we tested a linear model instead of the nonlinear model and found that the linear model was much less accurate than the proposed nonlinear model , as summarized in table 1 . two groups comprised young subjects ( 1926 years and 2024 years , respectively ) , whereas the remaining two comprised elderly subjects ( 6179 years and 6079 years , respectively ) . the results in table 1 appear to indicate that age does not play any significant role in the stai prediction problem . we note that a gender difference is discernible in that the highest rmse was 6.62 , followed by 6.38 in datasets 2 and 4 , respectively , where the result for the female subjects dominates that for the male subjects . potential differences in the results due to gender difference are not surprising because it is a known fact that gender differences exist in brain functions . in language processing tasks , for example , the right pfc is often activated in male subjects , whereas both the right and left pfc are activated in female subjects . fig. 7 appears to suggest that the subject could have started becoming tired as the trial proceeded . however , there were other cases where the prediction error decreased instead of increased over the four trials , as was shown in fig. 8 . on comparing our experiences with eeg - based experiments , both portable and non - portable , we determined that the two - channel portable nirs device is easier to equip than eeg devices . this is mainly because when conducting eeg measurements , one needs to carefully reduce the contact impedance between the head and the probe , whereas there is no such intricacy associated with the nirs device used in our study . the burden on the part of the subjects was also light compared with eeg measurements because the subjects could blink and carry out minor movements , whereas blinking and head movement significantly distort eeg signals . the fact that the nirs device was portable and lightweight also helped subjects to participate in the experiments with relative ease . the results of our prediction experiments , which we report in section iv , appear to indicate that the proposed algorithm is functional at least in the target datasets because the average prediction error is relatively small . the device is portable , weighs 100 g , and is easy to attach ; therefore , there could be potential applications in practical situations . one of the coauthors of this study , who is a neurosurgeon and routinely examines the stai index of patients before major operations , found that it helps when reasonable anxiety is predictable with this kind of simple device without a written self - report . the proposed method can be utilized in cases where patients are weak , in pain , or in acute anxiety states such that it is difficult for them to complete written questionnaires . one of the coauthors of this paper is a neurosurgery clinician and routinely acquires stai questionnaires from patients prior to major operations . sometimes , however , a patient is not able to answer the questionnaire in a credible manner . if the prediction method reported in this paper is functional , it could help in such scenarios . our predictions are based on a bayesian machine learning algorithm using the features extracted in terms of prediction errors . the fact that our predictions were reasonable means that the acquired nirs data contained information about the stai index via a complicated nonlinear manner provided appropriate features are found . this endeavor , however , necessitates a significant amount of effort and will therefore be left for future research . another limitation is that nirs measures the blood oxygen changes within illuminated pathways such that measured values of hemoglobin changes are also affected by extra - cranial tissues , not only intracranial tissues . in addition , it was suggested that the experiment itself could affect pfc activity at rest since the subject might feel the strain during nirs measurements , depending on their anxiety levels . the following possible future research projects are under consideration : i ) it would be interesting to study if the capability of the proposed prediction algorithm depends on gender and handedness , among other characteristics.ii ) it would also be worth investigating the prediction capability of the stai trait index , which is the feelings of stress , worry , discomfort , etc . that one experiences on a daily basis , instead of the stai state index , which is the feeling solely at the time of the experiment.iii ) nirs measurements are the building blocks for the proposed algorithm ; therefore , we need to eliminate possible uncertainties and examine its prediction capabilities . for instance , a project worth pursuing would be to consider a particular subject performing the experiment over several time intervals , e.g. , one or several weeks or several months , and examine the prediction capabilities of the proposed method . environmental factors worth considering include room temperature , humidity , lighting , time of a day , among others.iv ) an advantage of the present method is that it is not restricted to the stai data and the nirs data , as long as targeted written test data and associated sensor data are available.v ) providing experimental data considering both cases , i.e. , answering the questions before or after acquisition , could reveal useful information about nirs measurement sensitivity at resting protocols . it would be interesting to study if the capability of the proposed prediction algorithm depends on gender and handedness , among other characteristics . it would also be worth investigating the prediction capability of the stai trait index , which is the feelings of stress , worry , discomfort , etc . that one experiences on a daily basis , instead of the stai state index , which is the feeling solely at the time of the experiment . nirs measurements are the building blocks for the proposed algorithm ; therefore , we need to eliminate possible uncertainties and examine its prediction capabilities . for instance , a project worth pursuing would be to consider a particular subject performing the experiment over several time intervals , e.g. , one or several weeks or several months , and examine the prediction capabilities of the proposed method . environmental factors worth considering include room temperature , humidity , lighting , time of a day , among others . an advantage of the present method is that it is not restricted to the stai data and the nirs data , as long as targeted written test data and associated sensor data are available . providing experimental data considering both cases , i.e. , answering the questions before or after acquisition , could reveal useful information about nirs measurement sensitivity at resting protocols . in this paper , we reported on a study in which we attempted to make predictions of the anxiety index of subjects from data acquired by a two - channel nirs device placed on the pfc . the method utilized comprised several steps : i ) data acquisitionii ) feature extractioniii ) construction of machine learning algorithmiv ) prediction construction of machine learning algorithm data were acquired from four different groups two comprising young subjects and the remaining two comprising elderly subjects . care had to be taken in constructing the machine learning algorithm because the amount of data acquired was highly limited to 1720 subjects in each dataset , in addition to the potentially significant amount of uncertainties contained . since the stai score varies between 20 and 80 , the prediction accuracies appeared reasonably accurate . there appeared no significant difference in prediction capabilities between the young and the elderly subjects . the device is portable , weighs only 100 g , and is easy to position ; therefore , the method can be used in practical situations . in one of our ongoing research projects , a new algorithm for improving prediction accuracies is being developed .\noutput:\n" }, { "from": "agent", "value": "stress - induced psychological and somatic diseases are virtually endemic nowadays . written self - report anxiety measures are available ; however , these indices tend to be time consuming to acquire . for medical patients , completing written reports can be burdensome if they are weak , in pain , or in acute anxiety states . consequently , simple and fast non - invasive methods for assessing stress response from neurophysiological data are essential . in this paper , we report on a study that makes predictions of the state - trait anxiety inventory ( stai ) index from oxyhemoglobin and deoxyhemoglobin concentration changes of the prefrontal cortex using a two - channel portable near - infrared spectroscopy device . predictions are achieved by constructing machine learning algorithms within a bayesian framework with nonlinear basis function together with markov chain monte carlo implementation . in this paper , prediction experiments were performed against four different data sets , i.e. , two comprising young subjects , and the remaining two comprising elderly subjects . the number of subjects in each data set varied between 17 and 20 and each subject participated only once . they were not asked to perform any task ; instead , they were at rest . the root mean square errors for the four groups were 6.20 , 6.62 , 4.50 , and 6.38 , respectively . there appeared to be no significant distinctions of prediction accuracies between age groups and since the stai are defined between 20 and 80 , the predictions appeared reasonably accurate . the results indicate potential applications to practical situations such as stress management and medical practice ." } ]

[ { "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: integrins are plasma membrane proteins that generate complex and intracellular signals during morphogenesis , tissue remodeling , and repair . interactions of integrins with specific extracellular matrix proteins and growth factors or with certain small molecules generate ligand - specific signals . the integrin superfamily of heterodimeric glycoproteins consists of - and - monomers that associate in defined combinations that include more than twenty different mammalian subtypes , of which at least eight are characterized by the presence of an arg - gly - asp ( rgd ) site used in the process of recognition of different protein ligands . structural data have revealed that the extracellular segment of integrin v3 ( i.e. , lacking the transmembrane and cytoplasmic tails ) is v shaped with the 4 - domain v subunit and the 8 - domain 3 subunit bent by 135 . data for the rgd cyclic pentapeptide complex reveals that the rgd peptide occupies a shallow crevice between the propeller and a domains in the integrin head . the x - ray structure of apo v3 has been determined in the presence of ca ions and in the presence of mn as a complex with the cyclic pentapeptide arg - gly - asp - { d - phe } - { n - methyl - val } ( figure 1 ) . these data showed that replacement of ca with mn in the v3 integrin did not result in any important structural changes to the protein . there are also relatively small changes in the v3 structure with and without the cyclic pentapeptide bound in the rgd site of integrin . ligand binding to integrins is dependent upon bivalent - cation interactions that are generally stimulated by mg or mn and inhibited by ca . competitive binding data revealed preferential binding sites for one or more cations that could also be displaced by other cations and that their specific occupancy can lead to enhanced ligand binding in an allosteric or synergistic manner . the central core of the - propeller is one of the primary sites for cation binding . a common structural motif observed for integrins is the presence of a metal binding site , termed metal ion - dependent adhesion site ( midas ) , that is unique for mg / mn and is located in the integrin subunit i domain . mutagenesis data have shown that the midas motif and the nearby solvent exposed side chains are required for ligand binding . the integrin protein family has been studied both experimentally and theoretically . studies using nmr and molecular dynamics methods to map the interaction of the cyclic - peptide isodgr , a competitive antagonist of rgd - containing ligands of v3 integrin that inhibits endothelial cell adhesion , proliferation , and tumor growth , revealed a new recognition motif of the rgd binding pocket of v3 integrin . docking studies for a series of cyclic peptides further defined the structure - function relationships in binding to the rgd recognition site of v3 integrin . studies using a combination of experimental and computational approaches defined the role of divalent cations in mediating the binding of integrins to rgd peptides . structural data revealed that the divalent cation at the midas site in the a domain of integrin contacts the asp of the rgd peptide . this site is occupied by the divalent ion only in the rgd - liganded state . the results of these molecular dynamics studies support the stability of the orientation of asp residue of the rgd recognition site that interacts with the midas which is essential for binding , whereas the orientation of glu220 carboxyl oxygens of the 3 domain for the ligand associated metal binding sites ( limbss ) was maintained throughout the molecular dynamics simulations . the steered molecular dynamics studies of the unbinding of rgd cyclic peptides from v3 integrin revealed the importance of single water molecules tightly coordinated to the midas ion . these data suggest that this process is a general strategy for the stabilization of protein - protein adhesion against cell - derived forces through divalent cations . recently , a cell surface receptor for thyroid hormone has been identified on the extracellular domain of the v3 integrin that is relevant to the proliferative and proangiogenic activity of thyroid hormone . transduction of the hormone signal into proliferation and angiogenesis at the integrin is achieved by the mitogen - activated protein kinase ( mapk ; extracellular regulated kinase 1/2 , erk1 / 2 ) pathway or by the phosphatidylinositol 3 - kinase ( p3k ) / akt pathway . l - thyroxine ( t4 ) and 3,5,3 - triiodo - l - thyronine ( t3 ) are agonist thyroid hormone analogues at the integrin receptor , whereas a deaminated derivative of t4 , tetraiodothyroacetic acid ( t4ac ) , is a nonagonist inhibitor of the binding of t4 and t3 to integrin . competition data revealed that rgd peptides also block hormone binding by integrin , suggesting that the hormone - binding site is near the rgd recognition site on v3 . further analysis revealed that rgd peptides could inhibit the binding of other biologically active small molecules with estrogen - like structures , such as cis - and trans - resveratrol and stilbene ( figure 2 ) . these data reveal that t4 promotes cell proliferation in cancer cells whereas resveratrol is proapoptotic and that further shows that t4 inhibits resveratrol - induced apoptosis . this action is prevented by t4ac , shown to be an inhibitor of t4 binding to integrin . in the presence of t4 , t4ac does not affect the induction of apoptosis by resveratrol . these observations suggest that there is a discrete binding site for resveratrol and thyroid hormone on integrin . the noniodinated thyroid hormone analogue gc - 1 lacks the amino group of the alanine side chain , lacks the ether linkage between phenyl rings , and has methyl groups at the 3,5 - positions and an isopropyl group at the 3 - position , compared with the thyroid hormone t3 ( figure 2 ) . this thyroid hormone analogue is a selective agonist for nuclear thyroid hormone receptor tr1 and has the desirable metabolic effect of lowering circulating cholesterol without inducing tachycardia . gc - 1 was also demonstrated to be proangiogenic at the plasma membrane and require interaction with v3 integrin . to understand how these hormones and their analogues interact with integrin , modeling studies were carried out using the coordinates of the extracellular fragment of v3 integrin ( 1l5g . pdb ) as a starting model for their interactions near the rgd recognition site . these preliminary models revealed that the hormone analogues shown in figure 2 can bind in the rgd recognition site and that there may be two closely related binding pockets that can bind these hormone analogues . the smaller of these sites may be preferential for the more planar compounds such as estradiol , stilbene , or resveratrol . to provide more definitive details of the intermolecular interactions of these hormone analogues with the rgd recognition site in v3 integrin , quantitative molecular modeling including molecular dynamics ( md ) simulations and combined quantum mechanical molecular mechanical ( qm / mm ) methods were employed . these calculations also incorporated the effects of solvent and divalent cations on ligand - binding interactions . in order to calculate the desolvation energies of these ligands , an explicit water environment based on molecular dynamics ( md ) simulations was used in the qm / mm calculations . in the present study we utilized our own method of combined qm / mm calculations which are based on md . in this approach , standard md of the protein solvated by a sphere of explicit water moleculesthen a randomly chosen set of snapshots was selected from the md , and for each snapshot , full geometry optimization of the ligand ( qm ) in a fixed protein matrix ( mm ) was performed . in order to calculate the desolvation energy of the ligand , the same qm / mm was used to calculate the ligand surrounded by a sphere of explicit water molecules . the ligand - binding energy to the protein was calculated as a difference between the average ligand energy in the protein and the water environment . these computations were performed using the quantum - chemical program q - chem , which includes a modified version of an interface between qm and mm atoms . since the combined qm / mm calculations for each snapshot are independent of the other snapshots , this method referred to as the large - scale qm / mm method has the advantage of perfect parallel scalability . all calculations were performed using a large 1.000 node linus cluster where each node consists of two 3.2 ghz xeon processors and 2 gb of shared memory . coordinates from the x - ray structure of the v3 receptor ( 1l5 g pdb ) were used as a starting model . the cyclic rgd pentapeptide was removed from the file and original mn ions were replaced by mg or ca ions . parameters of the nag residues observed in this structure were obtained from the antechamber program of the amber programming suite . the positions of these cations were obtained from grid calculations of the protein electrostatic potential . the ligand structures ( figure 2 ) were obtained using quantum mechanical ( qm ) calculations at the b3lyp / 6 - 31 + g * level of theory . the qm calculations consisted of full geometry optimization of the ligands performed in the gas phase . these calculations , including iodine atoms of the thyroid hormones ( t4 , t3 , t4ac ) , were obtained using the lanl2dz effective core potential with a corresponding basis set . docking calculations were carried out using the auto dock 3 program . because of the lack of molecular mechanical parameters for iodine in the auto dock program , this atom was temporary replaced in the docking process by a carbon atom . the docking procedure was performed using a fixed internal geometry of these ligands . after docking , one snapshot of these compoundsthe precise selection of a docked structure is not important because geometry and orientation of the molecule inside the protein active site were recalculated in the following md simulations and in the qm / mm calculations . once these ligands were docked to the protein near the rgd recognition site of v3 integrin , another round of md simulations was carried out . the molecular system , including the protein , the ligand , and the metal ions , was placed into a center of tip3p water sphere of radius 80 . the md consisted of 100 ps heating dynamics from 0 to 300 k , followed by equilibration dynamics performed for 5 ns . the md simulation was also performed at constant temperature and volume , with application of constrained harmonic potentials outside the water sphere and for the metal ions . the md has been performed separately for each ligand ( figure 2 ) and separately for the protein system with ca and mg ions . following the md simulations , combined qm / mm calculations of the interaction between the ligand and the protein environment were carried out . first , a randomly selected protein snapshot from md was chosen that was then divided into qm part and mm contributions . the qm part included the ligand and the mm part included the rest of the protein system with water molecules and the metal ions . finally , full geometry optimization of the qm part inside the fixed positions of all atoms of the mm part was performed using the b3lyp / 6 - 31 + g * / amber method , as implemented in the q - chem program . during geometry optimization , the ligands were allowed to change their internal geometry and position relative to the fixed protein matrix . the calculations of the ligands , including those with iodine atoms ( t4 , t3 , t4ac ) , were performed using the lanl2dz effective core potential with a corresponding basis set . the interaction energy between the ligand and the protein was calculated as an energy difference between the energy of the molecule inside the protein and the energy of the molecule in the gas phase which was obtained from the optimal geometry of the molecule in the protein and in the gas phase , respectively . the same procedure was then applied to 600 randomly selected protein snapshots from the last 200 ps of md , and the results of the calculations are reported statistically based on the selected protein ensemble ( tables 1 and 2 ) . calculations of an induced dipole moment of the ligands ( figure 2 ) bound to the protein and in water were also carried out ( table 2 ) . the induced dipole moment is reported as a difference between the permanent dipole moment of the ligand in the protein ( water ) and the permanent dipole moment of the ligand in the gas phase , obtained from the optimal geometry of this molecule in the protein ( water ) and the gas phase , respectively . the calculated values of the interaction energies and induced dipole moments are reported as average values based on an ensemble of 600 protein ( solvent ) samples . use of a larger number of samples in the ensemble would represent the protein ( solvent ) system much more realistically ; however it requires more time - consuming calculations . therefore the number of samples ( snapshots ) chosen in the calculations was a compromise between computational accuracy and efficiency . structural data for the extracellular portion of v3 integrin reveals a heterodimer with 12 domains assembled into an ovoid head and two tails . the v and a domains form a seven - bladed propeller and the 3 portion of the integrinhead is composed of the a and hybrid domains ( figure 1 ) . the rgd cyclic peptide containing the rgd sequence binds in a crevice between the propeller and the a domains of the integrin head ( figure 1 ) . these data reveal interactions of the rgd peptide asp with the backbone of tyr122 and asn215 and the side chain atoms of arg214 of the 3 domain of v3 integrin and the arg of rgd interacts with asp150 and asp218 of the v domain ( figure 3 ) . also illustrated in figure 3 is the binding orientation of t4ac ( red ) and estradiol ( yellow ) as docked in the rgd cyclic peptide binding pocket . only small conformational changes were noted near the a domain between the apo integrin structure and the rgd cyclic peptide complex . these changes are also involved the metal ( ca or mn ) binding site in this region . to model thyroid or steroid hormone analogue interactions near the rgd cyclic peptide binding site , molecular docking experiments using quantum chemical calculations ( qm / mm ) were carried out in the presence of ca or mg for each of the ligands shown in figure 2 . furthermore , these calculations were carried out with the ligand in two different starting positions near the rgd binding site ( indicated as ca1 and ca2 ) to remove modeling bias from the calculations . similar calculations were made with the ligand starting position about 15 away from the rgd binding site . the results of the distant starting site calculations showed much smaller stabilization energies and suggest that the interaction between the ligand and metal cations is an important part of ligand binding ( data not shown ) . the results of the qm / mm modeling for the thyroid hormones , t4 , t3 , and t4ac , based on two starting orientations near the rgd binding site at the interface of the v and 3 domains , show that the thyroid hormones can bind in a wide range of orientations . in the case of t4 , the different starting positions result in binding modes in which the amino and hydroxyl ends of the molecule are flipped in the binding pocket . in one orientation , the 4 - hydroxyphenyl ring occupies a binding pocket deeper within the crevice between the v3 domains , while in the other binding mode , the phenolic ring occupies the interface between the integrin v3 domains ( figure 4 ) . consistent with pharmacokinetic / pharmacodynamic modeling reported elsewhere , the qm / mm modeling results for t3 differ significantly from those of t4 ( figure 5 ) . in one mode , the tyrosyl moiety lies along the arg side chain of the cyclic rgd peptide ( figure 6 ) . the second binding mode for t3 places the 4 - phenolic ring in a different binding pocket than observed for t4 ( figure 5 ) . the results for the two starting positions of t4ac reveal yet another variation in binding modes ( figure 7 ) . in this case , one of the t4ac orientations aligns along the side chain of arg in the rgd peptide binding site , as was observed for one of the orientations of t3 ( figure 6 ) . comparison of the other starting position for t3 and t4ac reveals a binding mode in which the phenolic ring of t4ac binds deeper within the rgd binding pocket , similar to that of t4 . the phenolic ring of t3 occupies an alternate pocket not occupied by either t4 or t4ac ( figure 8 ) . the one starting position calculated for the noniodinated thyroid analogue gc - 1 binds in a similar manner to that of t3 ( ca2 ) ( figure 9 ) . the differences in binding modes possible for the thyroid hormones are in agreement with competition data that indicate that rgd peptides block hormone binding by v3 integrin . these studies further show that t4ac is a nonagonist inhibitor of t4 and t3 binding to v3 integrin . the results of the qm / mm modeling of ligand interactions with cis - and trans - reservatrol based upon two starting positions show that these ligands have similar binding orientations near the rgd binding site ( figure 10 ) . in the case of the cis - resveratrol , both starting positions placed the ligand in similar orientations such that the dihydroxyphenyl ring makes interactions with asn215 of the 3 domain . in the case of trans - resveratrol , the two starting positions result in the molecule being flipped such that the dihydroxyphenyl ring is bound the opposite direction . the 4 - hydroxyphenyl ring still maintains contact to asn215 of the 3 domain ( figure 10 ) . these results are in agreement with biochemical data that indicate only the 3 monomer was essential for activation and induction of apoptosis by resveratrol and that the occlusion of the rgd binding site blocks the cellular actions of resveratrol . the modeling results for the qm / mm binding modes of cis - and trans - stilbene , the nonhydroxylated parent compound of resveratrol , revealed that the energy minimum conformation for the two starting positions of cis - stilbene were perpendicular to each other with one conformer bound deeper in the binding pocket than the other cis - conformer ( figure 11 ) . the results for the two starting positions of trans - stilbene show one molecule bound deeper in the rgd pocket than the other which is outside the binding pocket . the more hydrophobic nature of cis - and trans - stilbene compared with cis - and trans - resveratrol results in the greater variability of its binding modes as these molecules do not optimize binding involving specific hydrogen bonding interactions with residues in the rgd binding site . the binding data for estradiol show that the 3 - hydroxyl can interact with asn215 , as observed for resveratrol . an alternate orientation for estradiol binding shows the molecule perpendicular to that of the first and filling an alternate binding site ( figure 12 ) . the interaction energies between thyroid hormone analogues and the rgd recognition site of v3 integrin are presented in table 1 that also shows the interaction energies between these ligands and water . as illustrated in table 1 , all calculated interaction energies in the protein are more negative than the corresponding interaction energies of those molecules in the water environment , which indicates that these molecules are more strongly stabilized by the protein environment than by the water environment . among these ligands , estradiol shows the strongest interaction energy with the protein containing mg ions , namely , 72 kcal / mol , while gc - 1 shows the strongest interaction energy with the protein containing ca , namely , 33 kcal / mol . both values of the interaction energy include the calculated desolvation energies obtained in this study . t3 shows a relatively strong interaction with the v3 integrin and the type of metal binding present ; namely , the interaction energy with the protein containing the mg ions has a value of 60 kcal / mol , and the interaction energy with the protein containing the ca ions has a value of 35 kcal / mol . similarly , both values of the interaction energy include the calculated desolvation energies obtained in this study . it is interesting to note that the interaction energy of t3 with the protein containing both divalent metal ions is larger than the interaction energy of t4 , even though both compounds have similar interaction energies with water . this observation indicates that an additional iodine atom in t4 actually decreases its interaction energy with the protein . moreover , the interaction energy of t4 is larger than the interaction energy of t4ac indicating that the nh2 - group which is present in t4 and is absent in t4ac increases the interaction energy between the ligand and protein . generally , the protein environment with the ca ions stabilizes ligands such as resveratrol and stilbene , stronger than the protein environment with the mg ions . however , for the other ligands studied the protein environment with mg stabilizes the ligand more strongly than the protein environment with ca . resveratrol and stilbene both have less flexible geometries , where internal rotations around the single cc bonds between phenyl rings and a c = c double bond are constrained by steric interactions of phenyl hydrogen atoms . less flexible geometries prevent those molecules from penetrating deeper into the protein active site and keeps them constrained on the surface of the binding pocket . the other ligands show much more flexible geometries , giving greater opportunity to penetrate deeper into the protein active site . deeper penetration of the protein active site by estradiol , gc - 1 , t3 , t4 , and t4ac , increases the interaction between the ligand and the divalent cations , particular for mg , and this effect is observed in these calculations . table 2 shows the values of the induced dipole moment of the ligands , obtained in the protein and water environments . the largest induced dipole moment is observed for estradiol bound in the presence of mg , which has a value of 3.8 debye relative to the induced dipole moment of this ligand in water . the similarincreased induced dipole moment in the protein with mg is also observed in these calculations for t4 . although it is not systematically observed for all ligands , there is a correlation between a value of the induced dipole moment of the ligand and its interaction energy with the surrounding environment that is caused by two effects . the first is related to the change of the molecular geometry by steric interactions between atoms of the ligand and atoms of the active site pocket , or atoms of a first solvation shell of water . the second effect is related to polarization of the electronic density of the molecule by an electrostatic field of the protein or water surroundings . the change of the electronic density of the ligand inside the protein or water , observed as an induced dipole moment , generates a stronger attraction between polarized electrons of the ligand and the electrostatic field of the protein or water . as a consequence , the stronger attraction increases the total interaction energy between the ligand and the protein or water . the interaction energies show a strong stabilization effect of the bound ligand to integrin . however , these qm / mm calculations do not include polarization effects of the protein or water by the ligand that is inside these two environments . the qm / mm calculations have been performed using an approach in which all atoms of the protein or water are represented by molecular mechanical atoms , and therefore they can not be polarized . consequently , if polarization of the protein ( or water ) is included in the qm / mm calculation , the calculated interaction energy between the ligand and the surrounding environments is expected to be even larger . these studies reveal that there are two important effects responsible for the stabilization of the small molecules inside the active site of integrin binding domain . the first effect is related to internal flexibility of the molecule which yields better penetration of the molecule into the protein active site , and consequently it increases its stabilization . the second effect is related to polarization of electronic density of the molecule , by the electrostatic field of the protein ( or water ) . greater molecular polarization is responsible for a larger induced dipole moment , which consequently interacts more strongly with the surrounding protein ( or water ) environments . therefore , it can be finally concluded that both molecular flexibility and molecular polarizability of the ligands are the main forces responsible for strength of the binding process of the small molecules to v3 integrin . recent data have shown that the hormone receptor on v3 integrin enables the thyroid hormones t4 and t3 to stimulate cancer cell proliferation and angiogenesis and to regulate the activity of certain membrane pumps . the results of these qm / mm modeling studies for a series of thyroid or steroid - like ligands ( figure 2 ) bound to the v3 integrin reveal that these ligands have multiple modes of binding near the rgd peptide binding site that was shown to occupy a shallow crevice between the propeller and a domains of the integrin head ( figure 1 ) . the most notable observation from these studies is that the thyroid hormone analogues probe significantly different conformational space near the rgd recognition site and that these modes can be correlated with their biologic response to signaling via the integrin . furthermore , the binding modes for t3 and t4ac are consistent with pharmacodynamic data that indicate the presence of two discrete binding sites for t3 that control distinct downstream signal transduction pathways . comparison of the low - energy binding modes for thyroid hormones suggest that the positions of t4 and t4ac illustrated in figure 8 are consistent with data that shows t4ac blocks t4 binding to integrin . the different binding positions of t3 ( figure 5 ) are also consistent with data that suggest two discrete , but close , binding sites that activate different downstream signaling pathways . the binding of resveratrol has been shown to interact primarily with the 3 monomer of integrin , activating the erk1 / 2 pathway . these qm / mm modeling data for cis - and trans - resveratrol indicate that both conformers have intermolecular interactions with the side chain residues of the 3 domain , although the cis - conformer which is flipped end to end with those of the trans conformers can potentially be involved in more hydrogen bond interactions ( figure 10 ) . furthermore , comparison of the binding of resveratrol with t4 and t4ac ( figure 13 ) suggests a mechanism of ligand recognition that is compatible with the observed downstream biological responses . the qm / mm modeling data presented here show that these ligands have flexible binding modes and that some ligands can bind in either a forward or reverse direction near the rgd recognition site . this flexibility in their low energy conformations suggests that each ligand can selectively take advantage of specific interactions within the local environment and with the metal binding sites . the observation of multiple binding pockets near the rgd recognition site also indicates that there may be subtle changes in the integrin binding site that can dictate binding to alternate sites that influence downstream signaling pathways .\noutput:\n" }, { "from": "agent", "value": "recent biochemical studies have identified a cell surface receptor for thyroid and steroid hormones that bind near the arginine - glycine - aspartate ( rgd ) recognition site on the heterodimeric v3 integrin . to further characterize the intermolecular interactions for a series of hormone analogues , combined quantum mechanical and molecular mechanical ( qm / mm ) methods were used to calculate their interaction energies . all calculations were performed in the presence of either calcium ( ca2 + ) or magnesium ( mg2 + ) ions . these data reveal that 3,5 - triiodothyronine ( t3 ) and 3,5,3,5 - tetraiodothyroacetic acid ( t4ac ) bound in two different modes , occupying two alternate sites , one of which is along the arg side chain of the rgd cyclic peptide site . these orientations differ from those of the other ligands whose alternate binding modes placed the ligands deeper within the rgd binding pocket . these observations are consistent with biological data that indicate the presence of two discrete binding sites that control distinct downstream signal transduction pathways for t3 ." } ]

[ { "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: primary spontaneous pneumothorax ( psp ) is a benign disease , usually occurring in young patients without known underlying lung disorder . the occurrence rate is reported to be about 9 individuals per 100000 each year . depending on the individual severity , the therapeutic options include simple observation , needle aspiration , tube thoracostomy and definite operation . if surgery is indicated , video - assisted thoracoscopic surgery ( vats ) using an endoscopic linear cutter to resect the involved blebs is currently the most popular treatment . nevertheless , we try to avoid using the endoscopic staple device at our hospital because payment for the device is excluded by the national health insurance system in taiwan . thanks to the increased experience with therapeutic thoracoscopy that we have gained in recent years , we used the technique of thoracoscopic suturing to imbricate the blebs , without resection , to treat the air leakage in psp patients , and report here our early results . from january 2001 to april 2002 , we had 50 episodes of primary spontaneous pneumothorax in 49 patients referred for the operation . among them , 26 patients with 26 episodes received transaxillary thoracotomy with or without assisted - thoracoscopy inspection . twenty - one patients with 22 episodes of psp received vats wedge closure by suturing . in this study , we dealt solely with the vats group . study patients included 2 female and 19 male patients , with a mean age of 25 years , ranging from 16 to 52 years . these 2 female patients were much older than the other patients , being 52 and 45 years of age , respectively . because of no abnormal pulmonary disease except for the attack of pneumothoraxthe surgical indications included recurrences in 11 episodes ( 10 patients ) , prolonged air leakage for more than 5 days in 4 episodes ( 4 patients ) , and apical blebs seen on radiography in 2 episodes ( 2 patients ) . five patients in 5 episodes underwent the operation owing to fear of recurrence , thus not fitting the above indications . the patients were kept in the lateral decubitus position after anesthesia was administered with single - lung ventilation . the first 10 - mm port was created in the 7th intercostal space ( ics ) , mid - axillary line . the second 5 - mm and third 10 - mm ports were created in the 5th ics , anterior - axillary , and posterior - axillary line , respectively . after the full exploration of the lung surface , the involved blebs were sutured with an absorbable ( 3 - 0 ) vicryl polyglactin suture ( ethicon endo - surgery , inc , cincinatti , oh ) . the curved needle had to be straightened before it could be put into the trocar port . if no bleb was found , the apical scar area was sutured in the same way . coagulation of parietal pleura by the endo - instrument was routinely performed in all patients to achieve pleurodesis . the mean disease duration from attack to operation was 5 days , ranging from 1 to 30 days . the mean operation time was 133 minutes , ranging from 80 minutes to 270 minutes . the mean hospital stay after the operation was 4 days , ranging from 3 to 8 days . three patients complained of prolonged intermittent intercostal neuralgia during the follow - up period , and 1 patient suffered dehiscence at the chest tube port . during the mean 6 - month follow - up , ranging from 1 to 16 months , most patients recovered well , except 2 patients who experienced recurrences . vats endo - suturing of the leaking area was performed again , with apical pleurectomy for this patient . the suture - puncture of the leaking blebs , instead of the normal tissue , in the prior operation was condemned . no bleb was found in her prior vats . a relationship between the attack and her menstruationno matter what surgical approach is executed , the goal of treatment is to find the offending bleb , remove it , and perform some manipulations to encourage adhesion formation . recently , video - assisted thoracoscopic surgery ( vats ) has been shown to produce results comparable to those obtained following open thoracotomy , yet with a reduction of postoperative pain , respiratory dysfunction and catabolic response to trauma , and decrease in wound - related complications . we believe that for psp vats is the best treatment , as abdala et al recommend , because it allows us to treat the ruptured bleb radically avoiding any recurrence . however , it is not the treatment of choice for all physicians due to the high cost of the equipment and the stapling devices needed for the wedge resection of the involved blebs . in taiwan due to the financial policy of the national health system , the charge of the high price of the endo - stapling instruments to the patient always concerns us , which is just the same as that in yim 's report . finding a way to replace the endo - stapling methodendo - suturing is not a new skill , and it is widely applied in laparoscopic surgery . nevertheless , using the endosuturing method to treat spontaneous pneumothorax was only reported by yim in 1995 in the english literature . because the incurred blebs are always idiopathic in patients with primary spontaneous pneumothorax , we think that it is not necessary to remove them . furthermore , the preserved bleb tissues are of help in wound healing and prevent air leakage from the wound , which can shorten the duration of the chest tube insertion . therefore , the length of suturing is not a problem , and in 1 case a 10 - cm suturing - line was performed without prolonged air - leakage . without adequate treatment , the recurrence rate after the first pneumothorax on the same side is about 25 % , and after the second episode , more than 50 % . although no general agreement exists about the best time for surgical intervention ( ie , after the first or second episode ) , vats therapy is now accepted as a definite treatment even in the first episode . in this studythey were all well informed about the conventional indication of the surgery before being included in this study . ventilation of 1 lung is mandatory in this procedure because complete lung collapse promotes the effect of suturing . the suture tension becomes tight enough to stop any air leaks after the lung fully expands . in addition , the tissue of the bleb itself can be used as a buttress to enforce the suturing area . the recurrence rate after the vats operation is reported to be high , between 13.7 % and 20 % , due to newly formed blebs or bullae unidentified during operation . recently , a favorable 2.1 % recurrence rate by vats has been reported by maier et al who use a rotating brush as a supplement . , the cause of recurrence is thought to be improper suturing with direct puncture of the blebs during the operation and thus the leakage area is not repaired well . during reoperation by vats , the air leak was found near the previous sutured area , which adhered intensively to the parietal pleura . step - by - step dissection has to be carefully executed to prevent tissue damage during the second - look operation . therefore , we have an 9.1 % ( 2/22 ) recurrence rate , which is acceptable compared with that of the other vats reports . the coagulation pleurodesis seems ineffective if the definite treatment of the ruptured blebs is not accurately executed . it is thought that the limited pleura being applied via the 3 small ports during vats renders coagulation pleurodesis ineffective . the incidence of chronic postoperative complaints after minimally invasive procedures for spontaneous pneumothorax is relatively high . in the majority of the patients , two of our patients complained of intermittent anterior chest pain in the ipsilateral side , which may have been due to concurrent injury to the intercostal nerve at the trocar site . the vats wedge closure of the blebs by suturing , without resection of the involved blebs , is a feasible and effective alternative treatment for primary spontaneous pneumothorax if cost of the endo - stapler is regarded as a major problem .\noutput:\n" }, { "from": "agent", "value": "background and objectives : if surgery is indicated for primary spontaneous pneumothorax ( psp ) , video - assisted thoracoscopic surgery ( vats ) using an endoscopic linear cutter to resect the involved blebs is the most popular treatment . we tried to determine whether closure of the blebs with sutures without resection is also efficacious enough to treat psp.methods : we prospectively analyzed 22 episodes of psp in 21 patients from january 2001 to april 2002 . we endosutured the blebs , without removing them , no matter what the size and the number of the blebs were . coagulation pleurodesis was added in every case . only 3 ports were needed during the procedure.results : morbidity and cost efficiency were acceptable . two recurrences were experienced . the reasons for the recurrences were poor performance of the endo - suture in 1 patient , and no obvious blebs found in the other.conclusions : we believe that vats wedge closure of blebs by imbricating and buttressing them , without resection , is a feasible and effective alternative treatment for primary spontaneous pneumothorax ." } ]

[ { "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: anemia is a disease that can co - exist with depression , other mental disorders , or somatic diseases . anemia can imitate symptoms of depression , while depression symptoms can mask concurring symptoms of anemia . i am presenting a case of a 48 - year - old woman with addison biermer anemia , with co - existing mood disorders . the clinical analysis of the presented patient s history indicates diagnostic problems and a need for a detailed analysis of drug - related complications that occurred during previous treatment , eg , in the form of neuroleptic malignant syndrome . the presented case report contains valuable guidelines that can be of assistance in diagnostics and treatment of patients treated for mental disorders , who are also diagnosed with somatic diseases . pernicious anemia , also called addison biermer anemia , is an autoimmune disease most often occurring in people with a blood type , and caused by vitamin b12 absorption disturbances ( figure 1 ) . in the initial clinical presentation , symptoms of this anemia , including apathy , psychomotor retardation , lack of energy , fatigability , or excessive sleepiness , can indicate a possibility of concurring depression .1,2 furthermore , symptoms of depression can overlap with somatic symptoms of anemia , further complicating the clinical presentation , and therefore , the treatment of underlying disease , or even persisting when anemia symptoms have resolved . patients particularly susceptible to stress and suffering from anxious personality disorders concomitant with somatic diseases belong to a risk group prone to depressive disorders and anemia . depression can develop against a background of a chronic stress reaction related to the somatic disease .3 chronic stress can also lead to development of conversion disorders , with partial or complete loss of correct integration of past memories with a sense of own identity .4,5 increased conversion or depression symptoms in patients with addisonbiermer anemia can represent a difficult diagnostic and treatment challenge to hematology specialists , general practitioners , and psychiatrists . treatment of depression and conversion symptoms should combine pharmaco - and psychotherapy .6 for severe depression , treatment with anti - depressive drugs alone may be insufficient , requiring additional inclusion of atypical neuroleptics .7 it is worth noting that in people suffering from depression and with a positive history of somatic diseases , such as addisonbiermer anemia or endocrine diseases , the neuroleptic malignant syndrome ( nms ) is more likely to occur following neuroleptic treatment , than in people without somatic diseases . i am presenting a clinical case of a 48 - year - old patient , with a blood type , admitted to the surgical ward due to anemia . it is known from the interview that the patient was previously pharmacologically treated for hypothyroidism , but has not taken medications for several years . the patient felt weak , had concentration problems , and reduced tolerance of physical exercise for approximately 1 month . in physical examination , the patient underwent the following examinations : ultrasound scan of the abdominal cavity , gastroscopy , colonoscopy , computed tomography of the abdominal cavity , and ultrasound scan of the thyroid . laboratory tests conducted on admission day revealed : white blood corpuscules 4.56 k / l ; lymphocytes 2.41 ; red blood corpuscules 3.00 m / l ; hemoglobin 8.74 g / dl ; mean corpuscular volume 81.8 fl ; mean corpuscular hemoglobin 28.7 pg ; mean corpuscular hemoglobin concentration 35.7 g / dl ; platelets 158 k / l ; vitamin b12 level 120 pg / ml ( reference value 180900 pg / ml ) ; iron level 160 g / dl ( reference value 60160 g / dl ) . thyroid hormone levels for free thyroid hormone triiodothyronine , free thyroid hormone thyroxine , and thyroid - stimulating hormone levels were within the reference values . only in the tenth day of her hospitalization , the patient disclosed that in the past she had underwent psychiatric treatment for depression and conversion disorders . five years before current hospitalization , the patient had had nms due to treatment with olanzapine for psychotic depression . during psychiatric consultation , for the last 3 months , the patient has complained about deteriorating psychical condition revealing symptoms such as : low mood , apathy , anhedonia , anxiety , memory and concentration problems , sleep disturbances , and suicidal thoughts . depression diagnosis was based on clinical assessment of the patient and followed by performing beck depression inventory in which the patient received 26 scores .8 pharmacological treatment was commenced , with venlafaxine , 225 mg / day , and valproic acid , 1,000 mg / day . after 4 weeks of treatment , mirtazapine was added at a dose of 30 mg / day . mood and psychomotor drive were partially improved after 10 weeks of treatment . following 4 weeks of treatmentthis time the patient received 19 scores , which indicate improvement of the patient s mental status . the vitamin was administered intramuscularly daily for 10 days , then three times a week for 3 weeks , and then twice a week for the next 3 weeks . at the next stage of the treatment folic acidwas added at a dose of 15 g / d and after 10 weeks of therapy , anemia symptoms disappeared . when suffering from somatic symptoms of anemia or symptoms resulting from a thyroid function disorder , patients usually visit their general practitioner , hematologist , endocrinologist , or surgeon . the most important task of the doctor is to establish whether some or all of presented symptoms are of an organic origin , or not . the organic cause requires a clinical intervention , eg , in the form of pharmacological or surgical treatment .9 however , it should be remembered that the initial organic disease may be accompanied by concurrent secondary mental disorders .10,11 it is recommended to perform screening laboratory tests in patients with depression , excluding anemia and hypothyroidism , such as : complete blood count , serum iron level , total iron binding capacity , unsaturated iron binding capacity , serum vitamin b12 level , and thyroid - stimulating hormone . in patients belonging to a risk group susceptible to depression , it is recommended to determine oxidative stress markers , eg , chemokines , cytokines . these markers may constitute an early predictor of affective disorders .12 when the organic cause is excluded , or when concurrent symptoms of mental disorders are observed , then the basic medical procedure involves psychiatric consultation for correct diagnosis and treatment initiation . biermer anemia can co - exist with other somatic diseases or accompany mental disorders ( depression , anxiety disorders , conversion disorders ) .13 it is a strong predictor of adverse clinical incidents related to cardiac ischemia . anemia is associated with higher short - and long - term risk of death in coronary disease patients with a stable form of that disease , heart infarction with st segment elevation , and with acute coronary syndromes without st segment elevations , as well as in patients after coronary vessel interventions . a decrease in hemoglobin ( hb ) by 1 g / dl is associated with 14 % 18 % increase in mortality in a dialysis patient population , while hb level decrease below 8 g / dl doubles the risk of death versus patients with hb of 1011 g / dl . in depression , concurrence of somatic diseases , such as addisonbiermer anemia or thyroid hormone disturbances can delay therapy , for example , using electroconvulsive therapy in treatment of severe depression .14 in treatment of depression , delayed use of electroshocks can result in exacerbation of depression and contribute to the increased risk of suicide .15 moreover , in patients treated with atypical neuroleptics there is a risk of nms . according to the diagnostic and statistical manual of mental disorders , fourth edition ( dsm - iv ) , it is possible to diagnose nms when muscle rigidity and fever are found with at least two of the following symptoms concurring : diaphoresis , dysphagia , incontinence , changes in level of consciousness , mutism , tachycardia , increased or labile blood pressure , leukocytosis , and increased ck levels , indicating muscle injury . other criteria proposed by levenson include major symptoms ( fever , muscle rigidity , and increased ck levels ) and minor symptoms ( tachycardia , variable blood pressure , tachypnea , changes in level of consciousness , diaphoresis , and leukocytosis ) . the nms diagnosis is justified in cases with all major symptoms present , or when two of them are accompanied by at least twominor symptoms .16 nms can also develop in patients with positive history of somatic diseases , such as thyroid disorders , anemia , and neurological diseases , or in patients without chronic diseases .17 furthermore , patients who suffered from nms caused by olanzapine are predisposed to nms in the future also after administration of other drugs affecting the dopaminergic system .18,19 metabolic changes secondary to hypothyroidism or addison biermer disease , particularly in the dopaminergic pathways within the central nervous system , can also predispose to the development of nms .20 in treatment of depressive disorders , a possibility of concurrence of somatic disorders in the same patient should also be considered . taking into consideration the fact that mental disorders often represent prodromal signs of various somatic diseases , it is necessary to remember that additional tests and evaluation of the somatic status are of particular importance in psychiatric patients . it is worth noting that these patients focus on their emotional experience and ignore their somatic problems .\noutput:\n" }, { "from": "agent", "value": "backgroundanemia is a disease that can co - exist with depression , other mental disorders , or somatic diseases . anemia can imitate symptoms of depression , while depression symptoms can mask concurring symptoms of anemia.case presentationi am presenting a case of a 48 - year - old woman with addison biermer anemia , with co - existing mood disorders . the clinical analysis of the presented patient s history indicates diagnostic problems and a need for a detailed analysis of drug - related complications that occurred during previous treatment , eg , in the form of neuroleptic malignant syndrome.conclusionthe presented case report contains valuable guidelines that can be of assistance in diagnostics and treatment of patients treated for mental disorders , who are also diagnosed with somatic diseases ." } ]

[ { "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 material studied herein is deposited in the entomological collection of oswaldo cruz institute ( ceioc ) , oswaldo cruz foundation , rio de janeiro , brazil . the type specimens of t. b. macromelasoma and t. melanica have been lost ; therefore , these specimens were identified based on the literature and on comparisons with previously determined material deposited in the ceioc , including the holotypes of t. juazeirensis ( costa & felix 2007 ) and t. brasiliensis ( gonalves et al . 1993 ) . the redescription of t. b. macromelasoma is based on two specimens from its type locality ( municipality of petrolina , pe ) , as well as 15 males and 15 females from an f1 colony reared from insects collected in this locality . the manner of description and morphological terminology mainly follow the style of lent and wygodzinsky ( 1979 ) . t. b. macromelasoma galvo , 1956 , revalidated fig . 1 t. b. macromelasoma galvo ( 1956 ) t. brasiliensis lent and wygodzinsky ( 1979 ) length : males 19.4 - 24.3 mm , females 21.5 - 25.5 mm ; width of pronotum ( posterior lobe ) : males 3.9 - 5.4 mm , females 4.4 - 5.3 mm ; width of abdomen : males 6.0 - 7.6 mm , females 6.6 - 9.1 mm . tablemeasurements ( in mm ) of triatoma brasiliensis macromelasoma based on 15 males and 15 females from a f1 colony reared from insects collected in the type locality ( municipality of petrolina , state of pernambuco , brazil ) gender malefemalevariables minmaxxs sd minmaxxs sdtotal length19 .424.321.171.5731.25421.525.523.040.9370.968 length of head3 .74.74.190.0010.0274.14.84.400.0000.018 width of head1 .92.42.090.0000.0122.02.32.130.0000.008 synthlipsis1 .01.21.070.0000.0071.11.31.150.0000.007 width of eyes0 .50.60.500.0000.0030.50.60.510.0000.003 length of 1st antennal segment0 .71.00.820.0000.0070.81.00.930.0000.007 length of 2nd antennal segment3 .44.03.700.0000.0213.44.33.780.0010.023 length of 3rd antennal segment2 .32.82.520.0000.0142.42.92.610.0000.017 length of 4th antennal segment1 .82.11.950.0000.0132.02.42.140.0000.011 length of 1st rostral segment0 .91.10.980.0000.0061.01.11.040.0000.005 length of 2nd rostral segment2 .12.42.240.0000.0102.22.52.280.0000.009 length of 3rd rostral segment1 .01.21.150.0000.0061.11.41.200.0000.006 length of pronotum2 .83.93.160.0010.0303.13.93.340.0000.022 anterior width of pronotum2 .43.12.660.0000.0202.63.22.830.0000.016 posterior width of pronotum3 .95.44.390.0010.0374.45.34.690.0010.027 width of abdomen6 .07.66.690.0030.0526.69.17.440.0040.062 max ; maxima ; min : minimum ; sd : standard deviation ; s : variance ; x : average . max ; maxima ; min : minimum ; sd : standard deviation ; s : variance ; x : average . figs 1 - 5 : the five members of the triatoma brasiliensis species complex , dorsal habitus . 1 : triatoma brasiliensis macromelasoma , male ; 2 : triatoma brasiliensis brasiliensis , female ; 3 : triatoma juazeirensis , male ; 4 : triatoma melanica , male ; 5 : triatoma sherlocki , female . bars = 5 mm . twice as long as wide across the eyes ( males 1:0.35 - 0.42 ; females 1:0.35 - 0.41 ) and distinctly longer than the pronotum ( males 1:0.70 - 0.86 ; females 1:0.72 - 0.89 ) . genae tapering distally , but with apex narrowly rounded , not pointed , slightly projecting beyond the level of the apex of clypeus . eyes , in lateral view , approaching , but not attaining the level of the under surface and remote from the level of the upper surface of the head . ratio width of eye to synthlipsis 1:2.00 - 2.30 ( males ) and 1:1.91 - 2.67 ( females ) . first antennal segment attaining the level of the apex of clypeus ; second segment subcylindrical , beset with declivous setae shorter than diameter of the segment . ratio of antennal segments 1:4.0 - 5.3:2.4 - 3.8:2.0 - 2.8 ( males ) and 1:3.4 - 4.5:2.4 - 3.2:2.0 - 2.8 ( females ) . rostrum thick , as dark as the head capsule , with medium - sized hairs on the first and on the underside of the second segment , with long and very numerous hairs on the upper surface of the second and on the entire third segment ; hairs especially dense dorsally at the junction of the second and third segments . first rostral segment extending to the level of the apex of antenniferous tubercles , second one to the level of the apex of the middle of the eyes . ratio of rostral segments 1:1.9 - 2.7:1.1 - 1.4 ( males ) and 1:2.1 - 2.3:1.1 - 1.3 ( females ) . posterior lobe with submedian carinae evanescent on posterior fourth ; 1 + 1 narrow brownish - yellow stripes on carinae broadening posteriorly , not attaining pronotal apex . scutellum : black , posterior process with small yellow or brownish - yellow point on apex . posterior process as long as the main body of the scutellum , subcylindrical , but slightly compressed laterally ; apex slightly elevated , rounded . hemelytra : extending to variable levels from the base to the apex of the seventh urotergite . corium light yellow , with dark areas of variable extension , mainly in veins cu , m - cu and r + m , attaining sc . membrane fumose , yellowish - brown , as light as light - coloured areas of corium . veins of membrane black ; lumen of cells with a more or less extensive , irregularly shaped sooty spot extending over the central portion , mainly extending to the cu and pcu veins . legs : dark , with light markings on the trochantera ; incomplete brownish - yellow ring on the apical half of the femora and the subapical portion of the tibiae . fore and mid femora salient below subapically or with one or two weak denticles . males with spongy fossulae on tibiae of fore and mid legs ; absent in females . abdomen : slightly flattened below in both sexes , delicately striate transversally , sparsely setose . connexival segments presenting a black spot on anterior region , posterior edge rounded , followed by a larger light yellow spot ; wide black spot enclosing intersegmental sutures . male genitalia : as described by lent and jurberg ( 1978 ) { according to costa et al . ( 1997a ) , individual variations in the male genitalia of t. brasiliensis and the other members of the complex are not correlated with their different and stable chromatic forms . therefore , the genital structures are not useful for distinguishing t. b. macromelasoma . } . material examined - t. b. macromelasoma - pe : two males , petrolina , ceioc ; 15 males , 15 females , f1 colony reared from insects from petrolina , ceioc . t. b. brasiliensis - rn : one female ( holotype ) , caic , ceioc ; state of cear : five males , five females , jaguaru - ana , ceioc . t. juazeirensis - ba : one female ( holotype ) , three males ( paratypes ) , two females ( paratypes ) , juazeiro , ceioc ; seven males , 12 females , juazeiro , ceioc . t. melanica - mg : three males , three females , espinosa , ceioc . t. sherlocki - ba : one male , one female , gentio do ouro , ceioc . brachypterous specimens , hemelytra not extending posteriorly beyond the posterior margin of urotergite vi ; legs unusually long ; ground colour dark brown to black , connexivum and femora with orange to red marks ...................................... . t. sherlocki ( fig . macropterous specimens , hemelytra extending posteriorly at least as far as urotergite vii ; legs normally long ; ground colour brown , hemelytra and connexivum with brownish - yellow marks ............................................ 22a . pronotum and scutellum dark brown to black , rarely with few inconspicuous brownish - yellow marks ; femora entirely dark brown to black , without brownish - yellow rings ......................... . t. juazeirensis ( fig . pronotum with 1 + 1 elongate or subtriangular broad areas or narrow stripes , brownish - yellow ; scutellum with apex of posterior process brownish - yellow ; femora with complete or incomplete brownish - yellow rings ....................................................................................... 33a . pronotum with 1 + 1 narrow brownish - yellow stripes ; membrane of hemelytra with lumen of cells partially darkened ........ . t. b. macromelasoma ( fig .1 ) ( pe ) 3b . pronotum with 1 + 1 broad , elongated brownish - yellow areas ; membrane of hemelytra with lumen of cells entirely or not darkenedpronotum with 1 + 1 brownish - yellow areas extending from posterior portion of anterior lobe to posterior lobe ; femora with broad brownish - yellow rings ; membrane of hemelytra with lumen of cells not darkened ; males with spongy fossulae on fore and mid tibiae ......................... . t. b. brasiliensis ( fig .2 ) ( northeast region of brazil , state of gois and federal district ) 4b . pronotum with 1 + 1 brownish - yellow areas only on posterior lobe ; femora with narrow brownish - yellow rings ; membrane of hemelytra with lumen of cells entirely darkened ; males with spongy fossulae only on fore tibiae .......................... . t. melanica ( fig . triatoma b. brasiliensis and t. b. macromelasoma are the most closely related forms among all members of the t. brasiliensis complex . this was determined from an isoenzymatic analysis with nine loci conducted to calculate the values of nei 's genetic distance ( nei 1987 , costa et al .1997 b ) and the sequences of the mtdna cytochrome b gene and by applying phylogeographic approaches among 136 specimens representing 16 populations ( monteiro et al . the latter analysis revealed the existence of three discrete lineages : brasiliensis + macromelasoma , juazeiro ( t. juazeirensis ) and melanica . these clades are separated from each other by more than nine mutational steps , which is the 95 % confidence interval for the statistical parsimony process . despite this close relationship , the phylogenetic an - alyses showed that t. b. brasiliensis and t. b. macromelasoma have significant genetic differentiation , indicating their status as subspecies ( monteiro et al . ( 2009 ) used geometric morphometric techniques to compare the shape of the wings of the t. brasiliensis complex members . these authors proposed that t. b. macromelasoma could have originated by homoploid hybrid speciation ( greig et al .2006 , mallet 2007 ) via ancient contact between the neighbouring species t. brasiliensis and t. juazeirensis and the hybridisation of the putative parental forms most likely occurred in the area of pe . furthermore , the geometric morphometric analysis showed that t. b. macromelasoma is closely related to t. b. brasiliensis and is distinct from all other members of the t. brasiliensis complex ( costa et al . the mahalanobis distances were calculated for all members of the complex based on the shape ( conformation ) of the wings and these were convergent with the values of the matrices of genetic distances obtained either by isoenzyme analyses or mtdna sequences ( costa et al . in addition , despite all morphological , biological , genetic and ecological differences recorded among the members of the complex , they are all able to produce viable hybrids under laboratory conditions ( costa et al . however , no evidence of natural crosses was observed between the members of the complex , except for t. b. brasiliensis and t. b. macromelasoma . these multidisciplinary analyses revealed that t. b. macromelasoma has ( i ) a stable , homogeneous and differentiated colour pattern that is easily distinguished from those of the other members of the complex ( costa et al .1997 a , 2009 ) , ( ii ) a distinct egg shape and exochorion ornamentation ( costa et al . 1997a ) and ( iii ) a distinct geographic distribution , as it is found only in areas of pe ( costa et al . , the revalidation of t. b. macromelasoma as a subspecies agrees with the results of several independent taxonomic analyses , showing the closest relationship between this taxon and t. b. brasiliensis when compared to the other members of the complex . morphologically , t. b. macromelasoma can be distinguished from all members of the t. brasiliensis species complex by the following combination of features : ( i ) pronotum with 1 + 1 narrow brownish - yellow stripes on the submedian carinae , not attaining its apex , ( ii ) hemelytra with darkened membrane cells on the central portion and ( iii ) legs with an incomplete brownish - yellow ring on the apical half of the femora . the yellow marks on the pronotum are the more consistent feature that differentiates the members of the complex ( lent & wygodzinsky 1979 , costa 1997 ) . as expected , the females of t. b. macromelasoma tend to be slightly larger than the males , a pattern commonly observed in triatomines ( lent & wygodzinsky 1979 ) and , more specifically , in other members of the t. brasiliensis complex ( costa et al . a definition of the taxonomic status of the t. brasili - ensis complex members is important for epidemiological studies and control measures ( costa & felix 2007 ) and correct morphological identification is equally important . thus , the present key , which includes all members of the complex , can be considered a fundamental tool for the identification of specimens , especially in fieldwork .\noutput:\n" }, { "from": "agent", "value": "triatoma brasiliensis macromelasoma is revalidated based on the results of previous multidisciplinary studies on the triatoma brasiliensis complex , consisting of crossing experiments and morphological , biological , ecological and molecular analyses . these taxonomic tools showed the closest relationship between t. b. macromelasoma and triatoma brasiliensis brasiliensis . t. b. macromelasoma is redescribed based on specimens collected in the type locality and specimens from a f1 colony . the complex now comprises t. b. brasiliensis , t. b. macromelasoma , triatoma melanica , triatoma juazeirensis and triatoma sherlocki . an identification key for all members of the complex is presented . this detailed comparative study of the morphological features of t. b. macromelasoma and the remaining members of the complex corroborates results from multidisciplinary analyses , suggesting that the subspecific status is applicable . this subspecies can be distinguished by the following combination of features : a pronotum with 1 + 1 narrow brownish - yellow stripes on the submedian carinae , not attaining its apex , hemelytra with membrane cells darkened on the central portion and legs with an incomplete brownish - yellow ring on the apical half of the femora . because the t. brasiliensis complex is of distinct epidemiological importance throughout its geographic distribution , a precise identification of its five members is important for monitoring and controlling actions against chagas disease transmission ." } ]

[ { "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: but , these days , with advanced technology , brain receptors have been mapped . in 1957 , kuhn reported that imipramine has antidepressant properties . this was followed by other tricyclics such as amitriptyline , nortriptyline , doxepine , etc . and , later on , the selective serotonin reuptake inhibitor , i.e. fluvoxamine , fluoxetine , sertraline , etc . however , to date , the mechanism of action of these antidepressant drugs is yet to be precisely known . today , many antidepressants are available but they often cause adverse effects , particularly psychomotor and cognitive . this leads to patient maladjustment and may impair psychomotor performance , which plays important role in driving and operating complex machinery . therefore , it is desirable to develop antidepressant drugs with a minimal effect on these functions so that the patient 's productivity or social adjustment are not hampered . fluvoxamine is a newer antidepressant and hence the present study was planned to investigate its effect on psychomotor functions and compare with nortriptyline and record their adverse reactions . a total of 26 healthy volunteers , 20 males and six females , of age group -30 years with informed consent were included in this double - blind , placebocontrolled , crossover study . a single oral dose of fluvoxamine 50 mg , nortriptyline 50 mg and placebo was administered following a latin square design . the parameters were tested at 0 , 2 and 4 h. before the study volunteers received training till a performance plateau was reached . six - digit cancellation test ( 6dct ) : volunteers were required to cancel as many target digits as possible in a sheet consisting of 1,200 randomized digits in 3 min . digit symbol substitution test ( dsst ) : volunteers were required to insert the corresponding symbol in the space above each digit in a sheet consisting of 200 randomized digits in 2 min . critical flicker fusion test ( cfft ) : it is a reliable psychometric test as there is no learning curve effect . the apparatus consists of a viewing tube at the end of which a red circle of light flickers at the rate of 550 cycles / s . the critical fusion frequency was determined by increasing the frequency from 5 hz till a steady light source was seen and the critical flicker frequency by decreasing the frequency from 50 hz till flickering was seen . arithmetic ability test ( aa ) : the subjects had to solve simple mathematical problems , i.e. addition , subtraction , multiplication and division ( five of each ) within 2 min . this was tested by steadiness tester , which consists of holes of different size sand subjects had to insert stylus into the hole without touching its sides . the volunteers were asked to indicate the state of their current feeling by marking on a 100 mm horizontal line . the opposite mood - related adjectives at each end were as follows : wide awake - extreme sleepyalert - dullactive - tired wide awake - extreme sleepy volunteers marked their subjectively felt side effects on a sheet . the tests used were anova followed by post - hoc newman - keuls multiple comparison test . six - digit cancellation test ( 6dct ) : volunteers were required to cancel as many target digits as possible in a sheet consisting of 1,200 randomized digits in 3 min . digit symbol substitution test ( dsst ) : volunteers were required to insert the corresponding symbol in the space above each digit in a sheet consisting of 200 randomized digits in 2 min . critical flicker fusion test ( cfft ) : it is a reliable psychometric test as there is no learning curve effect . the apparatus consists of a viewing tube at the end of which a red circle of light flickers at the rate of 550 cycles / s . the critical fusion frequency was determined by increasing the frequency from 5 hz till a steady light source was seen and the critical flicker frequency by decreasing the frequency from 50 hz till flickering was seen . arithmetic ability test ( aa ) : the subjects had to solve simple mathematical problems , i.e. addition , subtraction , multiplication and division ( five of each ) within 2 min . six - digit cancellation test ( 6dct ) : volunteers were required to cancel as many target digits as possible in a sheet consisting of 1,200 randomized digits in 3 min . digit symbol substitution test ( dsst ) : volunteers were required to insert the corresponding symbol in the space above each digit in a sheet consisting of 200 randomized digits in 2 min . critical flicker fusion test ( cfft ) : it is a reliable psychometric test as there is no learning curve effect . the apparatus consists of a viewing tube at the end of which a red circle of light flickers at the rate of 550 cycles / s . the critical fusion frequency was determined by increasing the frequency from 5 hz till a steady light source was seen and the critical flicker frequency by decreasing the frequency from 50 hz till flickering was seen . arithmetic ability test ( aa ) : the subjects had to solve simple mathematical problems , i.e. addition , subtraction , multiplication and division ( five of each ) within 2 min . this was tested by steadiness tester , which consists of holes of different size sand subjects had to insert stylus into the hole without touching its sides . this was tested by steadiness tester , which consists of holes of different size sand subjects had to insert stylus into the hole without touching its sides . the volunteers were asked to indicate the state of their current feeling by marking on a 100 mm horizontal line . the opposite mood - related adjectives at each end were as follows : wide awake - extreme sleepyalert - dullactive - tired wide awake - extreme sleepy volunteers marked their subjectively felt side effects on a sheet . the tests used were anova followed by post - hoc newman - keuls multiple comparison test . the volunteers were asked to indicate the state of their current feeling by marking on a 100 mm horizontal line . the opposite mood - related adjectives at each end were as follows : wide awake - extreme sleepyalert - dullactive - tired wide awake - extreme sleepythe tests used were anova followed by post - hoc newman - keuls multiple comparison test . in the study , nortriptyline 50 mg dose decreased the substitution of symbols score on dsst and the cancellation of digits score on 6dct [ table 1 ] . it reduced the cfft threshold and aa score suggestive of impairment of central integrative capacity and central processing ability respectively [ table 1 ] it increased errors in the hand steadiness test , suggestive of motor impairment [ table 2 ] . these findings of nortriptyline on objective tests are also reflected in the subjective assessment of vas - 1 , vas - 2 and vas - 3 with a significant shift of the scale toward drowsiness , tiredness and dullness [ table 2 ] . nortriptyline when compared with fluvoxamine and placebo had shown significant impairment on objective [ table 3 ] and subjective tests at 4 h [ table 4 ] . thus , in the present study nortriptyline at the dose of 50 mg significantly affected the psychomotor functions . tricyclics like nortriptyline cause adverse effects of drowsiness and psychomotor impairment due to their antihistaminic , antimuscarinic and 1 - antagonist action . . effects of fluvoxamine and nortriptyline at 0 , 2 and 4 h effects of fluvoxamine and nortriptyline at 0 , 2 and 4 h interdrug comparison of mean difference at 2 and 4 h interdrug comparison of mean difference at 2 and 4 h it is seen from the studies of curran and lader fairweather , et al . fleishaker and hulst that fluvoxamine 50 mg had no significant effect on objective tests except the study of van harten in which performance was impaired . in our study , fluvoxamine in the dose of 50 mg did not show any significant effect on objective tests such as 6dct , dsst , cfft , aa test [ table 1 ] and hand steadiness test [ table 2 ] . however , on subjective parameters such as vas - 1 , vas - 2 and vas - 3 , there was a significant effect indicating a shift of the scale toward drowsiness , tiredness and dullness [ table 2 ] . also , nortriptyline in comparison with fluvoxamine impaired psychometric tests significantly [ tables 3 and 4 ] . in a recent study of the receptor binding of a wide range of antidepressants in human post - mortem brain , fluvoxamine was among the least - potent compounds at 1 , 2 , h1 and muscarinic receptor sites . this may account for its lack of sedation and consequently lack of impairment of psychomotor function . thus , the findings of effect of fluvoxamine on various psychometric tests in our study substantiate those of the other workers . further , there is limitation of analogue system as words may fail to describe the exactness of the subjective experience . the volunteers complained dryness of mouth with nortriptyline due to anticholinergic action and nausea headache with fluvoxamine [ table 5 ] . the cause for nausea , vomiting with fluvoxamine is increased synaptic availability of serotonin which stimulates 5ht3 receptors . nortriptyline significantly depresses the objective and subjective psychometric performance in comparison with placebo and fluvoxamine . dryness of mouth is the reported adverse effect of nortriptyline , whereas nausea and headache are the adverse effects of fluvoxamine . hence , fluvoxamine can be a better alternative to nortriptyline as it causes minimal psychomotor impairment .\noutput:\n" }, { "from": "agent", "value": "background : today , many antidepressants are available , but they often cause adverse effects , particularly psychomotor and cognitive . it leads to patient maladjustment and may impair psychomotor performance . fluvoxamine is a newer antidepressant and hence the present study was planned to investigate its effect on psychomotor functions and compare with nortriptyline and record their adverse reactions.materials and methods : a total of 26 healthy volunteers were included in this double - blind , placebocontrolled , crossover study . single oral doses of fluvoxamine 50 mg , nortriptyline 50 mg and placebo were administered following a latin square design . the objective parameters - six digit cancellation test , digit symbol substitution test , critical flicker fusion test , arithmetic ability test , hand steadiness test and subjective parameters such as visual analogue scale 1 , 2 , 3 were tested at 0 , 2 and 4 h. the side - effects were also investigated.results : nortriptyline impaired all subjective and objective psychomotor functions while fluvoxamine did not show any significant effect on objective tests . however , on subjective parameters , there was a significant effect . the side - effects observed were dryness of mouthwith the nortriptyline and nausea and headache with fluvoxamine.conclusion : fluvoxamine is a better antidepressant drug in comparison with nortriptyline as it causes a less impairment of psychomotor functions ." } ]

[ { "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 extracorporeal life support organization ( elso ) registry reports 64 uses of ecls during the period from 1986 to 2007 , including 13 patients from children 's healthcare of atlanta at egleston , as presented by hebbar and coworkers in their discussion of extracorporeal life support ( ecls ) for refractory severe status asthmaticus ( ssa ) . overall survival was 100 % in the egleston cohort and 92 % in the remaining 51 patients reported in the elso registry . it is of interest to note that all of the 13 survivors from the egleston series had no reported neurological sequelae . this outcome is comparable to the 6 % incidence of neurological complications ( seizure and intracranial hemorrhage ) observed in the larger group ; however , in neither group were neurological sequelae correlated with overall outcome . the observed characteristics of patients receiving ecls for ssa was similar between the two groups . in general , patients who received ecls had a median age of 10 years ; before ecls they had a serum ph of less than 7.0 , an arterial carbon dioxide tension ( paco2 ) above 120 torr , and an arterial oxygen tension above 50 torr . the percentage of patients in whom venovenous ( vv ) cannulation was used was higher in the egleston group than in the elso group ( 92 % versus 82 % ) , but over time more patients underwent vv cannulation . despite these demographic characteristics , although previous studies have considered outcomes for ecls for status asthmaticus in adults , the work of hebbar and coworkers is the first to discuss pediatric outcomes comprehensively . in our opinion , the clinical outcomes observed in both the egleston and the larger elso series support the early use of ecls in status asthmaticus , and moreover they highlight the need to define clinical parameters that should prompt strong consideration of ecls . we advocate a system that first identifies patients at high risk for developing refractory status asthmaticus : those with history of multiple intubations and / or respiratory failure requiring intubation within 6 hours of admission ; those with hemodynamic instability and / or neurological impairment at time of admission ; and those with a duration of respiratory failure greater than 12 hours despite maximal medical therapy , as defined by institutional availability . we are reluctant to propose distinct serum ph and paco2 values as pre - ecls criteria , given there is no correlation of these factors with survival . however , in general , sustained paco2 retention above 100 mmhg and persistent serum ph below 7.0 should warrant discussion of ecls . there are clear risks associated with ecls , but avoidance of cardiopulmonary arrest , attenuation of lung injury associated with prolonged mechanical ventilation at high pressures , and reduction in the systemic toxicities associated with medical therapies for ssa should be among the goals of therapy with ecls for refractory status asthmaticus . cannulation strategies should be patient specific . however , the recent trend toward vv cannulation for ssa reported in the elso registry is noted and reasonable , because this mode allows for preservation of arterial vascular integrity and provides sufficient pulmonary support during the acute period of illness in those patients without cardiovascular compromise . the recent availability of percutaneous insertion kits and new , double - lumen single cannulas that range in size from 13 to 32 fr make implementation of vv support in children and adults potentially even easier and safer . if ecls were considered at the time of presentation based on the aforementioned criteria , it is possible that patients could require shorter ecls courses , because they would not yet have developed the severe respiratory , hemodynamic , and metabolic derangements that may prolong the duration of ecls . the experience from children 's healthcare of atlanta at egleston successfully demonstrates the use of ecls as an adjunctive strategy for managing ssa . the work there is both important and relevant , because it illustrates consistent , positive outcomes over time with use of this therapy . it is of interest that although use of ecmo in adults is still a rarity , a recent review of adult ecmo also focused on use in status asthmaticus . both the adult and pediatric studies have found small numbers of patients , but it is unknown whether this reflects the small numbers of patients who develop refractory status asthmaticus or just the fact that ecmo is rarely considered , no matter how bad the respiratory failure associated with asthma becomes . ecmo is safer and easier to perform than it has ever been . perhaps raising the visibility of this techniqueas a support tool in severe asthma would decrease the mortality rate and improve patient care in children and adults alike . ecls : extracorporeal life support ; elso : extracorporeal life support organization ; paco2 : arterial carbon dioxide tension ; ssa : severe status asthmaticus ; vv : venovenous .\noutput:\n" }, { "from": "agent", "value": "status asthmaticus continues to be significant cause of intensive care admission , morbidity , and mortality in pediatric populations . furthermore , despite improved outpatient management and broader use of controller medications , patients with severe status asthmaticus account for a notable proportion of these admissions . there is variability in management and outcomes between institutions ; however , early and aggressive management to avoid respiratory failure is paramount . in those patients who progress to develop severe respiratory failure , extracorporeal life support ( ecls ) can be a life - saving therapy . here , we briefly overview the use of ecls for status asthmaticus , as reported through the extracorporeal life support organization , including the specific institutional experience at children 's healthcare of atlanta at egleston , and consider how earlier initiation of ecls may benefit patients with severe status asthmaticus refractory to conventional medical 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: gallstones ileus is defined as mechanical intestinal obstruction caused by a large gallstone lodged in the bowel lumen . this condition accounts for only 1 % of case with small bowel obstructions and 2 % of patients with gallstone disease . it is uncommon but it is seen most often in women and the elderly population which accounts for up to 20 % in the latter group . the pathophysiology of gallstone ileus is related to the formation of cholecystoenteric fistula which allows gallstones to enter the intestinal lumen . most ( 75 % ) of these fistulas develop between the gallbladder and duodenum , although it is possible that the gallstone gains entry to the duodenum via a fistula with the biliary tract . patients with gallstone ileus may have a history of gallbladder - related symptoms without previous surgery or hernia on physical examination . they usually present with acute intestinal obstruction , either partial or complete , depending on the size of the stone . classically , the stones are almost always 2.5 cm or more in diameter and can be found impacted at about 60 cm proximal to ileocaecal valve . abdominal radiograph findings include dilated small bowel , the presence of gas in the biliary system ( pneumobilia ) , and a gallstone in the right iliac fossa . although pneumobilia is one of the radiological features of gallstones ileus , other conditions may also demonstrate this finding , including incompetent sphincter of oddi , infection of the gallbladder ( emphysematous cholecystitis ) , and rarely gallbladder cancer and blunt trauma . the initial management of gallstone ileus is to relieve the bowel obstruction by performing a small enterotomy . the bowel is also inspected for any evidence of ischemic bowel with resection of any infracted segments . in patients who can tolerate it , cholecystectomy is also performed at the same time as the enterotomy . an 82 - year - old woman presented to the emergency department with a 1 week history of vomiting , mild abdominal discomfort , and absolute constipation . the latter was preceded by gradual worsening of bile - stained non - projectile vomiting . she was a non - smoker and denied recent alcohol consumption . on physical examination , she was apyrexial , pulse rate was 78 beats per minute , blood pressure was 110/60 mmhg , and respiratory rate was 25 breaths per minute . her abdomen was soft and non - distended , but there was mild generalized tenderness elicited on palpation . laboratory tests were as follows : white blood cells , 16.5510 / l ; hb , 14.1 g / dl ; platelet , 38710 / l 10 / l ; na , 118 mmol / l ; k , 2.8 mmol / l ; urea , 16.1 mmol / l ; creatinine , 101 mmol / l ; bilirubin ( total ) , 18 mol / l ; alkaline phosphatase , 72 iu / l ; and amylase , 69 iu / l . the arterial blood gas measurement suggested a hypochloremic metabolic alkalosis ( ph 7.55 , pco26 .17 kpa , bicarbonate 39.5 mmol / l , chloride 68 mmol / l , and lactate 1.7 mmol / l ) . urine dipstick was negative for glucose , bilirubin , ketone , blood , protein , nitrates , and leukocytes . an erect chest radiograph was normal with no evidence of subdiaphragmatic air [ figure 1 ] . abdominal radiograph showed dilated small bowel loop in the central of abdomen [ figure 2 ] . for a detailed evaluation of the level of bowel obstruction , a contrast computed tomography ( ct ) of the abdomen and pelvis was requested . ct examination of the abdomen and pelvis showed findings consistent with proximal small bowel obstruction , pneumobilia located in the right hepatic lobe [ figure 3 ] , and a gallstone in the distal small bowel [ figure 4 ] . an erect chest radiograph : no evidence of air beneath the diaphragm abdominal radiograph : central , dilated loops of small bowel ( white arrow ) . note the plicae circulares or valvulae conniventes ( yellow arrow ) , a feature of small bowel , which confirms that the dilated structure is small bowel . there is no gas within the large bowel suggesting a complete or nearly complete mechanical small bowel obstruction axial ct image of the upper abdomen : there is diffuse pneumobilia ( black arrow ) axial ct image of the pelvis : there is a calculus ( white arrow ) identified within the small bowel lumen . note the presence of both dilated and non - dilated small bowel after initial fluid resuscitation with 0.9 % sodium chloride , correction of electrolyte imbalance , and nasogastric decompression , the patient underwent midline laparotomy . numerous small bowel stones [ figure 5 ] of variable size were milked distally . the largest stone measured 3.5 cm in diameter was retrieved from the small bowel lumen [ figure 6 ] . each section of the bowels was inspected in a segmental fashion for sign of ischemia and other intra - luminal faceted gallstones . an abdominal washout was performed using warm saline in order to prevent gross peritoneal contamination . the abdominal incision was closed by a mass closure technique using an absorbable loop maxon suture and staples to the skin . the pathophysiology of formation of a fistula is associated with chronic inflammation of the gallbladder . a typical history of gallstone ileus is an intermittent and episodic abdominal complaint as the calculus passes down the intestinal tract . diagnosis of this rare condition should be suspected in the elderly who presented with symptoms and sign of bowel obstruction without a history of previous abdominal surgery or hernia on physical examination . a plain abdominal radiograph may show dilatation of small bowel ( small bowel obstruction ) , air in the biliary tree ( pneumobilia ) , and opacity in the right iliac fossa ( ectopic gallstone ) . the feature of small bowel obstruction , pneumobilia , and ectopic gallstone represents rigler 's triad which is consistent with a diagnosis of gallstone ileus . the triad presents only 14.81 % on plain film of the abdomen , 11.11 % on abdominal sonography , and 77.78 % on abdominal ct scan . this is not surprising because plain abdominal radiograph reveals radio opaque gallstones in only 10 % of cases . in the latter study , it was shown that pneumobilia can be detected up to 89 % of all cases of gallstone ileus . in the past , plain abdominal radiography and ultrasound are helpful in diagnosing gallstone ileus but the sensitivity of both modalities is low . ct scan is the investigation of choice for evaluating gallstone ileus as it has high sensitivity ( 93 % ) and specificity ( 100 % ) . a ct scan can accurately measure the size of the gallstone and establish the anatomical site and the nature of the obstruction . therefore , ct scan is usually a preferred diagnostic modality because of its high resolution in detecting gallstones and provides details of anatomical localization of the gallstone and fistula . sensitivity and specificity of different modalities in diagnosing gallstone ileus the initial management of gallstone ileus is to relieve the obstruction by removing the gallstone through a proximal enterotomy . spontaneous resolution of symptoms of gallstone ileus has been reported but uncommon . at presentthe choice of a one - stage or two - stage surgical procedure or enterotomy alone is still debatable . the reported mortality rates of gallstone ileus are generally consistent at about 20 % for the first time ileus presentation and at subsequent recurrent episodes . most of the retrospective studies conducted so far suggested that higher mortality rates were observed in the one - stage procedure [ table 2 ] . to date , the largest single published review of this condition , by reisner and cohen found that one - stage procedure carries higher risk of mortality compared to simple enterotomy . associated factors of a higher mortality rate may attribute to : ( 1 ) pre - operatively , ( 2 ) intra - operatively , and ( 3 ) post - operatively . first , pre - operatively : elderly patients with poor general medical conditions , delayed diagnosis , and prompt treatment of this uncommon condition as well as inadequate physiological state optimization pre - operatively prior to the time of emergency laparotomy may result in a poorer surgical outcome . second , intra - operatively : longer operating time for the one - stage procedure may lead to higher mortality . third , post - operatively : deaths may not be related to the surgery , for example , myocardial infarction or pulmonary embolism . comparison of mortality rates of two main surgical approaches in treating gallstone ileus , one - stage and two - stage procedure in this brief report , we compared mortality rates of the two main surgical approaches , one - stage procedure ( comprising enterotomy , cholecystectomy , and fistula repair ) and two - stage procedure ( enterotomy with or without subsequent cholecystectomy and fistula repair ) . there is no general consensus on gold standard surgical intervention and the controversy of these is still remaining arguable . of all selected 13 studies that provide adequate data comparing mortality rates in one - stage and two - stage procedures , we found a higher mortality rate in one - stage procedure ( 16.8 % ) compared to two - stage procedure ( 11.8 % ) . surprisingly , the results from these collective studies are similar to the previously reported data by reisner and cohen . a majority of the studies observed higher mortality rates in one - stage procedure except deitz et al . the author observed a higher mortality rate in two - stage procedure ( 16.7 % ) . pavlidis et al . , selectively performed two - stage operation for all patients with american society of anesthesiologists ( asa ) score three or more . he concluded that two - stage procedure should be performed in patients with unfavorable asa score . one can argue that laparoscopy increases operative time of the surgery due to technical difficulty finding the gallstone and requires specialist trained surgeons . on the other hand , laparoscopy inflicts less operative trauma on the patient , which may result in less morbidity and mortality . some recent reports have been published on the efficacy of the laparoscopic approach in the management of gallstone ileus . to date , there are five studies regarding the use of laparoscopy in the treatment of gallstone ileus . these reports demonstrate that laparoscopy is effective in both diagnosis and treatment of gallstone ileus . the number of patients in each study is small ; therefore , we do not have enough clinical data to allow comparison between one - stage and two - stage procedures performed laparoscopically . therefore , a prompt diagnosis followed by urgent optimization of patient prior to appropriate surgical intervention is essential . a two - stage procedure should be considered in all elderly patients with significant co - morbidities . a one - stage procedure , on the other hand , should be reserved for young , fit , and low - risk patient with a favorable asa score .\noutput:\n" }, { "from": "agent", "value": "gallstones ileus is an uncommon cause but important cause of small bowel obstruction . the gallstone enters the intestinal lumen via a fistula located in the duodenum ( cholecystoduodenal ) , or rarely , in the colon ( cholecystocolonic ) or stomach ( cholecystogastric ) . this may result in large bowel or gastric outlet obstruction ( bouveret 's syndrome ) . gallstone ileus affects the elderly females pre - dominantly and is associated with a high morbidity and mortality rate if diagnosis and urgent surgical intervention are delayed . in this paper , we report on the case of an elderly lady who presented with classical symptoms and signs of small bowel obstruction . she was subsequently diagnosed with gallstone ileus due to a large gallstones lodged in the intestinal lumen . we perform a literature review on this rare disease and discuss the two main surgical approaches in managing this condition . gallstone ileus should be considered in the differential diagnosis of small bowel obstruction especially in elderly women who have no history of abdominal surgery or abdominal hernia . early intervention is important because of the high mortality rate due to the poor general condition that often exists in this subgroup of patients . there is no general consensus on gold standard surgical approach in these cases but a two - stage procedure ( either enterotomy alone or enterotomy and subsequent cholecystectomy ) has been shown to be associated with lower mortality rates ." } ]

[ { "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: nurr1 also known as nr4a2 , belongs to the nuclear receptor superfamily of transcription factors , is highly expressed in midbrain dopaminergic ( da ) neurons , and plays an essential role in the development , survival and function maintenance of midbrain da neurons . nurr1 is a potential target for parkinson 's disease ( pd ) , which is the second common neurodegenerative disease and both genetic and environmental neurotoxin are important causes . nurr1 can activate the transcription of tyrosine hydroxylase and enhance the expression of da transporter . it was reported that homozygous nurr1 knockout mice failed to develop da neurons , and heterozygotes reduced their brain da and developed age - dependent locomotor deficits including impaired horizontal and vertical movement , difficultly performance on rotarod test compared to age - matched wild - type mice . reduction of nurr1 in the adult brain may increase the vulnerability of da neurons to stress and participate in the pathogenesis of pd . several polymorphisms of nurr1 gene including 291tdel and 245t -- g have been reported to result in a marked decrease of nurr1 mrna levels in transfected cell lines and lymphocytes of affected individuals . furthermore , le et al . reported a decreased nurr1 gene expression in peripheral blood mononuclear cells ( pbmcs ) of pd patients , which anticipated nurr1 as a potential biomarker for pd diagnosis . but to date , little has been done to investigate the association among nurr1 expression in pbmc , disease progression of pd , and da agents . this study was to measure the nurr1 mrna level in pbmc and evaluate the effect of nurr1 expression by da agents in vivo and in vitro . the 362 pd patients at department of neurology , the first affiliated hospital of sun yet - sen university between january 2012 and august 2014 were recruited . the diagnosis was made in accordance with the united kingdom pd society brain bank criteria . besides recent - onset pd patients without any anti - pd treatments ( de novo ) , each patient reported to have taken anti - pd medicines at least 2 years and all patients were assessed according to the hoehn and yahr ( h and y ) scale . meantime , 193 healthy controls ( hcs ) were enrolled either from physical examination center of sun yat - sen university or the spouses of the patients . the study was approved by the ethics committee of sun yat - sen university . peripheral blood samples ( 5 ml ) of pd patients and hcspbmc from venous blood of pd patients and hcs were prepared by ficoll - hypaque density gradient centrifugation . after centrifugation at 2200 r / min for 20 min , buffy coats were collected and washed three times with phosphate - buffered saline ( pbs ) , then centrifuged at 1800 r / min for 10 min to collect pbmc cells . then pbmc were lysed by adding 1 ml trizol reagent ( invitrogen , carlsbad , ca , usa ) and stored at 80c until used . in order to further explore the pattern of nurr1 expression , an in vitro analysis on cultured human pbmc was conducted . pbmc from venous blood of 10 hcs was prepared by ficoll - hypaque density gradient centrifugation through centrifuging at 2200 r / min for 20 min . the buffy coats were collected and washed twice with pbs , then washed once with complete rpmi 1640 medium ( gibco , german ) containing 2 mmol / l l - glutamine , 100 u / ml penicillin , 100 g / ml streptomycin , and 10 % fetal bovine serum and suspended at a concentration of 210 cells / ml with complete rpmi 1640 medium . pbmc was delivered in 3.5 cm diameter dishes with 210 cells separately with complete rpmi 1640 medium . after 12 h cultured , the cells were treated with 10 mol / l pramipexole ( sigma , st . louis , mo , usa ) for 2 , 4 , 8 , 12 and 24 h and cultured at 37c under the humidified 5 % co2 atmosphere . selected time , the pbmc cells were collected for rna extraction . then total rna was isolated using trizol ( invitrogen ) according to the manufacturer 's protocol . the 1 g of total rna was reverse transcribed into first - strand complementary dna ( cdna ) using a reverse transcription ( rt ) kit ( takara , japan ) according to the manufacturer 's protocol in a final volume of 20 l . for analysis , on nurr1 expression with quantitative real - time rt - polymerase chain reaction ( rt - pcr ) , human glyceraldehyde -3-phosphate dehydrogenase ( gapdh ) was used as internal control , and the sequences of primers as follows : nurr1 forward : 5 - tccaacgaggggctgtgcg - 3 ; nurr1 reverse : 5 - cactgtgcgcttaaagaagc - 3 ; and gapdh forward : 5 - gaaggtgaagg tcggagtc - 3 ; gapdh reverse : 5 - gaagatggtgatgggatttc - 3 . the 2 l of the synthesized cdna were used in all real - time pcr together with the sybr green i master mix ( sybr premix ex taq , takara , japan ) on mj research opticon2 real - time thermocycler ( bio - rad , hercules , ca , usa ) . fluorescent reading from real - time pcr reaction was quantitatively analyzed by determining the difference of ct ( delta ct ) between ct of nurr1 and its internal gapdh , and the nurr1 gene expression was determined by the formation of 2 . in addition , for all the analyzed samples , only triplicates with a standard deviation of the ct 0.20 were accepted . quantitative data ( age , h and y scale , the relative nurr1 mrna relative level ) were shown as mean standard error ( se ) or median and interquartile range , depending on the distribution of the data . the chi - square test was used to analyze the differences of gender between pd and hcs or among the subgroups of pd . the nonparametric mann - whitney u - test and kruskal - wallis test were performed to evaluate the differences between pd and hc or among the subgroups of pd . the multivariate linear regression models were used to simultaneously evaluate the cross - sectional association of dependent variables ( the nurr1 mrna relative level ) and independent variables ( h and y scale , age , and the different drug treatments ) . after adjustment of h and y scale and age , the covariance analysis was utilized to test the differences of nurr1 mrna relative level among different drug treatments . one - way analysis of variance was used to analyze the difference of nurr1 mrna level among the different hours treated with pramipexole . the 362 pd patients at department of neurology , the first affiliated hospital of sun yet - sen university between january 2012 and august 2014 were recruited . the diagnosis was made in accordance with the united kingdom pd society brain bank criteria . besides recent - onset pd patients without any anti - pd treatments ( de novo ) , each patient reported to have taken anti - pd medicines at least 2 years and all patients were assessed according to the hoehn and yahr ( h and y ) scale . meantime , 193 healthy controls ( hcs ) were enrolled either from physical examination center of sun yat - sen university or the spouses of the patients . peripheral blood samples ( 5 ml ) of pd patients and hcs were drawn from antecubital venous and put into natrium citricum - containing tubes . pbmc from venous blood of pd patients and hcs were prepared by ficoll - hypaque density gradient centrifugation . after centrifugation at 2200 r / min for 20 min , buffy coats were collected and washed three times with phosphate - buffered saline ( pbs ) , then centrifuged at 1800 r / min for 10 min to collect pbmc cells . then pbmc were lysed by adding 1 ml trizol reagent ( invitrogen , carlsbad , ca , usa ) and stored at 80c until used . in order to further explore the pattern of nurr1 expression , an in vitro analysis on cultured human pbmc was conducted . pbmc from venous blood of 10 hcs was prepared by ficoll - hypaque density gradient centrifugation through centrifuging at 2200 r / min for 20 min . the buffy coats were collected and washed twice with pbs , then washed once with complete rpmi 1640 medium ( gibco , german ) containing 2 mmol / l l - glutamine , 100 u / ml penicillin , 100 g / ml streptomycin , and 10 % fetal bovine serum and suspended at a concentration of 210 cells / ml with complete rpmi 1640 medium . pbmc was delivered in 3.5 cm diameter dishes with 210 cells separately with complete rpmi 1640 medium . after 12 h cultured , the cells were treated with 10 mol / l pramipexole ( sigma , st . louis , mo , usa ) for 2 , 4 , 8 , 12 and 24 h and cultured at 37c under the humidified 5 % co2 atmosphere . then total rna was isolated using trizol ( invitrogen ) according to the manufacturer 's protocol . the 1 g of total rna was reverse transcribed into first - strand complementary dna ( cdna ) using a reverse transcription ( rt ) kit ( takara , japan ) according to the manufacturer 's protocol in a final volume of 20 l . for analysis , on nurr1 expression with quantitative real - time rt - polymerase chain reaction ( rt - pcr ) , human glyceraldehyde -3-phosphate dehydrogenase ( gapdh ) was used as internal control , and the sequences of primers as follows : nurr1 forward : 5 - tccaacgaggggctgtgcg - 3 ; nurr1 reverse : 5 - cactgtgcgcttaaagaagc - 3 ; and gapdh forward : 5 - gaaggtgaagg tcggagtc - 3 ; gapdh reverse : 5 - gaagatggtgatgggatttc - 3 . the 2 l of the synthesized cdna were used in all real - time pcr together with the sybr green i master mix ( sybr premix ex taq , takara , japan ) on mj research opticon2 real - time thermocycler ( bio - rad , hercules , ca , usa ) . fluorescent reading from real - time pcr reaction was quantitatively analyzed by determining the difference of ct ( delta ct ) between ct of nurr1 and its internal gapdh , and the nurr1 gene expression was determined by the formation of 2 . in addition , for all the analyzed samples , only triplicates with a standard deviation of the ct 0.20 were accepted . quantitative data ( age , h and y scale , the relative nurr1 mrna relative level ) were shown as mean standard error ( se ) or median and interquartile range , depending on the distribution of the data . the chi - square test was used to analyze the differences of gender between pd and hcs or among the subgroups of pd . the nonparametric mann - whitney u - test and kruskal - wallis test were performed to evaluate the differences between pd and hc or among the subgroups of pd . the multivariate linear regression models were used to simultaneously evaluate the cross - sectional association of dependent variables ( the nurr1 mrna relative level ) and independent variables ( h and y scale , age , and the different drug treatments ) . after adjustment of h and y scale and age , the covariance analysis was utilized to test the differences of nurr1 mrna relative level among different drug treatments . one - way analysis of variance was used to analyze the difference of nurr1 mrna level among the different hours treated with pramipexole . the 362 pd patients ( 209 males , 153 females ) were enrolled in this study . among these 362 patients , 136 patients were recent - onset cases and did not receive any anti - pd treatment before blood drawing ( de novo ) ; 83 patients were administrated with l - dopa , 38 patients received d2 / d3 agonists ( piribedil or pramipexole ) , 105 patients took both l - dopa and da agonists . these patients were divided into four subgroups according to the different drug treatments : de novo , l - dopa , da agonist , and l - dopa and da agonist . the demographic and clinical characteristics of pd patients and hcs are summarized in table 1 , showing no significant differences ( p = 0.683 ) in gender between pd patients and hcs and among the four subgroups of pd patients . the average age of pd patients in l - dopa and l - dopa and da agonist subgroups was older than that of de novo subgroup or hcs ( p 0.05 ) . furthermore , the median scale of pd was 2.0 of h and y stage in all three subgroups ( l - dopa , da agonists and l - dopa and da agonist ) , which was significantly higher than de novo subgroup ( p 0.05 ) . demographic and clinical characteristics of the subjects da : dopaminergic ; hc : healthy control ; pd : parkinson s disease ; de novo : pd without any anti - pd treatment ; da agonists : pd treated with da agonists ; l - dopa : pd treated with l - dopa ; l - dopa and da agonists : pd treated with l - dopa and da agonists . * p 0.05 compared with de novo ; p 0.05 compared with hc . generalized estimating equations in linear regression models were performed on the data from all subjects . h and y scale , age and different drug treatments of pd patients were identified to be independently associated with nurr1 mrna relative level . in both the stepwise model and inclusive model , the independent predictors of nurr1 mrna relative level were da agonists , l - dopa , and da agonists . the formulae for nurr1 mrna relative level were created based on the regression coefficients ( ) : in stepwise model , for da agonists , = 4.551 ( 95 % confidence interval [ ci ] , 2.2006.903 ; p 0.001 ) ; for l - dopa and da agonists , = 4.398 ( 95 % ci , 2.8835.912 ; p 0.001 ) ; and in inclusive model , for age , = 0.024 ( 95 % ci , 0.0690.022 ; p = 0.311 ) ; for h and y scale , = 0.120 ( 95 % ci , 1.0920.852 ; p = 0.809 ) ; for de novo , = 0.633 ( 95 % ci , 2.7391.473 ; p = 0.555 ) ; for l - dopa , = 0.672 ( 95 % ci , 2.0583.402 ; p = 0.629 ) ; for da agonists , = 4.657 ( 95 % ci , 1.5527.762 ; p = 0.003 ) ; for l - dopa and da agonists , = 4.561 ( 95 % ci , 1.9737.147 ; p = 0.001 ) . the nurr1 mrna relative level was made using the following formulas : nurr1 mrna level = 2.973 + 4.551 da agonists + 4.398 l - dopa and da agonists , or nurr1 mrna level = 4.545 + 4.657 da agonists + 4.561 l - dopa and da agonists . according to different drug treatments , the pd patients were divided into 4 subgroups . as shown in figure 1 , the relative levels of nurr1 mrna in de novo subgroup and hcs were 2.380.42 versus 3.180.42 , respectively ( p = 0.307 ) , a slight decrease but no statistical significance in de novo subgroup without any da agonists , l - dopa or other anti - pd drugs . the relative level of nurr1 mrna in l - dopa pd group was 3.370.57 versus 3.180.42 in hc ( p = 0.841 ) , which showed no statistical significance . however , the relative nurr1 mrna level in da agonist subgroup was 7.521.82 , significant higher than those both in de novo group ( p 0.001 ) and hc ( p = 0.001 ) . the nurr1 mrna level in da agonist and l - dopa subgroup was up to 7.371.07 , which was significantly increased versus de novo subgroup or l - dopa subgroup ( p 0.001 ) . there were no significant differences of nurr1 mrna level between da agonist and da agonist and l - dopa subgroups . scatter plots of nurr1 mrna relative levels in peripheral blood mononuclear cells of subgroups of pd patients . fluorescent reading from real - time polymerase chain reaction was quantitatively analyzed by determining the difference of ct ( delta ct ) between ct of nurr1 and internal control . hc : healthy control ; pd : parkinson 's disease ; de novo : pd without any anti - pd treatment ; da agonists : pd treated with da agonists ; l - dopa : pd treated with l - dopa ; l - dopa and da agonists : pd treated with l - dopa and da agonists ; da : dopaminergic . in 136 recent - onset cases , 25 were treated with l - dopa and 19 were treated with da agonists . the nurr1 mrna level in 25 patients was 7.871.70 before l - dopa treatment , and 7.591.59 after l - dopa taken , but no significant difference ( p = 0.905 ) . the nurr1 mrna levels in 19 patients before and after da agonist treatment were 5.921.42 and 8.472.52 , respectively , indicating a slight but nonsignificant increase after da agonist treatment ( p = 0.066 ) . scatter plots of nurr1 mrna relative levels in peripheral blood mononuclear cells before and after treatment of l - dopa ( a ) ( n = 25 ) or da agonist ( b ) ( n = 19 ) in de novo subgroup . there were no obvious changes before and after l - dopa treatment neither for the whole group nor for each individual , while there were three individuals showed obvious increase of nurr1 mrna levels though there was no significance between before and after da agonist treatment as a whole group . da : dopaminergic . to further explore whether da agonists have effect on nurr1 expression , we measured the nurr1 mrna level in pbmc from 10 healthy volunteers with 10 mol / l pramipexole [ figure 3 ] . compared with control , the nurr1 mrna relative levels in pbmc by da agonistwere significantly increased to 199.6113.17 % , 171.7511.33 % , 173.1611.42 % in 2 , 4 and 8 h , respectively ( p 0.001 ) . in vitro experiment , the nurr1 mrna levels of pbmc treated by da agonist for 12 h and 24 h were 95.306.26 % and 104.604.32 % , respectively , and there were no significant differences compared with control ( p 0.05 ) , which was in accord with the half - life of 812 h. nurr1 mrna relative levels in vitro measured by real - time polymerase chain reaction treated with pramipexole . all experiments were performed at least three independent times ( * p 0.001 ) . the 362 pd patients ( 209 males , 153 females ) were enrolled in this study . among these 362 patients , 136 patients were recent - onset cases and did not receive any anti - pd treatment before blood drawing ( de novo ) ; 83 patients were administrated with l - dopa , 38 patients received d2 / d3 agonists ( piribedil or pramipexole ) , 105 patients took both l - dopa and da agonists . these patients were divided into four subgroups according to the different drug treatments : de novo , l - dopa , da agonist , and l - dopa and da agonist . the demographic and clinical characteristics of pd patients and hcs are summarized in table 1 , showing no significant differences ( p = 0.683 ) in gender between pd patients and hcs and among the four subgroups of pd patients . the average age of pd patients in l - dopa and l - dopa and da agonist subgroups was older than that of de novo subgroup or hcs ( p 0.05 ) . furthermore , the median scale of pd was 2.0 of h and y stage in all three subgroups ( l - dopa , da agonists and l - dopa and da agonist ) , which was significantly higher than de novo subgroup ( p 0.05 ) . demographic and clinical characteristics of the subjects da : dopaminergic ; hc : healthy control ; pd : parkinson s disease ; de novo : pd without any anti - pd treatment ; da agonists : pd treated with da agonists ; l - dopa : pd treated with l - dopa ; l - dopa and da agonists : pd treated with l - dopa and da agonists . generalized estimating equations in linear regression models were performed on the data from all subjects . h and y scale , age and different drug treatments of pd patientswere identified to be independently associated with nurr1 mrna relative level . in both the stepwise model and inclusive model , the independent predictors of nurr1 mrna relative level were da agonists , l - dopa , and da agonists . the formulae for nurr1 mrna relative level were created based on the regression coefficients ( ) : in stepwise model , for da agonists , = 4.551 ( 95 % confidence interval [ ci ] , 2.2006.903 ; p 0.001 ) ; for l - dopa and da agonists , = 4.398 ( 95 % ci , 2.8835.912 ; p 0.001 ) ; and in inclusive model , for age , = 0.024 ( 95 % ci , 0.0690.022 ; p = 0.311 ) ; for h and y scale , = 0.120 ( 95 % ci , 1.0920.852 ; p = 0.809 ) ; for de novo , = 0.633 ( 95 % ci , 2.7391.473 ; p = 0.555 ) ; for l - dopa , = 0.672 ( 95 % ci , 2.0583.402 ; p = 0.629 ) ; for da agonists , = 4.657 ( 95 % ci , 1.5527.762 ; p = 0.003 ) ; for l - dopa and da agonists , = 4.561 ( 95 % ci , 1.9737.147 ; p = 0.001 ) . the nurr1 mrna relative level was made using the following formulas : nurr1 mrna level = 2.973 + 4.551 da agonists + 4.398 l - dopa and da agonists , or nurr1 mrna level = 4.545 + 4.657 da agonists + 4.561 l - dopa and da agonists . according to different drug treatments , the pd patients were divided into 4 subgroups . as shown in figure 1 , the relative levels of nurr1 mrna in de novo subgroup and hcs were 2.380.42 versus 3.180.42 , respectively ( p = 0.307 ) , a slight decrease but no statistical significance in de novo subgroup without any da agonists , l - dopa or other anti - pd drugs . the relative level of nurr1 mrna in l - dopa pd group was 3.370.57 versus 3.180.42 in hc ( p = 0.841 ) , which showed no statistical significance . however , the relative nurr1 mrna level in da agonist subgroup was 7.521.82 , significant higher than those both in de novo group ( p 0.001 ) and hc ( p = 0.001 ) . the nurr1 mrna level in da agonist and l - dopa subgroup was up to 7.371.07 , which was significantly increased versus de novo subgroup or l - dopa subgroup ( p 0.001 ) . there were no significant differences of nurr1 mrna level between da agonist and da agonist and l - dopa subgroups . scatter plots of nurr1 mrna relative levels in peripheral blood mononuclear cells of subgroups of pd patients . fluorescent reading from real - time polymerase chain reaction was quantitatively analyzed by determining the difference of ct ( delta ct ) between ct of nurr1 and internal control . hc : healthy control ; pd : parkinson 's disease ; de novo : pd without any anti - pd treatment ; da agonists : pd treated with da agonists ; l - dopa : pd treated with l - dopa ; l - dopa and da agonists : pd treated with l - dopa and da agonists ; da : dopaminergic . in 136 recent - onset cases , 25 were treated with l - dopa and 19 were treated with da agonists . the nurr1 mrna level in 25 patients was 7.871.70 before l - dopa treatment , and 7.591.59 after l - dopa taken , but no significant difference ( p = 0.905 ) . the nurr1 mrna levels in 19 patients before and after da agonist treatment were 5.921.42 and 8.472.52 , respectively , indicating a slight but nonsignificant increase after da agonist treatment ( p = 0.066 ) . scatter plots of nurr1 mrna relative levels in peripheral blood mononuclear cells before and after treatment of l - dopa ( a ) ( n = 25 ) or da agonist ( b ) ( n = 19 ) in de novo subgroup . there were no obvious changes before and after l - dopa treatment neither for the whole group nor for each individual , while there were three individuals showed obvious increase of nurr1 mrna levels though there was no significance between before and after da agonist treatment as a whole group . da : dopaminergic . to further explore whether da agonists have effect on nurr1 expression , we measured the nurr1 mrna level in pbmc from 10 healthy volunteers with 10 mol / l pramipexole [ figure 3 ] . compared with control , the nurr1 mrna relative levels in pbmc by da agonistwere significantly increased to 199.6113.17 % , 171.7511.33 % , 173.1611.42 % in 2 , 4 and 8 h , respectively ( p 0.001 ) . in vitro experiment , the nurr1 mrna levels of pbmc treated by da agonist for 12 h and 24 h were 95.306.26 % and 104.604.32 % , respectively , and there were no significant differences compared with control ( p 0.05 ) , which was in accord with the half - life of 812 h. nurr1 mrna relative levels in vitro measured by real - time polymerase chain reaction treated with pramipexole . peripheral blood mononuclear cells from health volunteers were treated with 10 mol / l pramipexole for 024 h. glyceraldehyde -3-phosphate dehydrogenase was monitored as internal control . all experiments were performed at least three independent times ( * p 0.001 ) . nurr1 is highly expressed in the developing and adult ventral midbrain and required for the acquisition and maintenance of the da phenotype in nigrostriatal neurons . it has been reported that besides central nervous system , nurr1 is also an expression in many tissues including bone , endothelial cells , and pbmc . the key point for clinical evacuation of nurr1 is whether the alteration of nurr1expression is secondary to anti - pd drug effects . using rt - pcr , we analyzed the nurr1 mrna level in pbmc from 362 sporadic pd patients and 193 hcs from southern china , and found that the nurr1 expression level in de novo subgroup with a tendency of nonsignificant decrease compared to hcs , but a statistically significant increase in both da agonist or da agonist and l - dopa subgroups , which indicated that da agonists may exert an up - regulation effect on the expression of nurr1 in pbmc . as a transcription factors , the expression of nurr1 can be affected by many factors including growth factors , neurotransmitters , and drugs . for example , injection of 6 - hydroxydopamine into the striatum produced an increase in the number of cells expressing nurr1 in both substantia nigra compacta ( snc ) and substantia nigra reticulate . similar to our data , a series of evidence indicated that da receptor agonists may play an active role on the nurr1 expression . for instance , ropinirole has been documented to prevent the progression of pd in nurr1 deficient mouse , and pan et al . reported that sh - sy5y cells treated with d3 receptor agonist pramipexole enhanced the expression of nurr1 mrna and protein in vitro . studies on postmortem brains have been found that an age - related decline of da phenotypic markers was associated with down - regulation of nurr1 expression in human sn . reported the optical density of nurr1 immunofluorescence was significantly decreased in nigral neurons containing - synuclein - immunoreactive inclusions in pd patients . in addition , recent studies showed a significant decreased of nurr1 mrna in snc of d2 dopamine receptor / mice ( d2r ) . however , our data showed that the expression of nurr1 mrna in pbmc was affected by drugs like da agonist , but was no significant correlation with the disease severity ( h and y scale ) or age of onset of pd . for further exploring the pattern of nurr1 expression in vitro , we found that nurr1 mrna relative levels in pbmc increased significantly after treated with 10 mol / l pramipexole for 2 , 4 , and 8 h , which in accordance with our clinical investigation from blood cells of pd patients , demonstrating da agonist plays an active effect on nurr1 gene in pbmc . reported that levels of nurr1 mrna and protein in sh - sy5y increased after pramipexole treatment , indicating that the biological pattern of nurr1 expression in pbmc might be different from the changes in degeneration of da neurons in midbrain . in summary , we observed that nurr1 mrna level in pbmc from our pd patients was significantly influenced by antiparkinsonism drugs da agonists but not l - dopa , and such effect may contribute to da agonists - mediated neuroprotection on da neurons . furthermore , we found a slight insignificant reduction of nurr1 level in our de novo pd patients , which might present a correlation with the disease . a larger sample of de novo pd patients may be needed to evaluate whether reduced expression of nurr1 in pbmc can be used as a biomarker for early pd .\noutput:\n" }, { "from": "agent", "value": "background : nurr1 plays an essential role in the development , survival , and function maintenance of midbrain dopaminergic ( da ) neurons , and it is a potential target for parkinson 's disease ( pd ) . nurr1 mrna can be detected in peripheral blood mononuclear cells ( pbmcs ) , but whether there is any association of altered nurr1 expression in pbmc with the disease and da drug treatments remains elusive . this study aimed to measure the nurr1 mrna level in pbmc and evaluate the effect of nurr1 expression by da agents in vivo and in vitro.methods : the mrna levels of nurr1 in pbmc of four subgroups of 362 pd patients and 193 healthy controls ( hcs ) using real - time polymerase chain reaction were measured . the nonparametric mann - whitney u - test and kruskal - wallis test were performed to evaluate the differences between pd and hc , as well as the subgroups of pd . multivariate linear regression analysis was used to evaluate the independent association of nurr1 expression with hoehn and yahr scale , age , and drug treatments . besides , the nurr1 expression in cultured pbmc was measured to determine whether da agonist pramipexole affects its mrna level.results : the relative nurr1 mrna levels in da agonists treated subgroup were significant higher than those in recent - onset cases without any anti - pd treatments ( de novo ) ( p < 0.001 ) and hc groups ( p < 0.010 ) , respectively . furthermore , the increase in nurr1 mrna expression was seen in da agonist and l - dopa group . multivariate linear regression showed da agonists , l - dopa , and da agonists were independent predictors correlated with nurr1 mrna expression level in pbmc . in vitro , in the cultured pbmc treated with 10 mol / l pramipexole , the nurr1 mrna levels were significantly increased by 99.61 % , 71.75 % , 73.16 % in 2 , 4 , and 8 h , respectively ( p < 0.001 ) . conclusions : da agonists can induce nurr1 expression in pbmc , and such effect may contribute to da agonists - mediated neuroprotection on da neurons ." } ]

[ { "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: strain cbs10496 was isolated from a 31 - year - old aids patient from montreal , quebec , canada , who had traveled to mexico 15 months before cryptococcosis was diagnosed . the patient died despite extensive antifungal treatment with ketoconazole and amphotericin b ( 11 ) . cbs10496 has been identified as c. gattii serotype b ( cited as c. neoformans var . * aflp , amplified fragment length polymorphism ; cbs , fungal biodiversity centre ; amc , netherlands reference laboratory for bacterial meningitis , academic medical center , amsterdam , the netherlands ; na , not applicable ; csf , cerebrospinal fluid . origin and genetic composition of the strains are indicated . aflp fingerprint genotype ( 7 ) , followed by corresponding m13 pcr fingerprint genotype ( 8 ) . the ploidy of cbs10496 was determined by using flow cytometry ( 10 ) with the sequenced haploid strains cbs8710 and cbs10510 as references . coloration of colonies grown on canavanine - glycine - bromthymol blue ( cgb ) medium ( 12 ) was determined after incubation at 24c for 6 and 15 days . the serotype of cbs10496 was determined by using the cryptocheck serotyping kit ( iatron laboratories , tokyo , japan ) . dna of these colonies was used for amplified fragment length polymorphism ( aflp ) analysis ( 7 ) . the partial sequence of 6 nuclear regions was determined for reference isolates cbs10488cbs10490 , cbs1622 , cbs6992 , and the putative hybrid isolate cbs10496 . selected nuclear regions were those for internal transcribed spacer ( its ) region , intergenic spacer region , laccase ( cnlac1 ) , 2 rna polymerase ii subunits ( rpb1 and rpb2 ) , and translation elongation factor 1 ( tef1 ) ( 9,10 ) . the g1 peak of reference strains was located at positions 31.6 ( cbs8710 ) and 31.1 ( cbs10510 ) , and the g2 peak was located at positions 65.8 ( cbs8710 ) and 56.4 ( cbs10510 ) . the g1 peak of cbs10496 was located at position 57.5 , and the g2 peak was located at position 115.7 . thus , the g1 peak of cbs10496 coincided with the g2 peak of the haploid strains ( figure 1 , panel a ) , which indicates that cbs10496 has 2 more dna than haploid strains . staining with 4,6 - diamidino -2-phenylindole showed that cells of cbs10496 were monokaryotic ( figure 1 , panel b ) . a ) determination of ploidy of the novel cryptococcus neoformans c. gattii serotype ab hybrid isolate cbs10496 by flow cytometry . the first peak corresponds to the g1 phase ; the second peak corresponds to the g2 phase . haploid reference strain cbs10510 is shown by the red line ; cbs10496 is shown by the black line . the g1 peak of cbs10496 coincided with the g2 peak of strain cbs10510 , which indicated that strain cbs10496 has approximately twice the amount of dna than cbs10510 . b ) nuclear staining of isolate cbs10496 with 4,6 - diamidino -2-phenylindole , showing that cells are monokaryotic . reaction of cbs10496 on cgb medium was negative , which corresponds to c. neoformans ( 12 ) . the cryptocheck serotyping kit serum factors 5 ( corresponding to serotype b ) and 7 ( corresponding to serotype a ) agglutinated , which indicated that cbs10496 is a serotype ab strain . the aflp fingerprint obtained by analysis of colonies of cbs10496 did not match any of the previously defined aflp genotypes . the fingerprint of cbs10496 was compared with aflp fingerprints of reference strains cbs8710 and cbs9172 , which are aflp1 / vni , and e566 and cbs10510 , which are aflp4 / vgi . the aflp fingerprint of cbs10496 contained fragments characteristic of aflp1 / vni and aflp4 / vgi ( figure 2 ) , which indicated that genetic material from these 2 genotypes was present in this isolate . amplified fragment length polymorphism ( aflp ) fingerprint of 3 colonies of the novel cryptococcus neoformans c. gattii hybrid serotype ab isolate cbs10496 and 4 reference strains . cbs9172 and cbs8710 are c. neoformans var . grubii ( aflp1 / vni ) strains ; e566 and cbs10510 are c. gattii ( aflp4 / vgi ) strains . two alleles representing aflp1 / vni and aflp4 / vgi were found when fragments of rpb1 , rpb2 , cnlac1 , and intergenic spacer region of cbs10496 were cloned and sequenced . however , after 30 clones were sequenced , only 1 allele was obtained for tef1 , i.e. , aflp4 / vgi , and its , i.e. , aflp1 / vni . our results indicate that genetic material from aflp1 / vni and aflp4 / vgi was present in cbs10496 , although only 1 allele was obtained for tef1 and its . specific primer pair resulted in an amplicon . when mata and the mata serotype ain addition , cbs10510 , a mat serotype b strain , was amplified with the mat specific primer pair , and e566 , a mata serotype b strain , yielded an amplicon with the mata - specific pcr . these results indicate that a c. gattii and a mat serotype a background are present in cbs10496 . because the mating type of the c. gattii background within cbs10496 was unknown , 30 mat clones of cbs10496 were sequenced to determine whether a mat serotype b allele could be identified . however , all clones were mat serotype a ; no mat serotype b clones were found . our results indicated that cbs10496 is a monokaryotic , diploid , or aneuploid strain with the novel ab serotype . grubii ( serotype a , aflp1 / vni ) and c. gattii ( serotype b , aflp4 / vgi ) . cbs10496 had been identified as c. gattii on the basis of a weak positive reaction on cgb medium ( 11 ) . although a negative response on cgb medium has been shown for other c. neoformans c. gattii hybrids ( 10,14 ) , weak and delayed positive reactions on cgb medium may occur in c. neoformans c. gattii hybrid isolates ( 10,14 ) . inconsistent serotyping results have been reported for other hybrids ( 10,15 ) and may result from differences in specificity and potency among different batches of factor serum . all c. neoformans c. gattii hybrids discovered have originated from clinical sources ( 13 ; f. hagen and t. boekhout , unpub . although an amplicon was obtained with c. gattii specific mating - type primers , the c. gattii background could not be linked to a mating type . we hypothesize that the serotype ab c. neoformans c. gattii hybrid cbs10496 was formed by mating of a mata serotype b strain with a mat serotype a strain and subsequent loss of the mata serotype b allele . detection of single its and tef1 alleles in cbs10496 further supports our findings because it indicates that other alleles were also lost . loss of genetic material has been observed in other hybrids , such as serotype ad and bd hybrids ( 14 ) , and seems to be a normal process in cryptococcal hybrids . our results show that the c. gattii parent of the serotype ab hybrid belongs to the aflp4 / vgi genotype , as was the case for serotype bd hybrids ( 10 ) . the c. gattii parental sequence of all known serotype bd c. neoformans c. gattii hybrid isolates was identical to sequences of aflp4 / vgi strains cbs1622 and cbs6992 in all regions studied ( 9 ) . aflp4 / vgi subgroup in all isolated c. neoformans c. gattii hybrids may indicate that this subgroup preferentially forms interspecies hybrids .\noutput:\n" }, { "from": "agent", "value": "interspecies hybrids of cryptococcus neoformans and c. gattii have only recently been reported . we describe a novel c. neoformans c. gattii hybrid strain ( serotype ab ) that was previously described as c. gattii and that caused a lethal infection in an aids patient from canada ." } ]

[ { "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 population , from a myriad of islands both us governed ( e.g. , the state of hawaii and us territories , including american samoa , guam , commonwealth of the northern mariana islands ) and sovereign nations ( e.g. , fiji , federated states of micronesia , palau , papua new guinea , samoa , tonga ) , are often aggregated with asian americans , but are a distinct set of communities with different cultural norms , access to health , and health challenges . hepatitis b virus ( hbv ) infection , and the health problems associated with this ( including but not limited to liver conditions such as cirrhosis and hepatocellular carcinoma ) are highly prevalent among asians / pacific islanders ( apis ) in the us , and chronic hbv infection is endemic in the pacific islands . however , most studies on api populations tend to focus more on asians with less attention paid to pacific islanders , leading to an urgent need to examine the knowledge among us pacific islanders about hepatitis b transmission and testing behavior . in this paperwe analyze the results of a recent community needs assessment survey of a convenience sample of pacific islanders in southern california to investigate the associations among information sources , trust in sources , and self - reported hbv screening / testing and vaccination behavior . though respondents largely reported that they were screened and vaccinated for hbv because of recommendations by their physicians , and that if they had not been screened and vaccinated for hbv , they would seek screening vaccination on advice from their physicians , multivariate logistic regression analysis of the survey results suggest that obtaining information from and trust in physicians were not significant predictors of hbv screening or vaccination . instead , for those respondents who sought screening / testing or vaccination for hbv , significant factors included employment status and lack of knowledge about hbv . to present these findings , the paper proceeds in the following manner . first , we describe the data and methods used , including a description of the convenience sample and a comparison of this sample to us census data on the pacific islander population in southern california . we then provide descriptive analysis of pacific islander respondents knowledge about hbv transmission , questions about which sources of health information would lead respondents to be screened and vaccinated for hbv , and trusted health information sources . next , we present the results of multivariate logistic regression analysis of self - reported hbv screening and vaccination behavior . these results show that while respondents tend to report that physicians provide information and are highly trusted by these respondents as sources of information , information from and trust in physicians are not significant predictors of variations in self - reported hbv screening and vaccination . we conclude the paper with implications from this analysis for enhancing hbv screening and vaccination among pacific islanders in southern california , and elsewhere . a community needs assessment survey of pacific islander communities in the counties of los angeles , orange , and san diego in southern california was conducted to measure hepatitis b ( hbv ) knowledge , screening / testing , and vaccination , and trusted sources of health information . a survey questionnaire developed originally by the b free ceed at the center for the study of asian american health , new york university school of medicine ( originally designed for surveys of asian immigrants in new york city ) was revised by several of the co - authors to be more culturally appropriate for southern californian pacific islanders . in november 2008 , the center for the study of asian american health at nyu school of medicine reviewed the adapted questionnaire , and made additional suggestions , including deleting several questions . there were four english versions created of the survey questionnaire that targeted , respectively , chamorro , samoan , tongan , and other pacific islander respondents . the english versions targeting chamorro and samoan respondents were translated into chamorro and samoan by several of the co - authors , and backtranslated into english . the two english versions ( original and back - translated ) were compared by one of the co - authors ; minor revisions were made to the translated chamorro and samoan versions to improve clarity . the english and translated versions were pilot tested in late november 2008 with a total of 21 chamorros , 1 samoan , and 1 native hawaiian ; again , minor revisions were made to improve clarity . the questionnaires were copied such that both the english and in - language versions were included in all questionnaires ( english version on front and in - language version on back of each page ) . respondents could therefore complete the questionnaire entirely in english , entirely in - language , or could move between the two depending on the respondent s preferences . several of the co - authors distributed and collected the questionnaires from mid - february to mid april 2009 at community / church meetings , cultural gatherings , and other community venues in los angeles , orange , and san diego counties . to minimize potential respondent bias , individuals were asked to complete the self - administered questionnaire and deposit the completed questionnaire in a sealed box .1 each respondent was given a $ 5 gift card as an incentive for completing the questionnaire . the characteristics of the respondents overall and comparison to 20052007 public data microdata sample data2 are listed in the table 1 . compared to the pums sample , the convenience sample was more female , had lower annual household income , had larger household sizes , and was less often employed.table 1sample characteristics compared to 20052007 pumsdemographic or health variablerespondent characteristics ( n = 297 ) comparison to 20052007 pums ( n = 616 ) ethnic background51 % samoan53 % samoan49 % chamorro47 % chamorrogender55 % female49 % female44 % male51 % maleageaverage = 40 yearsaverage = 38 yearsrange : 1682 yearsrange = 1682 yearsplace of birth45 % california46 % california27 % guam18 % guam14 % american samoa10 % american samoa4 % samoa / western samoa8 % western samoanumber of years in us ( for immigrants only ) mean = 29 yearsmean = 28 yearsrange = 455 yearsrange = 455 yearsenglish language capacity62 % speak english fluently80 % speak english fluently24 % speak english very well8 % speak english wellpacific islander language capacity27 % speak pacific islander language fluently9 % speak chamorro / guamanian13 % speak very well27 % speak samoan11 % speak not at all45 % speak only englishmarital status43 % married51 % married31 % single or never married37 % single or never married10 % divorced or separated9 % divorced or separatedhealth insurance17 % no insurancen / aeducation9 % elementary school15 % elementary school8 % junior high school4 % junior high school51 % high school or ged28 % high school or ged 11 % tech / vocational school20 % some college19 % college or university graduate10 % junior college / college graduateemployment status63 % full / part time employed89 % full / part time employed19 % unemployed11 % unemployedhousehold sizeaverage : 5.6 average : 4.9 range : 140 personsrange : 112household members younger than 18average : 1.9 average : 0.85 range : 013 household members 18 yearsrange : 06 own children presenthouseholdcomposition95 % family99 % family or sub - familyapproximate total household income during last year5 % less than $ 10,0002 % less than $ 10,0007 % $ 10,000 $ 19,9995 % $ 10,000 $ 19,99917 % $ 20,000 $ 29,9999 % $ 20,000 $ 29,99912 % $ 30,000 $ 39,9996 % $ 30,000 $ 39,9997 % $ 40,000 $ 49,9998 % $ 40,00 $ 49,99928 % $ 50,000 or more70 % $ 50,000 or more24 % not sure / do nt know sample characteristics compared to 20052007 pumsa survey questionnaire developed originally by the b free ceed at the center for the study of asian american health , new york university school of medicine ( originally designed for surveys of asian immigrants in new york city ) was revised by several of the co - authors to be more culturally appropriate for southern californian pacific islanders . in november 2008 , the center for the study of asian american health at nyu school of medicine reviewed the adapted questionnaire , and made additional suggestions , including deleting several questions . there were four english versions created of the survey questionnaire that targeted , respectively , chamorro , samoan , tongan , and other pacific islander respondents . the english versions targeting chamorro and samoan respondents were translated into chamorro and samoan by several of the co - authors , and backtranslated into english . the two english versions ( original and back - translated ) were compared by one of the co - authors ; minor revisions were made to the translated chamorro and samoan versions to improve clarity . the english and translated versions were pilot tested in late november 2008 with a total of 21 chamorros , 1 samoan , and 1 native hawaiian ; again , minor revisions were made to improve clarity . the questionnaires were copied such that both the english and in - language versions were included in all questionnaires ( english version on front and in - language version on back of each page ) . respondents could therefore complete the questionnaire entirely in english , entirely in - language , or could move between the two depending on the respondent s preferences . several of the co - authors distributed and collected the questionnaires from mid - february to mid april 2009 at community / church meetings , cultural gatherings , and other community venues in los angeles , orange , and san diego counties . to minimize potential respondent bias , individuals were asked to complete the self - administered questionnaire and deposit the completed questionnaire in a sealed box .1 each respondent was given a $ 5 gift card as an incentive for completing the questionnaire . the characteristics of the respondents overall and comparison to 20052007 public data microdata sample data2 are listed in the table 1 . compared to the pums sample , the convenience sample was more female , had lower annual household income , had larger household sizes , and was less often employed.table 1sample characteristics compared to 20052007 pumsdemographic or health variablerespondent characteristics ( n = 297 ) comparison to 20052007 pums ( n = 616 ) ethnic background51 % samoan53 % samoan49 % chamorro47 % chamorrogender55 % female49 % female44 % male51 % maleageaverage = 40 yearsaverage = 38 yearsrange : 1682 yearsrange = 1682 yearsplace of birth45 % california46 % california27 % guam18 % guam14 % american samoa10 % american samoa4 % samoa / western samoa8 % western samoanumber of years in us ( for immigrants only ) mean = 29 yearsmean = 28 yearsrange = 455 yearsrange = 455 yearsenglish language capacity62 % speak english fluently80 % speak english fluently24 % speak english very well8 % speak english wellpacific islander language capacity27 % speak pacific islander language fluently9 % speak chamorro / guamanian13 % speak very well27 % speak samoan11 % speak not at all45 % speak only englishmarital status43 % married51 % married31 % single or never married37 % single or never married10 % divorced or separated9 % divorced or separatedhealth insurance17 % no insurancen / aeducation9 % elementary school15 % elementary school8 % junior high school4 % junior high school51 % high school or ged28 % high school or ged 11 % tech / vocational school20 % some college19 % college or university graduate10 % junior college / college graduateemployment status63 % full / part time employed89 % full / part time employed19 % unemployed11 % unemployedhousehold sizeaverage : 5.6 average : 4.9 range : 140 personsrange : 112household members younger than 18average : 1.9 average : 0.85 range : 013 household members 18 yearsrange : 06 own children presenthousehold composition95 % family99 % family or sub - familyapproximate total household income during last year5 % less than $ 10,0002 % less than $ 10,0007 % $ 10,000 $ 19,9995 % $ 10,000 $ 19,99917 % $ 20,000 $ 29,9999 % $ 20,000 $ 29,99912 % $ 30,000 $ 39,9996 % $ 30,000 $ 39,9997 % $ 40,000 $ 49,9998 % $ 40,00 $ 49,99928 % $ 50,000 or more70 % $ 50,000 or more24 % not sure / do nt know sample characteristics compared to 20052007 pumsrespondents were asked questions about hbv transmission and ethnic group prevalence to assess their knowledge , about whether they had been advised or referred for hbv screening / testing and vaccination , and their self assessment of risk of hbv transmission ( table 2 ) . a large proportion of respondents ( 63 % ) reported that they had heard of hbv , however , over half reported that they did not know which ethnic group ( s ) tends to most commonly have hbv . there also appears to be some confusion among respondents between hbv and hepatitis a ; 30 % of respondents , for example , reported that hbv could be transmitted by eating unclean food , 26 % reported that hbv could be transmitted via sharing food with an infected person and 21 % reported that hbv could be transmitted via sharing utensils or chopsticks ( these are transmission modes for hepatitis a ) . table 2knowledge of hepatitis b virus transmissionknowledge variableresponseheard of hepatitis b ( n = 289 ) 63 % yes23 % no14 % do nt knowin your opinion , in which ethnic group is hepatitis b most common ? ( n = 283 ) 3 % white8 % black1 % hispanic / latino4 % asian americans4 % pacific islanders24 % all equally common56 % do nt knowin your opinion , hepatitis b can be transmitted by : ( n = 250 ; more than one answer possible ) 63 % unprotected sex63 % using contaminated needles61 % contact blood or bodily fluids from an infected person38 % an infected mother to her baby at the time of delivery30 % heredity30 % eating unclean food26 % sharing food with an infected person21 % sharing utensils / chopsticks19 % kissing6 % other ( le ilor , raw food , ti utungo , toilet seat ) knowledge of hepatitis b virus transmission between 61 and 63 % of the respondents reported correctly that hbv could be transmitted via contact with blood or bodily fluids from an infected person , via unprotected sex , or via contaminated needles . of the total sample , 53 ( 19 % ) reported that they had been screened for hbv , and 61 ( 21 % ) reported that they had been vaccinated for hbv . these are much lower rates than reported in a recent study of cambodian and vietnamese americans drawing from the annual reach 2010 risk factor surveys . sizable proportions of respondents reported that they had not ever been told that they should be screened for hbv ( 40 % ) or that they had never heard of hbv before participating in this community needs assessment survey ( 26 % ) . of the one - third of total respondents who had been told that they should be screened for hbv , most had been advised to do so by a doctor and most of those respondents had been screened or tested for hbv ( though about 16 % of this group did not know or were unsure if they had been tested ) . the 40 % of the total respondents who reported that no one had suggested that they be screened for hbv indicated varying reasons for not being screened . the most common reasons were lack of knowledge , feeling well , not being suggested by a doctor , and not knowing where to get screened . similar patterns were exhibited concerning whether respondents were ever told that they should be vaccinated for hbv . about one - third of the respondents ( 36 % ) reported that they had been told that they should obtain a vaccination for hbv , while 39 % reported that they had not ever been told to obtain a hbv vaccination , and 25 % reported that they had never heard of hbv before participating in this community needs assessment survey . for the 36 % of the respondents who had ever been told that they should obtain a hbv vaccination , almost all of the respondents ( 87 % ) were told to do so by a doctor , and about two - thirds of those respondents reported that they had been vaccinated for hbv . for the 39 % of the respondents who reported not ever having been told to obtain an hbv vaccination , the most common reasons for not getting vaccinated included lack of knowledge and feeling well . over half ofthe respondents believed that they were not infected with hbv , but 41 % reported that they did not know ( 6 % believed that they might be infected ) ( table 3 ) . over three quarters of the respondents reported that they had not ever been diagnosed with hbv , but 21 % reported that they did not know or were not sure if they had ever been diagnosed with hbv . the most important influence appeared to be physicians recommendations ; almost two - thirds of the respondents reported that if a doctor recommended that the respondent be screened , then this would influence that respondent to obtain hbv screening and vaccination.table 3hepatitis b risk and most influence in screening / vaccinationawareness variableresponsewhat influenced or would influence you to get hepatitis b screening and vaccination ? ( n = 252 ) 64 % doctor told you to get screened35 % family member is a carrier34 % free screening / vaccination or if covered by insurance32 % fear of being infected by the virus31 % encouraged by family members28 % attended hepatitis b educational workshop22 % encouraged by spouse21 % encouraged by friends9 % other ( bakura , teacher , employer , galuega , travel ) do you think you could be infected with hepatitis b ? ( n = 280 ) 6 % yes52 % no41 % not sure / do nt knowhave you ever been diagnosed with hepatitis b infection ? ( n = 280 ) 1 % yes78 % no21 % not sure / do nt knowtotal percentages may add up to more than 100 % as respondents were asked to list all that apply ; the only responses that were highly correlated ( using pearson correlation coefficient ) were being encouraged by friends and family members hepatitis b risk and most influence in screening / vaccination total percentages may add up to more than 100 % as respondents were asked to list all that apply ; the only responses that were highly correlated ( using pearson correlation coefficient ) were being encouraged by friends and family membersrespondents were asked to indicate whether they had obtained information about health and health care from varied provider and community sources . the results are reported here by source , and then by utilization , and degree of trust depending on whether they had whether they had obtained information from specific sources ( table 4 ) . table 4health information sources and trust ( ranked by sources used by respondents ) information sourcereported getting information from this sourcereported not getting information from this sourcephysician / health care provider ( n = 275 ) 79 % yes21 % nofor respondents who answeredyesfor respondents who answered no 89 % used source in past year 51 % trusted information from this source 97 % trusted information from this sourcepharmacists ( n = 284 ) 53 % yes47 % nofor respondents who answered90 % used source in past year 31 % trusted information from this source 97 % trusted information from this sourcefamily members ( n = 280 ) 48 % yes52 % nofor respondents who answered yesfor respondents who answered no89 % used source in past year 25 % trusted information from this source 83 % trusted information from this sourcecommunity functions or health fairs ( n = 287 ) 46 % yes54 % nofor respondents who answeredyesfor respondents who answered no 84 % used source in past year 24 % trusted information from this source 92 % trusted information from this sourcechurch , spiritual or religious leaders ( n = 289 ) 31 % yes69 % nofor respondents who answered yesfor respondents who answered no 83 % used source in past year 18 % trusted information from this source 94 % trusted information from this sourcefriends ( n = 292 ) 29 % yes71 % nofor respondents who answeredyesfor respondents who answered no 87 % used source in past year 13 % trusted information from this source 91 % trusted information from this sourceemployee assistance programs ( n = 288 ) 26 % yes74 % nofor respondents who answeredyesfor respondents who answered no 90 % used source in past year 18 % trusted information from this source 97 % trusted information from this sourceco - workers ( n = 290 ) 20 % yes80 % nofor respondents who answered yesfor respondents who answered no 77 % used source in past year 14 % trusted information from this source 84 % trusted information from this sourcetraditional healers ( n = 283 ) 17 % yes83 % nofor respondents who answeredyesfor respondents who answered no 69 % used source in past year 16 % trusted information from this source 85 % trusted information from this sourcetelephone advice lines ( n = 288 ) 8 % yes92 % nofor respondents who answeredyesfor respondents who answered no 71 % used source in past year 13 % trusted information from this source 96 % trusted information from this source health information sources and trust ( ranked by sources used by respondents ) respondents reported most often that they had obtained health and health care information from the following sources : physicians / health care providers ( 79 % reported that they had obtained information ) , pharmacists ( 53 % reported that they had obtained information ) , family members ( 48 % reported that they had obtained information ) , and community functions or health fairs ( 46 % reported that they had received information ) . respondents reported less often obtaining information from church , spiritual , or religious leaders ( 31 % reported obtaining information ) , friends ( 29 % reported obtaining information ) , employee assistance programs ( 26 % reported obtaining information ) , co - workers ( 20 % reported obtaining information ) , traditional healers ( 17 % reported obtaining information ) , and telephone advice lines ( 8 % reported obtaining information ) . respondents who reported that they had obtained information from each of the sources also tended to report that they had used the source in the past year and trusted the information from that source . not surprisingly , respondents who reported that they had not used each of the sources less often reported that they trusted information from that source . similar to the results reported in the earlier section on the descriptive statistics on hbv knowledge , screening / testing , and vaccination , health care providers ( including physicians and pharmacists ) also appeared to be sources of information that these respondents would trust . in the following section , multivariate analyses are presented to ascertain socio - demographic or hbv knowledge association with trust in health information sources . logistic regression models were estimated for the binary dependent variables measuring self - reported hbv screening / testing and vaccination behavior to ascertain how important sources of information , and trust in those sources , were when controlling for socio - demographic and health coverage characteristics , and hbv transmission knowledge . the dependent variables ( whether respondents were screened for hbv and whether respondents were vaccinated for hbv ) only included those respondents who had ever been told that they should be screened or vaccinated for hbv . in other words , those respondents who had never been told they should be screened or vaccinated for hbv ( 40 % ) or who had never heard of hbv ( 26 % ) prior to completing the survey were not included in this analysis . though the resulting sample was smaller , it did provide the opportunity to assess the possible connections between screening / testing and vaccination self - reported behavior and other variables . to construct the logistic regression models , chi - square tests were conducted of the dependent variables ( respondent had been screened / tested for hbv , respondent had been vaccinated for hbv ) using each set of variables ( socio - demographic characteristics , health coverage , sources of health information , trust in health information sources , hbv transmission knowledge ) . only those variables that were statistically significant at the p 0.05 level or better were retained for additional analysis . pairwise pearson correlation coefficients were calculated to ensure that the independent variables were not highly correlated . using this variable screening process , the variables associated with physicians as sources of health information and trust associated with this health source were not retained ( i.e. , neither of these variables were significant at least at the p 0.05 level for either of the two dependent variables ) . this suggested that while a very large proportion of respondents reported that they received health information from their physicians , and that they trusted this source , this had little explanatory power with respect to hbv screening / testing or vaccination for those respondents who had been informed that they should be screened or vaccinated for hbv . as the number of observations in each of the models was relatively small ( n = 63 for the model for hbv screening / testing , and n = 78 for hbv vaccination ) , the results should be viewed as suggestive rather than conclusive . table 5 shows the results for a logistic regression model of hbv screening / testing for those respondents who had been informed that they should be screened for hbv . two sets of variables were retained for the model after chi - square and pearson correlation tests were conducted : socio - demographic and medical coverage characteristics , and information sources . two variables were statistically significant at least at the p 0.05 level in explaining the variation in having been screened / tested for hbv : being currently employed and getting health and health care information from friends . the results indicated that full - time employed respondents who have been informed that they should be screened / tested for hbv were over 6 times more likely to have been screened or tested for hbv compared to respondents who had been informed that they should be screened / tested for hbv but who did not report being full time workers ( e.g. , part time workers , retired , unemployed ) . in terms of health information sources , respondents who reported that they received health and health care information from their friends and who had been informed that they should be screened / tested for hbv were over 7 times more likely to also report that they had been screened or tested for hbv compared to respondents who had been informed that they should be screened / tested for hbv , but who did not report that they had received information about health or health care from their friends.table 5logistic regression results for hepatitis b screening / testing ( n = 63 ) variable ( bolded variables are statistically significant at least at p 0.05 ) odds ratiosezp | z | 95 % confidence intervaldemographics / medical coveragehas medicare coverage ( 1 = yes , 0 = no ) 0.320.291.270.200.061.86 highest grade of school completed ( 1 = elementary school , 6 = post - graduate school ) 1.590.531.390.160.833.07 currently employed full time ( 1 = yes , 0 = no ) 6.355.931.980.051.0239.60 currently retired ( 1 = yes , 0 = no ) 7.4210.191.460.150.50109.47 information sourcesgets information about health and health care from friends ( 1 = yes , 0 = no ) 7.677.981.960.051.0058.92 gets information about health and health care from the internet ( 1 = yes , 0 = no ) 1.751.630.590.550.2810.94 gets information about health and health care from pacific islander organizations ( 1 = yes , 0 = no ) 4.063.871.470.140.6326.24 model goodness of fit measureslr chi2 ( df = 7 ) 21.11 prob chi20 .01 pseudo r20 .33 log likelihood21 .52 logistic regression results for hepatitis b screening / testing ( n = 63 ) table 6 shows the results of the multivariate logistic regression model for the dependent variable measuring self - reports of vaccination for hbv ( only including those respondents who reported that they had been informed that they should be vaccinated ) . the only demographic or medical coverage variable that was a significant predictor of whether respondents reported that they had been vaccinated for hbv was whether the respondent reported being covered by medicare ; those who reported being covered by medicare were 0.02 times as likely as respondents who did not report that they were covered by medicare to also report that they had been vaccinated for hbv .3 table 6logistic regression results for hepatitis b vaccination ( n = 78 ) variable ( bolded variables are statistically significant at least at p 0.05 ) odds ratiosezp | z | 95 % confidence intervaldemographics / medical coveragehas medicare coverage ( 1 = yes , 0 = no ) 0.020.023.240.0010.000.21 highest grade of school completed ( 1 = elementary school , 6 = post - graduate school ) 1.040.300.130.900.591.81 currently employed part time ( one part time position ) ( 1 = yes , 0 = no ) 0.290.251.410.160.051.62 currently retired ( 1 = yes , 0 = no ) 4.045.461.030.300.2957.03 hepatitis b knowledgein your opinion , hepatitis b can be transmitted by eating unclean food ( 1 = true , 0 = false ) 8.347.662.310.021.3850.46 information sourcesgets information about health and health care from the employee assistance program ( 1 = yes , 0 = no ) 0.120.092.760.010.030.54 gets information about health and health care from social service provider or community health center ( 1 = yes , 0 = no ) 0.710.530.460.640.173.03 model goodness of fit measureslr chi2 ( df = 7 ) 35.32 prob chi20 .01 pseudo r20 .40 log likelihood26 .74 logistic regression results for hepatitis b vaccination ( n = 78 ) there is one hbv transmission knowledge question that was significant at least at the p 0.05 level ; responding that hepatitis b could be transmitted by eating unclean food ( an incorrect response ) was associated with also reporting being vaccinated for hbv . in other words , contrary to most interventions that might presume that more and better knowledge leads to protective and health promoting behavior , this result suggested that not understanding how hbv is transmitted ( i.e. , confusing hbv with hepatitis a ) was related to higher likelihood of being vaccinated for hbv . those who answered this question incorrectly were over 8 times more likely to report that they had been vaccinated for hbv compared to respondents who answered this question correctly . similar to the model presented previously on self - reported hbv screening / testing behavior , being employed again appeared to be important in explaining the variation in self - reported vaccination for hbv , however , in this model , employment had a negative association . obtaining information about health and health care from employee assistance programs was negatively associated with hbv vaccination for those respondents who had been informed that they should be vaccinated for hbv . in this paper , results were presented of an analysis of a recent community needs assessment survey of a convenience sample of pacific islanders in southern california . because this was a convenience sample and , in addition , because the multivariate analysis used a small subsample of the total sample , the results must be viewed as suggestive rather than conclusive . the findings indicated that though pacific islander respondents reported that physicians and pharmacists , i.e. , health care providers , were the most trustworthy and commonly used source of health care information and advice , when multivariate analysis was conducted to explain the variation in self - reported hbv screening / testing and vaccination behavior , trust in and use of physicians for health care information was not statistically significant . instead , the factors that were important in explaining hbv screening / testing for respondents who had been told that they should be screened or tested for hbv included being currently employed and receiving health and health care information from friends . being employed and receiving health and health care information from friends were both associated with much higher likelihoods of being screened or tested for hbv , compared to respondents who were not currently employed or who did not receive health information from friends . the factors that were important in explaining self - reported hbv vaccination behavior were different from those explaining the variation in hbv screening / testing . not being covered by medicare , having incorrect knowledge about hbv transmission ( confusing hbv with hepatitis a ) , and not receiving information from employee assistance programs were associated with self - reported hbv vaccination . these results were somewhat counterintuitive , as more and correct information is usually presumed to result in enhanced screening and health care access . these findings suggested that though these respondents viewed physicians and pharmacists positively , and a large proportion reported that they obtained health care information from health care providers , that other factors ( demographic , knowledge , and information source ) were more important in explaining hbv screening and vaccination behavior . one possible interpretation of these findings is that health recommendations for hbv screening and vaccination may need to come from physicians , who are highly trusted sources , but that additional motivations ( information from friends ) or opportunities for access to health care ( being full time employed , presumably with health care benefits ) may also be necessary to expand the number of pacific islanders who are screened and vaccinated for hepatitis b. additional research is needed to ascertain whether these findings hold for other pacific islander groups in california , nationally , and on the island jurisdictions .\noutput:\n" }, { "from": "agent", "value": "we measured hepatitis b virus ( hbv ) transmission knowledge and self - reported screening / testing behavior among pacific islanders ( guamanians / chamorros , samoans , and tongans ) in southern california . we also examined access and trust by pacific islanders of varying health information sources . we administered and analyzed survey data ( n = 297 ) , using a convenience sample in los angeles , orange , and san diego counties in spring 2009 . we found that while pacific islander respondents reported that they receive health information from physicians , and largely trust this source , information from and trust in physicians were not statistically significant in explaining whether respondents sought hbv screening or vaccination ." } ]

[ { "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: bacille calmette guerin ( bcg ) vaccination is recommended under expanded program for immunization by world health organization at birth in developing countries . it is a live vaccine which is contraindicated in immunodeficiency states like acquired immunodeficiency syndrome ( aids ) and severe combined immunodeficiency disease ( scid ) . skin manifestations in disseminated bcg lesions in infants with scid have been reported in the past . we report disseminated bcg vaccine disease with skin lesions in one of the twins suffering from scid . a 7 - month - old first born male twin infant , adopted by his uncle , presented with loose stools for 3 days in a private clinic . after 48 hours loose stools improved but he developed fever , cough and fast breathing . a diagnosis of viral or nosocomial infection was made and child was transferred to pediatric intensive care unit . the child was brought back to the clinic after 3 days with history of fever , cough , fast breathing and skin rashes . past medical history revealed frequent infections since birth , including episode of documented rota virus diarrhea , bronchiolitis and oral thrush . he was an adopted child from his paternal uncle and product of in vitro fertilization and twin gestation ( first twin ) . the infant was on formula feeds and few sessions of breastfeeding daily by his biological mother since birth who was living in the same premises . infant received hepatitis b , bcg and oral polio vaccine ( opv ) vaccine at birth followed by three doses of dpt , hepatitis b and opv at 6 , 10 and 14 weeks age . on examination child had fever ( 102f ) , respiratory rate 56 breaths per minute , mild pallor , oral thrush and red to purple , papulo - nodular , fixed and non - itching subcutaneous lesions , 0.5 - 2 cm in size , over neck , back and abdomen [ figure 1a ] . the differential diagnosis for the rash was drug reaction , panniculitis and vitamin k - dependent bleeding ( vkdb ) from prolonged use of broad spectrum antibiotics . a skin biopsy was taken from three sites . an abnormal prothrombin time ( pt ) 16 sec ( 12 sec control ) suggested vkdb and was treated with vitamin k ( 5 mg intravenously for 3 days ) . investigations showed anemia ( hb 10.0 g / dl ) , positive c - reactive protein ( 8 mg / dl ) , and normal total leukocyte count ( 6200 cells / mm : neutophils 42 % , lymphocytes 48 % , monocytes 9 % , eosinophils 1 % , basophils 0 ) , platelets ( 28010 / mm ) and sterile blood and urine cultures . in view of non - improvement andpersistent pneumonitis after 72 hours of intravenous antibiotics and supportive treatment ( repeat chest x - ray revealed bilateral infiltrates ) infant was investigated for tuberculosis . mantoux test was non - reactive and gastric aspirates were negative for acid fast bacilli . a skin biopsy showed sheets of macrophages with neutrophilic micro abscess ; species stain was acid fast bacilli ( afb ) strongly positive ( 6 + ) with infiltrate of macrophages laden with bacilli ( globii ) [ figure 1b ] . a diagnosis of disseminated tuberculosis was made and antitubercular therapy ( isoniazid , rifampicin , pyrazinamide and ethambutol ) with prednisolone ( 2 mg / kg ) was started . skin lesions in infant modified ziehl nelson staining of skin biopsy revealed numerous acid fast bacilli with globi formation . zn stain 400 in view of non - resolving pneumonia , lymphopenia ( 2976 / mm ) and history of recurrent past infections immunodeficiency was suspected . an immunological profile showed low immunoglobulins , normal b lymphocytes and decreased t cells and natural killer ( nk ) cell counts [ table 1 ] suggestive of scid . a skin biopsy was sent for culture and polymerase chain reaction ( pcr ) analysis . culture rapid ( automated bact alert 3 d system ; biomerieux , france ) after 3 weeks was positive for acid fast bacilli and immune chromatographic test mpt64 implying mycobacterium tuberculosis complex ( mtb ) which was further confirmed by oligonucleotide probe liquid hybridization protection assay ( accuprobe , genprobe , sa ) . pyrazinamidase screening results showed resistance , and further molecular typing and biochemical tests confirmed mycobacterium bovis . the infant deteriorated and on day 10 of admission , was put on mechanical ventilator and died after 5 days . family was counseled and the mother and another twin offered to be screened for immunodeficiency . there was no history of recurrent infections and failure to thrive in parents or other twin . the facial features and blood groups of both the twins were different suggesting dizygosity . immunological profile of the infantdisseminated bcg disease is a rare complication ( approximately 1 / million ) of bcg vaccination in immunocompetent children . talbot et al . and loette et al . have reported the occurrence of disseminated bcg disease in 86 % and 100 % children with immune defects , respectively . disseminated bcg disease generally manifests as fever , malnutrition , and pneumonitis 3 - 6 months after receiving bcg vaccination . skin manifestations like subcutaneous nodules , rash , ulcers , and erythema in scid infants with disseminated bcg disease have been reported by some authors . more than 30 genetic defects are known in scid which may be inherited as x - linked recessive or autosomal recessive . x - linked scid in 50 % and adenosine deaminase ( ada ) deficiency ( autosomal recessive ) in 15 - 20 % cases of scid are most common disorders . unless treated scid is uniformly fatal in first 2 years of life . disseminated bcg infection also carries very high fatality ( 1 ) in children with scid . routine newborn screening by t - cell receptor excision circles ( trecs ) by pcr , using dna extracted from newborn dried blood spots ( guthrie cards ) , has been recently implemented in wisconsin ( usa ) . as routine bcg vaccinationis recommended at birth to all newborns in most developing countries and children with immunodeficiency are symptomatic afterwards , most of these children remain at risk of fatal disseminated bcg disease .\noutput:\n" }, { "from": "agent", "value": "fatal - disseminated bacillus calmette guerin ( bcg ) disease is well known in infants with severe combined immunodeficiency after bcg vaccination . we report a 7 month male infant delivered as a product of in vitro fertilization and twin gestation that presented with fever , cough and multiple nodular skin lesions . a biopsy of skin lesions revealed the presence of acid fast bacilli . mycobacterium bovis infection was confirmed by polymerase chain reaction ( pcr ) and molecular studies . immunological profile confirmed the diagnosis of severe combined immunodeficiency . only few reports of similar case exist in the 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: multifocal motor neuropathy ( mmn ) and chronic inflammatory demyelinating polyradiculoneuropathy ( cidp ) are acquired immune - mediated peripheral neuropathies ( pn ) . mmn is a pure motor neuropathy syndrome usually beginning in one or both hands and principally affecting the upper extremities , characterized by a chronic or stepwise progressive asymmetrical limb weakness and muscle atrophy . cidp is an immune - mediated peripheral neuropathy that may cause weakness , paralysis , and / or impairment in both motor and sensory functions , usually affecting both sides of the body ( symmetrical ) . the neurophysiological hallmark of mmn is conduction blocks ( cb ) outside the usual sites of nerve compression , while cidp typical features are cb , slowed motor , and sensory nerves conduction velocities and prolonged distal latencies . in addition , both diseases may present a variable extent of axonal loss , which has been attributed both to recurrent demyelinating insults and intrinsic pathogenic features , especially in the case of mmn . neuromuscular ultrasound ( us ) is a noninvasive , painless , and radiation - free complementary imaging technique for the diagnostic work - up of pn . focal nerve enlargements can be observed in the majority of mmn patients and generalized nerve enlargements can be observed in cidp patients , interestingly showing alterations also in limbs without signs of neurophysiological dysfunction . however , the correlation between us , neurophysiological findings , and functional disability is still partially controversial . some authors have found an association between disease duration and the extent of nerve enlargement , while others have suggested a specific us pattern in relation to different mechanisms of injury : demyelinating insults might result in swollen , enlarged , and hypoechoic nerves , while axonal damage may be characterized by hyperechoic atrophic bundles of fascicles . in addition , a variable combination of axonal and demyelinating insults may also coexist , resulting in hyperechoic and hypertrophic nerves . most of literature data have been collected on cidp patients , while a few sonographic - clinical - electrophysiological studies have been currently reported in mmn . the aim of this study is to analyze us findings in patients with cidp and mmn at different functional disability , in order to correlate us qualitative and quantitative measures with clinical and neurophysiological features . this cross - sectional observational study includes 22 cidp ( 5 females ; 17 males ) and 10 mmn ( 4 females ; 6 males ) patients recruited from the neuromuscular unit of turin university hospital between may 2014 and may 2015 and 70 healthy controls ( 43 men and 27 women ) . patients were evaluated by means of a clinical , us , electrophysiological assessment , and a structured clinical interview . all subjects fulfilled the european federation of neurological society / peripheral nerve society ( efns / pns ) criteria for cidp or mmn and , at the time of us examination , were receiving a monthly treatment with intravenous immunoglobulin ( ivig ) ( 1 - 2 g / kg / month ) for at least 6 months . written informed consent and local ethical committee ( aou san giovanni battista di torino ) approval were obtained . the authors acted in accordance with the ethical standards laid down in the 1964 declaration of helsinki . a complete neurological examination was performed by means of the inflammatory neuropathy cause and treatment ( incat ) disability scale , the medical research council ( mrc ) score in 8 muscle groups bilaterally ( shoulder abduction , elbow flexion , wrist flexion , first dorsal interosseous , hip flexion , knee extension , and ankle flexion / extension ) , and the overall neuropathy limitation scale ( onls ) . according to the incat disability scale , upper limb activities were scored as no / minimal impairment ( not affected ) , moderate impairment ( affected but not prevented ) , or severe impairment ( prevented ) , while the evaluation of walking difficulties was based on the use of aids : no / minimal impairment ( moderate gait impairment , independent or with unilateral support ) ; severe impairment ( severe gait impairment , bilateral supports or wheelchair ) . the us assessment was performed by means of a sonosite m - turbo ultrasound machine equipped with a broadband linear transducer ( frequency band 615 mhz ) . the us scan was performed the same day of the neurological assessment by an evaluator ( michela rosso ) , who was blinded to the clinical and neurophysiological data . the following quantitative and qualitative us parameters were collected for the median , ulnar , peroneal , tibial , and sural nerves bilaterally . csa was measured by tracing the nerve just inside the hyperechoic rims with the ellipse method when applicable ( when the nerve in the transverse scan had an elliptical or roundish shape ) or alternatively tracing the nerve shape ( when the nerve had an irregular shape ) . csa was evaluated for each nerve at predetermined sites : median nerve was evaluated at wrist ( entrance of carpal tunnel ) , middle third of the forearm , elbow ( before penetrating the pronator teres muscle next to the brachial artery ) , and middle third of the arm ( middle of the distance between medial epicondyle and axillary fossa ) ; ulnar nerve at wrist ( guyon 's canal ) , middle third of the forearm , elbow ( between medial epicondyle and olecranon ) , and middle third of the arm ( middle of the distance between medial epicondyle and axillary fossa ) ; peroneal nerve at the fibular head and popliteal fossa ; tibial nerve at popliteal fossa and at medial malleolus before its division into plantar nerves ( ankle ) ; sural nerve at the ankle . maximal csa ( csa ) enlargement was recorded for each nerve ; median and ulnar nerves were scanned along the entire viewable tract , from the wrist to the middle third of the arm . abnormal csa values at entrapment sites ( wrist , elbow , and fibular head ) were excluded to avoid confounding local neuropathies . intranerve csa variability . intranerve csa variability was calculated as the ratio between csa / csa , for each nerve ( available for median and ulnar nerves ) . side - to - side intranerve variability was calculated as the side - to - side ratio of the intranerve csa variability . qualitative analysis of nerve fascicles . nerves were classified as abnormal if 3 fascicles showed a cross - sectional area 2 mm , regardless of the csa value . normative us reference values were obtained by the assessment of healthy controls ( table 1 ) , considering the upper threshold of the normality range ( ut ) to be the average value + 2 standard deviations . then , in order to compare the csa of different nerves taking into account their relative normative values , a normalized csa ( csa ) was calculated by dividing the csa of each nerve to the corresponding ut value ( csa = csa / csa ) . nerve conduction studies were performed by means of a keypoint ( natus medical incorporated , san carlos , ca , usa ) electromyography ( emg ) machine by evaluators blinded to the us study , assessing the bilateral peroneal , tibial , ulnar , and median motor nerves and the bilateral sural , median , and ulnar sensory nerves . nerve conduction velocities ( cv ) , compound muscle action potentials ( cmap ) , and sensory action potentials ( snap ) were collected and compared to the normality cut - off values of our laboratory ; all patients were checked for skin temperature with a probe on the emg machine . if needed , the body temperature was maintained above + 34c by means of an infrared lamp . cb was defined in accordance with the efns / pns criteria , excluding possible sites of entrapment ( wrist , elbow , and fibular head ) to avoid confounding focal neuropathies . moreover , neurophysiological alterations of nerve segments were stratified in predominantly myelin damage oraxonal damage in accordance with the classification already proposed by di pasquale et al . . descriptive statistics ( mean , standard deviation , and range ) were used for continuous variables . mann - whitney and cramer 's v tests were used for comparison between patients with different disease severity and neurophysiological alterations and between cidp and mmn patients . spearman 's rho , kendall 's tau - b , and pearson 's correlations were used to estimate correlations between clinical , us , and electrophysiological characteristics , while a linear regression model was applied to estimate the influence of age , disease and treatment duration , and ivig doses on csa values . bonferroni 's correction for multiple comparisons was applied to avoid statistical biases of repeated testing effects . the average csa values in bilaterally measured nerves were obtained pooling together data of the two sides . however , in order to take into account the asymmetrical involvement typical of mmn , we also considered the side - to - side intranerve variability , calculated by dividing the intranerve variability of the most affected side with the intranerve variability of the less affected side . complete clinical , us , and neurophysiological data were available for 22 cidp and 10 mmn patients with similar age ( 62.713.8 versus 55.114.9 years old ; p : 0.119 ) and disease duration ( 81.560.0 versus 87.346.6 months ; p : 0.734 ) . us data of 70 healthy controls ( 58.416.1 years old ; range 3082 ) with normal clinical and neurophysiological assessments were used as normative reference values ( table 1 ) . according to the incat disability score ( table 2 ) , 7/32 subjects required a bilateral support / wheelchair ( cidp = 18 % ; mmn = 30 % ) ; 17/32 required a unilateral support ( cidp = 64 % ; mmn = 30 % ) ; and 8/32 did not show any significant impairment of gait ( cidp = 18 % ; mmn = 40 % ) . the upper limbs score showed that 9/32 subjects had a severe impairment in daily living activities ( cidp = 23 % ; mmn = 40 % ) ; 12/32 reported a moderate impairment ( cidp = 41 % ; mmn = 30 % ) ; and 11/32 did not report any significant impairment ( cidp = 36 % ; mmn = 30 % ) . no differences were observed between cidp and mmn patients at the incat ( p : 0.519 ) , onls ( p : 0.724 ) , and mrc ( p : 0.327 ) scores ( table 2 ) . a total of 320 nerves ( 220 cidp and 100 mmn ) were evaluated by means of nerve conduction studies and us assessments : neurophysiological alterations were found in 78.0 % of cidp nerve segments ( predominant myelin damage = 41.6 % ; predominant axonal damage = 36.4 % ) and in 62.5 % of mmn nerve segments ( predominant myelin damage = 35.0 % ; predominant axonal damage = 27.5 % ) . quantitative and / or qualitative us alterations were observed in 43.2 % ( 95/220 ) of cipd nerve segments and in 40.0 % ( 40/100 ) of mmn nerve segments . in both cases these alterationswere found more frequently in nerves with predominantly myelin versus axonal damage ( cidp = 74.6 % versus 25 % [ p : 0.001 ] ; mmn = 78.3 % versus 20 % [ p : 0.010 ] ) . usabnormal features were additionally observed in 14.4 % of cidp and 10.1 % of mmn nerve segments without significant neurophysiological alterations . as shown in figure 1 ( a ) andtable 3 , cidp and mmn patients with intermediate functional disability ( gait disturbance that might require a unilateral support ) showed higher csa values than patients with no / minimal gait difficulties ( p : 0.001 for cidp and p : 0.002 for mmn ) or higher functional disability ( p : 0.041 for cidp and p : 0.034 for mmn ) . moreover , higher csa values were observed ( figure 1 ( c ) ) in nerves with demyelinating features versus axonal damage ( p : 0.048 for cidp and p : 0.049 for mmn ) . the quantitative us analyses showed higher csa in cidp than in mmn patients in peroneal nerve ( 16.813.01 mm versus 13.602.27 mm ; p : 0.024 ) , tibial nerve ( 23.462.23 mm versus 18.642.66 mm ; p : 0.027 ) , and sural nerve ( 3.560.31 mm versus 2.600.49 mm ; p : 0.047 ) . the qualitative us analyses revealed abnormal fascicles in 40 % of mmn versus 22.7 % of cidp peroneal nerve segments ( p : 0.171 ) and in 35 % of mmn versus 15.9 % of cidp tibial nerve segments ( p : 0.087 ) . additionally , a significant correlation was found between abnormal nerve fascicles and cb ( peroneal nerve : tau = 0.411 [ p : 0.015 ] in cidp and tau = 0.302 [ p : 0.046 ] in mmn ; tibial nerve : tau = 0.365 [ p : 0.042 ] in cidp and tau = 0.282 [ p : 0.048 ] in mmn ) and between abnormal nerve fascicles and csa values , both in cidp ( peroneal nerve : rho = 0.329 [ p : 0.033 ] ; tibial nerve : rho = 0.296 [ p : 0.049 ] ) and in mmn ( peroneal nerve : rho = 0.229 [ p : 0.046 ] ; tibial nerve : rho = 0.454 [ p : 0.044 ] ) . median and ulnar nerves csa were significantly higher in patients with moderate impairment compared to subjects with either a more severe functional impairment ( p : 0.037 for cidp and p : 0.047 for mmn ) or milder disability ( p : 0.042 for cidp and p : 0.037 for mmn ) ( table 4 , figures 1 ( b ) and 2 ) . the quantitative us analyses showed higher csa in cidp than in mmn patients in median nerve ( 18.702.30 versus 14.852.58 ; p : 0.042 ) and ulnar nerve ( 13.272.64 versus 10.752.23 ; p : 0.040 ) , while the side - to - side intranerve variability was higher in mmn ( median nerve : 1.90.6 versus 1.50.6 [ p : 0.035 ] ; ulnar nerve : 1.80.4 versus 1.40.4 [ p : 0.007 ] ) ( table 4 ) . the correlation between abnormal fascicles and cb was also confirmed for the upper limbs ( median nerve : tau = 0.310 [ p : 0.046 ] in cidp and tau = 0.213 [ p : 0.045 ] in mmn ; ulnar nerve : tau = 0.260 [ p : 0.049 ] in cidp and tau = 0.271 [ p : 0.048 ] in mmn ) , as was for the correlation between altered fascicles and csa , both in cidp ( median nerve : rho = 0.315 [ p : 0.037 ] ; ulnar nerve : rho = 0.447 [ p : 0.002 ] ) and in mmn subjects ( median nerve : rho = 0.331 [ p : 0.043 ] ; ulnar nerve : rho = 0.564 [ p : 0.001 ] ) . qualitative us analyses showed an inverse pattern compared to that observed at the lower limbs , with a moderately higher prevalence of altered fascicles in cidp than in mmn nerve segments ( median nerve : 38.6 % versus 15 % [ p : 0.059 ] ; ulnar nerve : 36.4 % versus 20 % [ p : 0.194 ] ) . as observed in the lower limbs , the csa values were higher in nerve segments with predominantly demyelinating features versus axonal damage ( p : 0.001 for cidp and p : 0.049 for mmn ) ( figure 1 ( d ) ) . there was a direct correlation between axonal damage and gait impairment at the lower limbs ( cidp : r = 0.456 [ p : 0.002 ] ; mmn : r = 0.450 [ p : 0.036 ] ) and between axonal damage and functional disability at the upper limbs ( cidp : r = 0.402 [ p : 0.001 ] ; mmn : r = 0.325 [ p : 0.047 ] ) . no linear correlations were observed between us data and incat score ( cidp : r = 0.121 [ p : 0.110 ] ; mmn : r = 0.239 [ p = 0.190 ] ) or between us data and onls score ( cidp : r = 0.053 [ p = 0.415 ] ; mmn : r : 0.211 [ p : 0.140 ] ) , while an inverse correlation was observed in cidp patients between mrc scores of muscles innervated by median and ulnar nerves and the corresponding intranerve variability ( table 5 ) . csa values were not influenced by age ( cidp : = 0.141 [ p : 0.456 ] ; mmn : = 0.205 [ p : 0.437 ] ) , disease duration ( cidp : = 0.005 [ p : 0.954 ] ; mmn : = 0.195 [ p : 0.305 ] ) , treatment duration ( cidp : = 0.027 [ p : 0.749 ] ; mmn : = 0.295 [ p : 0.247 ] ) , or ivig dose ( cidp : = 0.023 [ p : 0.809 ] ; mmn : = 0.186 [ p : 0.663 ] ) . this study reports the peripheral nerve us findings of 32 cidp and mmn patients at different functional disabilities . lower csa values were associated with more severe clinical alterations and / or axonal damage , while higher csa values were associated with intermediate functional disability ( clinical alterations without loss of functionality ) and / or demyelinating damage . these data are in accordance with the findings reported by di pasquale et al . , who observed that nerve segments characterized by predominantly myelin damage had greater csa than nerves with predominantly axonal damage and normal nerves , which virtually overlapped . in addition , we found some differential aspects between mmn and cidp : greater side - to - side intranerve variability was observed in mmn , in line with the pattern of heterogeneous and multifocal involvement characteristic of the disease ; patients with cidp showed higher csa values , potentially indicating more prominent demyelinating processes ; qualitative us analyses revealed a different distribution of abnormal fascicles in the upper and lower limbs , with more prominent us alterations in district affected by predominantly demyelinating damage ( frequently associated with a less marked functional impairment ) compared to district affected by secondary axonal degeneration . the majority of literature data reported increased csa values in cidp , with a possible association between intranerve variability and functional scores . less data are available for mmn , where asymmetric and focal csa enlargements have also been reported in nerves without neurophysiological alterations , suggesting disease processes that could extend beyond the sensitivity of standard diagnostic techniques . several complex phenomena , such as segmental demyelination , proliferation of schwann cells in response to repeated inflammatory insults , onion bulbs formation , and a variable degree of axonal loss might underlie these us findings . however , their correlation with the mechanisms of nerve damage and repair still remains to be clarified . our data support the complementary role of us in the assessment of cidp and mmn , suggesting a different pattern in nerves with demyelinating versus axonal damage and in cidp versus mmn patients , in possible relationship with the different pathological processes involved . previous studies reported a correlation between disease duration and csa values , while in our heterogeneous sample of patients we observed awe speculate that different disease phases might be associated with different us patterns , with an initial / intermediate phase of inflammation and myelin damage , characterized by increased csa and enlarged swollen fascicles and a late phase of severe axonal degeneration , characterized by small atrophic fascicles , reduced csa and greater functional impairment . other factors , such as ivig pharmacological treatment and / or individual inflammatory response , might also be implicated in the morphological modifications of peripheral nerves . however , the similar therapeutic regimen ( ivig ) administered to our patients did not allow a post hoc analysis of treatment effects on csa values . finally , patients with cidp , characterized by more prominent inflammatory and demyelinating features , might display greater nerve enlargement compared to mmn or to peripheral neuropathies characterized by primary axonal degeneration ( i.e. , chronic idiopathic axonal polyneuropathy ) . taken together , these findings suggest variable applications for us in the field of immune - mediated peripheral neuropathies , ranging from the more accurate clinicopathophysiologic phenotyping to the early detection of morphological changes associated with critical disease milestones . in additioninnovative us score , such as the bochum ultrasound score , will likely allow a more accurate differentiation between cidp and other acquired or inherited peripheral neuropathies . our findings suggest that cidp and mmn patients with an intermediate functional disability may present more pronounced quantitative and qualitative us alterations than patients with higher disability . moreover , some differential aspects can be recognized in cidp versus mmn and greater us alterations might be observed in nerve segments with demyelinating versus axonal damage . the strength of our findings is partially limited by the relatively small sample size and the lack of serial prospective follow - up assessments . in addition , two aspects should be considered in the interpretation of data : ( a ) the u - shapedrelationship between us findings and functional impairment , which might result in a similar us pattern in patients with either minimal or severe disability ; ( b ) the association of csa reduction with two different factors ( axonal damage and functional impairment ) , indicating the need of further prospective studies to analyze which of the two features primarily correlates with nerve size reduction .\noutput:\n" }, { "from": "agent", "value": "objective . this cross - sectional study analyzes the pattern of ultrasound peripheral nerve alterations in patients with chronic inflammatory demyelinating polyradiculoneuropathy ( cidp ) and multifocal motor neuropathy ( mmn ) at different stages of functional disability . material and methods . 22 cidp and 10 mmn patients and a group of 70 healthy controls were evaluated with an ultrasound scan of the median , ulnar , peroneal , tibial , and sural nerves . results were correlated with clinical disability scales and nerve conduction studies . results . patients with intermediate functional impairment showed relatively larger cross - sectional areas than subjects with either a milder ( p < 0.05 ) or more severe impairment ( p < 0.05 ) , both in cidp and in mmn . in addition , mmn was associated with greater side - to - side intranerve variability ( p < 0.05 ) , while higher cross - sectional areas were observed in cidp ( p < 0.05 ) and in nerve segments with predominantly demyelinating features ( p < 0.05 ) . higher csa values were observed in nerves with demyelinating features versus axonal damage ( p < 0.05 for cidp ; p < 0.05 for mmn ) . discussion and conclusions . greater extent of quantitative and qualitative us alterations was observed in patients at intermediate versus higher functional disability and in nerves with demyelinating versus axonal damage . cidp and mmn showed differential us aspects , with greater side - to - side intranerve variability in mmn and higher cross - sectional areas in cidp ." } ]

[ { "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: urine is composed of numerous harmful metabolites , which are stored for prolonged time in the urinary bladder .1 for that , the primary function of urinary bladder is to prevent internalization of metabolites from bladder lumen into the underlying tissues and blood .2 this blood - urine permeability barrier has to remain functional during the stretching - contraction of the urinary bladder .3,4 the permeability barrier is formed by the apical plasma membrane of superficial urothelial cells , tight junctions , and inhibited endocytosis .4 the apical plasma membrane of normal superficial urothelial cells is characterized by the formation of urothelial plaques , which are detergent - resistant membrane domains made of ordered transmembrane proteins known as uroplakins .511 urothelial plaques cover 70 % 90 % of the apical plasma membrane , where they contribute to the transcellular permeability barrier for ie , urea , water , ammonia or small non - electrolytes ,2,12 but do not prevent co2 transport through the urothelium .13 in the urothelium , where superficial cells do not reach their terminal differentiation , as is the case during urothelial carcinogenesis ,1417 the permeability barrier function is decreased .4,18 urothelial plaques also cover cytoplasmic fusiform vesicles ( fvs ) , which are implicated in the transport and incorporation of the urothelial plaques into the apical plasma membrane .3,4,19 nevertheless , involvement of fvs in the endocytosis of urothelial plaques from the apical plasma membrane is controversially discussed .3,4,19 if fvs are involved in the endocytosis from the luminal side of the bladder , they would inevitably capture some urine despite their fattened shape .20,21 therefore , demonstrating whether fvs are involved or not in the internalization of urine constituents would enhance our understanding of the permeability barrier function of the urothelium . a physiological approach to study the internalization of urine would be the introduction of nanoparticles as urine constituents . nanoparticles are small enough to be filtered through the kidneys and are accumulated in the bladder lumen , they are biologically inert , and they do not influence endocytotic processes .22,23 in this study , we tested 1.9 nm ultra - small gold nanoparticles ( aunps ) , covered by a highly water soluble organic shell , as markers for studying endocytosis in normal and neoplastic urothelium under in vivo conditions . using light and electron microscopy , we show that intravenously injected aunps reach the urinary bladder and act as physiological constituents of urine . experiments were approved by the veterinary administration of the slovenian ministry of agriculture and forestry ( permit no 34401 - 29 / 2007/3 ) in compliance with the animal health protection act and the instructions for granting permits for animal experimentation for scientific purposes . adult male mice , strain a / j ola hsd , were housed in plastic cages at 23c 2c , at 50 % 60 % relative humidity and at 12 - hour light / dark circadian cycle . ten animals were divided into three groups by simple random sampling : two animals were fed normal diet and were not injected with aunps , but were injected with a 0.9 % nacl physiological solution ( control animals ) , four animals were fed normal diet and were then injected with aunps ( aunps - n animals ) , and four animals were n - butyl - n - ( 4 - hydroxybutyl ) nitrosamine ( bbn ) treated and were then injected with aunps ( aunps - bbn animals ) . bbn ( tokyo chemical industry co , ltd tokyo , japan ) was diluted to 0.05 % with tap water and this mixture was provided as drinking water ( ad libitum ) to aunps - bbn animals for 10 weeks . animals were anesthetized with 2 % chanazine ( chanelle pharmaceuticals manufacturing ltd loughrea , ireland ; 5 l / 100 g body weight ) and 10 % bioketan ( vetoquinol biowet , gorzw , poland ; 10 l / 100 g body weight ) . once sedated aunps - n and aunps - bbn animals were injected with 200 l of the aunps solution into the tail vein . the aunps solution was prepared as follows : forty milligrams of 1.9 nm aurovist gold nanoparticles ( nanoprobes , yaphank , ny , usa ) were diluted in 400 l of physiologic solution according to manufacturer recommended protocol to obtain the final concentration of approximately 1.4 g au / kg body mass . the animals from the control group were injected with 200 l of physiologic solution into the tail vein . the urinary bladders were exposed with abdominal incision and fixed with 4 % paraformaldehyde in phosphate saline buffer without potassium ( pbs - k ) for 3 minutes , applied from the serosa side in situ . next bladders were removed from the animals and dissected into multiple pieces in the same fixative . samples from each of the bladders were further processed for light , transmission ( tem ) , and scanning ( sem ) electron microscopy . urine was collected ; a 5 l drop of urine was put on gold electron microscopy grids , dried and either directly observed or processed for aunps intensification . hq silver enhancement ( nanoprobes ) and gold enhanced ( nanoprobes ) were used to enlarge gold nanoparticles . both silver and gold enhanced solutions were prepared and used according to manufacturer recommended protocols with enhancement times of 4 and 5 minutes , respectively . the urinary bladder samples were fixed in 4 % paraformaldehyde in pbs ( k ) at 4c overnight , dehydrated and embedded in paraffin . paraffin blocks were cut into serial sections and counterstained with hematoxylin and eosin and examined by a uropathologist . histological urothelial changes of aunps - bbn animals were classified according to world health organization ( who ) classification of tumors of the urinary tract .24 the urinary bladder samples were fixed in 4 % paraformaldehyde in pbs ( k ) at room temperature for a total of 45 minutes . after fixation , the samples were washed in pbs ( k ) , then in deionized water , and finally in the citrate buffer . the samples were then incubated in the hq silver enhancement solution ( nanoprobes ) and prepared according to manufacturer protocol in the dark for 5.5 minutes . after washing in deionized water , the samples were post - fixed in 0.2 % oso4 for 75 minutes , washed in 0.1 m cacodylate buffer , dehydrated in graded ethanol , and embedded in epon . semi - thin sections ( thickness 1 m ) , were stained with 1 % toluidine and examined with an eclipse te300 inverted microscope ( nikon , tokyo , japan ) . from the regions of interest , the ultrathin sections ( 50 nm ) were cut and counterstained with lead citrate and uranyl acetate . next , they were examined with a cm100 tem ( philips ) running at 80 kv the urinary bladder samples from aunps - bbn animals were also prepared using the modified tokuyasu method .25 briefly , urothelium , cut into 1 mm pieces , was fixed in 4 % paraformaldehyde in pbs ( k ) at room temperature for 2 hours , washed in pbs ( k ) , embedded into 12 % gelatine , and cryoprotected by incubation in 2.3 m saharose at 4c overnight . subsequently , 300 nm thick cryosections were cut with fcs cryo - ultramicrotome ( leica microsystems , wetzlar , germany ) at 100c and collected on glass cover slips . nanoparticles in cryo - sections were silver enhanced with the hq silver enhancement solution ( nanoprobes ) in the dark for 6 minutes , washed in deionized water , and counterstained with toluidine and examined with an eclipse te300 inverted microscope ( nikon ) . from the regions of interest the cryo - ultrathin sections ( 50 nm ) were cut and counterstained with uranil acetate - methyl cellulose mixture . energy dispersive x - ray spectroscopy ( edxs ) analysiswas performed using a transmission electron microscope 2100 ( jeol , tokyo , japan ) equipped with an edx system ex-23003bu ( jeol ) . the tem was operated at 200 kv the urinary bladder samples were fixed in 4 % paraformaldehyde plus 2 % glutaraldehyde in 0.1 m cacodylate buffer at 4c for 3 hours , washed overnight in cacodylate buffer , dehydrated in a series of ethanol , and critical - point dried ( cpd030 baltec , balzers , liechtenstein ) . after sputter - coating with gold ( balzers union scd040 , balzers , liechtenstein ) , samples were examined with a jsm840a scanning electron microscope ( jeol ) at 15 kv . the cultures of normal porcine urothelial cells ( 5th passage ) were established on 12 - well culture inserts with 0.4 m porous membranes ( bd falcon , san jose , ca , usa ) and maintained in urom media as described previously .26,27 when cultures reached confluence , they were divided into two groups by simple random sampling : treated cells and control cells . aurovist aunps ( nanoprobes ) , in the same concentration as were injected into experimental animals , were added to the urom media of treated cells . control cells were kept in the urom media without aunps . after 90 minutes , cells were detached by using triple select ( gibco , life technologies , carlsbad , ca , usa ) , centrifuged , and re - suspended in fresh urom media . the survival of cells treated with aunps is presented as the percentage of the trypan blue - labeled cells versus non - labeled cells ; average , standard deviation ( sd ) , and student s t - test were performed with excel 2010 software ( microsoft corporation , redmond , wa , usa ) . experiments were approved by the veterinary administration of the slovenian ministry of agriculture and forestry ( permit no 34401 - 29 / 2007/3 ) in compliance with the animal health protection act and the instructions for granting permits for animal experimentation for scientific purposes . adult male mice , strain a / j ola hsd , were housed in plastic cages at 23c 2c , at 50 % 60 % relative humidity and at 12 - hour light / dark circadian cycle . ten animals were divided into three groups by simple random sampling : two animals were fed normal diet and were not injected with aunps , but were injected with a 0.9 % nacl physiological solution ( control animals ) , four animals were fed normal diet and were then injected with aunps ( aunps - n animals ) , and four animals were n - butyl - n - ( 4 - hydroxybutyl ) nitrosamine ( bbn ) treated and were then injected with aunps ( aunps - bbn animals ) . bbn ( tokyo chemical industry co , ltd tokyo , japan ) was diluted to 0.05 % with tap water and this mixture was provided as drinking water ( ad libitum ) to aunps - bbn animals for 10 weeks . animals were anesthetized with 2 % chanazine ( chanelle pharmaceuticals manufacturing ltd loughrea , ireland ; 5 l / 100 g body weight ) and 10 % bioketan ( vetoquinol biowet , gorzw , poland ; 10 l / 100 g body weight ) . once sedated aunps - n and aunps - bbn animals were injected with 200 l of the aunps solution into the tail vein . the aunps solution was prepared as follows : forty milligrams of 1.9 nm aurovist gold nanoparticles ( nanoprobes , yaphank , ny , usa ) were diluted in 400 l of physiologic solution according to manufacturer recommended protocol to obtain the final concentration of approximately 1.4 g au / kg body mass . the animals from the control group were injected with 200 l of physiologic solution into the tail vein . the urinary bladders were exposed with abdominal incision and fixed with 4 % paraformaldehyde in phosphate saline buffer without potassium ( pbs - k ) for 3 minutes , applied from the serosa side in situ . next bladders were removed from the animals and dissected into multiple pieces in the same fixative . samples from each of the bladders were further processed for light , transmission ( tem ) , and scanning ( sem ) electron microscopy . urine was collected ; a 5 l drop of urine was put on gold electron microscopy grids , dried and either directly observed or processed for aunps intensification . hq silver enhancement ( nanoprobes ) and gold enhanced ( nanoprobes ) were used to enlarge gold nanoparticles . both silver and gold enhanced solutions were prepared and used according to manufacturer recommended protocols with enhancement times of 4 and 5 minutes , respectively . the urinary bladder samples were fixed in 4 % paraformaldehyde in pbs ( k ) at 4c overnight , dehydrated and embedded in paraffin . paraffin blocks were cut into serial sections and counterstained with hematoxylin and eosin and examined by a uropathologist . histological urothelial changes of aunps - bbn animals were classified according to world health organization ( who ) classification of tumors of the urinary tract .24 the urinary bladder samples were fixed in 4 % paraformaldehyde in pbs ( k ) at room temperature for a total of 45 minutes . after fixation , the samples were washed in pbs ( k ) , then in deionized water , and finally in the citrate buffer . the samples were then incubated in the hq silver enhancement solution ( nanoprobes ) and prepared according to manufacturer protocol in the dark for 5.5 minutes . after washing in deionized water , the samples were post - fixed in 0.2 % oso4 for 75 minutes , washed in 0.1 m cacodylate buffer , dehydrated in graded ethanol , and embedded in epon . semi - thin sections ( thickness 1 m ) , were stained with 1 % toluidine and examined with an eclipse te300 inverted microscope ( nikon , tokyo , japan ) . from the regions of interest , the ultrathin sections ( 50 nm ) were cut and counterstained with lead citrate and uranyl acetate . next , they were examined with a cm100 tem ( philips ) running at 80 kv the urinary bladder samples from aunps - bbn animals were also prepared using the modified tokuyasu method .25 briefly , urothelium , cut into 1 mm pieces , was fixed in 4 % paraformaldehyde in pbs ( k ) at room temperature for 2 hours , washed in pbs ( k ) , embedded into 12 % gelatine , and cryoprotected by incubation in 2.3 m saharose at 4c overnight . subsequently , 300 nm thick cryosections were cut with fcs cryo - ultramicrotome ( leica microsystems , wetzlar , germany ) at 100c and collected on glass cover slips . nanoparticles in cryo - sections were silver enhanced with the hq silver enhancement solution ( nanoprobes ) in the dark for 6 minutes , washed in deionized water , and counterstained with toluidine and examined with an eclipse te300 inverted microscope ( nikon ) . from the regions of interest the cryo - ultrathin sections ( 50 nm ) were cut and counterstained with uranil acetate - methyl cellulose mixture . energy dispersive x - ray spectroscopy ( edxs ) analysis was performed using a transmission electron microscope 2100 ( jeol , tokyo , japan ) equipped with an edx system ex-23003bu ( jeol ) . the urinary bladder samples were fixed in 4 % paraformaldehyde plus 2 % glutaraldehyde in 0.1 m cacodylate buffer at 4c for 3 hours , washed overnight in cacodylate buffer , dehydrated in a series of ethanol , and critical - point dried ( cpd030 baltec , balzers , liechtenstein ) . after sputter - coating with gold ( balzers union scd040 , balzers , liechtenstein ) , samples were examined with a jsm840a scanning electron microscope ( jeol ) at 15 kv . the cultures of normal porcine urothelial cells ( 5th passage ) were established on 12 - well culture inserts with 0.4 m porous membranes ( bd falcon , san jose , ca , usa ) and maintained in urom media as described previously .26,27 when cultures reached confluence , they were divided into two groups by simple random sampling : treated cells and control cells . aurovist aunps ( nanoprobes ) , in the same concentration as were injected into experimental animals , were added to the urom media of treated cells . after 90 minutes , cells were detached by using triple select ( gibco , life technologies , carlsbad , ca , usa ) , centrifuged , and re - suspended in fresh urom media . the survival of cells treated with aunps is presented as the percentage of the trypan blue - labeled cells versus non - labeled cells ; average , standard deviation ( sd ) , and student s t - test were performed with excel 2010 software ( microsoft corporation , redmond , wa , usa ) . all animals survived the injection of aunps or physiologic solution into the tail vein and fully recovered after anesthesia . aunps were filtered through the kidneys and reached the urinary bladder after 90 minutes , which was evaluated both macro - and microscopically ( figure 1 ) . macroscopically , lumen of the urinary bladders turned black in the aunps - n ( figure 1a and b ) and aunps - bbn animals , while in the control animals they remained translucent . the presence of aunps was confirmed in the urine ( figure 1c ) by tem ( figure 1d ) . the concentration of aunps in the urine was high ( figure 1d ) , so that it was not a limiting factor for detection . to make aunps easily detected by tem , we tested if they were suitable for silver or gold enhancement . the results showed that the gold core of nanoparticles can be enlarged by both methods ( figure 1e and f ) . gold enhancement provided a more uniform size of enlarged nanoparticles than silver enhancement , but on the other hand , many particles remained unenhanced . therefore , silver enhancement was used in further experiments . under light microscopy ( lm ) , the reaction product of silver enhancement was brown . to prove that the silver enhancement reaction specifically enlarges aunps in the tissue , results have confirmed that nanoparticles seen as accumulation of electron - dense material in tem contained elementary gold ( figure 1 g ) . analysis of a large number of the individual nanoparticles always showed co - localization of ag ( silver ) and au , whereas in areas of the samples without the nanoparticles , au could not be detected . to verify the low toxicity of aunps , they were added to the medium of urothelial cell culture at the same concentration as the aunps - n and aunps - bbn in experimental animals . after 90 minutes , the viability of control cells was 90.3 % 12 % , while the treated cells had a viability of 78.2 % 5 % ; the difference was statistically significant , p 0.001 . to test if aunps are internalized by the superficial urothelial cells , we analyzed urinary bladder samples under light and electron microscopes . under lm , the urothelia of control and aunps - n animals consisted of three cell layers : small basal , intermediate , and large superficial cells ( figure 2a ) . brown - labeled product of silver enhancement was not seen in any layer of the urothelial or in the blood vessels of the urinary bladder wall ( figure 2a ) . under electron microscopes , the superficial urothelial cells of control and aunps - n animalswere observed as large , homogenous , and polygonal shaped ( figure 2b ) , and contained numerous fvs in their cytoplasm ( figure 2c ) . in the aunps - n animals , aunps were not detected in approximately three out of four superficial cells ( figure 2c ) . in one fourth of the superficial urothelial cells , aunps were observed in membrane compartments with 3001200 nm diameter , which were presumably endosomes ( figure 2d and e ) . epithelial intracellular spaces , lamina propria , blood vessels , and bladder muscles were also unlabeled ( figure 2f ) . occasionally , the regions of exfoliated urothelium were observed in semi - thin sections of the normal urothelium of control and aunps - n animals . these regions were limited to one or a few superficial cells ( figure 3a ) . in the aunps - n animals , regions of exfoliated urothelium were surrounded by apically labeled cells ( figure 3a and b ) . labeling was seen only in the superficial cell layer and was present in an all - or - nothing manner ; eg , by observing two cells , one contained a relatively constant amount of brown labeling while the neighboring superficial cell contained no labeling at all ( figure 3b ) . sem analysis of the apical urothelial surface revealed cells of different sizes ; relatively small cells next to exfoliated regions and large polygonal cells further away from these areas ( figure 3c ) . under tem , labeled cells showed fvs , which are characteristic of highly differentiated urothelial cells ( figure 3d and e ) . these cells were heavily loaded with aunps with the majority of them found in the cytosol ( figure 3d and e ) . the sharp boundary between labeled and non - labeled cells was seen ( figure 3e ) . in order to follow the internalization of aunps into the neoplastic urotheliumafter 10 weeks of bbn administration , the urothelium of aunps - bbn animals developed flat hyperplasia with moderate dysplasia . in these regions , the brown labeling was observed in the majority of superficial cells , in the significant portion of intermediate cells , and in some basal cells ( figure 4a ) . relatively small superficial cells of dysplastic urothelium were covered with microvilli and ropy ridges ( figure 4b ) and their apical cytoplasm contained no fvs ( figure 4c ) . the labeling was seen in the vesicular compartments , presumably endosomes , as well as in the cytosol ( figure 4d ) . all animals survived the injection of aunps or physiologic solution into the tail vein and fully recovered after anesthesia . aunps were filtered through the kidneys and reached the urinary bladder after 90 minutes , which was evaluated both macro - and microscopically ( figure 1 ) . macroscopically , lumen of the urinary bladders turned black in the aunps - n ( figure 1a and b ) and aunps - bbn animals , while in the control animals they remained translucent . the presence of aunps was confirmed in the urine ( figure 1c ) by tem ( figure 1d ) . the concentration of aunps in the urine was high ( figure 1d ) , so that it was not a limiting factor for detection . to make aunps easily detected by tem , we tested if they were suitable for silver or gold enhancement . the results showed that the gold core of nanoparticles can be enlarged by both methods ( figure 1e and f ) . gold enhancement provided a more uniform size of enlarged nanoparticles than silver enhancement , but on the other hand , many particles remained unenhanced . therefore , silver enhancement was used in further experiments . under light microscopy ( lm ) , the reaction product of silver enhancement was brown . to prove that the silver enhancement reaction specifically enlarges aunps in the tissue , results have confirmed that nanoparticles seen as accumulation of electron - dense material in tem contained elementary gold ( figure 1 g ) . analysis of a large number of the individual nanoparticles always showed co - localization of ag ( silver ) and au , whereas in areas of the samples without the nanoparticles , au could not be detected . to verify the low toxicity of aunps , they were added to the medium of urothelial cell culture at the same concentration as the aunps - n and aunps - bbn in experimental animals . after 90 minutes , the viability of control cells was 90.3 % 12 % , while the treated cells had a viability of 78.2 % 5 % ; the difference was statistically significant , p 0.001 . to test if aunps are internalized by the superficial urothelial cells , we analyzed urinary bladder samples under light and electron microscopes . under lm , the urothelia of control and aunps - n animals consisted of three cell layers : small basal , intermediate , and large superficial cells ( figure 2a ) . brown - labeled product of silver enhancement was not seen in any layer of the urothelial or in the blood vessels of the urinary bladder wall ( figure 2a ) . under electron microscopes , the superficial urothelial cells of control and aunps - n animalswere observed as large , homogenous , and polygonal shaped ( figure 2b ) , and contained numerous fvs in their cytoplasm ( figure 2c ) . in the aunps - n animals , aunps were not detected in approximately three out of four superficial cells ( figure 2c ) . in one fourth of the superficial urothelial cells , aunps were observed in membrane compartments with 3001200 nm diameter , which were presumably endosomes ( figure 2d and e ) . epithelial intracellular spaces , lamina propria , blood vessels , and bladder muscles were also unlabeled ( figure 2f ) . occasionally , the regions of exfoliated urothelium were observed in semi - thin sections of the normal urothelium of control and aunps - n animals . these regions were limited to one or a few superficial cells ( figure 3a ) . in the aunps - n animals , regions of exfoliated urothelium were surrounded by apically labeled cells ( figure 3a and b ) . labeling was seen only in the superficial cell layer and was present in an all - or - nothing manner ; eg , by observing two cells , one contained a relatively constant amount of brown labeling while the neighboring superficial cell contained no labeling at all ( figure 3b ) . sem analysis of the apical urothelial surface revealed cells of different sizes ; relatively small cells next to exfoliated regions and large polygonal cells further away from these areas ( figure 3c ) . under tem , labeled cells showed fvs , which are characteristic of highly differentiated urothelial cells ( figure 3d and e ) . these cells were heavily loaded with aunps with the majority of them found in the cytosol ( figure 3d and e ) . the sharp boundary between labeled and non - labeled cells was seen ( figure 3e ) . in order to follow the internalization of aunps into the neoplastic urothelium , we induced urothelial carcinogenesis with 0.05 % bbn in drinking water . after 10 weeks of bbn administration , the urothelium of aunps - bbn animals developed flat hyperplasia with moderate dysplasia . in these regions , the brown labeling was observed in the majority of superficial cells , in the significant portion of intermediate cells , and in some basal cells ( figure 4a ) . relatively small superficial cells of dysplastic urothelium were covered with microvilli and ropy ridges ( figure 4b ) and their apical cytoplasm contained no fvs ( figure 4c ) . the labeling was seen in the vesicular compartments , presumably endosomes , as well as in the cytosol ( figure 4d ) . great care should be devoted to the choice of endocytotic markers and the method of their application in order to study endocytosis in vivo under physiological conditions . we have selected aunps that fulfill three requests : ( 1 ) biocompatibility , ( 2 ) size , and ( 3 ) ability to detect . aunps have a relatively long history in biological applications and have been confirmed biocompatible by various in vitro and in vivo experiments .23,2832 in our study , the viability of cultured cells exposed to the highest recommended concentration of aunps was lower than of control cultured cells ( 78.2 % 5 % versus 90.3 % 12 % ) ; however , the survival rate was still acceptable and well above ld50 ( median lethal dose ) . moreover , all animals survived the tail vein injection of aunps and fully recovered after 90 minutes of anesthesia . . size of nanoparticles . based on the standard definition of the american society for testing and materials , nanoparticles are particles with lengths that range from 1 to 100 nm in two or three dimensions . the aunps we used , with their gold core 1.9 nm in diameter , are on the smaller side of the nanoparticle definition scale that is a prerequisite for substances to pass the macromolecular filter in the kidney . in our study , intravenously injected aunps were detected in the urine , which suggests that aunps are filtered in the kidneys and become constituents of the urine under physiological conditions . colloidal gold with diameters above 5 nm have sufficient electron density to be visualized in ultrathin sections of biological samples by tem . aunps used in our study can be seen under tem when directly applied to a tem grid , but are too small to be easily recognized in the ultrathin sections of the tissues . however , after silver or gold enhancement ,3336 nanoparticles are clearly seen . we confirmed specificity of the enhancement reaction by tem and edxs analysis and showed that silver enhancement enlarges a higher percentage of nanoparticles than gold enhancement . with the three basic requests fulfilled , the aunps can be used as a potential marker to follow internalization into urothelial cells from the luminal side of the urinary bladder under physiological conditions in vivo . since there are contradicting results regarding endocytosis in urothelial cells ,3,19,37,38 we used the aunps to follow internalization into superficial urothelial cells of normal and neoplastic urothelium . in the terminally differentiated superficial urothelial cells of normalurothelium , internalization of the aunps was minimal , which is in agreement with our previous study on urothelial cells in vitro .38 despite the high concentration of nanoparticles in the bladder lumen , only one quarter of cells contained a few labeled endosomes , which shows extremely low dynamics of endocytosis compared to other cell types .38 nanoparticles were not found in the fvs , demonstrating that fvs are not involved in the removal of urothelial plaques from the apical plasma membrane . limited internalization of nanoparticles into terminally differentiated superficial urothelial cells hence supports the idea that internalization of urine and its constituents is minimized , which contributes to the barrier function of the urothelium .4 in the normal urothelium , terminally differentiated superficial cells have an extremely long life time ; 39,40 however , they are occasionally removed by exfoliation and the exfoliated areas are rapidly resealed .4144 in our study , we observed regions of exfoliated urothelium in control and in aunps - n animals , and in either case exfoliated regions were surrounded by differentiated , but smaller urothelial cells . in aunps - n animals , these cells contained nanoparticles indicating that what is observed are regenerating cells , which have not yet established a fully functional permeability barrier . to further explore the functionality of the permeability barrier during alternative differentiation , we applied aunps to aunps - bbn animals . bbn is widely used in the urothelial carcinogenesis model systems and prevents urothelial cells reaching their terminal differentiation .45,46 a consequence of low cellular differentiation is leaky epithelium ,38,47 which was also observed in our study . the increased internalization into superficial cells of dysplastic urothelium in comparison to normal superficial cells reveals the potential that nanoparticles could be used in improved diagnostic and optimized treatment of urinary bladder cancer .31,4851 however , the increased nanoparticle internalization is not an explicit property of the partially differentiated cells found in the neoplastically transformed urothelium , but is also seen in normal urothelial cells located next to the exfoliated regions of the urothelium . therefore , the aunps above can all be used to follow endocytosis as well as be used as a sensitive marker of differentiation and functionality in urothelial cells . our experiments were intended to determine the physiological conditions for studying internalization in superficial urothelial cells in vivo . we provide evidence that the aunps we used are an excellent choice for the given studies , both on normal and in neoplastic urinary bladders . our results support the hypothesis that endocytosis is very limited in terminally differentiated urothelial cells , while the internalization of urine constituents increases significantly when the urothelial cells are at a lower differentiation stage . the conception of the latter provides solid ground for the developing novel , more effective bladder cancer diagnostic and treatment tools using nanoparticles .\noutput:\n" }, { "from": "agent", "value": "backgroundurothelial bladder is the reservoir of urine and the urothelium minimizes the exchange of urine constituents with this tissue . our aim was to test 1.9 nm biocompatible gold nanoparticles as a novel marker of internalization into the urothelial cells under physiological conditions in vivo.methodswe compared normal and neoplastic mice urothelium . neoplastic lesions were induced by 0.05 % n - butyl - n - ( 4 - hydroxybutyl ) nitrosamine ( bbn ) in drinking water for 10 weeks . nanoparticles , intravenously injected into normal and bbn - treated mice , were filtered through the kidneys and became constituents of the urine within 90 minutes after injection.resultsgold nanoparticles were densely accumulated in the urine , while their internalization into urothelial cells depended on the cell differentiation stage . in the terminally differentiated superficial urothelial cells of normal animals , nanoparticles were occasionally found in the endosomes , but not in the fusiform vesicles . regions of exfoliated cells were occasionally found in the normal urothelium . superficial urothelial cells located next to exfoliated regions contained gold nanoparticles in the endosomes and in the cytosol beneath the apical plasma membrane . the urothelium of bbn - treated animals developed fat hyperplasia with moderate dysplasia . the superficial cells of bbn - treated animals were partially differentiated as demonstrated by the lack of fusiform vesicles . these cells contained the gold nanoparticles distributed in the endosomes and throughout their cytosol.conclusiongold nanoparticles are a valuable marker to study urine internalization into urothelial cells in vivo . moreover , they can be used as a sensitive marker of differentiation and functionality of urothelial 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: transthoracic echocardiography is a commonly performed non - invasive investigation of cardiac anatomy and physiology and is indicated for the diagnosis of common cardiac pathologies . these include valvular heart disease , ischaemic heart disease , cardiomyopathies and infective endocarditis , to name a few . echocardiography is also indicated in the diagnosis and assessment of intra - cardiac masses , but additional investigations may be required to evaluate them further . it is recognised that non - cardiac pathology can present with cardiac symptoms and artefact on cardiovascular investigations . we present the case of a patient diagnosed with hiatus hernia presenting with cardiovascular symptoms and appearance of intra - cardiac mass on transthoracic echocardiography , and also review the relevant literature . an 81 - year - old female with a background of stable ischaemic heart disease and hypertension was referred to the cardiology department complaining of dyspnoea on exertion over a period of 12 months . she denied fever , weight loss , change in appetite , dyspepsia or gastrointestinal bleeding . her medication list included aspirin , a statin , a proton - pump inhibitor and an angiotensin receptor blocker . physical examination was normal ; in particular there were no finger clubbing , no cardiac murmurs on auscultation and no signs of fluid retention such as elevated jugular venous pressure and peripheral oedema . her haemoglobin , leukocyte count , renal and liver function blood tests were all normal . b - type natriuretic peptide was within normal limits . given her past medical history of cardiovascular disease , she was referred for echocardiography to assess for structural or functional cardiac disease possibly contributing to her unexplained dyspnoea . alarmingly , the study demonstrated a large echolucent mass with the appearance of a left atrial space - occupying lesion ( fig .1 ) . left ventricular size and contractile function were preserved and there was no significant valvular disease . right ventricular size and function were normal and there was no pericardial effusion . to further delineate the intra - cardiac mass , the patient underwent cardiac magnetic resonance imaging ( mri ) the study revealed no intra - cardiac masses , with normal heart structure and function . it demonstrated a large hiatus hernia containing food and compressing and distorting the posterior wall of the left atrium ( fig . although often asymptomatic , hiatus hernia can present with symptoms mimicking those of cardiovascular pathology such as dyspnoea , chest pain and syncope . furthermore , by cardiac compression , hiatus hernia can produce dynamic electrocardiography changes and simulate the appearances of cardiac masses on echocardiography . our patient presented with symptoms of breathlessness and was suspected of having congestive cardiac failure , given a past history of ischaemic heart disease and hypertension . it is believed that extrinsic compression of the left atrium results in these symptoms due to impaired left atrial filling leading to pulmonary venous hypertension . a case series of patients with significant left atrial compression by gastric structures presenting with haemodynamic instability and respiratory failure has been reported . the differential diagnosis of an intra - cardiac mass includes tumours ( benign or malignant ) , thrombi , vegetation , normal anatomical variants ( such as eustachian valve , chiari network , etc . ) and artefact . hiatus hernia mimicking intra - cardiac mass due to sonographic artefact was diagnosed in this case using multi - modality imaging . although transthoracic echocardiography is an excellent initial diagnostic technique to evaluate and diagnose cardiac masses , invariably definitive diagnosis and comprehensive view of these structures is confirmed by other imaging modalities such as cardiac mri , through the excellent spatial resolution and range of sequences of this modality to characterize tissue . cardiac mri has been found to have greater efficacy in the detection and morphological evaluation of cardiac masses compared to echocardiography , which may be limited by poor sonographic windows . the growing number of indications for performing echocardiography will undoubtedly result in misdiagnosis of cardiac masses in these patients , irrespective of symptoms . this in turn will have implications for the patient as well as for clinical resources . in conclusion , as highlighted by this case , one should consider extra - cardiac pathology such as hiatus hernia in the assessment of cardiac masses demonstrated on echocardiography , and appreciate that these can present with symptoms resembling those from primary cardiac disorders . the patient presented in this report gave informed consent to her case being submitted for publication and is aware that there are no patient - identifying details in the text or images submitted .\noutput:\n" }, { "from": "agent", "value": "hiatus hernia is a common medical condition . an elderly woman being investigated for dyspnoea of unknown aetiology had a transthoracic echocardiogram as part of her investigations . this alarmingly demonstrated a large left atrial mass . further assessment with cardiac magnetic resonance imaging revealed a large hiatus hernia compressing the left atrium and no intra - cardiac mass . the case succinctly highlights gastrointestinal pathology simulating cardiac symptoms and masses ." } ]

[ { "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 , an inflammatory disease of multifactorial origin seems to be the leading cause of tooth loss worldwide . this disease in its wake leaves behind a trail of destruction mainly pertaining to the tooth supporting structures . periodontal therapy consists of treatment modalities aimed at arresting infection , restoring the lost structure and to maintain a healthy periodontium . the mechanical removal of bacterial plaque , calculus and toxic material is an effective means of altering the etiology of periodontal disease . historically , periodontal surgery was used to treat patients with generalized disease and because of this the surgical approach was usually designed to treat multiple adjacent teeth . the goal of periodontal surgery has always been to alleviate or eliminate the degeneration associated with the progressive periodontal disease . in order to accomplish this goal , access to the periodontal defect for debridementthe current pendulum of clinical opinion in some areas of periodontal education and research has swung away from traditional mechanical and surgical therapy toward advanced treatment applications . the application of magnification to periodontics has tremendously refined the periodontal surgical care . as recent developments in medicinemicrosurgery is a treatment philosophy whose clinical horizons will continue to improve with operator experience and willingness to employ previously unused basic optical magnification and ergonomic techniques and technology . as of today , no clinical study has demonstrated the use and possible advantages of dental loupes in periodontal open flap debridement . so the aim of the present study is to evaluate the treatment outcomes of microsurgery and compare it with conventional open flap debridement procedures . written informed consent was signed and obtained from all the patients who participated in the study . totally , 13 patients ( 7 male and 6 female ) with the age range of 3050 years were included in the study . a total of 13 chronic generalized periodontitis patients attending the department of periodontics presenting with similar horizontal bone loss and probing pocket depth 5 mm in contralateral quadrants were included in the study . patients with any systemic diseases or under antibiotics in the past 6 months , smokers and with poor oral hygiene were excluded . three teeth per quadrant with identical pattern of bone loss and probing depth were included for treatment either by microsurgical ( test site ) or conventional approach ( control site ) in a split mouth design . at baseline , 3 , 6 and 9 months , the following clinical parameters were evaluated : probing pocket depth , relative attachment level , gingival recession , gingival bleeding index - ainamo and bay 1975 , patient comfort was assessed by visual analog scale for 7 days postoperatively . a stent was individually fabricated to create fixed landmarks and to standardize the location and angulation of periodontal probes at all the six sites . the position of the gingival margin was measured from the stent to the gingival margin , and the relative attachment level from the stent to the bottom of the periodontal pocket . the probing depth was calculated based on the difference between relative attachment level and gingival margin level . the patient was asked to rinse the mouth with 10 ml of 0.2 % chlorhexidine digluconate solution for 60 s. the operative site was anaesthetized with 2 % lignocaine hcl with adrenaline ( 1:80,000 ) . after achieving adequate anesthesia , in the control sitessurgical debridement was carried out to remove subgingival plaque , calculus , diseased granulation tissue and pocket epithelium . surgical flaps were sutured to the presurgical level with 3 - 0 silk suture utilizing an interdental , direct suturing technique achieving primary closure . antibiotic prescription of amoxicillin 500 mg thrice daily for 5 days and a nonsteroidal anti - inflammatory agent thrice daily for 2 days was given . in test sites , microsurgery was carried out with 3.5 optical magnification dental loupe . after local anaesthesia , sulcular incisions were placed with microsurgical ophthalmic blades [ figure 1 ] . granulation tissue adherent to the inner surface of flaps were carefully removed with curettes to provide full access and visibility to root surfaces . any remaining plaque and calculusconventional versus microsurgical blade conventional versus microsurgical periosteal elevator statistical analysis was carried out using spss software version 17.0 ( ibm corporation , chicago , il , usa ) . paired t - test was used to compare means on the same or related subjects over time or in differing circumstances , and unpaired t - test was applied to compare the means of the two groups . a total of 13 chronic generalized periodontitis patients attending the department of periodontics presenting with similar horizontal bone loss and probing pocket depth 5 mm in contralateral quadrants were included in the study . patients with any systemic diseases or under antibiotics in the past 6 months , smokers and with poor oral hygiene were excluded . three teeth per quadrant with identical pattern of bone loss and probing depth were included for treatment either by microsurgical ( test site ) or conventional approach ( control site ) in a split mouth design . at baseline , 3 , 6 and 9 months , the following clinical parameters were evaluated : probing pocket depth , relative attachment level , gingival recession , gingival bleeding index - ainamo and bay 1975 , patient comfort was assessed by visual analog scale for 7 days postoperatively . a stent was individually fabricated to create fixed landmarks and to standardize the location and angulation of periodontal probes at all the six sites . the position of the gingival margin was measured from the stent to the gingival margin , and the relative attachment level from the stent to the bottom of the periodontal pocket . the probing depth was calculated based on the difference between relative attachment level and gingival margin level . the patient was asked to rinse the mouth with 10 ml of 0.2 % chlorhexidine digluconate solution for 60 s. the operative site was anaesthetized with 2 % lignocaine hcl with adrenaline ( 1:80,000 ) . after achieving adequate anesthesia , in the control sitessurgical debridement was carried out to remove subgingival plaque , calculus , diseased granulation tissue and pocket epithelium . surgical flaps were sutured to the presurgical level with 3 - 0 silk suture utilizing an interdental , direct suturing technique achieving primary closure . antibiotic prescription of amoxicillin 500 mg thrice daily for 5 days and a nonsteroidal anti - inflammatory agent thrice daily for 2 days was given . in test sites , microsurgery was carried out with 3.5 optical magnification dental loupe . after local anaesthesia , sulcular incisions were placed with microsurgical ophthalmic blades [ figure 1 ] . granulation tissue adherent to the inner surface of flaps were carefully removed with curettes to provide full access and visibility to root surfaces . conventional versus microsurgical blade conventional versus microsurgical periosteal elevator statistical analysis was carried out using spss software version 17.0 ( ibm corporation , chicago , il , usa ) . paired t - test was used to compare means on the same or related subjects over time or in differing circumstances , and unpaired t - test was applied to compare the means of the two groups . a total of 13 chronic generalized periodontitis patients attending the department of periodontics presenting with similar horizontal bone loss and probing pocket depth 5 mm in contralateral quadrants were included in the study . patients with any systemic diseases or under antibiotics in the past 6 months , smokers and with poor oral hygiene were excluded . three teeth per quadrant with identical pattern of bone loss and probing depth were included for treatment either by microsurgical ( test site ) or conventional approach ( control site ) in a split mouth design . at baseline , 3 , 6 and 9 months , the following clinical parameters were evaluated : probing pocket depth , relative attachment level , gingival recession , gingival bleeding index - ainamo and bay 1975 , patient comfort was assessed by visual analog scale for 7 days postoperatively . a stent was individually fabricated to create fixed landmarks and to standardize the location and angulation of periodontal probes at all the six sites . the position of the gingival margin was measured from the stent to the gingival margin , and the relative attachment level from the stent to the bottom of the periodontal pocket . the probing depth was calculated based on the difference between relative attachment level and gingival margin level . the patient was asked to rinse the mouth with 10 ml of 0.2 % chlorhexidine digluconate solution for 60 s. the operative site was anaesthetized with 2 % lignocaine hcl with adrenaline ( 1:80,000 ) . after achieving adequate anesthesia , in the control sitessurgical debridement was carried out to remove subgingival plaque , calculus , diseased granulation tissue and pocket epithelium . surgical flaps were sutured to the presurgical level with 3 - 0 silk suture utilizing an interdental , direct suturing technique achieving primary closure . antibiotic prescription of amoxicillin 500 mg thrice daily for 5 days and a nonsteroidal anti - inflammatory agent thrice daily for 2 days was given . in test sites , microsurgery was carried out with 3.5 optical magnification dental loupe . after local anaesthesia , sulcular incisions were placed with microsurgical ophthalmic blades [ figure 1 ] . granulation tissue adherent to the inner surface of flaps were carefully removed with curettes to provide full access and visibility to root surfaces . conventional versus microsurgical blade conventional versus microsurgical periosteal elevator statistical analysis was carried out using spss software version 17.0 ( ibm corporation , chicago , il , usa ) . paired t - test was used to compare means on the same or related subjects over time or in differing circumstances , and unpaired t - test was applied to compare the means of the two groups . there was no significant difference between the groups for probing pocket depth , relative attachment level , gingival recession , gingival bleeding index , gingival margin level , as shown in table 1 . the changes in probing pocket depth , relative attachment level , gingival recession , gingival bleeding index , between the groups in different visits are depicted in figures 36 respectively . figure 7 signifies the frequency distribution of early healing index , with a lesser score of 1 was more with the test site ( 85 % ) , and more percentage of the control site showed a higher score of 2 ( 71.70 % ) . comparison between the parameters from baseline and at 3 , 6 and 9 months changes in the relative attachment level between the groups at different visits changes in the probing pocket depth between the groups at different visits changes in the gingival recession between the groups at different visits changes in the gingival bleeding index between the groups at different visits comparison of early healing index between test and control sites at baseline and 1 week post operatively at day 1 post operatively , the mean pain scale of the test site patients was 0 , for the control site was 1.070.75 and the difference was statistically significant . from day 27 , there was score 0 on the scale for both the groups , and there was no statistically significant difference . the present clinical study has demonstrated that open flap debridement procedures for chronic periodontitis using the microsurgical procedures has improved the early healing of the wound and decreased postoperative pain when compared to the clinical performance under conventional techniques . scaling and root planing are widely used techniques to remove the irritants from the surfaces of teeth and also to reduce root roughness that may facilitate the accumulation of irritants . small areas of calculus are often left behind , with anywhere from about 3 % to 80 % of instrumented root surfaces showing some residual calculus . it was also observed that more residual calculus is left behind on proximal surfaces , in deep sites , and in furcation areas . complete removal of calculus is a primary part of achieving a biologically acceptable tooth surface in the treatment of periodontitis . however , residual calculus exists not only on teeth treated by scaling alone but also on teeth treated by flap surgery followed by scaling and root planing . periodontal flaps for access provide a means to reduce residual calculus , especially more efficient even in deeper pockets , both in anterior and posterior teethscaling and root planing with flap showed better removal of calculus than after scaling and root planing alone . microsurgical procedures have been studied for various regenerative procedures , root coverage and papilla reconstruction procedures . the benefits of microsurgical approaches have been described only in a few case reports , and one prospective cohort study . a case control study was conducted similar to our present study design to assess the clinical outcome in localized gingival recessions . as of today , there is no clinical study to compare microsurgical and conventional open flap debridement procedures . in the present split mouth study , three teeth with probing pocket depth 5 mmwere considered as test site , and the contralateral teeth with same probing pocket depth were considered as controls . both test and control sites showed almost similar radiographic and clinical parameters . the only difference / variable over conventional technique was that there was improved visual and tactile perception through microsurgical technique . postoperative pain and early healing assessed for 7 days after the procedure showed that the test sites were significantly better than the controls . this may be due to delicate handling of the tissues and precise wound closure , which are similar to some of the earlier studies . a frequency of once every 3 months recall appears to be sufficient to maintain the beneficial effects of therapy even in the presence of individual variations of personal oral hygiene and gingival inflammation . although studies demonstrate that healing may continue for a period of 9 months following initial therapy , most of the healing seems to complete at 3 months following therapy . in our study , although the clinical parameters , probing pocket depth , relative attachment level , gingival margin level showed significant difference from baseline to 3 , 6 and 9 months , there was no significant difference between the groups in the present study . in our study , there was no statistically significant increase in gingival recession between the test and control sites . the test sites showed an increase of 0.12 mm as against 0.14 mm in control sites . however , studies have shown minimal gingival recession ( 0.4 mm ) with microsurgery due to atraumatic manipulation during surgery and excellent soft tissue preservation . however , the mean surgical operation time for test site is 1 h and 30 min that is 6 % more than in control sites 1 h and 16 min . in oral surgical procedures , studies have shown that the incidence and severity of complications following periodontal surgery correlated well with the duration of the procedure . it may be speculated that the extended operation time may compensate for the beneficial treatment effect of minimally invasive techniques . however in the present study microsurgical open flap debridement resulted in faster healing and less postoperative pain . the test sites were treated after the control sites , the less postoperative pain may be due to the less apprehension for the second surgery . within the limitations of the present study , it can be concluded that microsurgical approach resulted in early healing and less postoperative pain compared to the conventional approach . the choice of micro or macro surgical approaches should be decided based on the treatment outcomes , cost and the patient - centered parameters .\noutput:\n" }, { "from": "agent", "value": "background : residual calculus exists not only on teeth treated by scaling alone but also on teeth treated by flap surgery . periodontal microsurgery enables more definite removal of calculus , atraumatic handling of tissues through optical magnification . the purpose of this study was to compare the clinical outcomes of microsurgery with conventional open flap debridement in patients with chronic periodontitis.materials and methods : thirteen chronic periodontitis patients were randomly assigned for test ( microsurgical ) and control ( conventional ) open flap debridement in a split mouth design . at baseline , 3 , 6 and 9 months the following clinical parameters were recorded : probing pocket depth , relative attachment level , gingival recession , gingival bleeding index . postoperative healing at 1 - week by early healing index and pain scale for 7 days were assessed.results : paired t - test was used to compare means within the groups , and unpaired t - test was applied to compare the means of the two groups . at 3 , 6 and 9 months postoperatively there was a significant reduction in gingival bleeding index , probing pocket depth , relative attachment level within both the groups and there was no significant difference between both the groups . gingival margin level and gingival recession increased in both the groups , but it was not statistically significant . early healing index score of 1 was found in 85 % of test sites and 28 % of control sites . the mean pain scale was 0 in test site and 1.07 0.75 in control site.conclusions : in open flap debridement procedure , a microsurgical approach can substantially improve the early healing index and induce less postoperative pain compared with applying a conventional macroscopic approach ." } ]

[ { "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 melanoma is a relatively common malignancy in the united states and is responsible for the majority of skin cancer deaths . approximately 70,230 cases of melanoma were diagnosed , and approximately 8,790 people died from melanoma in the united states in 2011 . the incidence of cutaneous melanoma in the united states has been steadily rising since 1975 , with the most prominent risk factor being sun exposure . mucosal melanoma of the head and neck ( mmhn ) is a rare and aggressive disease that makes up less than 1 % of all melanoma cases in the united states . to date , it is unknown whether the incidence of mmhn , which occurs outside of sun exposed areas , has followed the same incidence trend over time as cutaneous melanoma . in our study , we describe trends in incidence rates ( irs ) for mmhn in the united states using the national cancer institute 's surveillance , epidemiology , and end results ( seer ) database . we identified patients using the seer 9 registries , which encompass nine geographic regions in the united states ( atlanta , connecticut , detroit , hawaii , iowa , new mexico , san francisco - oakland , seattle - puget sound , and utah ) and include approximately 9.5 % of the us population . the seer 9 registries were chosen for this purpose because each of the member registries has been continuously active throughout the duration of the study period . using seerstat version 7.0.9 , we identified patients within the seer 9 registries with international classification of diseases in oncology ( icd - 03 ) diagnosis codes for all histologic variants of melanoma ( 8720 / 38723 / 3 , 8730/3 , 8740 / 38746 / 3 , 8761/3 , 8770 / 38772 / 3 ) . we included any of the above histologies associated with topography codes for mucosal lip ( c00 .3 c00 .8 ) , tongue ( c01 .9 c02 .9 ) , salivary glands ( c07 .9 c08 .9 ) , floor of mouth ( c04 .0 c04 .9 ) , gums ( c03 .0 c03 .9 ) , other mouth ( c05 .0 c06 .9 ) , nasopharynx ( c11 .0 c11 .9 ) , tonsils ( c09 .0 c09 .9 ) , oropharynx ( c10 .0 c10 .9 ) , hypopharynx ( c12 .9 c13 .9 ) , other pharynx ( c14 .0 c14 .8 ) , nasal cavity ( c30 .0 ) , middle ear ( c30 .1 ) , paranasal sinuses ( c31 .0 c31 .9 ) , or larynx ( c32 .0 c32 .9 ) . cases that were designated as autopsy or death certificate only were excluded . all data was obtained using seerstat version 7.0.9 , and statistical analysis was performed with spss version 19 ( ibm corporation , armonk , ny , usa ) , and joinpoint regression program version 3.5.3 . our primary endpoints were the percent change ( pc ) and the annual percent change ( apc ) in the age - adjusted ir of mmhn from 1987 to 2009 , and we evaluated incidence trends for several subgroups according to gender , race , age , and anatomic subsite by a stratified analysis . while incidence data is available for mmhn going back to 1973 , there were not enough cases from 1973 to 1986 to perform a meaningful incidence trend analysis . therefore , we made the decision to limit our analysis of incidence trends to the time period from 1987 to 2009 . incidence was defined as the number of new cancers diagnosed per year , and all irs represent the number of cases per 1,000,000 persons per year . the pc represents the age - adjusted ir in 2009 divided by the age - adjusted ir in 1987 . the apc is estimated by weighted - least squares regression to the natural logarithm of age - adjusted incidence rates by year . apcs are presented with their associated p values ( representing the likelihood that the apc is not significantly different from zero ) . a p value of 0.05 was considered statistically significant . the statistical methods employed in this analysis were similar to those used in prior studies that have reported on trends in cancer incidence . we identified 452 cases of mmhn in the seer 9 registry between 1987 and 2009 . of these patients , 237 ( 52.4 % ) were female , and 215 ( 47.6 % ) were male . the cohort included 383 white patients ( 84.7 % ) , 24 black patients ( 5.3 % ) , 44 patients ( 9.7 % ) classified as ( including american indian / alaska native and asian / pacific islander ) , and one patient ( 0.2 % ) with unknown race . by comparison , the racial distribution of the general us population is 75.1 % white , 12.3 % black , and 12.5 % other races ( including american indian / alaska native , asian , hawaiian / pacific islander , other race , and two or more races ) . the most common site of disease was the nasal cavity , comprising 237 patients ( 52.4 % ) , and 328 patients ( 72.6 % ) had disease in a sinonasal location . the age - adjusted incidence of mmhn in the united states has increased over time . from 1987 to 2009 , the total pc in the age - adjusted ir for all patients with mmhn was 50.0 % , and the apc was 2.4 % ( p 0.01 ) . joinpoint analysis demonstrates that this trend was most pronounced from 1999 to 2009 , with an apc of 5.8 % over that time period , as illustrated in figure 1 . details of the total pc and apc in age - adjusted irs for mmhn by subgroup from 1987 to 2009 are shown in table 2 . by subsite , the rate increase was most pronounced in nasal cavity lesions , with a total pc of 102.9 % and apc of 2.7 % over the study period ( p 0.01 ) , as illustrated in figure 2 . , there was no statistically significant change in the age - adjusted ir over time for lesions outside of the nasal cavity . stratified by gender , there was a significant increase in the age - adjusted ir over time for female patients , with a total pc of 45.5 % and an apc of 3.4 % ( p 0.01 ) , while there was no significant change in incidence for male patients over the same time period ( pc 35.2 % , apc 1.0 % , p = 0.30 ) . there was increased incidence in white patients , with a total pc of 52.5 % and apc of 2.2 % ( p = 0.01 ) ; however , due to low patient numbers , incidence trends for other racial groups were unable to be calculated . for white females with nasal cavity lesions , the total pc and apc were 50.4 % and 3.5 % , respectively ( p = 0.01 ) . for patients of ages 55 to 84 there was a significant trend demonstrating higher age - adjusted irs over time , with a total pc of 184.4 % and an apc of 2.9 % from 1987 to 2009 . for patients ages 2054 and 85 , there were insufficient patient numbers to determine an apc ; however , the pc in age - adjusted irs between 1987 and 2009 for these subgroups were 42.1 % and 34.4 % , respectively . the specific subset of patients that had the highest total pc and apc in the age - adjusted ir for mmhn from 1987 to 2009 were white females ages 55 to 84 . in this cohort , the total pc in age - adjusted incidence of mmhn was 306.3 % , and the apc was 5.1 % over the study period ( p 0.01 ) . age - adjusted irs for white females ages 55 to 84 with mmhn by year are illustrated in figure 3 . mmhn is a rare malignancy that makes up less than one percent of all melanomas . outcomes for patients with mmhn are generally poor , with reported five - year overall survival ( os ) rates for all stages ranging from 20 to 48 % . sinonasal lesions often present with epistaxis and nasal obstruction , and oral cavity lesions typically present as flat pigmented lesions that may be found on dental examination . there is no firm consensus regarding the optimal management of these tumors ; however , the usual primary treatment is surgical resection . postoperative radiotherapy has been shown to improve local control but has no demonstrated impact on survival . because of the rarity of mmhn , the majority of studies on this disease are single institution reports with limited patient numbers , and reliable data regarding both outcomes and epidemiology are sparse . it is firmly established that the incidence of cutaneous melanoma is increasing over time . the 2000 joint annual report on cancer reported that the incidence of cutaneous melanoma in the united states increased by approximately 2.6 % per year from 1991 to 1997 . more recently , simard et al . demonstrated that the apc in the age - adjusted ir for cutaneous melanoma was 2.1 % per year for white men and 2.4 % per year for white women from 1999 to 2009 in the united states , with subset analysis demonstrating that these trends were mainly due to increasing incidence in men aged older than 55 years and women of all ages . this trend may be due to changes in sun exposure patterns ; however , it is also possible that improved detection has played a role . in contrast to the well - documented rise in incidence for cutaneous melanoma , however , there has been no published data to date describing the incidence trend for mmhn . our analysis of the seer data demonstrates that the incidence of mmhn in the united states has been rising steadily from 1987 to 2009 , with an apc ( 2.4 % ) similar to that of cutaneous melanoma over a similar time period . furthermore , joinpoint regression analysis demonstrates that the rise in incidence of mmhn was particularly prominent from 1999 to 2009 , with an apc of 5.8 % over this time period . there is a particularly notable increase in mmhn in white females , with the highest rates of increase observed in white females ages 55 to 84 . these findings suggest that there are dynamic etiologic factors that are causing a change in the patterns of presentation in this disease . however , it is unclear what specific risk factors are contributing to the particularly rapid increase in mmhn incidence in this subgroup , and further study is needed to better understand this trend . risk factors for the development of cutaneous melanoma are well understood and include exposure to ultraviolet radiation , family history of melanoma , and multiple benign or atypical nevi . melanocytes in the mucosal layers of the head and neck are thought to be histologically identical to melanocytes in the skin ; however , the pathogenesis of mmhn is largely unknown . several etiologic agents for mmhn have been proposed , including tobacco exposure , occupational exposure to formaldehyde , and infection with the human papilloma virus ( hpv ) , none of which are thought to be important risk factors for the development of cutaneous melanoma . studies have shown an association with mutations in the kit proto - oncogene , which encodes the protein c - kit and is not typically mutated in cutaneous melanoma . given that cutaneous melanoma and mmhn do not appear to share etiologic factors , it is of interest that the incidence rates of these diseases are rising at similar rates . a possible explanation for our findings is that advances in endoscopy and imaging may have improved detection of this disease over the last 25 years . however , given the infrequency of screening mucosal surfaces of the head and neck in asymptomatic patients and the inherent difficulty in identifying many of these lesions on physical exam , it is unlikely that improved screening would be singularly responsible for such a pronounced increase in incidence over time . additionally , this explanation would not account for the differences in the rates of increase in irs between gender , racial , and age - based subgroups . one of the notable findings of our study was the fact that mmhn incidence is rising in nasal cavity lesions , but the age - adjusted ir for tumors outside of the nasal cavity has remained stable . this finding suggests that there is a specific etiologic agent contributing to nasal cavity melanomas that is either not present or does not have the same carcinogenic effects in other subsites . in a separate recently published seer analysis , jethanamest et al . demonstrated that nasal cavity melanomas are associated with superior survival compared to mucosal melanomas in other head and neck subsites , which lends further support to the hypothesis that nasal cavity melanomas are somehow biologically distinct from other mmhns . of the patients identified in our seer analysis from 1987 to 2009 , patients with mmhn ( n = 452 ) made up less than 0.5 percent of all patients with melanoma ( n = 110 , 537 ) . there was a slight predominance of female patients ( 52.4 % ) compared to male patients ( 47.6 % ) . in contrast to our data , prior reports have described a modest male predominance in mmhn . given that our study is derived from a population - based dataset , our findings may reflect more accurately the true distribution of mmhn in the community . the most common site of disease in our study was the nasal cavity , comprising 52.4 % of patients , and 72.6 % of cases occurred in a sinonasal subsite . this finding is consistent with previous reports that have shown that the majority of cases of mmhn present in a sinonasal location . second , by using the seer data , we were able to identify patients diagnosed with mmhn over a long period of time who were diagnosed in multiple geographic regions of the united states . limitations of our study include the potential for underreporting of minority data in the seer registries , possible mistakes in coding , possible inconsistencies of coding across registries , and the relatively low number of cases . additionally , the seer data is limited in its ability to identify specific patient and disease factors that may contribute to the development of mmhn . these include ( but are not limited to ) family history , sun exposure history , occupational exposures , smoking history , and comorbid illnesses . finally , as mmhn is often misclassified pathologically , it would be useful to have the ability to confirm each patient 's pathologic diagnosis . unfortunately , there is no mechanism within the seer database for review of the original pathologic material . overall , however , the seer database is an excellent resource for reporting cancer trends over time , and we believe that our study forms a strong foundation for future work in this disease . in summary , mmhn is a rare and often fatal malignancy that is increasing rapidly in incidence in the united states . the most profound increasing incidence is primarily in patients with nasal cavity tumors and in white women , with the most significant increases in incidence observed in white women ages 55 to 84 . while mmhn and cutaneous melanoma do not appear to have a common etiologic basis , the rates of increase in the incidence of these diseases are similar . further research on mmhn is needed , and we hope that our hypothesis - generating study will help to form a basis for future investigation that may elucidate the etiology and epidemiology of this aggressive disease .\noutput:\n" }, { "from": "agent", "value": "background . while it is established that the incidence of cutaneous melanoma has risen over time in the united states , the incidence trend for mucosal melanoma of the head and neck ( mmhn ) is unknown . methods . we used the surveillance , epidemiology , and end results ( seer ) database to determine incidence trends for mmhn from 1987 to 2009 in the united states . we determined annual percent change ( apc ) by weighted least squares and joinpoint regression analysis . results . mmhn incidence increased from 1987 to 2009 ( apc 2.4 % ; p < 0.01 ) . nasal cavity lesions increased in incidence ( apc 2.7 % ; p < 0.01 ) over this duration , while the incidence of non - nasal cavity lesions remained stable . the highest rate of increase was in white females ages 55 to 84 ( apc 5.1 % ; p = 0.01 ) . conclusions . the incidence of mmhn in the united states has been rising since 1987 . this trend is driven primarily by increased incidence of nasal cavity melanomas ." } ]

[ { "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 online version of this article ( doi : 10.1007 / s40261 - 016 - 0376 - 0 ) contains supplementary material , which is available to authorized users . this analysis examined data from the early weeks ( 4 , 8 , and 12 ) of the dual i and ii studies in patients with type 2 diabetes , comparing the fixed - ratio combination product ideglira to its monocomponents.the results showed lower hba1c and fpg values at all time points assessed with ideglira compared with each of its monocomponents , as well as higher percentages of patients reaching the hba1c target 7 % at weeks 8 and 12 and fpg target 7.2 mmol / l at weeks 4 , 8 , and 12 . ideglira also compared favorably with insulin degludec for the composite endpoint of hba1c 7 % without hypoglycemia weight gain at weeks 8 and 12 . despite the well accepted benefits of good glycemic control , many patients with type 2 diabetes mellitus ( t2 dm ) have plasma glucose ( pg ) levels chronically elevated above guideline recommendations because potentially beneficial changes are not made to their treatment regimens . one reason for this clinical inertia is anxiety on the part of patients and their clinicians that introduction of insulin therapy will be restrictive and result in hypoglycemic events and weight gain . a recent survey of more than 4000 patients showed that even when insulin was introduced , more than 80 % of patients still had a glycated hemoglobin ( hba1c ) 7.0 % ( 53 mmol / mol ) 6 months later , with 75 % having had no intensification beyond dose titration of their original insulin therapy . therefore , both insulin - treated patients and those on oral antidiabetic drugs ( oads ) are potentially left at increased risk of diabetic complications as a result of clinical inertia , although it must be acknowledged that hba1c targets 7.0 % are appropriate for some individual patients . the prevalence of poor control is perhaps surprising , however , given that patients treatment satisfaction is largely influenced by clinical outcomes , especially improvement in glycemic control . clearly there is a need to address clinical inertia , and given that improving glycemia increases treatment satisfaction , it seems likely that therapies able to tolerably reduce pg without increasing the risk of hypoglycemia within short time intervals could benefit patient engagement with self - management . in recent years , several new drug classes for t2 dm have been introduced providing opportunities to study various combinations with different but complementary mechanisms of action . it is possible that a combination of different agents with different actions could accelerate and enhance the initial pg - lowering response . one such combination is that of basal insulin plus glucagon - like peptide - 1 receptor agonist ( glp - 1ra ) since these agents have pharmacological actions that complement each other . the speed with which glycemic control can be established with this combination has hitherto not been studied , but together these agents provide dynamic control of both fasting and postprandial glycemia with low risks of hypoglycemia and weight gain . this is achieved together with , and partly as a consequence of , a minimization of the insulin dose requirement . many clinical studies have demonstrated such clinical benefits with this regimen , and the tolerability of this combination relative to intensified insulin therapy is especially appealing and may benefit treatment adherence . in this respect , the improved or relative treatment satisfaction / quality - of - life benefits reported with the incorporation of a glp - 1ra into a basal insulin - based regimen may be relevant . following the clinical use of basal insulin plus glp - 1ra therapy given in parallel , and as an approach to simplifying therapy with a goal of improving adherence and convenience , novel , one such product ( ideglira ) consists of insulin degludec and the glp - 1 analog liraglutide . insulin degludec provides a flat and stable steady - state basal insulin profile , and effectively reduces fasting plasma glucose ( fpg ) levels , while liraglutide benefits both fpg and postprandial plasma glucose ( ppg ) levels . the effects of liraglutide on beta - cell and alpha - cell function are strictly glucose dependent , hence when combined , liraglutide and insulin degludec have the potential to mitigate the risk of hypoglycemia that might otherwise limit intensive glycemic control with insulin therapy . as a glp - 1 analog , liraglutide also reduces hunger , promoting weight loss , hence ideglira also provides weight advantages when compared with basal insulin - based regimens . ideglira is administered as dose steps given once daily , titrated in a similar way to basal insulin . one dose step contains a fixed combination of 1 unit of insulin degludec and 0.036 mg of liraglutide . the pen enables injections in increments of single dose steps ( maximum dose : 50 units of degludec and 1.8 mg liraglutide ) . two phase iii trials ( including an extension study ) involving ideglira have currently been completed and published and a further five are soon to be published or are still on - going . these studies have demonstrated the complementary effects of the components of ideglira , also demonstrating its good efficacy and tolerability profile . however , data concerning the relative speed of glycemic improvement during ideglira therapy have not been reported . increased speed of improvement could potentially translate into enhanced perseverance / adherence with therapy , which could be particularly important with an injectable therapy . this post hoc analysis therefore sought to investigate , in patients with t2 dm previously treated with oad or basal insulin + oad , the time - course over which differences in glycemic control as well as hypoglycemia risk and changes in body weight occurred . this analysis thus assessed the hypothesis that responses to ideglira would be faster versus insulin degludec or liraglutide alone . data suitable for assessment had been collected at weeks 4 , 8 , and 12 in the dual action of liraglutide and insulin degludec in type 2 diabetes ( dual ) i and ii studies . in these studies , all procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation ( institutional and national ) and with the helsinki declaration of 1975 , as revised in 2000 and 2008 . patients included in dual i were 1663 adults ( mean age 55 years ) with a mean hba1c of 8.3 % ( inclusion criterion 710 % ) and a mean body mass index ( bmi ) of 31.2 kg / m ( inclusion criterion 40 kg / m ) who were previously treated with metformin with or without pioglitazone for at least 90 days before screening . patients were randomized ( 2:1:1 ) to daily injections of ideglira , insulin degludec , or liraglutide . dual ii included 413 adults ( mean age 5758 years ) with a mean hba1c of 8.78.8 % ( inclusion criterion 7.510 % inclusive ) and a mean bmi of 33.7 kg / m ( inclusion criterion 27 kg / m ) who had prior treatment for at least 90 days with basal insulin at a stable dose ( 2040 units / day ) in combination with metformin with or without sulfonylurea or glinides . in dual ii , patients were randomized to ideglira or insulin degludec titrated to a maximum dose of 50 units . in both studies , doses of ideglira ( and insulin degludec ) were adjusted twice weekly during a telephone consultation with a study nurse and using a titration algorithm based on the mean self - measured pre - breakfast pg value from 3 consecutive days , aiming for a pre - breakfast glucose concentration target of 4.05.0 mmol / l . efficacy endpoints assessed in this analysis were change in hba1c , change in fpg , and change in body weight over time . in addition , responder endpoints were assessed including proportion of patients achieving hba1c 7.0 % ( 53 mmol / mol ) , and proportion of patients achieving fpg 7.2 mmol / l , these values being in line with the current american diabetes association ( ada ) / european association for the study of diabetes ( easd ) treatment position statement . two composite responder endpoints were assessed : proportion of patients achieving hba1c 7.0 % without confirmed hypoglycemia ( details below ) , and proportion of patients achieving hba1c 7.0 % without confirmed hypoglycemia and without weight gain . for the responder endpoints that included hba1c 7.0 % , week 4 data were not included in the analysis due to this interval being relatively short compared with the time - scale over which hba1c changes in response to mean pg exposure , and the timing of increments in dose steps . confirmed hypoglycemia rates over the first 12 weeks and the cumulative incidence at weeks 4 , 8 , and 12 were assessed to investigate the balance between early glycemic control and development of early hypoglycemia risk . confirmed hypoglycemic episodes were defined as severe events requiring third - party assistance , or non - severe episodes dealt with by the patient and confirmed by a pg value 3.1 mmol / l ( 56 mg / dl ) . the responder endpoints were analyzed using logistic regression adjusting for treatment , region , and antidiabetic treatment at screening as fixed factors , and baseline values as covariates . absolute values for hba1c , fpg , and body weight change were analyzed using analysis of covariance , also adjusting for these fixed factors and baseline values as covariates , and hypoglycemia rates were analyzed using a negative binomial model adjusting for treatment , region , gender , and antidiabetic treatment at screening as fixed factors . dual i data were also adjusted for baseline hba1c stratum and sub - study participation . in the logistic regression a logit - link was used . in the negative binomial modelanalyses were based on the full analysis set , using the last observation carried forward to impute missing data . the patient baseline characteristics for the dual i and ii studies are given in supplementary table 1 ; within each study the comparator groups were well matched . in both dual i and ii , reduction in mean hba1c values occurred faster in patients treated with ideglira , such that significant differences were demonstrated at weeks 4 , 8 , and 12 versus insulin degludec ( both studies ) and at weeks 8 and 12 versus liraglutide ( dual i ) . the proportion of patients achieving hba1c 7.0 % at weeks 8 and 12 was significantly higher with ideglira than comparators ( fig . 2 ) . the proportions of patients achieving this target without hypoglycemia , and without hypoglycemia and weight gain were also higher with ideglira than with insulin degludec in both studies at weeks 8 and 12 . the proportion of patients achieving the target without hypoglycemia were similar for ideglira and liraglutide at week 12 in dual i , but there was a significant difference favoring ideglira at week 8 ( fig . the proportion of patients achieving the target without either hypoglycemia or weight gain was higher for liraglutide than ideglira at week 12 ( fig .2 c ) . table 1confirmed hypoglycemia incidence and cumulative incidence during initial 12 weeks of the dual i and ii studiesstudy / week of studyideglirainsulin degludecliraglutidehypoglycemic events per patient yearcumulative % of patients reporting a hypoglycemic eventhypoglycemic events per patient yearcumulative % of patients reporting a hypoglycemic eventhypoglycemic events per patient yearcumulative % of patients reporting a hypoglycemic eventdual i study 41.186.40.875.80.54 * 3.281.1811.61.2111.90.34 ** 3.6121.4819.61.6219.70.26 ** 4.4 dual ii study 40.774.00.783.581.089.51.6710.6121.3315.12.2416.1 p values are for rate ratio for the observed mean number of events per patient per year , for which there were no statistically significant differences between ideglira and insulin degludec cumulative % percent of cohort having recorded at least one confirmed hypoglycemic event by the time - points of week 4 , 8 , and 12 , ideglira insulin degludec + liraglutide fixed combination * p 0.02 vs. ideglira , * * p 0.0001 vs. ideglirafig . * p 0.0001 vs. insulin degludec ; p 0.0001 vs. liraglutide . ci confidence interval , hba 1c glycated hemoglobin , ideg insulin degludec , ideglira insulin degludec + liraglutide fixed combination , lira liraglutidefig .2 proportion of patients achieving hba1c and composite endpoint targets in weeks 8 and 12 in the dual i and dual ii studies . ci confidence interval , hba 1c glycated hemoglobin , ideg insulin degludec , ideglira insulin degludec + liraglutide fixed combination , lira liraglutide confirmed hypoglycemia incidence and cumulative incidence during initial 12 weeks of the dual i and ii studies p values are for rate ratio for the observed mean number of events per patient per year , for which there were no statistically significant differences between ideglira and insulin degludec cumulative % percent of cohort having recorded at least one confirmed hypoglycemic event by the time - points of week 4 , 8 , and 12 , ideglira insulin degludec + liraglutide fixed combination * p 0.02 vs. ideglira , * * p 0.0001 vs. ideglira change in hba1c in weeks 012 in the dual i and dual ii studies . * p 0.0001 vs. insulin degludec ; p 0.0001 vs. liraglutide . ci confidence interval , hba 1c glycated hemoglobin , ideg insulin degludec , ideglira insulin degludec + liraglutide fixed combination , lira liraglutide proportion of patients achieving hba1c and composite endpoint targets in weeks 8 and 12 in the dual i and dual ii studies . ci confidence interval , hba 1c glycated hemoglobin , ideg insulin degludec , ideglira insulin degludec + liraglutide fixed combination , lira liraglutide fpg data are shown in figs . 3 and 4 . in dual i , mean fpg was lower with ideglira versus individual components at weeks 4 , 8 , and 12 ( all p 0.0001 ) ( fig . mean fpg was also lower with ideglira versus insulin degludec from week 4 , continuing through weeks 8 and 12 ( fig . the proportion of patients who reached fpg 7.2 mmol / l at week 4 was greater with ideglira versus its individual components , and this was also observed at week 8 ( fig .4 a ) . in dual ii , the proportions of patients reaching fpg 7.2 mmol / l at weeks 4 and 8 were higher with ideglira than with insulin degludec , and a diminished but statistically significant between - treatment difference was still evident at week 12 ( fig .3 change in fasting plasma glucose in weeks 012 in the dual i and dual ii studies . * p ci confidence interval , fpg fasting plasma glucose , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combinationfig . mmol / l in weeks 4 , 8 , and 12 in the dual i and dual ii studies . ci confidence interval , fpg fasting plasma glucose , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combination change in fasting plasma glucose in weeks 012 in the dual i and dual ii studies . * p 0.0001 vs. insulin degludec , p 0.0001 vs. liraglutide . ci confidence interval , fpg fasting plasma glucose , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combination proportion of patients achieving fasting glucose 7.2 mmol / l in weeks 4 , 8 , and 12 in the dual i and dual ii studies . ci confidence interval , fpg fasting plasma glucose , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combination trajectories for body weight change are shown in fig .5 . in dual i , mean weight reduction from baseline to 4 weeks was greater with ideglira versus insulin degludec , but lower with ideglira versus liraglutide , and these differences in trajectories continued over weeks 8 and 12 ( fig . mean weight reduction from baseline was greater with ideglira versus insulin degludec after 4 , 8 , and 12 weeks ( fig .5 change in weight in weeks 012 in the dual i and dual ii studies . * p 0.0001 vs. ideg ; p 0.0001 vs. liraglutide . ci confidence interval , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combination change in weight in weeks 012 in the dual i and dual ii studies . * p 0.0001 vs. ideg ; p 0.0001 vs. liraglutide . ci confidence interval , ideg insulin degludec , lira liraglutide , ideglira insulin degludec + liraglutide fixed combination hypoglycemia data during the initial 12 weeks are presented in table 1 . the absolute event rates and cumulative incidence were low in the initial weeks with all treatments . there was no difference in hypoglycemia rate between ideglira and insulin degludec in either study , but hypoglycemia was more frequent with ideglira than with liraglutide in dual i.in dual i , baseline mean hba1c was 8.3 % ( 67 mmol / mol ) and this was reduced at 26 weeks by 1.9 % ( 21 mmol / mol ) with ideglira [ final mean dose , 38 dose steps ( 38 units insulin , 1.37 mg liraglutide ) ] , versus 1.4 % ( 15 mmol / mol ) with insulin degludec ( final mean dose 53 units ) , and 1.3 % ( 14 mmol / mol ) with liraglutide ( final dose 1.8 mg ) , estimated treatment differences p 0.0001 for ideglira versus each comparator . a higher proportion of patients reached hba1c 7.0 % ( 53 mmol / mol ) with ideglira ( 80.6 % ) than with insulin degludec ( 65.1 % ) or liraglutide ( 60.4 % ; p 0.0001 both comparisons ) . these advantages for ideglira were preserved through to 52 weeks in an extension study . in dual ii , mean hba1c improvement from baseline was greater with ideglira than with insulin degludec , with respective mean reductions of 1.9 % ( 21 mmol / mol ) and 0.9 % ( 10 mmol / mol ; p 0.0001 ) from respective baseline values of 8.7 and 8.8 % ( 72 and 73 mmol / mol ) at equal final mean insulin doses of 45 units . again , more patients achieved hba1c 7.0 % with ideglira ( 60 % ) than with insulin degludec ( 23 % ; p 0.0001 ) . data collected from the first few weeks of these studies and analyzed here clearly show that much of the improvement with ideglira occurred in the early weeks , with relatively rapid improvement of fpg and hba1c , resulting in lower mean values and higher proportions of patients achieving target values early on therapy when compared with insulin degludec or liraglutide given alone . a relative mean body weight reduction versus insulin degludec was apparent from 4 weeks in both studies , although body weight reduction was not as substantial with ideglira as with liraglutide alone in the initial weeks of treatment in the dual i study . importantly , these early clinical benefits are likely to be meaningful to patients . illustrative of the relative differences in the early improvement in glycemic control is the observation that the proportion of patients achieving the hba1c target at week 8 with ideglira was similar to the proportion achieving this target at week 12 with insulin degludec in both studies , and the proportion of liraglutide - treated patients achieving this target at week 12 in dual i ( not statistically tested ) ( fig . 2 ) . similar observations apply to fpg ( figs . 3 , 4 ) , where greater reductions early in treatment were again seen for ideglira in both studies . fasting glycemia is likely to be especially important for early establishment of treatment satisfaction since immediate improvements are seen for this clinical endpoint , and since titration of ideglira was directed to an fpg target , patients are likely to view fpg as a direct measure of treatment success . hypoglycemia rate and weight gain with ideglira were relatively reduced compared with insulin degludec alone in the dual i and ii studies , although not when compared with liraglutide alone . each of these potential insulin therapy side effects may be particularly important in treatment initiation and the early stages of insulin therapy since their early occurrence might discourage subsequent dose titration to appropriate levels and affect future adherence behaviors , and they have been recognized as psychological barriers to insulin initiation and adherence . hypoglycemia and weight gain were therefore included in the composite endpoints , and the proportions of patients achieving the hba1c target without these adverse events remained higher with ideglira than with insulin degludec alone ; indeed , the relative advantage became larger . in patientspreviously treated with oads ( dual i ) , a higher percentage of patients achieved the hba1c target without hypoglycemia and without weight gain with liraglutide than with ideglira at week 12 . one question of interest is whether patients with different degrees of disease progression will all respond equally well to ideglira . post hoc analyses have demonstrated that the efficacy of ideglira in the dual i and ii studies was independent of several parameters that can be considered markers of disease progression including , baseline hba1c , disease duration , and bmi . however , further research is merited to assess the efficacy of ideglira in advanced t2 dm . another consideration with the use of glp - 1ras is gastrointestinal ( gi ) side effects , with transient nausea being the most frequently reported event . the results from dual i showed a lower rate of nausea with ideglira compared to liraglutide alone , probably attributable to the much slower titration of the liraglutide dose when using the ideglira combination . inblinded comparison in dual ii , the difference between ideglira and insulin degludec was very small . our analysis , together with these previous data , therefore suggests that patients treated with ideglira can expect to observe relatively early therapeutic benefits in terms of glycemic control , but with a relatively low risk of the adverse reactions that might be expected from the components . it should be noted , however , that the maximum dose of liraglutide was not reached with ideglira in either the dual i or dual ii study , hence the therapeutic potential of the glp - 1ra component of the regimen may not have been realized to the full extent that is possible with a free combination regimen . nevertheless , clinically relevant efficacy and safety outcomes were achieved with the convenient fixed combination regimen in these studies . it can be hypothesized that a therapeutic profile characterized by the prospect of clinical benefits combined with good tolerability might help patients and their healthcare professionals overcome clinical inertia as well as enhancing treatment adherence . it should be noted , however , that treatment satisfaction and adherence to ideglira relative to comparators was not studied in the dual i and ii studies , although treatment satisfaction was included as an endpoint in other recently completed ideglira trials . within a strictly monitored , controlled clinical trial , in fact , the subject of how the speed of clinical improvement in response to pharmacological intervention affects patient self - management behaviors appears to have been little studied in any field of medicine , including diabetes . the gold standard used for judging success in glycemic control has long been hba1c , and improvement in this endpoint is typically assessed after a period of at least 16 weeks of treatment or longer . a patient s attitude to their therapy , however , may be shaped more by their experiences of side effects and the clinical responses they can observe ( e.g. , self - measured blood glucose - determined fpg ) in the earlier stages of therapy . diabetes is a condition where self - management behavior and good glycemic control are critical determinants for long - term prognosis , but where suboptimal control and adherence do not produce immediate unpleasant consequences for the patient . one caveat in this assessment is that to achieve parity in insulin dosing in dual ii ( which was designed to assess the clinical contribution of liraglutide in ideglira ) , both ideglira and insulin degludec were initiated at 16 dose - steps / units . this basal insulin dose reduction ( from a mean of 29 units ) in patients randomized to insulin degludec would have compromised the early efficacy that might have been achieved had patients applied the same titration algorithm to their pre - trial insulin dose . therefore , the relative differences in speed of improvement may not reflect what might be expected where the choice is to switch patients from their basal insulin regimen to ideglira , or to continue and optimize their basal insulin regimen . nevertheless , mean hba1c had decreased by approximately 1 % ( and fpg by more than 2.5 mmol / l ) by week 8 ( figs . 1 , 3 ) in patients commencing ideglira , despite the reduction in insulin dose , hence this transfer was made without any immediate loss in glycemic control . it is also important to note that , depending on the patient s hba1c , a reduction in basal insulin dose is appropriate when glp - 1ra therapy is introduced to the regimen of a patient on basal insulin . a further consideration with dual ii is that the maximum dose of insulin degludec was limited to 50 units . this should not have impacted early between - treatment differences during titration , but might have affected outcomes by week 12 when doses were approaching final mean values . another limitation of our analysis is that the greater speed of glucose reduction might merely reflect the more potent total glucose - lowering effect of ideglira versus its comparators , with both the rates and final totals of glucose reduction largely determined by the titration algorithms . the same 202 titration algorithm was used for both ideglira and insulin degludec , and while ideglira contains two agents in one injection , these findings indicate that glycemic target could be achieved more quickly with ideglira versus insulin degludec , with a similar number of injections and effort in terms of titration , and without an increased risk of hypoglycemia and weight gain . the titration algorithms used in the trialsare those recommended for everyday clinical practice , although we are aware that this may be challenging in a regular ( non - trial ) out - patient setting . in summary , the present analysis complements the original dual i and ii study publications by providing data from the early phases of ideglira therapy in patients previously treated with oads with or without basal insulin . these data are of clinical importance as they show that the improved balance between glycemic control , hypoglycemia , and weight change , comparing ideglira with its individual components , manifested early during therapy ( remaining thereafter throughout the duration of the studies ) . indeed , ideglira produced marked improvements in glycemic control , with beneficial effects on body weight , as early as 4 weeks after initiation , not achieved at the expense of early side effects such as hypoglycemia . these findings support the hypothesis that drug combinations with complementary actions could accelerate the onset of therapeutic benefits in t2 dm patients . early improvement in glycemic control could enhance patient perception of progress and hence their satisfaction and perseverance with treatment , and may also help overcome clinical inertia in the drive for improved glycemic control . novo nordisk funded the study , participated in study design , data analysis , and manuscript preparation and review . the decision to publish was the authors.tina vilsbll has received lecture fees from astrazeneca , boehringer ingelheim pharmaceuticals , bristol - myers squibb , eli lilly and company , merck sharp & dohme , novo nordisk , novartis , sanofi , and zealand pharma , and is a member of the advisory boards of astrazeneca , boehringer ingelheim pharmaceuticals , bristol - myers squibb , eli lilly and company , merck sharp & dohme , novo nordisk , and sanofi . jiten vora has served on advisory boards and received support for research and attendance for national and international educational meetings and honoraria for lecturing from novo nordisk , eli lilly and company , sanofi , merck sharp & dohme , takeda , novartis , and abbott . merck & co , novo nordisk and sanofi , consultancy honoraria from astrazeneca , glaxosmithkline , intarcia therapeutics inc , janssen pharmaceuticals inc . , merck & co , novo nordisk , quest diagnostics , and sanofi and research grants to his institution from eli lilly and company , novo nordisk , and sanofi . all procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation ( institutional and national ) and with the helsinki declaration of 1975 , as revised in 2000 and 2008 .\noutput:\n" }, { "from": "agent", "value": "background and objectivesthe time - course when changes in glycemic control and body weight were first manifest in patients with type 2 diabetes mellitus ( t2 dm ) treated with a combination of insulin degludec and liraglutide ( ideglira ) was assessed , comparing ideglira to its individual components.methodsdata from weeks 012 from two studies were analyzed , one comparing ideglira to each component ( dual i ) , and one comparing ideglira to insulin degludec titrated to a maximum 50 units ( dual ii ) . efficacy endpoints included glycated hemoglobin ( hba1c ) and fasting plasma glucose ( fpg ) reduction , proportion of patients achieving hba1c [ < 7.0 % ( < 53.0 mmol / mol ) ] and fpg ( 7.2 mmol / l ) targets , and proportion achieving hba1c target without hypoglycemia and without hypoglycemia and weight gain.resultsmean hba1c was lower , and the proportion of patients reaching target hba1c greater , with ideglira versus comparators ( both studies ) at weeks 8 and 12 . proportions of patients reaching target hba1c without hypoglycemia and without hypoglycemia and weight gain were higher for ideglira versus insulin degludec , though not versus liraglutide . mean fpg was lower with ideglira , and the proportion achieving target fpg higher , versus components ( both studies ) from weeks 412 . ideglira was associated with mean weight reduction from weeks 412 , although less than with liraglutide alone . hypoglycemia occurred infrequently in weeks 012 , with no difference in incidence between ideglira and insulin degludec in either study.conclusionsideglira reduces plasma glucose to a greater extent than its components , measurable within the first 12 weeks of therapy , and without weight gain or an increased hypoglycemia risk versus insulin degludec.electronic supplementary materialthe online version of this article ( doi : 10.1007 / s40261 - 016 - 0376 - 0 ) contains supplementary material , which is available to authorized users ." } ]

[ { "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 analysis of cancer predisposition syndromes has been an important approach towards the identification of oncogenes and tumor suppressor genes . some hereditary cancer syndromes , such as li - fraumeni syndrome , are caused by the mutation of critical tumor suppressor genes ( tp53 ) and lead to wide - spread tumorigenesis including many different tumor types . however , other hereditary cancer syndromes appear to have a more limited tumor spectrum.for example , individuals with syndromes such as wagr ( wilms tumor , aniridia , genitourinary abnormalities , and mental retardation syndrome ) and denys - drash syndrome have mutations in the wt1 gene , and these patients are primarily at risk for wilms tumor . the identification of an underlying genetic mutation or predisposition to develop specific cancers is helpful not only to family members with that syndrome , but also to many other individuals who develop cancer without known risk factors . knowledge of how specific tumors arise can be applied to targeted prevention , surveillance , and even therapeutic strategies . ewing 's sarcoma , first described by james ewing in 1921 , is the second most common pediatric bone cancer after osteosarcoma . it is an aggressive cancer of children and young adults , with 30 % 60 % survival depending on tumor site and the presence or absence of metastases at diagnosis . while osteosarcoma is thought to arise from bone cell progenitors , the cell of origin of ewing 's sarcoma remains unknown . james ewing himself initially described this disease as an endothelioma of bone , and later suggested that it arises from perivascular lymphatic endothelium . since that time , other investigators have suggested myriad cells of origin , including hematologic , mesenchymal / fibroblastic , and neural crest derivatives . more recently , emerging evidence has suggested that ewing 's sarcoma arises from a mesenchymal stem or progenitor cell . a definitive answer to the cell of origin question will require additional analyses . while the cell of origin of ewing 's sarcoma is not yet known , the molecular genetics of the tumor are better understood . ewing 's sarcomas are highly associated with a limited set of recurring , somatic chromosomal rearrangements . the most common of these , t ( 11 ; 22 ) ( q24 ; q12 ) , is found in approximately 85 % of cases , while t ( 21 ; 22 ) ( q22 ; q12 ) is found in 10 % of cases . the remaining translocations are found in 5 % each . these translocations fuse the ewsr1 gene on chromosome 22 with an ets family member , most commonly the fli1 gene on chromosome 11 . this ewing 's sarcoma - specific translocation generates an ews / ets fusion protein . the ewing 's sarcoma fusion proteins contain a strong transcriptional activation domain fused to an ets type dna binding domain and thus function as aberrant transcription factors that dysregulate target genes contributing to oncogenic transformation . a number of genes that are dysregulated by ews / fli have been identified , and their roles in the oncogenic process are under active investigation . the presence of ews / ets translocations is specific to ewing 's sarcoma , and the presence of an ews / ets fusion protein can be used clinically to diagnose patients with ewing 's sarcoma who have small round blue cell tumors . two main cooperating mutations have been identified in ewing 's sarcoma : p53 and rb pathway mutations . mutations in tp53 ( encoding the p53 protein ) occur with a frequency of 5 % 20 % in ewing 's sarcoma , amplifications of mdm2 occur in 0 % 10 % of cases , and deletions of the cdkn2a locus ( encoding overlapping p16 and p14 transcripts ) occur in about 15 % of cases . a similar percentage of ewing 's sarcoma tumors also have alterations in the rb pathway . alterations in these pathways may be required to bypass a growth inhibitory effect mediated by the ews / ets fusion protein . although alterations in the p53 and / or rb pathways may cooperate with ews / ets fusion proteins to induce ewing 's sarcoma , this disease is not traditionally considered to be a part of the li - fraumeni syndrome andhas rarely been reported as a second tumor in patients with heritable retinoblastoma . ewing 's sarcoma does not appear to be a component of other tumor susceptibility syndromes , either . there are no well - documented environmental causes of this disease and only a handful of epidemiological studies have focused on ewing 's sarcoma . while ewing 's sarcoma is not common , with an incidence of about 3 per one million people under 20 years of age , it remains uniformly deadly when untreated . interestingly , ewing 's sarcoma has a strong predilection for caucasians , being far more common in this population than in asians and ten times more common than in those of african descent . a molecular postulate has been proposed for the racial predilection noted : intron 6 , near the molecular breakpoint region , is at least fifty percent smaller due to diminished interspersed repeat sequences ( alu elements ) in about 10 percent of the african population . it is hypothesized that ( alu elements are preferential sites for genetic recombinations in cancer . beyond the observation of different rates by ethnicity , ewing 's sarcoma is considered to be nonfamilial , with no genetic lineage predisposition . we reviewed the english literature to find any evidence in the demographics and epidemiology of ewing 's sarcoma to suggest a familial predisposition . we considered cases of consanguinity and any onco - syndromic conditions that might imply a predisposition genotype . additional tumors beyond classic ewing 's sarcoma have been found to have similar histologic and molecular phenotypes , including the specific t ( 11 ; 22 ) translocation . ewing 's sarcoma and another small round blue cell malignancy often seen in soft tissues , termed primitive neuroectodermal tumor ( pnet ) , were found to not only have similar histologic features but also to contain the identical translocation in greater than 95 % of cases . ewing 's sarcoma family of tumors to encompass ewing 's sarcoma , pnet , as well as atypical ewing 's sarcoma and askin tumor ( ewing 's sarcoma of the chest wall ) . because of the consistent genetic lesion , we will continue to refer to this entire group as ewing 's sarcoma . there are currently no known cancer syndromes of which ewing 's sarcoma tumors are included , and ewing 's sarcoma tumors do not seem to be associated with any other types of tumors either in pediatric or adult oncology . chronologically , ninety percent of cases occur in patients between 5 and 25 years of age . about 25 % of cases occur before age 10 , while 65 % arise between ages 10 and 20 years old . boys and young men are affected more frequently than girls and young women . males also do less well than females . the pelvis is the most common location , followed by the femur , tibia , humerus , and scapula . however , ewing 's sarcoma can be found in any part in the body . several reports have highlighted the general association of ewing 's sarcoma and parental exposure to pesticides , solvents , and farming or agricultural occupation . hernia , both inguinal and umbilical have also been linked to ewing 's sarcoma . valery et al . surmised that ewing 's sarcoma and hernia have common embryologic neuroectodermal pathways . interestingly , these cases arose in farming families perhaps suggesting some unknown environmental influence the link of the two entities . at least one report discounts this association . in a case - control study , winn et al . matched 208 ewing 's cases with one sibling control and one age matched regional population control . although hernia was seen 6 times more frequently among ewing 's patients compared to regional controls , sibling controls experienced hernias with the same frequency as ewing 's patients . reports of patient height and onset of pubertal growth have been varied with no clear or consistent pattern developing in their association with ewing 's sarcoma . the ethnic epidemiology of ewing 's sarcoma is fascinating as it uniquely follows racial boundaries , similar to wilms ' tumor . ewing 's sarcoma has a strong predilection for caucasians , being far more common than in asians and those of african descent . have noted that intron 6 , near the molecular breakpoint region , is at least fifty percent smaller due to diminished interspersed repeat sequences ( alu elements ) in about 10 percent of the african population . alu elements are a type of sine , or short interspersed element , and are approximately 300 bp in length with approximately 1,000,000 copies in the human genome , accounting for approximately 10 % of genetic material . it is hypothesized that alu elements are preferential sites for genetic recombinations in cancer . perhaps in families with ewing 's sarcoma probands that develop remote ewing 's sarcoma in their descendents , increased genomic predominance of alu elements leads to subsequent rechimerization of ews / fli and related translocations . large - scale studies on germline dna from ewing 's sarcoma patients have yet to be performed which could support this hypothesis . most recently , johnson et al . explored the association between parental age and risk of all childhood cancers . the previous studies had explored the association between advanced maternal and paternal age with congenital syndromes ( including several which predispose to cancer ) and a handful of other reports had provided preliminary support of an association between older parental age and an increased risk of some childhood cancers . johnson et al . followed up on these investigations and performed a pooled analysis on 17,672 childhood cancer cases diagnosed during 19802004 and 57,9666 controls born during 19702004 . cancer and birth registry records from new york , washington , minnesota , texas , and california were linked , and johnson et al . calculated logistic regression for parental age and specific childhood cancers adjusting for sex , birth weight , gestational age , birth order , plurality , maternal race , birth year , and state . report that older maternal age seemed to increase the risk for most common childhood cancers . interestingly , ewing 's sarcoma was found to be associated with the highest risk of all childhood cancer subtypes in relation to a 5 - year increase in both maternal age ( odds ratio 1.18 [ 1.021.35 ] ) and paternal age ( odds ratio 1.19 [ 1.061.34 ] ) . they speculate that the increased risk of cancer in older mothers could be due to age - related increases in de novo epimutations in oocyte genes transmitted to offspring . a similar phenomenon in epimutations could be occurring in the spermatocytes of older fathers . although limited to a single pooled analysis , this large study provides intriguing data to suggest a slight but possible contribution of genetic risk to the development of ewing 's sarcoma . the association between ewing 's sarcoma and other forms of cancer seen in a proband 's pedigree has been reported , some as early as 1952 . . noted that 9 of 80 patients ( 11 % ) were noted to have close family relatives , usually a grandfather or aunt , with some form of malignant tumor . in their series , eight years later the first reported incidence of ewing 's sarcoma in siblings was reported by huntington et al . . two sisters , each diagnosed in their teens , eventually died of metastatic disease . none of their other siblings ( five boys and two girls ) showed any evidence of disease . hutter et al . reported the case of two siblings , both female . one sister was diagnosed at age 3 and died of metastatic disease shortly thereafter . her sister was diagnosed at age 16 and at the time of reporting was alive and disease free . interestingly , their mother was treated for breast carcinoma , and their maternal grandfather died of carcinoma of the colon . joyce et al . reported the third case of ewing 's sarcoma in siblings in 1983 . the first sibling was diagnosed at age 9 and treated successfully with chemotherapy and radiation . her sister was diagnosed at age 19 and at the time of publication was alive with pulmonary disease that seemed responsive to chemotherapy . a careful history showed no reports of neoplastic disease in the immediate or extended family . although isolated to case reports , these siblings with ewing 's sarcoma also would imply a slight but definitely suggestible contribution of genetics to the risk of developing ewing 's sarcoma . however , given their limited numbers and lack of genomic dna for analysis , environmental contributions also can not be ruled out . it is also interesting to note that these isolated siblings with familial ewing 's sarcoma were all females . finally , several authors have reported on the association of ewing 's sarcoma after diagnoses and treatment for retinoblastoma . . published on a cohort of 6 ewing 's patients diagnosed after treatment for various cancers including lymphoma , leukemia , wilms tumor , and retinoblastoma . , via meta - analysis , found that while ewing 's has been reported after a number of different malignancies . only the predominance of retinoblastomaprior to ewing 's differs dramatically from the low frequency of retinoblastoma among childhood cancers in the general population . in contrast , cancers other than retinoblastoma were proportionate to those in the general population . the mechanisms by which oncogenic ets fusion proteins , which are dna - binding transcription factors , target genes necessary for tumorigenesis are not well understood . analyzed promoters of these target genes and described a significant overrepresentation of highly repetitive ggaa - containing elements ( microsatellites ) . they also reported that ews / fli uses ggaa microsatellites to regulate the expression of target genes , and that the ability to do so depends on the number of consecutive ggaa motifs . speculated that these microsatellite polymorphisms may contribute to differences in individual and population susceptibility to ewing 's sarcoma , and that this may also be true of other diseases mediated by ets transcription factors . most recently , this same group combined transcriptional analysis , whole genome localization data , and rna interference knockdown to identify glutathione s - transferase m4 ( gstm4 ) as a critical ews / fli target gene in ewing 's sarcoma . they found that the recurrent ewing 's sarcoma translocation t ( 11 ; 22 ) directly binds and regulates gstm4 expression through the same ggaa - microsatellite described above . microsatellite sizes differ between individuals , and so in addition to possible genetic contribution to ewing 's sarcoma susceptibility , there may be inherited differences in ewing 's sarcoma therapeutic responses . ewing 's sarcoma case - control studies analyzing microsatellite size and frequency are now required to support these findings . the epidemiological evidence supports a slight but possible genetic contribution to the risk of developing ewing 's sarcoma . however , due to its rarity , many of these studies lack statistical power to definitely prove or disprove a genetic susceptibility to this sarcoma . there is no smoking gun to suggest an underlying cancer predisposition in the majority of cases of ewing 's sarcoma . large - scale studies investigating the genetic epidemiology of ewing 's sarcoma are sorely needed to answer the question of genetic disease risk . because of its rarity , a remote familiality may have evaded detection thus far . we believe that an in depth investigation into the genetic epidemiology of ewing 's sarcoma is required to see if a predisposition gene or set of genes might contribute to this deadly disease in some subtle manner . this will only be accomplished through a stringent analysis of existing ewing 's sarcoma registries or large population databases .\noutput:\n" }, { "from": "agent", "value": "ewing 's sarcoma is a highly malignant tumor of children and young adults . the molecular mechanisms that underlie ewing 's sarcoma development are beginning to be understood . for example , most cases of this disease harbor somatic chromosomal translocations that fuse the ewsr1 gene on chromosome 22 with members of the ets family . while some cooperative genetic events have been identified , such as mutations in tp53 or deletions of the cdkn2a locus , these appear to be absent in the vast majority of cases . it is therefore uncertain whether ews / ets translocations are the only consistently present alteration in this tumor , or whether there are other recurrent abnormalities yet to be discovered . one method to discover such mutations is to identify familial cases of ewing 's sarcoma and to then map the susceptibility locus using traditional genetic mapping techniques . although cases of sibling pairs with ewing 's sarcoma exist , familial cases of ewing 's sarcoma have not been reported . while ewing 's sarcoma has been reported as a 2nd malignancy after retinoblastoma , significant associations of ewing 's sarcoma with classic tumor susceptibility syndromes have not been identified . we will review the current evidence , or lack thereof , regarding the potential of a heritable condition predisposing to ewing 's sarcoma ." } ]

[ { "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: ewing sarcoma is the second most common malignancy of bone and soft tissues in children and young adults and is characterized by a chromosomal translocation that generates a fusion oncogene between ews and an ets family transcription factor , most commonly fli - 1 . ewing sarcoma is an aggressive tumor with relatively poor long - term outcome . overall survival is approximately 60 % , and the five - year survival of recurrent cases is less than 10 % . considering that current cytotoxic chemotherapies used for ewing sarcoma are not improving the survival of metastatic or recurrent disease , a new approach for targeted therapy needs to be developed . the growth and survival of ewing sarcoma cells critically depend on the ews - fli - 1 fusion oncoprotein . thereforehowever , despite a number of attempts , an ews - fli -1-targeted therapy has not materialized to date and ews - fli - 1 continues to be the perfect target without a therapeutic agent . ews - fli - 1 is a transcription factor that controls the expression of a number of genes important for cell proliferation and transformation . transcriptional regulation by ews - fli - 1 has been studied extensively , but little is known about the biochemical properties of the ews - fli - 1 protein . to gain insight into the biochemical nature of the ews - fli - 1 protein , we undertook proteomic analyses of the ews - fli - 1 interactome . the result from the interactome analyses was used to provide leads for subsequent molecular biological analyses . using a tandem affinity purification approach , we identified known ews - fli - 1 interactors such as ews and rna helicase a. using a proximity - dependent biotinylation technique , bioid , we identified cation - independent mannose 6 - phosphate receptor ( cimpr ) as a protein located in the vicinity of ews - fli - 1 within a cell . cimpr is a cargo that mediates the sorting of lysosomal hydrolase precursors from the trans - golgi network to endosomes . additional molecular cell biological analyses revealed that the ews - fli - 1 protein turns over by a lysosome - dependent mechanism . we show that torin 1 , which is an active - site inhibitor of mtorc1 that was shown to stimulate the tfeb - lysosome pathway , can reduce ews - fli - 1 protein levels in ewing sarcoma cells , suggesting a potential utility of mtorc1 active - site inhibitors as therapy for ewing sarcoma . the target sequences for shrnas are as follows : human cimpr shrna , ctacctgtatgagatccaa ; human vps26a shrna , ctctattaagatggaagtg ; luciferase shrna , gcactctgattgacaaatacgattt . cathepsin d and firefly luciferase ews - fli - 1 fusion cdnas were cloned into pcdf1 lentiviral vector ( system biosciences ) .293 cells and 293 t cells were cultured in dulbecco s modified eagle s medium ( dmem ) supplemented with 10 % calf serum . a673 cells and hela cells were cultured in dmem supplemented with 10 % fetal calf serum . lentiviruses were prepared by transfection in 293 t cells following system biosciences protocol , and the cells infected with lentiviruses were selected with 2 g / ml puromycin for 48 h as described . luciferase assays were done as described . forty 15 - cm plates of 293 t cells were transfected with flag - his - ews - fli - 1 ( type 1 fusion ) ; 48 h after transfection , the cells were lysed in tn buffer ( 10 mm tris ph 7.4 / 150 mm nacl / 1 % np - 40/1 mm aebsf / 10 g / ml aprotinin / 10 g / ml leupeptin / 1 g / ml pepstatin a / 20 mm sodium fluoride ) . the lysate was incubated with ni - nta agarose ( qiagen ) , flag - his - ews - fli - 1 and its interacting proteins were collected by centrifugation , washed three times with tn buffer , and eluted with 50 mm sodium phosphate buffer ph 8.0 / 150 mm nacl / 250 mm imidazole . the eluted sample was immunoprecipitated with anti - flag antibody ( m2 , sigma - aldrich ) , the immunoprecipitate was eluted with flag peptide ( sigma - aldrich ) , and the eluted protein sample was processed with an amicon ultra 0.53 k centrifugal filter device ( millipore ) for concentration and buffer exchange to 50 mm tris ph 8.5 . proteins were digested at 37 c overnight with trypsin ( promega ; 1:10 , enzyme / substrate ) in the presence of 10 % acetonitrile ( acn ) . the ph of the digestion solution was adjusted to 7.5 with 1 mm ammonium bicarbonate , if necessary . the resulting tryptic peptides were analyzed by hplc - esi - tandem mass spectrometry ( hplc - esi - ms / ms ) on a thermo fisher ltq orbitrap velos mass spectrometer fitted with a new objective digital picoview 550 nanoesi source . online hplc separation of the digests was accomplished with an eksigent / ab sciex nanolc - ultra 2 - d hplc system : column , picofrit ( new objective ; 75 m i.d . ) packed to 15 - cm with c18 adsorbent ( vydac ; 218msb55 m , 300 ) ; mobile phase a , 0.5 % acetic acid ( hac ) / 0.005 % trifluoroacetic acid ( tfa ) ; mobile phase b , 90 % acn / 0.5 % hac / 0.005 % tfa ; gradient 242 % b in 120 min ; flow rate , 0.4 l / min . precursor ions were acquired in the orbitrap in centroid mode at 60,000 resolution ( m / z 400 ) ; data - dependent collision - induced dissociation ( cid ) spectra of the 10 most intense ions in the precursor scan above a threshold of 3,000 were acquired at the same time in the linear trap ( isolation window for ms / ms , 3 ; relative collision energy , 30 ) . ions with a 1 + or unassigned charge state were not fragmented . dynamic exclusion settings were : repeat count , 1 ; repeat duration , 30 s ; exclusion list size , 500 ; exclusion duration , 30 s. three 15 - cm plates of 293 cells were transfected with bioid - ews - fli - 1 ( myc tag and bira r118 g mutant fused to the n - terminus of ews - fli - 1 ) . twenty - four hours after transfection , biotinylation of proteins in the vicinity of bioid - ews - fli - 1 within the cells was induced for 24 h by the addition of 50 m biotin to the culture medium . the cells were lysed by boiling in a lysis buffer ( 50 mm tris , ph 7.4 / 500 mm nacl / 0.4 % sds / 5 mm edta / 1 mm dtt / 1 mm aebsf / 10 g / ml aprotinin / 10 g / ml leupeptin / 1 g / ml pepstatin a / 20 mm sodium fluoride ) . the viscosity of the sample was reduced by passing it through an 18 - gauge needle followed by sonication . triton x-100 was added to 2 % final concentration , and the biotinylated proteins were purified using streptavidin agarose ( pierce / thermo fisher ) and eluted in an sds - page sample buffer . the proteins in each sample were fractionated by sds - page and visualized by coomassie blue . each gel lane was divided into six slices , and the proteins in each slice were digested in situ with trypsin ( promega modified ) in 40 mm nh4hco3 overnight at 37 c . the resulting tryptic peptides were analyzed by hplc - esi - ms / ms as described above , except that a 30 min hplc gradient was employed and the six most intense ions in the precursor scan were fragmented . the xcalibur raw files were converted to mzxml format using readw ( http://tools.proteomecenter.org/wiki/index.php?title=software:readw ) and were searched against the ipi human protein database ( v 3.24 ; 66,923 protein entries ) using x ! tandem . methionine oxidation was considered as a variable modification in all searches , and lysine biotinylation was included for the bioid experiments . tandem search results were analyzed by the trans - proteomic pipeline version 4.3 . a proteinprophet score of 0.9 was used as a cutoff , which corresponded to false identification rates of 1.1 % and 0.7 % in the flag - his - ews - fli - 1 and bioid - ews - fli - 1 data sets , respectively . the following antibodies were used : rabbit polyclonal anti - cimpr ( ab32815 , abcam ) ; mouse monoclonal anti - cyclin d1 ( 2926 , cell signaling technologies ) ; mouse monoclonal anti - flag ( m2 , sigma - aldrich ) ; rabbit polyclonal anti - flag ( immunology consultants laboratory , inc . ) ; rabbit polyclonal anti - fli - 1 ( ab15289 , abcam ) ; mouse monoclonal anti - ha ( 16b12 , covance ) ; mouse monoclonal anti - lamp2 ( 55803 , bd biosciences ) ; rabbit polyclonal anti - msin3a ( k - 20 , santa cruz biotechnology ) ; rabbit polyclonal anti - myc ( n262 , santa cruz biotechnology ) ; mouse monoclonal anti - nucleolin ( c23 , santa cruz biotechnology ) ; mouse monoclonal anti - p62 / sqstm1 ( 610832 , bd biosciences ) ; and mouse monoclonal anti - tubulin ( dm1a , lab vision ) . a673 cells were treated with 100 m chloroquine for 12 h or left untreated . lysosomes were prepared using the lysosome enrichment kit for tissue and cultured cells ( # 89839 , pierce / thermo scientific ) following the manufacturer s protocol . briefly , cells were lysed by sonication in the manufacturer s lysis buffer and centrifuged at 500 g for 10 min . the resulting supernatant was placed on top of a density gradient comprising of 17 % - 30 % iodixanol -5,5 - [ ( 2 - hydroxy -1,3-propanediyl ) - bis ( acetylamino ) ] bis [ n , n - bis ( 2,3 dihydroxypropyl -2,4,6-triiodo-1,3-benzenecarboxamide ) ] in the manufacture s gradient dilution buffer , with an aliquot of the supernatant saved as the input fraction . the lysosome enrichment gradient was centrifuged at 145,000 g using a sw60ti rotor ( beckman - coulter ) for 2 h at 4 c . the top layer of the gradient , which contains the lysosomes , was collected , diluted with two volumes phosphate - buffered saline , and centrifuged at 16,000 g for 30 min at 4 c . the resulting lysosome pellet was washed once in gradient dilution buffer and dissolved in sds - page sample buffer . for immunoblotting analysis , to dissect the ews - fli - 1 interactome , we initially employed a tandem affinity purification approach . we expressed flag - his - tagged ews - fli - 1 in human embryonic kidney 293 t cells and isolated the ews - fli -1-containing protein complex by nickel agarose chromatography followed by anti - flag immunoprecipitation , which was subsequently analyzed by hplc - esi - ms / ms as described in the experimental procedures ( figure 1a ) . at a protein prophet probability score of 0.9 or higher ,105 different proteins were identified ( table s1 ) . to exclude the false positive identifications , we employed the data sets obtained using two unrelated nuclear proteins , p21 ( cdkn1a ) and histone macroh2a . the proteins commonly identified by flag - his - ews - fli - 1 and flag - his - p21 or flag - his - macroh2a with a protein prophet probability score of 0.9 or higher were considered as false positive identifications ( the list of these proteins is shown in table s2 ) . after subtracting these false positive identifications , 54 proteins remained in the flag - his - ews - fli - 1 data set ( shown in table s3 ) , including known ews - fli - 1 interactors such as ews ( figure 1b ; note that two ews c - terminal peptides , which are absent in ews - fli - 1 , were identified ) and rna helicase a ( figure 1c ) . while the tandem affinity purification approach identified known interactors for ews - fli - 1 , we noticed that the majority of flag - his - ews - fli - 1 expressed in 293 t cells was not solubilized under the non - denaturing solubilization conditions used for tandem affinity purification ( figure 1d ) . forty - eight hours after transfection , flag - his - ews - fli - 1 and its interacting proteins were isolated by nickel affinity chromatography followed by anti - flag immunoprecipitation and the protein sample was analyzed by tandem mass spectrometry . ( d ) flag - his - ews - fli - 1 is mostly insoluble under the lysis conditions used for tandem affinity purification . the abundance of flag - his - ews - fli - 1 in whole cell lysate ( lane 1 and 4 ) , tandem affinity purification lysate ( lane 2 and 5 ) , and postlysis pellet ( lane 3 and 6 ) was determined by anti - flag immunoblotting . therefore , as an alternative approach to dissect the ews - fli - 1 interactome , we used the proximity - dependent biotinylation technique , bioid . in the bioid approach , a bait protein is fused to a mutated bira biotinylase ( bira r118 g ) which promiscuously biotinylates the lysine residues of proteins in the vicinity ( within 2030 nm ) . the biotinylated vicinal proteins are purified by streptavidin affinity chromatography and are identified by mass spectrometry . the bioid approach does not require the purification of a stable protein complex under non - denaturing conditions and is useful for the analysis of insoluble protein complexes or transient low - affinity interactions . it has been successfully applied to identify interactors for nuclear lamin a , whose insolubility has hampered the analysis of its interactors , and to identify the protein components of bilobe , an insoluble cytoskeletal structure in trypanosoma brucei . we expressed bioid - tagged ews - fli - 1 in human embryonic kidney 293 cells , induced the biotinylation of the proteins in the vicinity of bioid - ews - fli - 1 by 50 m biotin , and isolated the biotinylated proteins by streptavidin affinity chromatography ( figure 2a ) . the biotinylated proteins were analyzed as described in the experimental procedures . at a protein prophet probability score of 0.9 or higher ,561 different proteins were identified ( table s4 ) . to exclude the false positive identifications , we employed the crapome database , which is a contaminant repository for affinity purification . using crapome version 1.1 ( http://www.crapome.org/ ) , 12 control proximity - dependent biotinylation experiments performed in 293 cells were compiled . the proteins detected with five or more spectral counts per control experiment were considered as false positive identifications by the proximity - dependent biotinylation approach . the list of these false positive identifications is shown in table s5 , which contains 656 proteins . after subtracting these false positive identifications from table s4 , 366 proteins remained ( table s6 ) , including ews , which was shown to form a hetero - oligomer with ews - fli - 1 .293 cells were transfected with bioid - ews - fli - 1 ( myc tag and bira r118 g mutant fused to ews - fli - 1 ) , and the biotinylation of proteins in the vicinity of bioid - ews - fli - 1 was induced by the addition of 50 m biotin to the culture medium . the biotinylated vicinal proteins were purified by streptavidin agarose chromatography and were analyzed by tandem mass spectrometry .293 t cells were transfected with flag - ews - fli - 1 or flag - vector . the transfected cells were treated with 100 m chloroquine for 12 h where indicated . the physical interaction of flag - ews - fli - 1 and cimpr was examined by anti - flag immunoprecipitation followed by anti - cimpr immunoblotting . the immunoprecipitation of flag - ews - fli - 1 was verified by anti - flag immunoblotting . after excluding the false positive identifications , 54 proteins were identified from flag - his - ews - fli - 1 affinity purification and 366 proteins were identified from bioid - ews - fli - 1 analysis , and of these , four proteins were in common : ews - fli - 1 , hnrnpa3 , u2af1 , and ewsadditionally , different isoforms of sumo proteins were identified in both flag - his - ews - fli - 1 and bioid - ews - fli - 1 experiments . we note that there is a possible sumo - binding motif ( lellsds , residues 340346 ) in ews - fli - 1 , which could mediate the interaction with sumo proteins . ews - fli - 1 does not contain a sumoylation motif ( hydrophobic - k - x - e ) , and we have not been able to detect its sumoylation ( data not shown ) . among the high - scoring proteins identified by the bioid approach , cation - independent mannose 6 - phosphate receptor ( cimpr ) caught our attention because the detection of cimpr , which is a cargo that mediates the sorting of lysosomal hydrolase precursors from the trans - golgi network to endosomes , using bioid - ews - fli - 1 suggested a possible new link between ews - fli - 1 and the endosomemolecular biological characterization of ews - fli - 1 , performed in parallel with the proteomic analyses , demonstrated that ews - fli - 1 is a relatively stable protein and does not turn over by a proteasome - dependent mechanism ( described below ) , which led us to consider a possibility that ews - fli - 1 turns over by a lysosome - dependent mechanism . in the bioid - ews - fli - 1 experiment , 17 unique and 19 total peptides from cimpr were identified ( figure 2b and table s6 ) . consistent with the identification of cimpr by the bioid approach , we observed the coimmunoprecipitation of flag - ews - fli - 1 and endogenous cimpr upon treatment with chloroquine , an inhibitor of lysosomal degradation ( figure 2c ) . it is noteworthy that cimpr was identified by the bioid approach using only three 15 - cm plates of cells whereas it was not identified by the tandem affinity purification approach using 4015 - cm plates of cells ( even though the latter used 293 t cells which generally result in higher protein expression levels than 293 cells employed in the former ) . we believe this is related to the insolubility of ews - fli - 1 under the solubilization conditions used for tandem affinity purification ( figure 1d ) .348 peptides derived from ews - fli - 1 were identified by the bioid approach using three 15 - cm plates ( table s6 ) whereas 120 peptides derived from ews - fli - 1 were identified by the tandem affinity purification approach using 4015 - cm plates ( table s3 ) , suggesting the efficient solubilization of ews - fli - 1 by the bioid lysis buffer which contains 0.4 % sds . our result as well as two previous bioid studies suggest the utility of the bioid approach for the dissection of protein protein interactions involving insoluble proteins . the protein transport function of cimpr is regulated by the retromer complex , which redirects cimpr from the endosome to the trans - golgi network . interestingly , knockdown of cimpr or vps26a , an essential component of the retromer , resulted in reduced ews - fli - 1 protein expression ( figure 3a ) . this raised a possibility that ews - fli - 1 is transported to the late endosome and degraded by the lysosome , especially when cimpr and retromer functions are compromised . importantly , we found that coexpression of tfeb , a potent inducer of lysosomal biogenesis , resulted in striking degradation of ews - fli - 1 ( figure 3b ) . conversely , inhibition of lysosomal degradation by chloroquine stabilized ews - fli - 1 ( figure 3c ) . we found that one of the lysosomal proteases , cathepsin d , can degrade ews - fli - 1 , which was inhibited by chloroquine or a cathepsin d inhibitor , pepstatin a ( figure 3d ) . cathepsin d did not degrade p53 ( figure 3d ) , indicating that cathepsin d does not degrade proteins non - selectively . furthermore , we found that endogenous ews - fli - 1 in a673 ewing sarcoma cells is degraded upon expression of cathepsin d ( figure 3e ) and is stabilized by chloroquine , an inhibitor of lysosomal degradation ( figure 3f , left ) . endogenous ews - fli - 1 in a673 cells was not stabilized by a proteasome inhibitor , mg - 132 ( figure 3f , right ) . using subcellular fractionation , we detected endogenous ews - fli - 1 in the lysosomal fraction , which increased upon chloroquine treatment ( figure 3 g ) . an abundant lysosomal glycoprotein , lamp2 , was readily detectable in the lysosomal fraction whereas a nuclear transcriptional corepressor msin3a , which is not known to be located in the lysosome , was absent ( figure 3 g ) . p62 / sqstm1 , a known substrate of lysosomal degradation , displayed increased lysosomal location upon chloroquine treatment ( figure 3 g ) . ews - fli - 1 turns over by a lysosome - dependent mechanism : ( a ) knockdown of cimpr or vps26a results in destabilization of flag - ews - fli - 1 .293 cells were cotransfected with flag - ews - fli - 1 and shrna against luciferase ( control ) , cimpr , or vps26a . forty - eight hours after transfection , the levels of flag - ews - fli - 1 were examined by anti - flag immunoblotting .293 cells were cotransfected with flag - ews - fli - 1 and ha - tfeb or empty vector . forty - eight hours after transfection , the levels of flag - ews - fli - 1 were examined by anti - flag immunoblotting . transfected cells were left untreated ( control ) or treated with 100 m chloroquine for 12 h. the levels of flag - ews - fli - 1 were examined by anti - flag immunoblotting . ( d ) cathepsin d degrades ews - fli - 1 , but not p53 , in 293 cells .293 cells were cotransfected with flag - ews - fli - 1 and cathepsin d or empty vector . transfected cellswere left untreated or treated with 100 m chloroquine for 12 h or 100 nm pepstatin a for 12 h. 293 cells were cotransfected with flag - p53 and cathepsin d or empty vector . the levels of flag - ews - fli - 1 and flag - p53 were examined by anti - flag immunoblotting . ( e ) cathepsin d degrades endogenous ews - fli - 1 in a673 ewing sarcoma cells . a673 cells were infected with a lentivirus vector expressing cathepsin d or an empty vector , the infected cells were selected with puromycin , and the levels of endogenous ews - fli - 1 were examined by anti - fli - 1 c - terminus antibody immunoblotting at 4 days after infection . a673 cells were left untreated , treated with 100 m chloroquine for 12 h , or treated with 10 m mg - 132 for 12 h. the levels of ews - fli - 1 were examined by anti - fli - 1 c - terminus immunoblotting . while chloroquine increased the levels of endogenous ews - fli - 1 , mg - 132 had no effect on the ews - fli - 1 protein levels , suggesting that ews - fli - 1 turns over by a lysosomal , but not proteasomal mechanism . ( g ) endogenous ews - fli - 1 in a673 cells displays increased lysosomal location upon chloroquine treatment . a673 cells were treated with 100 m chloroquine for 12 h or left untreated , and the whole cell extract ( wce ) and lysosomal fraction were isolated . the abundance of ews - fli - 1 , lamp2 , p62 / sqstm1 , and msin3a in each fraction was determined by immunoblotting . we employed a translational inhibitor , cycloheximide , to inhibit the new protein synthesis in ewing sarcoma cells and analyzed the turnover of endogenous ews - fli - 1 protein . while the ews - fli - 1 protein levels did not exhibit any significant decrease after 24 h treatment with cycloheximide , the sensitivity of ewing sarcoma cells to cycloheximide did not allow us to continue the cycloheximide treatment to observe the turnover of ews - fli - 1 , which is consistent with a previous report . the toxicity of translation inhibitors such as cycloheximide was attributed to the depletion of ubiquitin . therefore , we exogenously expressed ubiquitin in ewing sarcoma cells , which made the cells less sensitive to cycloheximide , and analyzed ews - fli - 1 turnover upon prolonged cycloheximide treatment . we observed some decay of ews - fli - 1 after 72 h treatment with cycloheximide ( figure 4a ) . in contrast , c - myc [ half - life = 30 min ] and cyclin d1 [ half - life 30 min ] displayed the expected rapid decay upon cycloheximide treatment ( figure 4a ) . our data suggest that endogenous ews - fli - 1 is a relatively stable protein , which agrees with the previous findings on transfected ews - fli - 1 and fli - 1 . targeting ews - fli - 1 for degradation : ( a ) the effects of cycloheximide on endogenous ews - fli - 1 levels in ewing sarcoma cells . to reduce the toxicity of cycloheximidesubsequently , a673 and tc71 cells were treated with 100 g / ml cycloheximide for 24 , 48 , or 72 h and the levels of ews - fli - 1 , c - myc , and cyclin d1 were determined by anti - fli - 1 c - terminus , anti - c - myc , and anti - cyclin d1 immunoblotting , respectively . ( b ) the effects of cytosine arabinoside on endogenous ews - fli - 1 levels in ewing sarcoma cells . a673 and tc71 cells were treated with 300 nm cytosine arabinoside for 48 h , and the levels of endogenous ews - fli - 1 were determined by anti - fli - 1 c - terminus immunoblotting . ( c ) the effects of doxorubicin on endogenous ews - fli - 1 levels in ewing sarcoma cells . a673 and tc71 cells were treated with 60 or 120 nm doxorubicin for 72 h , and the levels of endogenous ews - fli - 1 were determined by anti - fli - 1 c - terminus immunoblotting . ( d ) the effects of rapamycin on endogenous ews - fli - 1 levels in ewing sarcoma cells . a673 and tc71 cells were treated with 10 ng / ml rapamycin for 48 h , and the levels of endogenous ews - fli - 1 were determined by anti - fli - 1 c - terminus immunoblotting . ( e ) torin 1 reduces the ews - fli - 1 protein levels in ewing sarcoma . a673 andtc71 cells were left untreated or treated with 150 or 300 nm torin 1 for 24 or 48 h. the levels of endogenous ews - fli - 1 were determined by anti - fli - 1 c - terminus immunoblotting . the experiment was repeated three times with similar results .293 cells were infected with a lentivirus vector expressing luciferase ews - fli - 1 fusion protein , and the infected cells were selected with puromycin . the cells were treated with 100 m chloroquine for 12 h or left untreated , and the luciferase activity was determined using the same amount of protein lysate ( left ) . the cells were treated with 300 nm torin 1 for 24 h or left untreated , and the luciferase activity was determined using the same amount of protein lysate ( right ) . sinceews - fli - 1 is a stable protein , there is a large therapeutic window to enhance its degradation . there are a few previously reported compounds that reduce ews - fli - 1 protein levels . rapamycin , an mtor allosteric inhibitor , was reported to diminish ews - fli - 1 protein levels in several ewing sarcoma cell lines . a screening for chemical compounds that inhibit the ews - fli -1-mediated gene expression signature identified cytosine arabinoside , which was later shown to reduce the ews - fli - 1 protein levels in ewing sarcoma cells . the same study also demonstrated that doxorubicin , one of the standard chemotherapeutic agents for treating ewing sarcoma , can reduce ews - fli - 1 protein levels in ewing sarcoma cells . however , using the conditions described in refs ( 28 ) and ( 29 ) , we have been unable to reproduce the reported effects of cytosine arabinoside , doxorubicin , and rapamycin on ews - fli - 1 protein levels ( figure 4b d ) . a transcription factor tfeb recently emerged as a master regulator of lysosomal biogenesis . the activity of tfeb is controlled by cytoplasmic sequestration , which is regulated by mtor - mediated phosphorylation . a potent mtor active - site inhibitor , torin 1 , was shown to efficiently induce the nuclear translocation of tfeb . in contrast , rapamycin , an mtor allosteric inhibitor that only incompletely inhibits mtor activity , did not induce tfeb nuclear translocation at any of the concentrations that are routinely used ( 10 nm 10 m ) . we found that torin 1 treatment of ewing sarcoma cells resulted in reduced ews - fli - 1 protein levels ( figure 4e ) , suggesting a potential therapeutic utility of mtor active - site inhibitors against ewing sarcoma . we also devised the fusion of ews - fli - 1 and firefly luciferase to monitor the ews - fli - 1 protein levels . the luciferase activity derived from the luciferase ews - fli - 1 fusion protein increased upon chloroquine treatment and decreased by torin 1 treatment ( figure 4f ) , further supporting that ews - fli - 1 turns over by a lysosome - dependent mechanism , which can be enhanced by torin 1 . in addition , this luciferase reporter can be used in the future to screen for compounds that target ews - fli - 1 for degradation . since the discovery of chromosomal translocation generating the ews - fli - 1 fusion oncogene and the pivotal role played by the transcriptional activity of ews - fli - 1 in ewing sarcoma , several attempts have been made to target the transcriptional activity of ews - fli - 1 . stegmaier et al . screened a small molecule library for compounds that inhibit the gene expression signature mediated by ews - fli - 1 in a673 ewing sarcoma cells and identified cytosine arabinoside as an ews - fli - 1 modulator . employed surface plasmon resonance screening for compounds that bind ews - fli - 1 and identified a small molecule that blocks the interaction of ews - fli - 1 and rna helicase a , leading to suppression of ews - fli - 1 transcriptional activity and ewing sarcoma growth . grohar et al . employed a high throughput screen ( luciferase reporter screen followed by a gene signature secondary screen ) to evaluate over 50,000 compounds for inhibition of ews - fli - 1 transcriptional activity and identified mithramycin as an ews - fli - 1 inhibitor displaying anti - ewing sarcoma activity . used four ews - fli - 1 transcriptional target genes as readout to screen for compounds that abrogate ews - fli - 1 transcriptional activity and identified a kinase inhibitor , midostaurin , which induced apoptosis in ewing sarcoma cells . while these seminal attempts provided important insights into ewing sarcoma biology , an ews - fli -1-targeted therapy has not reached clinical translation and ews - fli - 1 remains the perfect target without a therapeutic agent . our findings that ews - fli - 1 turns over by a lysosome - dependent mechanism and that an mtorc1 active - site inhibitor can reduce the ews - fli - 1 protein levels in ewing sarcoma cells suggest a potential therapy by targeting ews - fli - 1 for degradation . proteomic analysis of the ews - fli - 1 interactome led to the discovery of the role for the lysosome in ews - fli - 1 protein turnover . we demonstrated that ews - fli - 1 is a stable protein , which provides a large therapeutic window to enhance its degradation . we found that an mtorc1 active - site inhibitor , torin 1 , which stimulates the tfeb - lysosome pathway , can induce the degradation of ews - fli - 1 in ewing sarcoma cells . mtorc1 active - site inhibitors could target both the dependence of ewing sarcoma on igf - mtor signaling and ews - fli - 1 protein turnover and are potentially more effective than mtor allosteric inhibitors as therapy for ewing sarcoma .\noutput:\n" }, { "from": "agent", "value": "ewing sarcoma is a cancer of bone and soft tissue in children that is characterized by a chromosomal translocation involving ews and an ets family transcription factor , most commonly fli - 1 . ews - fli - 1 fusion accounts for 85 % of cases . the growth and survival of ewing sarcoma cells are critically dependent on ews - fli - 1 . a large body of evidence has established that ews - fli - 1 functions as a dna - binding transcription factor that regulates the expression of a number of genes important for cell proliferation and transformation . however , little is known about the biochemical properties of the ews - fli - 1 protein . we undertook a series of proteomic analyses to dissect the ews - fli - 1 interactome . employing a proximity - dependent biotinylation technique , bioid , we identified cation - independent mannose 6 - phosphate receptor ( cimpr ) as a protein located in the vicinity of ews - fli - 1 within a cell . cimpr is a cargo that mediates the delivery of lysosomal hydrolases from the trans - golgi network to the endosome , which are subsequently transferred to the lysosomes . further molecular cell biological analyses uncovered a role for lysosomes in the turnover of the ews - fli - 1 protein . we demonstrate that an mtorc1 active - site inhibitor , torin 1 , which stimulates the tfeb - lysosome pathway , can induce the degradation of ews - fli - 1 , suggesting a potential therapeutic approach to target ews - fli - 1 for degradation ." } ]

[ { "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 all domains of life , nucleotide - based second messengers allow a rapid integration of external and internal signals into fine - tuned regulatory pathways that control cellular responses to changing conditions . as a unifying theme , a basic second messenger control module consists of two distinct enzymes for synthesis and degradation of the second messenger and a nucleotide sensor that , upon ligand binding , interacts with a target to produce a cellular output ( hengge , 2009 ) .3 , 5 - cyclic diguanylic acid ( c - di - gmp ) , which is not produced in archaea or eukaryotes , was first discovered as an allosteric effector of cellulose synthase in gluconacetobacter xylinus and is now recognized as one of the most important and widespread second messengers in bacteria . c - di - gmp is synthesized from two molecules of gtp by diguanylate cyclases ( dgcs ) , which are characterized by active site ggdef motifs ( a - site ) ( paul et al . , 2004 ; chan et al . , the majority of active dgcs also carry a so - called inhibitory or i - site motif , rxxd , which is involved in feedback inhibition ( christen et al . , 2006 ; schirmer and jenal , 2009 ) . specific phosphodiesterases ( pdes ) , which harbor eal or hd - gyp domains , degrade the cyclic dinucleotide ( schmidt et al . , 2005 ; christen et al . , 2005 ; the enzymatically active domains involved in c - di - gmp turnover are often associated with diverse sensory domains , thus enabling cells to adjust second messenger levels in response to different environmental stimuli ( hengge , 2009 ) . the binding of c - di - gmp to effector proteins impacts diverse processes such as adhesion , virulence , motility , and biofilm formation in unicellular , flagellated bacteria ( rmling et al . , the known c - di - gmp - binding motifs of these proteins are limited but include degenerate ggdef domain proteins carrying i - site motifs ( duerig et al . , 2009 ; , 2007b ; petters et al . , 2012 ) , inactive eal domain receptors ( navarro et al . , 2009 ; 2009 ) , and pilz domain - containing proteins ( amikam and galperin , 2006 ) . transcription factors that sense c - di - gmp lack these common c - di - gmp - binding motifs and thus must be identified experimentally . the sparse list of known c - di - gmp - responsive transcriptional regulators includes the tetr - like activator ltma from mycobacterium smegmatis ( li and he , 2012 ) , the crp - fnr - like transcription factor clp from xanthomonas ( chin et al . , 2010 ; leduc and roberts , 2009 ) , bcam1349 from burkholderia ( fazli et al . , 2011 ) , the ntrc - type protein fleq from pseudomonas aeruginosa ( baraquet and harwood , 2013 ) , and vpsr from vibrio cholerae ( srivastava et al . , 2011 ) . the only c - di - gmp - responsive transcription factor for which structural information is available and hence c - di - gmp binding is understood is vpst , which is a member of the well - studied fixj - luxr - csgd family of response regulators . the vpst structure revealed a characteristic response regulator fold and a w ( f / l / m ) ( t / s ) r c - di - gmp - binding motif ( krasteva et al . , 2010 ) . notably , in all known structures of c - di - gmp - binding effector proteins or enzymes , the c - di - gmp is bound either as a monomer or intercalated dimer . biophysical studies suggest the possibility of higher order oligomeric forms of c - di - gmp , but they have yet to be observed in any biological context ( gentner et al . , 2012 ) . while the roles played by c - di - gmp in controlling cellular processes in unicellular bacteria are becoming clear , the function ( s ) of c - di - gmp in multicellular , nonmotile bacteria such as streptomyces are unknown . the complex streptomyces life cycle involves two distinct filamentous cell forms : the growing or vegetative hyphae and the reproductive or aerial hyphae , which differentiate into exospores for dispersion through a massive synchronous septation event ( flrdh and buttner , 2009 ) . in the model species streptomyces venezuelae , there are three ggdef proteins , two proteins with hd - gyp domains , and five proteins containing both a ggdef and an eal domain ( figure 1a ) . altered expression of the ggdef proteins , cdga and cdgb , and deletions of the eal proteins , rmda and rmdb , have a significant impact on streptomyces growth progression , suggesting that c - di - gmp plays a role in controlling developmental processes in multicellular bacteria ( den hengst et al . , 2010 ; interestingly , cdga and cdgb have recently been identified as direct regulatory targets of the developmental master regulator bldd ( den hengst et al . , 2010 ; tran et al . , mutations in the bld loci block the formation of aerial hyphae , resulting in a baldphenotype , and also affect the production of antibiotics ( mccormick and flrdh , 2012 ) . bldd sits at the top of the regulatory cascade controlling development , serving to repress expression of sporulation genes during vegetative growth ( den hengst et al . , 2010 ) . in streptomyces coelicolor , bldd controls the expression of at least 167 genes , including 42 genes ( 25 % of the regulon ) that encode regulatory proteins ( elliot et al . , 2001 ; den hengst et al . , are many genes known to play critical roles in streptomyces development , including other bld regulators ( e.g. , blda , bldc , bldh / adpa , bldm , and bldn ) , several whi ( white ) regulators required for the differentiation of aerial hyphae into spores ( e.g. , whig and whib ) , and genes encoding critical components of the cell division and chromosome segregation machineries such as ftsz , ssga , ssgb , and the dna translocase sffa ( den hengst et al . , 2010 ; mccormick , 2009 ) . we show that bldd is a c - di - gmp - binding effector protein , thus revealing a link between c - di - gmp signaling and the development of multicellular bacteria . specifically , structural and biochemical analyses show that the second messenger c - di - gmp activates bldd dna binding by driving a unique form of dimerization that is mediated by a tetrameric form of c - di - gmp . the c - di - gmp tetramer performs its oligomerization function by adjoining two bldd c - terminal domain ( ctd ) protomers , the polypeptide chains of which are separated by 10 . bldd recognizes the c - di - gmp tetramer using a bipartite rxd - x8 - rxxd c - di - gmp interaction signature sequence from each subunit . thus , tetrameric c - di - gmp acts as a small - molecule dimerizing agent that controls the dna - binding activity of bldd , leading to repression of the bldd regulon of sporulation genes during vegetative growth , thereby controlling the hypha - to - spore transition in multicellular bacteria . to gain insight into the cellular processes controlled by c - di - gmp in streptomycetes , we overexpressed either the active dgc cdgb from s. coelicolor ( tran et al . , 2011 ) or the active pde yhjh from e. coli ( pesavento et al . , strikingly , overexpression of both cdgb and yhjh blocked the generation of aerial mycelium by s. venezuelae ( figure 1b ) . however , scanning electron micrographs ( sems ) revealed that , whereas overexpression of cdgb blocked development , resulting in a classical bald phenotype , overexpression of the pde yhjh in fact promoted sporulation , but the colonies appeared bald to the naked eye because aerial mycelium formation had been bypassed ( figure 1c ) . as judged by heat resistance , the spores made by the yhjh overexpression strain were as robust as those of the wild - type ( wt ) ( figure s1a available online ) . moreover , overexpression of catalytically inactive versions of yhjh or cdgb had no effect on s. venezuelae development ( figure s1b ) . these data suggest that intracellular levels of c - di - gmp influence the timing of development . in particular , they suggest that increased c - di - gmp levels delay differentiation , arresting the colonies in the vegetative growth stage , whereas decreased levels of the second messenger accelerate development , favoring sporulation . s. venezuelae has no pilz domain - containing proteins , and no putative c - di - gmp - binding effector proteins have so far been identified in the streptomyces genus . thus , to address the mechanism by which s. venezuelae senses c - di - gmp to control sporulation , we sought to identify c - di - gmp effector proteins involved in development . to selectively enrich putative c - di - gmp - binding proteins from s. venezuelae cell extracts , we performed an affinity pull - down assay using a c - di - gmp capture compound ( nesper et al . , 2012 ) . remarkably , the developmental master regulator bldd was repeatedly recovered in our c - di - gmp - based capture compound experiments . bldd is an 18 kda dna - binding protein ( elliot and leskiw , 1999 ) consisting of two distinct domains connected by a flexible linker ( figure 2a ) . the n - terminal domain is the dna - binding domain ( dbd ) and has a xenobiotic response element ( xre ) helix - turn - helix ( hth ) dna - binding motif ( kim et al . , 2006 ) . the bldd ctd harbors a largely helical fold with no known function ( kim et al . , 2014 ) . to probe the interaction between bldd and c - di - gmp further and to identify the c - di - gmp - binding domain , we used differential radial capillary action of ligand assays ( dracala ) ( roelofs et al . , 2011 ) . dracala allows the visualization of protein - bound radiolabeled ligand as a concentrated spot after the application of the protein - ligand mixture onto nitrocellulose . using this assay , we confirmed that full - length ( fl ) bldd ( expressed as an n - terminally his6 - tagged protein ) from both s. venezuelae ( figures 2b and s2b ) and s. coelicolor ( data not shown ) bind p - labeled c - di - gmp . importantly , the dracala assays demonstrated that the previously uncharacterized ctd of bldd functions as the c - di - gmp - binding domain ( figure 2b ) . further , excess unlabeled c - di - gmp , but not gtp , competed with the labeled c - di - gmp for binding to fl bldd and to bldd - ctd . thus , these data reveal that the ctd of the key developmental regulator bldd is a c - di - gmp - binding domain . using global chromatin immunoprecipitation - microarray analysis ( chip - chip ) , we previously identified the complete bldd regulon in s. coelicolor , showing that it encompasses 167 transcription units ( den hengst et al . ,2010 ) . through meme - based sequence analysis of all the promoter regions directly targeted by bldd , we defined a 13 bp pseudo - palindromic sequence , 5 - tnac ( n ) 5gtna - 3 , designated the bldd box , which functions as a specific binding sequence for bldd ( den hengst et al . , 2010 ) . sequence analysis showed that the bldd box was conserved between s. coelicolor and s. venezuelae for most key bldd target promoters ( den hengst et al . , 2010 ) . further , bldd from s. coelicolor and s. venezuelae contain an identical dbd and differ by only two residues in the dbd - ctd linker and five residues in the ctd , suggesting that bldd function is broadly conserved between the two species . having shown that bldd binds c - di - gmp , we tested the effect of c - di - gmp on bldd dna binding . radiolabeled s. venezuelae dna fragments encompassing the promoter regions of two well - characterized bldd target genes , bldm and whig , including the bioinformatically identified bldd box ( figure 2c ) , were used as target dnas in electrophoretic mobility shift assays ( emsas ) ( figure 2d ) . the fixed concentration of bldd used in these assays ( 0.6 m ) was insufficient to elicit a dna mobility shift . however , the addition of increasing concentrations of c - di - gmp ( 0.251.75 m ) strongly induced bldd binding to both the tested promoter regions ( figure 2d ) . to confirm and extend these results into cells , we manipulated the levels of c - di - gmp in s. venezuelae and monitored the effect on bldd binding to the bldm and whig promoters in vivo using chip - sequencing ( chip - seq ) . the degree of bldd binding was assayed at a single time point in wt s. venezuelae and the wt overexpressing either the dgc cdgb or the pde yhjh ( the strains whose phenotypes are described above ) . consistent with the in vitro emsa data , overexpression of the dgc enhanced chip - seq peak height at the bldd target promoters relative to the wt control ( figure 2e ) . conversely , overexpression of the pde lowered chip - seq peak heights at bldd target promoters relative to the wt ( figure 2e ) . these data demonstrate that c - di - gmp enhances the binding of bldd to the bldd box , stimulating bldd - mediated repression of its target regulon . thus , it is not bldd , but a bldd - ( c - di - gmp ) complex , that serves to turn off sporulation genes during vegetative growth . the opposing effects of the overexpression of the dgc cdgb and the pde yhjh suggested that high levels of c - di - gmp retard sporulation and low levels of c - di - gmp accelerate sporulation . because the bldd - ( c - di - gmp ) complex serves to keep sporulation genes shut off during vegetative growth , loss of blddshould have a similar effect on streptomyces development as depletion of c - di - gmp levels . to test this hypothesisstrikingly , the bldd null mutant formed small colonies lacking aerial hyphae , but when examined by sem even young colonies of the bldd mutant were found to contain spore chains embedded in an excess of extracellular matrix ( figure 3a ) . heat resistance tests showed the bldd mutant spores were mildly defective ( figure s1a ) . by contrast , equivalent young colonies of the wt that were grown and imaged in parallel had not yet developed aerial hyphae or spores ( figure 3b ) . thus , loss of bldd mimics the effects of overexpressing the pde yhjh ( compare figures 1c and 3a ) . in addition , overexpression of cdgb had no effect on the phenotype of the bldd mutant ( figure s2a ) , further supporting the idea that c - di - gmp signals through bldd to control the hypha - to - spore transition . to elucidate the molecular basis for c - di - gmp recognition and binding by the bldd ctd and to gain insight into how this interaction may elicit developmental signaling , we determined structures of the s. venezuelae bldd ctd ( residues 80166 ) and s. coelicolor bldd ctd ( residues 80167 ) in complex with c - di - gmp . three s. venezuelae bldd c - domain - ( c - di - gmp ) structures and one s. coelicolor bldd c - domain - ( c - di - gmp ) structure were determined to resolutions of 1.95 , 2.33 , 1.75 , and 2.25 , respectively ( figure 4 ) ( see extended experimental procedures and tables s1 and s2 ) . the bldd ctd structures are composed of two ( -- ) repeats followed by a short c - terminal helix and are similar to the apo form studied by nmr ( kim et al . , 2014 ) ( figure 4 ) . database searches revealed that the bldd ctd harbors a new fold , but reduced stringency revealed that it shows limited structural similarity with winged hth proteins , in particular , the winged hth domain of eukaryotic heat shock factor 1 ( hsf1 ) ( littlefield and nelson , 1999 ) . the bldd ctd and hsf1 bind c - di - gmp and dna , respectively , but the motifs they employ to interact with their nucleotide ligands are completely different ( figure s3 ) . the bldd ctd uses a previously unseen mode of c - di - gmp binding in which two noninteracting ctds are glued together by a c - di - gmp tetramer composed of two interlocked c - di - gmp dimers ( figure 4a ) . thus , in the bldd ctd - ( c - di - gmp ) complex , c - di - gmp functions as a macromolecular dimerizer . indeed , the closest approach of any c atoms of the two tethered ctds is 10 . the bldd ctd interacts with c - di - gmp using two contiguous surface motifs , herein called motif 1 and motif 2 , which are located between the two -- repeats . motif 1 is composed of residues 114116 ( rgd ) and motif 2 is composed of residues 125128 ( rqdd ) ( figure 5a ) . these motifs are located on a solvent exposed region at one end of each ctd protomer and not within a pocket or cavity ( figures 4a and 5a ) . the combined motifs from two ctd subunits provide ideal shape and electrostatic complementarity for encasing the unusual cage - like c - di - gmp tetramer ( figures 4a and 4b ) . strikingly , although the bldd ctd is overall acidic ( pi5 .0 ) , the c - di - gmp - binding surface between two bldd protomers is electropositive ( figure 4b ) . in addition to shape and charge complementary , contacts from the arginine and aspartic acid residues within motifs 1 and 2 provide specificity for recognition of guanine cyclic nucleotides ; the multiple interactions effectively exclude binding to adenine cyclic nucleotides . specifically , motif 2 from each ctd protomer combine to mediate contacts to one intercalated c - di - gmp dimer , asp116 of motif 1 from each protomer combine to mediate contacts to the other c - di - gmp dimer , while arg114 sits centrally and anchors both dimers ( figures 5a and 5b ) . the guanine bases wedged between the two motif 2 regions are specified by contacts from residues arg125 and asp128 ( figures 5a and 5b ) . residue asp128 makes two hydrogen bonds to the n1 and the exocyclic n2 atoms of the guanine bases on each end ( top and bottom layers ) of the intercalated dimer , while arg125 flanks the guanines in the center ( middle layers ) of the dimer and makes hydrogen bonds to the guanine o6 and n7 atoms ( figures 5b5d ) . notably , the stacking interactions between the arg125 side chains are the only direct contacts between the two ctd protomers but are clearly not sufficient to promote bldd dimerization . arg114 is the only ctd residue that makes contacts to both intercalated c - di - gmp dimers . arg114 hydrogen bonds to the guanines contacted by asp128 , as well as the o6 atoms of the adjacent guanines of the other c - di - gmp dimer ( figures 5a and 5b ) . thus , arg114 plays a key role in the recognition and stabilization of this unique c - di - gmp tetramer . the c - di - gmp dimer bound between the motif 1 regions has fewer contacts and is more exposed ( figure 5a ) . in addition to contacts from arg114 , asp116 of motif 1 hydrogen bonds to the guanine n1 and n2 atoms in a manner analogous to the contacts from asp128 of motif 2 ( figure 5 ) . notably , the specific hydrogen bonds from motif 1 and 2 residues to guanine exocyclic o6 and n2 atoms dictate that bldd binds to c - di - gmp but not to c - di - amp , which is missing an exocyclic atom at the 2 position and harbors a hydrogen bond donor rather than an acceptor at the exocyclic 6 position . bldd motifs 1 ( rxd ) and 2 ( rxxd ) , although similar in sequence to the inhibitory i - site ( rxxd ) , which is involved in product inhibition feedback control of dgc activity ( christen et al . , further , mutagenesis of either bldd motif 1 or motif 2 abolishes c - di - gmp binding in dracala assays ( figure s2b ) , confirming that , unlike i - site c - di - gmp binding , both motifs 1 and 2 in bldd are required to construct the complete binding site for the tetrameric c - di - gmp complex . this dual signature sequence is unlike any previously characterized c - di - gmp - binding motif . moreover , specific binding of the c - di - gmp tetramer requires encasement by two such bipartite motifs from precisely oriented bldd protomers . while the arginine and aspartic acid residues in bldd motifs 1 and 2 dictate the c - di - gmp - binding arrangement and read the guanine bases , contacts to the c - di - gmp phosphate groups are provided by lys84 from 1 and arg130 from 3 . further , ile110 makes van der waals interactions and residues asn118 and ser123 hydrogen bond with the guanine bases on the top and bottom layers of the c - di - gmp tetramer ( figure 5a ) . the combination of the optimally positioned bipartite signature sequences from two bldd protomers exquisitely templates binding of the specific and unusual c - di - gmp tetramer structure . c - di - gmp is monomeric in solution at physiological concentrations ( gentner et al . , 2012 ) . however , intercalated c - di - gmp dimers have been observed in crystal structures of the nucleotide alone and in complexes with effector proteins . higher order c - di - gmp structures such as tetramers and octamers have thus far only been inferred from nmr and spectroscopic studies and require very high c - di - gmp concentrations ( up to 30 mm ) and monovalent cations ( zhang et al . , 2006 ) . these higher order structures are characterized by g - quartet interactions with a centrally bound potassium ion coordinated by four guanines . there are minimal base contacts and no base stacking interactions in these structures ( figure s4a ) ( zhang et al . , 2006 ; gentner et al . ,2012 ) . by sharp contrast , the bldd - bound tetrameric c - di - gmp is a tightly packed structure that is not secured by ions . rather , the c - di - gmp molecules are closely spaced and optimally positioned for interbase pairing , leading to the formation of a multistranded , base - stacked structure with top , middle , and bottom layers ( figures 5d and s4a ) . there are 12 hydrogen bonds between the two intercalated dimers within the c - di - gmp tetramer , including contacts between the n3 atoms and exocyclic nh2 amides of an adjacent base ( figures 5c and s4b ) . such contacts could not be formed with c - di - amp due to its lack of an exocyclic nh2 atom . therefore , in addition to contacts from motifs 1 and 2 , guanine - guanine base hydrogen bonds serve to specify c - di - gmp tetramer binding to bldd . notably , formation of the c - di - gmp tetramer buries 24 % of the total surface area ( buried surface area [ bsa ] ) of the c - di - gmp molecules ( figure s4b ) . by comparison , in most protein oligomersthe bsa between protomers is 15 % ( wang et al . , 2009 ) . finally , the interface between the intercalated c - di - gmp dimers that forms the tetramer is remarkably complementary in shape ( figure s4b ) . thus , the combination of multiple contacts between the c - di - gmp moieties along with its extensive bsa and molecular shape complementarity lead to the creation of a compact and highly specific c - di - gmp tetramer . however , bldd is necessary to stabilize this tetramer and template its formation . the bldd ctd - ( c - di - gmp ) crystal structures reveal that c - di - gmp acts as a dimerizer to link two ctd protomers . to examine the effect of c - di - gmp on the oligomeric state of the bldd ctd in solution , we carried out chemical crosslinking and size exclusion chromatography ( sec ) studies . chemical crosslinking experiments were performed using disuccinimidyl suberate ( dss ) , which contains amine - reactive n - hydroxysuccinimide esters at both ends of an 11 spacer arm . this reagent should therefore be able to crosslink even the distantly anchored ctd protomers observed in our ctd - ( c - di - gmp ) structures ( figure 4a ) . in the absence of dss , the bldd dbd and ctd migrate on sds - page gels as single bands with the expected monomeric molecular weights of 11 and 12 kda , respectively ( figure 6a ) . upon incubation with dss , the bldd dbd forms a covalent dimer of 21 kda , consistent with previous biochemical and structural analyses of this domain ( kim et al . , 2006 ; lee et al . , 2007a ) , and oligomerization is unaffected by the addition of c - di - gmp ( figure 6a ) . however , in the presence of c - di - gmp , addition of dss results in the clear formation of covalent ctd dimers ( figure 6a ) . to examine c - di - gmp - induced ctd oligomerization further , we performed sec analyses . as part of this study , we mutagenized the rgd ( motif 1 ) - x8 - rqdd ( motif 2 ) c - di - gmp - binding signature of the bldd ctd . to retain the charge of these surface residues , we made the charge - swapped dgr - x8 - dqdr ctd mutant , changing the key arg residues within the two motifs to asp , and vice versa . dracala assays showed that this mutant ctd was unable to bind c - di - gmp ( figure s2b ) . sec experiments in the presence of 3 m c - di - gmp showed that the wt ctd forms a dimer , while the mutant ctd is monomeric ( figure 6b ) . hence , the crosslinking and sec data support our structural finding that c - di - gmp is required for bldd ctd dimerization . further , we constructed a bldd mutant allele encoding a protein solely defective in c - di - gmp binding ( carrying the dgr - x8 - dqdr mutation ) and found that it had no ability to complement a bldd mutant ( figure s2a ) , confirming that the major in vivo functions of bldd are indeed mediated by its binding to c - di - gmp . our structures reveal a unique interaction between the bldd ctd and a c - di - gmp tetramer . remarkably , every guanine in this complex is read specifically by either bldd arginines , aspartic acids , and / or other guanine bases , suggesting that bldd binds only c - di - gmp , and not other cyclic nucleotides . to test this hypothesis and further probe the c - di - gmp - binding affinity of bldd , we performed fluorescence polarization ( fp ) experiments . these studies were performed with bldd ctd that was expressed and purified from sf9 insect cells to ensure no c - di - gmp was present , as eukaryotes do not produce c - di - gmp ( extended experimental procedures ) . the bldd - ( c - di - gmp ) structures show that one ribose of each c - di - gmp bound to bldd must be unmodified to permit formation of the bldd - ( c - di - gmp ) complex ( figure s5a ) . hence , for these studies we used the fluoresceinated probe , 2 - fluo - ahc - c - di - gmp , which harbors the fluorescein dye on only one ribose ( figure s5a ) . these studies revealed bldd ctd bound to 2 - fluo - ahc - c - di - gmp , with an apparent kd of 2.5 m 0.6 ( figure s5b ) . consistent with our dracala assays ( figure s2b ) , the dgr - x8 - dqdr ctd mutant failed to bind 2 - fluo - ahc - c - di - gmp in fp assays ( figure s5b ) . wt bldd ctd showed no binding to the identically fluoresceinated c - di - amp tagged molecule , 2 - fluo - ahc - c - di - amp ( figure s5b ) . next , to ascertain the stoichiometry of c - di - gmp binding in solution , we used an fp - based binding assay . the resulting data ( figure s5c ) a single inflection point can be fitted at a bldd monomer concentration of 12 m , which equates to a stoichiometry of four c - di - gmp molecules per ctd dimer . however , careful inspection of the data reveals another potential inflection point at a bldd monomer concentration of 6 m , which would be consistent with an initial binding event of two c - di - gmp molecules per ctd dimer . this putative initial binding event is also apparent in the equilibrium - binding isotherm yielding an apparent kd of 1.7 m ( figure s5b ) . two - step binding is not inconsistent with the structure , but the nearly identical affinities observed for each binding event suggest positive cooperativity . overall , these data demonstrate unequivocally that c - di - gmp binds the ctd with a stoichiometry of four c - di - gmp molecules per ctd dimer , concordant with our structures . these studies also demonstrate that the bldd ctd binds specifically and with high affinity to c - di - gmp but not c - di - amp and that both motifs 1 and 2 are essential for this interaction . dimeric bldd binds pseudo - palindromic dna sites that contain a 5 - tnac ( n ) 5gtna - 3 consensus ( den hengst et al . ,2010 ) . our data and those of others ( lee et al . ,2007 a ) show that the bldd dbd alone can dimerize at higher concentrations ( 10 m ) . consistent with these findings , the crystal structure of the s. coelicolor bldd dbd revealed a dimer with a small contact interface ( kim et al . , 2006 ) . we obtained additional views of the bldd dbd by solving the s. venezuelae bldd dbd structure to 2.80 resolution . comparison of these dimers with the dimer from the s. coelicolor dbd structure showed that , although hydrophobic residues within the c - terminal regions of the dbds make contacts between the subunits in each case , all three dimers take distinct conformations ( figure s6a ) . moreover , there is less than 300 bsa per subunit in this dimer , which is far less than the 1000 bsa per subunit typically observed for biologically relevant dimers ( krissinel and henrick , 2007 ) . these data indicate that the bldd dbd is unlikely to form a stable dna - binding active dimer at physiologically relevant concentrations . in addition , although the bldd dbd resembles the equivalent dbd of repressor , previous modeling studies suggested that the bldd dbds would not interact specifically with dna if bldd employed a dna - binding mechanism similar to that utilized by repressor ( kim et al . , 2006 ) . our finding that c - di - gmp binding leads to the formation of a c - di - gmp bridged ctd dimer provides the missing link to this puzzle . however , how c - di - gmp binding to the ctds is signaled to the dbds to bring about dna binding remained unclear . to deduce the mechanism by which c - di - gmp activates bldd to bind dna , we determined the structure of a bldd - ( c - di - gmp ) -21-mer dna complex to 4.5 resolution ( extended experimental procedures ; figure s6b ) . while the low resolution of the structure precludes a detailed analysis , the electron density maps show the overall arrangement of the domains and how the dbds dock onto the dna . critically , the structure reveals that bldd binding to cognate dna is more similar to the dna binding mode of the xre protein sinr ( lewis et al . , 1998 ; 2013 ) than to that of the repressor , as the two bldd dbds are juxtaposed when bldd is bound to dna ( figures 7a and 7b ) . the dbd - dbd interacting surfaces observed in the bldd - dna complex correspond to the hydrophobic regions near the dbd c terminus that interact in the apo dbd structures . however , the interfaces are yet again different , supporting the notion that dbd dimerization is weak and malleable . such malleability is critical to allow the dimeric bldd hth elements to bind the dna , which is bent by 30 . the bldd dbds are tethered to the ctd via a linker that was previously shown to be highly flexible ( kim et al . not surprisingly , this linker ( pgttpggaaeppp ; residues 7184 ) is disordered in the bldd - ( c - di - gmp ) -21-mer structure . its flexibility is underscored by the different orientation of the two ctds in the structure relative to the dbd - dna complex ( figure 7a ) . the ctd subunits in the dimer make different interactions that help anchor them in the bldd - ( c - di - gmp ) - dna crystal ; one of the ctds interacts with a hydrophobic patch on its cognate dbd , while the other ctd makes crystal contacts with a symmetry mate ( figures 7a and s6c ) . however , the ctds in the fl bldd - ( c - di - gmp ) - dna structure are dimerized in a manner identical to that observed in our ctd - ( c - di - gmp ) structures ( figures 4d , 5a , 7a , and s6c ) . additional evidence that the linker region between the dbd and ctd is flexible was provided by proteolysis experiments employing endoproteinase glu - c , which cleaves exposed peptide bonds on the carboxyl side of glutamic or aspartic acid residues . hence , if the bldd linker region is unstructured , glu - c should selectively cleave after bldd residue glu80 . glu - c proteolysis experiments were carried out on the fl bldd protein , the fl protein with the 21 - mer dna present , and the fl protein in the presence of both c - di - gmp and the 21 - mer dna . in all three cases blddwas readily cleaved into two bands , corresponding to the dbd and the ctd ( figure s6d ) . thus , neither the presence of dna , nor of c - di - gmp and dna , protected bldd from proteolysis , indicating the linker is exposed even in the presence of cognate ligands . therefore , the combined data suggest a molecular model for c - di - gmp activation of bldd dna binding in which binding of c - di - gmp leads to the formation of a c - di - gmp - linked bldd ctd dimer ( figure 7c ) . such ctd dimerization effectively brings the two dbds into proximity , thereby increasing their local concentration to allow germane dbd dimerization on cognate dna ( figure 7c ) . the inherent flexibility afforded by the dbd - ctd linker allows the dbds to adjust for optimal binding to multiple pseudo - palindromic bldd dna boxes . the role of c - di - gmp has been studied extensively in unicellular gram - negative bacteria , in which most c - di - gmp - dependent signaling pathways control the transition from a planktonic , motile lifestyle to a surface - associated , sessile lifestyle ( stick or swim ) . herewe show that the activity of the streptomyces master regulator bldd is also controlled by c - di - gmp , thus bringing the regulatory role of this key second messenger into a new physiological arena , that of differentiation in gram - positive multicellular bacteria . our studies indicate that c - di - gmp binding to bldd controls the developmental switch between vegetative growth and sporulation . specifically , we demonstrate that c - di - gmp binding to bldd activates its dna - binding activity , which results in repression of sporulation genes during vegetative growth . consistent with this , genetic studies revealed that bldd null mutants sporulate precociously , mimicking the effect of overexpressing a c - di - gmp phosphodiesterase . thus , c - di - gmp signals through bldd to control the hypha - to - spore developmental transition in streptomyces . few c - di - gmp effector - binding motifs have been identified to date .2009 ; lee et al . , 2007b ; petters et al . , 2012 ) , inactive eal domains ( navarro et al . , 2009 ; qi et al . , 2011 ; newell et al . , structures have shown that c - di - gmp interacts with these motifs as either a monomer or intercalated dimer . the bldd protein does not contain any previously characterized c - di - gmp effector - binding motifs . thus , to elucidate the mechanism by which c - di - gmp acts as a switch to turn on the dna - binding activity of bldd , we determined several structures of the bldd ctd complexed to c - di - gmp as well as a 4.5 structure of the bldd - ( c - di - gmp ) - dna complex . these structures revealed that bldd interacts with c - di - gmp using a heretofore unseen c - di - gmp binding mode involving a unique c - di - gmp - binding signature sequence consisting of two proximal arginine and aspartic acid containing motifs , motif 1 ( rxd ) and motif 2 ( rxxd ) , separated by eight residues . remarkably , in this binding mode , a tetrameric form of the c - di - gmp functions as a small - molecule dimerizer to adjoin two noninteracting bldd protomers . notably , the identical ctd dimer - ( c - di - gmp ) tetramer structure was seen in multiple crystal forms . finally , binding studies confirmed that the bldd ctd binds c - di - gmp with a stoichiometry of four c - di - gmp molecules to one bldd ctd dimer . the c - di - gmp tetramer revealed in these structures represents a previously unknown form of this nucleotide second messenger . indeed , we do not know of any other example in which a signaling molecule can assume different oligomeric states to effect its function . bldd is present throughout the sporulating actinomycetes ( den hengst et al . , 2010 ) , including , for example , nitrogen - fixing frankia that live in symbiosis within the root nodules of alder trees , and members of the marine genus salinospora , which have recently emerged as an important source of antibiotics and other medically significant compounds . outside of the genus streptomyces , the only actinomycete in which bldd has been investigated is saccharopolyspora erythraea , where bldd directly controls expression of the biosynthetic cluster of the clinically important antibiotic erythromycin ( chng et al . , 2008 ) . homologs from across the sporulating actinomycetes share 77 % 99 % sequence identity with s. venezuelae bldd . the main region of conservation between these proteins is the n - terminal dna - binding domain , which shares 95 % 100 % identity . although our bldd - ( c - di - gmp ) - dna structure is too low resolution to ascribe specific protein - dna contacts , it reveals the location of the hth motif and residues that likely contact the dna . notably , these amino acids are the most conserved among bldd homologs ( essentially 100 % ; figure s7 ) . by contrast , the ctd regions of bldd proteins are less well conserved ( as low as 48 % identity ) . hence , it is striking , given this low conservation , that the residues that interact with c - di - gmp are strictly conserved ( figure s7 ) . the only exception is lys84 , which contacts c - di - gmp phosphate groups . however , in all bldd homologs this residue is either a lysine or arginine and thus able to make the same electrostatic interaction . of particular note , residues r114 , d116 , r125 , and d128 ( from motifs 1 and 2 ) , which mediate essential specifying contacts with c - di - gmp , further , all of the actinomycetes that encode an ortholog of bldd also encode ggdef domain - containing dgcs . these combined findings indicate that bldd - ( c - di - gmp ) is likely to control key developmental processes throughout the sporulating actinomycetes , using tetrameric c - di - gmp as a second messenger . for a full explanation of the experimental protocols , see extended experimental procedures in supplemental information . strains and plasmids used are shown in table s3 , and oligonucleotides used are shown in table s4 . a bldd null mutant ( sv77 ) was constructed by redirect pcr targeting , and the bldd : : apr mutant allele was moved into a new wt background by generalized transduction using the s. venezuelae - specific phage sv1 . transduction of the bldd : : apr allele was confirmed by pcr and the strain was named sv74 . cyclic di - gmp capture compound experiments were performed as described previously ( nesper et al . , 2012 ) but with the minor modifications described in extended experimental procedures . briefly , the c - di - gmp capture compound was added to the soluble lysates and , following uv irradiation in the caprobox , magnetic streptavidin beads were added to the reaction . after incubation the beads were collected , washed , and boiled in sample buffer , the proteins released were run on sds - pa gels and cut out for mass spectrometry analysis . the dracala assays used his6 - bldd or n - terminally his - tagged domains , which were incubated with 11 nm p - c - di - gmp . the competition experiments had 266 m cold c - di - gmp or gtp added to the reaction . dna fragments spanning the bldm ( 158 bp ) and whig ( 151 bp ) promoter regions of s. venezuelae were generated by pcr and 5 end labeled using [ - p ] - atp and t4 polynucleotide kinase . the binding reactions were performed using 0.6 m his6 - bldd and radiolabeled dna ( 8,000 cpm ) as well as 0.5 g poly [ d ( i - c ) ] as nonspecific competitor dna . when appropriate , increasing amounts of c - di - gmp ( 0.251.75 m ) were added to the mixture . the reaction samples were incubated for 20 min at room temperature and then run on 5 % polyacrylamide gels . chromatin immunoprecipitations were performed as described ( bush et al . , 2013 ) using an anti - bldd polyclonal antibody . the oligomeric states of bldd and its domains were analyzed via chemical crosslinking using dss in the presence and absence of c - di - gmp ( see the extended experimental procedures ) and visualized on sds - pa gels . molecular weight analyses using sec experiments were performed with a hiload 16/600 superdex 75 pg column . for detailed descriptions of the protein expression , purification , crystallization , structure determination , and refinement protocols , see the extended experimental procedures . extended experimental proceduresbacterial strains , growth conditions , and conjugationsall e. coli strains used in this study ( table s3 ) were grown in lb medium under aeration at 37c . e. coli dh5 was used for plasmid and cosmid propagation and bl21 ( de3 ) plyss for protein overexpression . bw25113 ( datsenko and wanner , 2000 ) containing a red plasmid , pij790 , was used to create the bldd disruption cosmid and et12567 containing puz8002 ( paget et al . , 1999 ) s. venezuelae strains ( table s3 ) were grown at 30c on maltose - yeast extract - malt extract ( mym ) medium ( stuttard , 1982 ) containing 50 % tap water ( mym - tap ) and 200 l trace element solution ( kieser et al . , 2000 ) per 100 ml . conjugations between e. coli and s. venezuelae were carried out as previously described ( bibb et al . , 2012 ) . construction of plasmidsthe oligonucleotides used for plasmid constructions are listed in table s4 . for protein overexpression and purification , bldd and its individual domainswere cloned into pet15b resulting in n - terminally his - tagged fl ( full - length ) bldd ( amino acid residues 1 - 166 ) , bldd - dbd ( amino acid residues 1 - 79 ) and bldd - ctd ( amino acid residues 80 - 166 ) . for overexpression of yhjh in s. venezuelae , an n - terminally codon optimized variant of yhjh was cloned downstream of the ermep promoter in the bt1 attb site - specific integrative vector pij10257 ( hong et al . , 2005 ) . point mutations in bldd were introduced by following the four - primer / two - step pcr protocol ( germer et al . , 2001 ) . for complementation analysis the bldd gene carrying its native promoter and the r114d , d116r , r125d and d128r mutations was expressed from the integrative vector pms82.construction of a bldd null mutant derivative of s. venezuelae and phage transductionthe bldd mutant was generated according to the redirect pcr targeting protocol ( gust et al . , 2003 , 2004 ) . the sv -4-h05 cosmid was introduced into e. coli bw25113 and bldd was replaced with the apramycin - resistance ( apr ) cassette containing orit , which was amplified from pij773 using primers with bldd - specific extensions ( table s4 ) . the disrupted cosmid was confirmed by restriction and pcr analyses and introduced into e. coli et12567 / puz8002 for conjugation into s. venezuelae . a null mutant generated by double crossing over was identified by its apramycin - resistant and kanamycin - sensitive phenotype and named sv77 after confirmation by pcr using test primers listed in table s4 . the mutant allele bldd : : apr was moved into a new wt background by generalized transduction using the s. venezuelae - specific phage sv1 ( stuttard , 1979 ) . to prepare sv1 - lysate ,10 phage were added to 10 sv77 donor spores in 800 l pre - warmed ( 45c ) soft nutrient agar ( sna ) and poured onto difco nutrient agar plates containing 0.5 % glucose , 10 mm mgso4 and 10 mm ca ( no3 ) 2 . the plates were incubated at 30c overnight , then flooded with 2.5 ml difco nutrient broth ( dnb ) and incubated for 3 - 4the phage - containing dnb soak - out was harvested and filtered through a 0.45 m filter to eliminate bacterial contamination . for transduction of the bldd : : apr allele , 10 phage particles harvested from the bldd : : apr mutant strain sv77 , were mixed with 10 - 10 wt spores and incubated overnight on mym agar at room temperature before overlaying with apramycin for selection . transduction of the bldd : : apr allele was confirmed by pcr using test primers listed in table s4 , and the strain was named sv74.c - di - gmp protein capture experimentscyclic di - gmp capture compound experiments were performed as described previously ( nesper et al . , 2012 ) with minor modifications . s. venezuelae cultures were grown in mym - tap supplemented with trace element solution until late transition phase for 24 hr at 30c and then pelleted by centrifugation for 10 min at 6,000 rpm . the pellet was resuspended in lysis buffer ( 6.7 mm mes , 6.7 mm hepes , 200 mm nacl , 6.7 mm potassium acetate ( kac ) , ph 7.5 ) containing protease inhibitor and dnase i. cells were put through a french press four times at 18,000 psi and then centrifuged at 100,000 x g for 1 hr . for the capture experiments , the protein concentration of the soluble fractionwas determined using a uv / vis nanodrop spectrophotometer and 400 g protein were mixed with 10 m c - di - gmp capture compound and with 20 l 5 x capture buffer ( 100 mm hepes , 250 mm kac , 50 mm magnesium acetate ( mgac ) , 50 % glycerol , ph 7.5 ) .1 mm c - di - gmp was added to the control reaction and incubated for 30 min prior to capture compound addition . the reaction volume was adjusted with h2o to 100 l and incubated for 2 hr at 4c in the dark on a rotary wheel . after uv irradiation for 4 min in a caprobox , 50 l magnetic streptavidin beads and 25 l 5 x wash buffer ( 250 mm tris ph 7.5 , 5 m nacl , 0.1 % n - octyl -- glucopyranoside ) were added to the reaction and the mixture was incubated for 45 min at 4c on a rotary wheel . the beads were then collected with a magnet and washed 6 times with 200 l wash buffer . the beads were resuspended in 20 l sample buffer and run for 10 min on a 15 % sds polyacrylamide gel after 10 min incubation at 95c . the gel was stained using instantblue coomassie stain solution , and a 11 cm gel slice containing all captured proteins was excised for analysis by mass spectrometry.electrophoretic mobility shift assaysdna fragments spanning the bldm ( 158 bp ) and whig ( 151 bp ) promoter regions of s. venezuelae were generated by pcr using oligonucleotides listed in table s4 and then 5 end - labeled using [ - p ] - atp and t4 polynucleotide kinase . the binding reactions were performed in bandshift buffer ( 10 mm tris ph 7.5 , 1 mm edta , 5 % glycerol , 10 mm nacl , 1 mm mgcl2 ) in 20 l reaction mixture containing 0.6 m bldd and radiolabeled dna ( 8,000 c.p.m . ) as well as 0.5 g poly [ d ( i - c ) ] as nonspecific competitor dna . when appropriate , increasing amounts of c - di - gmp ( 0.251.75 m ) were added to the mixture . the reaction samples were incubated for 20 min at room temperature followed by electrophoresis on a 5 % polyacrylamide gel in 0.5 x tbe ( tris - borate - edta ) buffer at 80v for 105 min . the gels were dried before being analyzed on a phosphorimager.bldd chip - seq experimentss . chromatin immunoprecipitations were performed as previously described ( bush et al . , 2013 ) , except that an anti - bldd polyclonal antibody was used and pulled down with protein a - sepharose beads . library construction , sequencing and chip - seq data analyses were all carried out as previously described ( bush et al . , 2013 ) . chemical crosslinking and sds polyacrylamide gel electrophoresisthe his6 - bldd - dbd and his6 - bldd - ctd proteins were dialyzed into crosslinking buffer ( 100 mm nah2po4 , 150 mm nacl , ph 8 ) and then incubated at room temperature for 30 min in 20 l reaction samples containing 10 m protein , 1 mm disuccinimidyl suberate ( dss ) in dimethylsulfoxide ( dmso ) , and c - di - gmp as indicated . the reaction was stopped by adding 50 mm tris ph 8 and incubation for 15 min followed by addition of sds sample buffer and heating to 95c for 10 min . samples were separated on a 15 % sds polyacrylamide gel and visualized by coomassie staining.determination of c - di - gmp binding to proteins by differential radial capillary action of ligand assayradiolabeled c - di - gmp was synthesized in vitro using [ - p ] - gtp and the purified diguanylate cyclase pled as described ( paul et al . , 2004 ) . the dracala assays ( roelofs et al . , 2011 ) were performed using 2 g of his6 - bldd or its n - terminally his - tagged domains that were incubated with 11 nm p - c - di - gmp in dgc buffer ( 250 mm nacl , 25 mm tris ph 8 , 10 mm mgcl2 , 5 mm - mercaptoethanol ) . for competition experiments ,266 m cold c - di - gmp or gtp were added to the reaction . after a 5 min incubation at room temperature ,5 l of the binding sample were spotted onto nitrocellulose membrane and the dried membranes were analyzed using a phosphorimager.purification , crystallization , and structure determination of s. venezuelae and s. coelicolor bldd ctd - ( c - di - gmp ) complexesfor structural studies on the ctd , the regions encoding residues 80 - 166 ( s. venezuelae bldd ) and 80 - 167 ( s. coelicolor bldd ) were cloned into the pet15b vector and the proteins induced at 37c and purified via ni - nta chromatography . the his - tags were removed from the proteins used for structural studies by thrombin cleavage . crystals of the s. venezuelae bldd ctd - ( c - di - gmp ) complex , which assumed the trigonal space group , p32 , were obtained using protein at 30 mg / ml and 1 mm c - di - gmp . crystals were produced via the hanging drop vapor diffusion method and mixing the complex 1:1 with 28 % peg 1500 , 100 mm sodium acetate , ph 5.5 . the s. venezuelae bldd ctd contains no methionines and hence for phasing , leu92 and ile135 were substituted with methionines . semet ( l92m / i135 m ) bldd ctd was expressed using the methionine inhibitory pathway and the protein purified and crystallized with c - di - gmp as per the wt ctd . the selenomethionine - substituted l92m / i135 m protein crystallized in the wild - type protein p32 space group . a second crystal form of the s. venezuelae bldd ctd - ( c - di - gmp ) complex was grown with protein at 20 - 40 mg / ml and 1 mm c - di - gmp using 20 % peg 2000 monomethyl ether , 100 mm mes , ph 6.0 , as a crystallization reagent and took the orthorhombic space group p21212 . the third crystal form of the s. venezuelae bldd ctd - ( c - di - gmp ) complex was produced with protein at 10 mg / ml and 1 mm c - di - gmp using 1.2 m sodium / potassium phosphate , 50 mm citrate ph 5.6 . crystals were obtained for the s. coelicolor bldd ctd - ( c - di - gmp ) complex using 25 mg / ml protein , 1 mm c - di - gmp and mixing the complex 1:1 with a reservoir comprised of 1.4 m sodium / potassium phosphate , 100 mm hepes ph 7.5 . these crystals take the c2221 space group.multiple wavelength anomalous diffraction ( mad ) data were collected for a semet ( l92m / i135 m ) s. venezuelae bldd ctd - ( c - di - gmp ) crystal to 2.28 resolution at als ( advanced light source , berkeley , ca , usa ) beamline 8.3.1 ( table s1 ) . the data were processed using mosflm and the heavy atom substructure was obtained via solve ( terwilliger and berendzen , 1999 ) . phenix was used for final phasing and density modification ( adams et al . , 2010 ) . the crystal contains 12 protein molecules in the asymmetric unit ( asu ) and each of the six dimers is glued together by four c - di - gmp molecules . the six c - di - gmp complexed dimers are essentially identical ( figure 4d ) . final refinement was done using a data set collected to 1.95 resolution for a semet ( blddl92 m ) ctd - ( c - di - gmp ) crystal . a wt data set was also collected to 2.2 resolution and the structure was identical to the l92 m and l92m / i135 m structures . the final 1.95 resolution - structure contains residues 84 - 161 for each of the 12 subunits and 24 c - di - gmp molecules ( table s2 ) . data were collected to 1.75 , 2.25 and 2.33 resolution for the s. venezuelae and s. coelicolor bldd ctd - ( c - di - gmp ) c2221 forms and the s. venezuelae bldd ctd - ( c - di - gmp ) p21212 crystal form , respectively , and the structures solved by molecular replacement ( mr ) . the s. coelicolor bldd ctd and s. venezuelae bldd ctd c2221 crystal forms contain a ctd dimer and four c - di - gmp molecules in the asu and the s. venezuelae bldd c - domain - ( c - di - gmp ) p21212 crystal form contains 10 subunits ( five dimers ) , and 20 c - di - gmp molecules . the structures were solved by mr using the program phaser ( mccoy et al . , 2007 ) . the topology of every bldd ctd is 1 ( residues 84 - 88 ) - 1 ( residues 89 - 93 ) - 2 ( residues 98 - 113 ) - 2 ( residues 120 - 124 ) - 3 ( residues 128 - 136 ) - 4 ( residues 140 - 149 ) - 5 ( residues 154 - 160 ) . crystallization and structure determination of the s. venezuelae bldd dbdthe bldd dna binding domain ( bldd dbd ) , encoding residues 1 - 79 , was cloned into pet15b , expressed in e. coli bl21 ( de3 ) and the protein purified via ni - nta chromatography . prior to crystallization , the hexa - his tag was removed via thrombin cleavage and the protein further purified by size exclusion chromatography . crystals were grown by mixing the protein ( 40 mg / ml ) 1:1 with a reservoir consisting of 35 % peg 400 , 0.1 m mgcl2 and 0.1 m tris ph 7.5 . x - ray intensity data were collected to 2.8 resolution at als beamline 8.3.1 and processed with mosflm . the rsym and i / ( i ) for the data are 11.3 % ( 38.4 % ) and 11.4 ( 4.3 ) , respectively , where the values in parentheses indicate data from the highest resolution shell . the structure , which contains 3 subunits in the asu ( 2 subunits form a dimer and crystal symmetry generates a second dimer ) , was solved with phaser using a single s. coelicolor dbd subunit ( pdb code 2ewt ) as the search model . the final model contains residues 3 - 71 of each subunit and was refined using phenix to final rwork / rfree values of 23.7 % / 28.9 % , respectively ( adams et al . , 2010 ) . crystallization and structure determination of the s. venezuelae bldd - ( c - di - gmp ) -21-mer complexcrystals of the full - length ( fl ) s. venezuelae bldd - ( c - di - gmp ) -21-mer complex were grown by using protein in which the n - terminal hexa - his tag had been cleaved and incubated with 1 mm c - di - gmp ( final concentration ) . this bldd - ( c - di - gmp ) solution was mixed in a 1:1 molar ratio of bldd dimer to 21 - mer dna duplex ( 5 - cccctcacgctgcgtgacggg - 3 , with the canonical bldd box underlined , annealed to its complementary oligodeoxynucleotide ) for crystallization trials . crystals were grown by mixing the protein - dna complex 1:1 with the crystallization solution composed of 100 mm sodium citrate tribasic / citric acid ph 4.0 and 200 mm ammonium sulfate . the crystals take the trigonal space group , p3221 , with a = b = 114.0 , c = 95.2 and contain a bldd dimer - ( c - di - gmp ) -21-mer duplex in the asu . data were collected to the limiting resolution of 4.5 . the rsym = 9.0 % ( 86.0 % ) and i / ( i ) = 5.8 ( 1.8 ) , where the values in parentheses are for the highest resolution shell . first , bldd dna binding domain - dna complex models were constructed based on the sinr - dna ( pdb code 3zkc ) or repressor - dna ( pdb code 1lmb ) complex structures and used in the mr program phaser ( mccoy et al . , 2007 ) . this solution was then used as a static model with the ctd - ( c - di - gmp ) dimeric structure as a search model . due to its low resolution , the structure was subjected to rigid body refinement only ( rwork / rfree = 33.0 % / 38.9 % , respectively ) . proteolysis of fl bldd by endoproteinase glu - cto examine the flexibility of the linker region that connects the bldd dbd and ctd , limited proteolysis experiments were carried out . specifically , the accessibility of residue glu80 , which is the only acidic residue in the bldd linker region , was determined by the ability of the glu - c protease to cleave after this residue . in these experiments , endo - glu - c ( 100 units / ml ) was a diluted 50 fold into samples of 1 ) fl bldd ( 1 mg / ml ) , 2 ) fl bldd -21-mer dna ( 1 mg / ml protein with 100 m dna ) or 3 ) fl bldd - ( c - di - gmp ) -21-mer ( 1 mg / ml protein with 100 m 21 - mer dna and 1 mm c - di - gmp ) . the proteolysis buffer was 50 mm sodium phosphate , ph 7.5 and the final protein concentration of each sample was 4 mg / ml . the samples shown in figure s6d were taken at a time point of 4 hr . notably , proteolysis of each sample was identical , demonstrating that ligand binding of neither cognate dna nor c - di - gmp by bldd affect the accessibility of the linker region , which remains flexible and unstructured.size exclusion chromatographic analyses of wild - type bldd ctd and the bldd ctd quadruple mutantsize exclusion chromatography experiments were carried out using a hiload 16/600 superdex 75 pg column .5 mg of either the wild - type bldd ctd or the quadruple mutant were loaded onto a column that had been pre - equilibrated with 150 mm nacl , 5 % glycerol , 20 mm tris hcl ph 7.5 and 3 m c - di - gmp . the samples were run and eluted with the same c - di - gmp containing buffer . the elution volume was plotted against a standard curve to determine the relative molecular weights of the samples . the standard curve was determined using cytochrome c ( 12 kda ) , carbonic anhydrase ( 29 kda ) and albumin ( 66 kda ) . cryo - scanning electron microscopycryo - sem was performed as previously described ( bush et al . , 2013 ) . bldd ctd expression and purification from sf9 cellswhen induced in e. coli bl21 ( de3 ) at 37c , bldd ctd samples contained little to no c - di - gmp contamination , which was supported by a280 / a260 values of the purified protein , which were approximately 1.6 . however , to ensure that there was no endogenous c - di - gmp present in samples used for binding affinity measurements , the bldd ctd was expressed and purified in sf9 insect cells . for these studies , a gene encoding the same s. venezuelae bldd ctd region that was expressed in e. coli was codon optimized for expression in insect cells ( genscript , piscataway , nj , usa ; http://www.genscript.com ) and subcloned into the expression vector f1 , which was transfected into the dh10bac strain for generation of the recombinant bacmid . rbacmids were then transfected in sf9 insect cells with cellfectin ii and the cells incubated in sf - 900 ii sfm for 56 days before harvest . the supernatant was collected for the p1 viral stock and p2 was amplified for later infection . sf9 cells expressing bldd ctd were harvested at 72 hr post infection and cells were lysed into 25 mm tris ph 7.5 , 300 mm nacl and 5 % glycerol with protease inhibitors . the protein was purified from the supernatant by ni - nta followed by size exclusion chromatography and was 90 % pure as assessed by sds - page analysis.determination of the affinity , stoichiometry , and specificity of c - di - gmp for sf9 - purified bldd ctd by fluorescence polarizationto measure binding , 2 - o - ( 6 - [ fluoresceinyl ] aminohexylcarbamoyl ) - cyclic diguanosine monophosphate ( 2 - fluo - ahc - c - di - gmp ) , was used as the fluoresceinated ligand . this molecule is conjugated via a 9 atom spacer to one of the 2 hydroxyl groups of the c - di - gmp , hence meeting the structural requirement for bldd binding that only one 2 hydroxyl group be unmodified and the other available for the interactions observed in the bldd - ( c - di - gmp ) structures ( figure 5 ) . binding was carried out at 25c in a buffer of 150 mm nacl and 25 mm tris - hcl ph 7.5 , which contained 1 nm 2 - fluo - ahc - c - di - gmp . increasing concentrations of bldd ctd were titrated into the reaction mixture to obtain the binding isotherms . after each addition of protein the reaction sample was incubated for 30 min to ensure equilibrium had been reached . c - di - gmp binding to bldd appears to have the characteristics of a high affinity / slow binding ligand . the resulting data were plotted using kaleidagraph and curves were fitted to deduce binding affinities . to determine the binding stoichiometry of the bldd ctd - ( c - di - gmp ) complex , the same fp binding conditions were used but the total concentration of c - di - gmp ( c - di - gmp + 2 - fluo - ahc - c - di - gmp ) was 25 m , 10-fold above the kd of 2.5 m ensuring stoichiometric binding . close inspection of the binding isotherm revealed the possibility that there are two nearly identical binding events ( likely corresponding to the binding of each intercalated c - di - gmp dimer ) . the graph of the resulting data shows a linear increase in the observed mps until saturation of the binding sites , after which the line is flat . importantly , the final inflection occurs at a bldd monomer concentrations of 12 m , which , when divided by the concentrations of c - di - gmp ( 25 m ) , indicates a stoichiometry of two ctd protomers per four c - di - gmps . as anticipated from a purely chemical complementarity - orientated argument , fp studies carried out in the same buffer also revealed that wild - type bldd ctd does not bind to c - di - amp . in addition , the bldd dgr - x8 - dqdr ctd mutant did not bind the c - di - gmp probe . all e. coli strains used in this study ( table s3 ) were grown in lb medium under aeration at 37c . e. coli dh5 was used for plasmid and cosmid propagation and bl21 ( de3 ) plyss for protein overexpression . bw25113 ( datsenko and wanner , 2000 ) containing a red plasmid , pij790 , was used to create the bldd disruption cosmid and et12567 containing puz8002 ( paget et al . , 1999 ) s. venezuelae strains ( table s3 ) were grown at 30c on maltose - yeast extract - malt extract ( mym ) medium ( stuttard , 1982 ) containing 50 % tap water ( mym - tap ) and 200 l trace element solution ( kieser et al . , 2000 ) per 100 ml . conjugations between e. coli and s. venezuelae were carried out as previously described ( bibb et al . , 2012 ) . for protein overexpression and purification , bldd and its individual domains were cloned into pet15b resulting in n - terminally his - tagged fl ( full - length ) bldd ( amino acid residues 1 - 166 ) , bldd - dbd ( amino acid residues 1 - 79 ) and bldd - ctd ( amino acid residues 80 - 166 ) . for overexpression of yhjh in s. venezuelae , an n - terminally codon optimized variant of yhjh was cloned downstream of the ermep promoter in the bt1 attb site - specific integrative vector pij10257 ( hong et al . , 2005 ) . point mutations in bldd were introduced by following the four - primer / two - step pcr protocol ( germer et al . , 2001 ) . for complementation analysis the bldd gene carrying its native promoter and the r114d , d116r , r125d and d128r mutations was expressed from the integrative vector pms82 . the bldd mutant was generated according to the redirect pcr targeting protocol ( gust et al . the sv -4-h05 cosmid was introduced into e. coli bw25113 and bldd was replaced with the apramycin - resistance ( apr ) cassette containing orit , which was amplified from pij773 using primers with bldd - specific extensions ( table s4 ) . the disrupted cosmid was confirmed by restriction and pcr analyses and introduced into e. coli et12567 / puz8002 for conjugation into s. venezuelae . a null mutant generated by double crossing over was identified by its apramycin - resistant and kanamycin - sensitive phenotype and named sv77 after confirmation by pcr using test primers listed in table s4 . the mutant allele bldd : : apr was moved into a new wt background by generalized transduction using the s. venezuelae - specific phage sv1 ( stuttard , 1979 ) . to prepare sv1 - lysate ,10 phage were added to 10 sv77 donor spores in 800 l pre - warmed ( 45c ) soft nutrient agar ( sna ) and poured onto difco nutrient agar plates containing 0.5 % glucose , 10 mm mgso4 and 10 mm ca ( no3 ) 2 . the plates were incubated at 30c overnight , then flooded with 2.5 ml difco nutrient broth ( dnb ) and incubated for 3 - 4 hr at room temperature . the phage - containing dnb soak - out was harvested and filtered through a 0.45 m filter to eliminate bacterial contamination . for transduction of the bldd : : apr allele , 10 phage particles harvested from the bldd : : apr mutant strain sv77 , were mixed with 10 - 10 wt spores and incubated overnight on mym agar at room temperature before overlaying with apramycin for selection . transduction of the bldd : : apr allele was confirmed by pcr using test primers listed in table s4 , and the strain was named sv74 . cyclic di - gmp capture compound experiments were performed as described previously ( nesper et al . , 2012 ) with minor modifications . s. venezuelae cultures were grown in mym - tap supplemented with trace element solution until late transition phase for 24 hr at 30c and then pelleted by centrifugation for 10 min at 6,000 rpm . the pellet was resuspended in lysis buffer ( 6.7 mm mes , 6.7 mm hepes , 200 mm nacl , 6.7 mm potassium acetate ( kac ) , ph 7.5 ) containing protease inhibitor and dnase i. cells were put through a french press four times at 18,000 psi and then centrifuged at 100,000 x g for 1 hr . for the capture experiments , the protein concentration of the soluble fraction was determined using a uv / vis nanodrop spectrophotometer and 400 g protein were mixed with 10 m c - di - gmp capture compound and with 20 l 5 x capture buffer ( 100 mm hepes , 250 mm kac , 50 mm magnesium acetate ( mgac ) , 50 % glycerol , ph 7.5 ) . 1 mm c - di - gmp was added to the control reaction and incubated for 30 min prior to capture compound addition . the reaction volume was adjusted with h2o to 100 l and incubated for 2 hr at 4c in the dark on a rotary wheel . after uv irradiation for 4 min in a caprobox , 50 l magnetic streptavidin beads and 25 l 5 x wash buffer ( 250 mm tris ph 7.5 , 5 m nacl , 0.1 % n - octyl -- glucopyranoside ) were added to the reaction and the mixture was incubated for 45 min at 4c on a rotary wheel . the beads were then collected with a magnet and washed 6 times with 200 l wash buffer . the beads were resuspended in 20 l sample buffer and run for 10 min on a 15 % sds polyacrylamide gel after 10 min incubation at 95c . the gel was stained using instantblue coomassie stain solution , and a 11 cm gel slice containing all captured proteins was excised for analysis by mass spectrometry . dna fragments spanning the bldm ( 158 bp ) and whig ( 151 bp ) promoter regions of s. venezuelae were generated by pcr using oligonucleotides listed in table s4 and then 5 end - labeled using [ - p ] - atp and t4 polynucleotide kinase . the binding reactions were performed in bandshift buffer ( 10 mm tris ph 7.5 , 1 mm edta , 5 % glycerol , 10 mm nacl , 1 mm mgcl2 ) in 20 l reaction mixture containing 0.6 m bldd and radiolabeled dna ( 8,000 c.p.m . ) as well as 0.5 g poly [ d ( i - c ) ] as nonspecific competitor dna . when appropriate , increasing amounts of c - di - gmp ( 0.251.75 m ) were added to the mixture . the reaction samples were incubated for 20 min at room temperature followed by electrophoresis on a 5 % polyacrylamide gel in 0.5 x tbe ( tris - borate - edta ) buffer at 80v for 105 min . chromatin immunoprecipitations were performed as previously described ( bush et al . , 2013 ) , except that an anti - bldd polyclonal antibody was used and pulled down with protein a - sepharose beads . library construction , sequencing and chip - seq data analyses were all carried out as previously described ( bush et al . , 2013 ) . the his6 - bldd - dbd and his6 - bldd - ctd proteins were dialyzed into crosslinking buffer ( 100 mm nah2po4 , 150 mm nacl , ph 8 ) and then incubated at room temperature for 30 min in 20 l reaction samples containing 10 m protein , 1 mm disuccinimidyl suberate ( dss ) in dimethylsulfoxide ( dmso ) , and c - di - gmp as indicated . the reaction was stopped by adding 50 mm tris ph 8 and incubation for 15 min followed by addition of sds sample buffer and heating to 95c for 10 min . samples were separated on a 15 % sds polyacrylamide gel and visualized by coomassie staining . radiolabeled c - di - gmp was synthesized in vitro using [ - p ] - gtp and the purified diguanylate cyclase pled as described ( paul et al . , 2004 ) . the dracala assays ( roelofs et al . , 2011 ) were performed using 2 g of his6 - bldd or its n - terminally his - tagged domains that were incubated with 11 nm p - c - di - gmp in dgc buffer ( 250 mm nacl , 25 mm tris ph 8 , 10 mm mgcl2 , 5 mm - mercaptoethanol ) . for competition experiments ,266 m cold c - di - gmp or gtp were added to the reaction . after a 5 min incubation at room temperature , 5 l of the binding sample were spotted onto nitrocellulose membrane and the dried membranes were analyzed using a phosphorimager . for structural studies on the ctd , the regions encoding residues 80 - 166 ( s. venezuelae bldd ) and 80 - 167 ( s. coelicolor bldd ) were cloned into the pet15b vector and the proteins induced at 37c and purified via ni - nta chromatography . the his - tags were removed from the proteins used for structural studies by thrombin cleavage . crystals of the s. venezuelae bldd ctd - ( c - di - gmp ) complex , which assumed the trigonal space group , p32 , were obtained using protein at 30 mg / ml and 1 mm c - di - gmp . crystals were produced via the hanging drop vapor diffusion method and mixing the complex 1:1 with 28 % peg 1500 , 100 mm sodium acetate , ph 5.5 . the s. venezuelae bldd ctd contains no methionines and hence for phasing , leu92 and ile135 were substituted with methionines . semet ( l92m / i135 m ) bldd ctd was expressed using the methionine inhibitory pathway and the protein purified and crystallized with c - di - gmp as per the wt ctd . the selenomethionine - substituted l92m / i135 m protein crystallized in the wild - type protein p32 space group . a second crystal form of the s. venezuelae bldd ctd - ( c - di - gmp ) complex was grown with protein at 20 - 40 mg / ml and 1 mm c - di - gmp using 20 % peg 2000 monomethyl ether , 100 mm mes , ph 6.0 , as a crystallization reagent and took the orthorhombic space group p21212 . the third crystal form of the s. venezuelae bldd ctd - ( c - di - gmp ) complex was produced with protein at 10 mg / ml and 1 mm c - di - gmp using 1.2 m sodium / potassium phosphate , 50 mm citrate ph 5.6 . crystals were obtained for the s. coelicolor bldd ctd - ( c - di - gmp ) complex using 25 mg / ml protein , 1 mm c - di - gmp and mixing the complex 1:1 with a reservoir comprised of 1.4 m sodium / potassium phosphate , 100 mm hepes ph 7.5 . multiple wavelength anomalous diffraction ( mad ) data were collected for a semet ( l92m / i135 m ) s. venezuelae bldd ctd - ( c - di - gmp ) crystal to 2.28 resolution at als ( advanced light source , berkeley , ca , usa ) beamline 8.3.1 ( table s1 ) . the data were processed using mosflm and the heavy atom substructure was obtained via solve ( terwilliger and berendzen , 1999 ) . phenix was used for final phasing and density modification ( adams et al . , 2010 ) . the crystal contains 12 protein molecules in the asymmetric unit ( asu ) and each of the six dimers is glued together by four c - di - gmp molecules . the six c - di - gmp complexed dimers are essentially identical ( figure 4d ) . final refinement was done using a data set collected to 1.95 resolution for a semet ( blddl92 m ) ctd - ( c - di - gmp ) crystal . a wt data set was also collected to 2.2 resolution and the structure was identical to the l92 m and l92m / i135 m structures . the final 1.95 resolution - structure contains residues 84 - 161 for each of the 12 subunits and 24 c - di - gmp molecules ( table s2 ) . data were collected to 1.75 , 2.25 and 2.33 resolution for the s. venezuelae and s. coelicolor bldd ctd - ( c - di - gmp ) c2221 forms and the s. venezuelae bldd ctd - ( c - di - gmp ) p21212 crystal form , respectively , and the structures solved by molecular replacement ( mr ) . the s. coelicolor bldd ctd and s. venezuelae bldd ctd c2221 crystal forms contain a ctd dimer and four c - di - gmp molecules in the asu and the s. venezuelae bldd c - domain - ( c - di - gmp ) p21212 crystal form contains 10 subunits ( five dimers ) , and 20 c - di - gmp molecules . the structures were solved by mr using the program phaser ( mccoy et al . , 2007 ) . the topology of every bldd ctd is 1 ( residues 84 - 88 ) - 1 ( residues 89 - 93 ) - 2 ( residues 98 - 113 ) - 2 ( residues 120 - 124 ) - 3 ( residues 128 - 136 ) - 4 ( residues 140 - 149 ) - 5 ( residues 154 - 160 ) . the bldd dna binding domain ( bldd dbd ) , encoding residues 1 - 79 , was cloned into pet15b , expressed in e. coli bl21 ( de3 ) and the protein purified via ni - nta chromatography . prior to crystallization , the hexa - his tag was removed via thrombin cleavage and the protein further purified by size exclusion chromatography . crystals were grown by mixing the protein ( 40 mg / ml ) 1:1 with a reservoir consisting of 35 % peg 400 , 0.1 m mgcl2 and 0.1 m tris ph 7.5 . x - ray intensity data were collected to 2.8 resolution at als beamline 8.3.1 and processed with mosflm . the rsym and i / ( i ) for the data are 11.3 % ( 38.4 % ) and 11.4 ( 4.3 ) , respectively , where the values in parentheses indicate data from the highest resolution shell . the structure , which contains 3 subunits in the asu ( 2 subunits form a dimer and crystal symmetry generates a second dimer ) , was solved with phaser using a single s. coelicolor dbd subunit ( pdb code 2ewt ) as the search model . the final model contains residues 3 - 71 of each subunit and was refined using phenix to final rwork / rfree values of 23.7 % / 28.9 % , respectively ( adams et al . , 2010 ) . crystals of the full - length ( fl ) s. venezuelae bldd - ( c - di - gmp ) -21-mer complex were grown by using protein in which the n - terminal hexa - his tag had been cleaved and incubated with 1 mm c - di - gmp ( final concentration ) . this bldd - ( c - di - gmp ) solution was mixed in a 1:1 molar ratio of bldd dimer to 21 - mer dna duplex ( 5 - cccctcacgctgcgtgacggg - 3 , with the canonical bldd box underlined , annealed to its complementary oligodeoxynucleotide ) for crystallization trials . crystals were grown by mixing the protein - dna complex 1:1 with the crystallization solution composed of 100 mm sodium citrate tribasic / citric acid ph 4.0 and 200 mm ammonium sulfate . the crystals take the trigonal space group , p3221 , with a = b = 114.0 , c = 95.2 and contain a bldd dimer - ( c - di - gmp ) -21-mer duplex in the asu . data were collected to the limiting resolution of 4.5 . the rsym = 9.0 % ( 86.0 % ) and i / ( i ) = 5.8 ( 1.8 ) , where the values in parentheses are for the highest resolution shell . first , bldd dna binding domain - dna complex models were constructed based on the sinr - dna ( pdb code 3zkc ) or repressor - dna ( pdb code 1lmb ) complex structures and used in the mr program phaser ( mccoy et al . , 2007 ) . this solution was then used as a static model with the ctd - ( c - di - gmp ) dimeric structure as a search model . , the structure was subjected to rigid body refinement only ( rwork / rfree = 33.0 % / 38.9 % , respectively ) . to examine the flexibility of the linker region that connects the bldd dbd and ctd , specifically , the accessibility of residue glu80 , which is the only acidic residue in the bldd linker region , was determined by the ability of the glu - c protease to cleave after this residue . in these experiments , endo - glu - c ( 100 units / ml ) was a diluted 50 fold into samples of 1 ) fl bldd ( 1 mg / ml ) , 2 ) fl bldd -21-mer dna ( 1 mg / ml protein with 100 m dna ) or 3 ) fl bldd - ( c - di - gmp ) -21-mer ( 1 mg / ml protein with 100 m 21 - mer dna and 1 mm c - di - gmp ) . the proteolysis buffer was 50 mm sodium phosphate , ph 7.5 and the final protein concentration of each sample was 4 mg / ml . the samples shown in figure s6d were taken at a time point of 4 hr . notably , proteolysis of each sample was identical , demonstrating that ligand binding of neither cognate dna nor c - di - gmp by bldd affect the accessibility of the linker region , which remains flexible and unstructured . size exclusion chromatography experiments were carried out using a hiload 16/600 superdex 75 pg column .5 mg of either the wild - type bldd ctd or the quadruple mutant were loaded onto a column that had been pre - equilibrated with 150 mm nacl , 5 % glycerol , 20 mm tris hcl ph 7.5 and 3 m c - di - gmp . the samples were run and eluted with the same c - di - gmp containing buffer . the elution volume was plotted against a standard curve to determine the relative molecular weights of the samples . the standard curve was determined using cytochrome c ( 12 kda ) , carbonic anhydrase ( 29 kda ) and albumin ( 66 kda ) . cryo - sem was performed as previously described ( bush et al . , 2013 ) . when induced in e. coli bl21 ( de3 ) at 37c , bldd ctd samples contained little to no c - di - gmp contamination , which was supported by a280 / a260 values of the purified protein , which were approximately 1.6 . however , to ensure that there was no endogenous c - di - gmp present in samples used for binding affinity measurements , the bldd ctd was expressed and purified in sf9 insect cells . for these studies , a gene encoding the same s. venezuelae bldd ctd region that was expressed in e. coli was codon optimized for expression in insect cells ( genscript , piscataway , nj , usa ; http://www.genscript.com ) and subcloned into the expression vector f1 , which was transfected into the dh10bac strain for generation of the recombinant bacmid . rbacmids were then transfected in sf9 insect cells with cellfectin ii and the cells incubated in sf - 900 ii sfm for 56 days before harvest . the supernatant was collected for the p1 viral stock and p2 was amplified for later infection . sf9 cells expressing bldd ctd were harvested at 72 hr post infection and cells were lysed into 25 mm tris ph 7.5 , 300 mm nacl and 5 % glycerol with protease inhibitors . the protein was purified from the supernatant by ni - nta followed by size exclusion chromatography and was 90 % pure as assessed by sds - page analysis . to measure binding , 2 - o - ( 6 - [ fluoresceinyl ] aminohexylcarbamoyl ) - cyclic diguanosine monophosphate ( 2 - fluo - ahc - c - di - gmp ) , this molecule is conjugated via a 9 atom spacer to one of the 2 hydroxyl groups of the c - di - gmp , hence meeting the structural requirement for bldd binding that only one 2 hydroxyl group be unmodified and the other available for the interactions observed in the bldd - ( c - di - gmp ) structures ( figure 5 ) . binding was carried out at 25c in a buffer of 150 mm nacl and 25 mm tris - hcl ph 7.5 , which contained 1 nm 2 - fluo - ahc - c - di - gmp . increasing concentrations of bldd ctd were titrated into the reaction mixture to obtain the binding isotherms . after each addition of protein the reaction sample was incubated for 30 min to ensure equilibrium had been reached . c - di - gmp binding to bldd appears to have the characteristics of a high affinity / slow binding ligand . the resulting data were plotted using kaleidagraph and curves were fitted to deduce binding affinities . to determine the binding stoichiometry of the bldd ctd - ( c - di - gmp ) complex , the same fp binding conditions were used but the total concentration of c - di - gmp ( c - di - gmp + 2 - fluo - ahc - c - di - gmp ) was 25 m , 10-fold above the kd of 2.5 m ensuring stoichiometric binding . close inspection of the binding isotherm revealed the possibility that there are two nearly identical binding events ( likely corresponding to the binding of each intercalated c - di - gmp dimer ) . the graph of the resulting data shows a linear increase in the observed mps until saturation of the binding sites , after which the line is flat . importantly , the final inflection occurs at a bldd monomer concentrations of 12 m , which , when divided by the concentrations of c - di - gmp ( 25 m ) , indicates a stoichiometry of two ctd protomers per four c - di - gmps . as anticipated from a purely chemical complementarity - orientated argument , fp studies carried out in the same buffer also revealed that wild - type bldd ctd does not bind to c - di - amp . in addition , the bldd dgr - x8 - dqdr ctd mutant did not bind the c - di - gmp probe . n.t . designed , performed , and interpreted experiments , created figures , and wrote the paper . m.a.s . designed , performed , and interpreted experiments , created figures , and wrote the paper . r.g.b . designed and interpreted experiments and wrote the paper . m.j.b . designed and interpreted experiments and wrote the paper\noutput:\n" }, { "from": "agent", "value": "summarythe cyclic dinucleotide c - di - gmp is a signaling molecule with diverse functions in cellular physiology . here , we report that c - di - gmp can assemble into a tetramer that mediates the effective dimerization of a transcription factor , bldd , which controls the progression of multicellular differentiation in sporulating actinomycete bacteria . bldd represses expression of sporulation genes during vegetative growth in a manner that depends on c - di - gmp - mediated dimerization . structural and biochemical analyses show that tetrameric c - di - gmp links two subunits of bldd through their c - terminal domains , which are otherwise separated by 10 and thus can not effect dimerization directly . binding of the c - di - gmp tetramer by bldd is selective and requires a bipartite rxd - x8 - rxxd signature . the findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions ." } ]

[ { "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: during follow - up , patients with known malignancies commonly undergo screening studies to detect recurrence or metastasis . 18f - fluorodeoxyglucose positron emission tomography ( fdg - pet ) is increasingly being used for screening , often in conjunction with computed tomography ( ct ) . overall , in the setting of an indeterminate nodule greater than 1 cm , fdg - pet has a sensitivity of 96.8 % and specificity of 77.8 % in the detection of malignancy . however , little is known about the accuracy of fdg - pet in detecting extrathoracic malignancies that have spread to the lungs . recently , video assisted thoracoscopic surgery ( vats ) has been performed for the resection of small pulmonary lesions . this technique is less painful and invasive , and is thus more acceptable to patients than thoracotomy . in this studythe aims of the study were to determine the accuracy of fdg - pet in detecting pulmonary metastasis through the vats technique , which allows the excisional biopsy of small pulmonary nodules in patients with known malignancies . between july 2007 and april 2010 , we prospectively studied 28 patients who were in follow - up care for a previously treated malignancy . the malignancies included the colorectum ( 9 ) , breast ( 6 ) , head and neck ( 5 ) , stomach ( 3 ) , lymph ( 1 ) , ovary , uterus , liver , bladder ( table 1 ) . small pulmonary nodules had been found on chest ct and fdg - pet during routine follow - up care . diagnostic vats was then performed as part of a metastatic evaluation within a mean 20 days ( range , 2 to 90 days ) . medical records were reviewed for age , gender , primary tumor type , chest ct , and fdg - pet results , as well as histopathology of the removed nodules . chest ct results were transcribed based on the clinical report , as well as review of the images , with nodule measurement . fdg - pet imaging results with the maximum standardized uptake values ( suvmax ) were abstracted from the radiology reading at our institution . in operating room , the patient was positioned for vats . after prepping and draping , three working ports were created and the lung was visualized . an autosuture stapling device that was 45 or 60 mm long and used 4.8 mm staples was placed on an area of the lung with palpation and was fired . there were 16 men and 12 women whose median age was 56.7 years old ( range , 38 to 77 years ) . postoperative median length of chest tube drainage was 3.9 days ( range , 2 to 8 days ) . the histopathology of the nodules was metastatic adenocarcinoma in 6 ( 5 in the colorectum , 1 in the breast ) , primary adenocarcinoma in 1 ( breast ) , squamous cell in 4 ( 3 in the head and neck , 1 in the uterus ) , urothelial carcinoma in 1 , and bronchioloalveolar carcinoma in 1 . benign diagnoses included pulmonary tulberculosis in 6 , fibrosis in 5 , organizing pneumonia in 3 , and lymphoid hyperplasia in 1 ( table 2 ) . overall sensitivity of 18f - fdg - pet in the 28 patients who underwent resection was 39.2 % . no association was found between malignant and benign tissue in the suvmax and tumor sizes ( table 3 ) . a receiver operating characteristics curve was constructed and a cut - off value was determined for the diagnosis of metastatic small pulmonary nodules . using the cut - off of 2.5 for the suvmax , the sensitivity and specificity for predicting metastatic small pulmonary nodules were 60.0 % and 43.7 % , respectively . using the cut - off of 1 mm for tumor size , the sensitivity and specificity for predicting metastatic small pulmonary nodules were 45.0 % and 50.0 % , respectively ( figs . 1 , 2 ) . the presumed diagnosis of small pulmonary nodules is based on several factors : the age of the patient , associated symptoms , appearance of the lesion on a radiograph , and the length of time the lesion has been present . a single pulmonary nodule is more likely to be malignant in patients with known cancer . the idea of whole body cancer surveillance is very appealing and has , for some , compelled the use of fdg - pet as a screening tool for recurrence of various malignancies . integrated fdg - pet / ct can evaluate nodules as small as 7 or 8 mm in size . a high suvmax , especially in a small pulmonary nodule , provides important information and helps guide therapy . moreover , an integrated fdg - pet / ct may provide other targets ( lymph nodes or m1 sites ) that harbor metastatic disease that require biopsy prior to resection . the optimal value of the suvmax for mediastinal and hilar lymph nodes has recently been evaluated . the usefulness of 18f - fdg - pet for differentiation of benign and malignant pulmonary lesions has been investigated in various studies [ 4 - 6 ] . the reported sensitivity and specificity of the 18f - fdg - pet ranges between 0.75 and 1.0 . suvmax were significantly increased in malignant lesions compared to benign lesions , and the value of 2.5 is accepted as the cut - off point for malignancy . suv expresses fdg uptake by the lesion normalized according to the dose administered and the subject 's body weight . in fact , having defined the many factors that can affect the uptake of labeled glucose and , therefore , the suv , it is not easy to establish fixed values that serve to distinguish between the benign and malignant nature of a small pulmonary nodule . a number of formulas designed to correct the underestimation of the suv caused by hyperglycemia , such as adjusting the value of this parameter according to the patient 's serum glucose level , have also been studied . using this method , while much has been published about the sensitivity of fdg - pet for pulmonary nodules in primary lung cancer , little information has been available on the sensitivity of pet for metastatic pulmonary lesions from extrathoracic malignancies . modern ct scanners have a far higher detection rate than ct scanners of 15 years ago . even in the case of small nodulesthe accurate and timely diagnosis of pulmonary nodules is essential for the proper management of patients with known malignancies . the implications of metastatic lung lesions , no matter what size , on treatment selection for patients who have received a diagnosis of a malignancy are enormous . definitive diagnosis of lung lesions can sometimes not be made because of the inaccessibility of the true lesion or the inadequacy of the sample size . bronchoscopic biopsy and percutaneous needle biopsy under ct are useful methods ; however , they are not always able to yield a definite diagnosis , since results depend on the technique and tumor size . moreover , specimens may be too small to be diagnosed , and negative biopsy results might require further examination . surgical lung biopsy is considered the final diagnostic modality to be used in patients with undiagnosed small pulmonary nodules . vats has replaced thoracotomy as the preferred surgical modality for diagnostic excisional biopsy of indeterminate pulmonary nodules because of decreased morbidity . we do use finger palpation through the port if we have difficulty identifying the lesion or the margins . we also use long roberts haemostatic clamps to feel the surface of the lung when we search for the lesion . it is generally accepted that vats biopsy reduces postoperative pain and disability , causes fewer operative scars , and is equally effective in obtaining histologic diagnosis . in patients with a history of an extrathoracic malignancy and newly diagnosed small pulmonary nodules , fdg - pet is not sensitive enough to dictate treatment . the results of this study in patients with known malignant disease reinforce the need for timely vats wedge excision of small pulmonary nodules .\noutput:\n" }, { "from": "agent", "value": "backgroundthe aims of the study were to determine the accuracy of fluorodeoxyglucose positron emission tomography ( fdg - pet ) in detecting pulmonary metastasis through video - assisted thoracoscopic surgery ( vats ) , a technique that allows the excisional biopsy of small pulmonary nodules in patients with known malignancies.materials and methodsbetween october 2007 and april 2010 , 28 patients with known malignancies and small pulmonary nodules underwent vats excisional biopsies . all patients were in follow - up for a previously treated malignancy . the malignancies included the following : colorectum ( 9 ) , breast ( 6 ) , head and neck ( 5 ) , stomach ( 3 ) , lymph ( 1 ) , ovary ( 1 ) , uterus ( 1 ) , bladder ( 1 ) , and liver ( 1 ) . resultsthere were 16 men and 12 women whose mean age was 56.7 years old ( range , 38 to 77 years ) . the sizes of the mean nodules removed were 11.3 mm ( range , 7 to 21 mm ) . diagnoses included metastatic ( 11 ) , bronchioloalveolar carcinoma ( 1 ) , primary adenocarcinoma ( 1 ) , pulmonary tuberculosis ( 6 ) , fibrosis ( 5 ) , organizing pneumonia ( 3 ) , lymphoid hyperplasia ( 1 ) . among these lesions , 46.4 % were malignant.conclusiontrue positive fdg - pet was 39.2 % . fdg - pet is not a sensitive test in the evaluation of patients with a history of an extrathoracic malignancy and newly diagnosed small pulmonary nodules . vats excision allows the early diagnosis of small pulmonary nodules , with low morbidity , in patients with known malignancies ." } ]

[ { "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 cases of acute mesenteric ischemia , 5 - 15 % cases are caused by superior mesenteric vein ( smv ) thrombosis .1 in cases of mesenteric vein thrombosis ( mvt ) , intestinal ischemia can occur if there is mesenteric venous blood flow obstruction , resulting in critical bowel wall edema and fluid efflux into the lumen . this can result in diminished arterial blood flow , leading to submucosal hemorrhage and bowel infarction . mvt can be fatal if the diagnosis and subsequent treatment is delayed .2 in the present report , we describe the case of a patient with smv thrombosis who presented with abdominal pain and was treated with systematic anticoagulation therapy for a 6 - month period . myelodysplastic syndrome ( mds ) was diagnosed during the work - up that was performed to identify the cause of the smv thrombosis . a 62 - year - old woman who was admitted to the hospital presented with a 7 - day history of abdominal pain , which had worsened over time and was associated with postprandial bloating . the patient had been diagnosed with rheumatoid arthritis 7 years previously and was taking the following medications : low - dose glucocorticoids such as prednisolone ( 5 mg / day ) and methotrexate ( 15 mg / week ) , as well as the nonsteroidal anti - inflammatory drug celecoxib ( 200 mg / day ) . the patient had no history of surgery or trauma , and there was no family history of venous thromboembolism . on admission , initial laboratory findings revealed pancytopenia ( hemoglobin concentration , 9.8 g / dl ; white blood cell count , 3,100 / mm ; and platelet count , 32,000 / mm ) . the prothrombin time ( international normalized ratio , 1.43 ) and activated partial thromboplastin time ( 42 seconds ) were prolonged . the levels of fibrinogen and fibrinogen degradation product were 186 mg / dl and 20 g / ml , respectively , whereas the d - dimer level was elevated by 6 g / ml . ct scan of the abdomen and pelvis showed a moderate amount of ascites with omental and mesenteric infiltration , which was associated with a 4.5 - cm thrombus in the smv and its tributary ( fig . in addition , there was no evidence of paroxysmal nocturnal hemoglobinuria , antiphospholipid syndrome , or other autoimmune disease . the protein c concentration ( 46 % ) and s activity ( 26 % ) were below the normal ranges . anticoagulation therapy was initiated , and the patient was closely monitored for signs of bowel infarction . moreover , low - molecular - weight heparin was initiated . on the third day of admission , the patient 's bone marrow was examined in order to identify the cause of the pancytopenia and the recent thrombotic event . a diagnosis of mds was made , which was believed to involve refractory cytopenia with multilineage dysplasia ( fig .2 ) . thereafter , the patient experienced sustained hematochezia and vague abdominal pain . on the fourth day , capsule endoscopy was performed to exclude bowel ischemia . through small bowel endoscopy , we identified the presence of diffuse mucosal edema from the distal jejunum to terminal ileum and erythematous patches in the ascending colon , which were compatible with smv territories ( fig . after 6 months of anticoagulation therapy , follow - up ct of the abdomen and pelvis showed complete dissolution of the smv thrombosis ( fig . the patient experienced no recurrence of smv thrombosis during the 2 - year follow - up period . acute mvt is a rare but potentially fatal condition , with a mortality rate of 20 - 30 % .3,4 however , diagnosis of this condition is difficult because the symptoms are nonspecific . critical symptoms such as hemodynamic instability and peritonitis are important indicators as to whether surgery is required . suspicion of mvt is important for avoiding delays in diagnosis and therapy , particularly in elderly patients . the development of imagining modalities over the past 2 decades has improved the ability to make an accurate diagnosis of mvt . in this patient , the sensitivity of diagnosis by contrast - enhanced abdominal ct is approximately 90 % .2 mvt is classified as either primary or secondary . primary smv thrombosis is idiopathic , whereas secondary smv thrombosis can result from various underlying causes , including hypercoagulable states , pregnancy , or recent abdominal surgery .5 after an mvt diagnosis is made , the clinician should attempt to identify the cause of the thrombosis . our patient had been diagnosed with rheumatoid arthritis 7 years prior to the current admission . reports have shown that there is an increased risk of developing deep vein thrombosis in patients with rheumatoid arthritis compared with patients who did not have rheumatoid arthritis .6 however , whether treatment or disease activity can modify the risk of venous thromboembolism in patients with rheumatoid arthritis remains controversial .7 slight decreases in antithrombin iii and protein c levels , and s activity were identified in the present case . after a hematological specialist was consulted , these findings were confirmed to be the result - as opposed to the cause - of the recent massive thrombosis . the pancytopenia that was noted on peripheral blood examination and multilineage dysplasia indicated by the assessment of bone marrow aspirate led to the diagnosis of mds . although myeloproliferative disease and malignancy are the most frequently diagnosed thrombophilic conditions ,8,9 other studies have reported the presence of thrombosis in association with mds , as in the present case .10,11 kimura et al. 12 found that patients with mds and trisomy 8 were more likely to develop thrombosis and intestinal ulcers . chen et al. 11 reported a case of large - vessel thrombosis that was complicated by mds and trisomy 8 . although no definite cause of thrombosis has been identified , thrombosis and hemorrhage complicated by mds most likely occur as a result of quantitative and qualitative platelet anomalies .10 other researchers have noted that in cases of mds , immunological disorders caused by neutrophil dysfunction and inflammatory cytokine overproduction may lead to injury and inflammation of the endothelium .11,13,14 there have been reports of patients with mds and autoimmune disease , including behet 's disease , particularly in japan .15,16 another interesting point of our case is the capsule endoscopic findings . to our knowledge , capsule endoscopic findings have not been reported for smv thrombosis .17 the patient experienced sustained symptoms during initial anticoagulation therapy , and bowel ischemia should be excluded in such cases . therefore , capsule endoscopy can play a major role as a noninvasive procedure in cases where clinicians are determining whether surgery is warranted , particularly in cases involving sustained symptoms or controversial imaging findings . a patient 's clinical status typically determines the initial management of mvt . if the patient is clinically unstable , immediate surgical exploration is warranted . if a patient is clinically stable , conservative management , including systemic anticoagulation , is considered appropriate .18,19 catheter - directed thrombolysis is a safe and effective treatment in cases of main trunk involvement .20 the typical duration of anticoagulation treatment is 6 - 12 months .3 the immediate initiation of anticoagulation with low - molecular - weight heparin and a subsequent 6 - month course of warfarin proved to be successful in the present case . this case demonstrates the importance of early detection of smv thrombosis followed by active systemic anticoagulation . thus , we believe that clinicians should adopt a high degree of suspicion in such cases , and this increased awareness along with the early initiation of systemic anticoagulation therapy are essential for successful treatment of mvt .\noutput:\n" }, { "from": "agent", "value": "mesenteric venous thrombosis ( mvt ) is a serious condition due to its potential association with mesenteric ischemia and infarction of the small bowel . symptoms of mvt are often vague , making accurate diagnosis and sufficient treatment difficult . however , increased awareness and new imaging modalities for this condition have improved outcomes for patients with mvt . treatment includes anticoagulation , transcatheter therapy , and surgery . in the present report , we describe the case study of a 62 - year - old woman with a presenting diagnosis of superior mvt , who was finally diagnosed with myelodysplastic syndrome . the superior mvt spontaneously dissolved after the patient underwent 6 months of systemic anticoagulation therapy . invasive surgery or bowel resection was not required ." } ]

[ { "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 must constantly absorb light energy and phagocyte lipid rich photoreceptor outer segment shed from neural retina due to normal physiological visual cycle . oxidative stress refers to progressive cellular damage that contributes to protein misfolding and functional abnormalities in the rpe cells during cellular senescence . the accumulation of this damage in the postmitotic rpe cells seems to be one of the key events in the development of age - related macular degeneration ( amd ) , the leading cause of blindness in the elderly in the developed countries . the rpe cells ensure the survival of neural cells , rod , and cones . in senescent rpe cells , this ability is reduced causing secondary adverse effects on the neural retina , ultimately leading to loss of vision . both intra - and extracellular . efficient removal of misfolded proteins from cytoplasm is critical for cellular survival and adaptation . however , potentially toxic misfolded protein aggregates accumulate during the aging process . control of protein turnover is particularly important in postmitotic cells , since the accumulation of malfunctioning proteins may be highly detrimental to the cells . once heat shock protein - mediated protein folding fails , the misfolded proteins are usually tagged with a ubiquitin ( ub ) moiety that directs the complex to the ubiquitin / proteasomal protein degradation pathway ( upp ) . it is believed that the aggregation of oxidized and ubiquinated proteins is due to a decline in the proteasomal activity with age , and that this also occurs in rpe cells . protein aggregates formed in the cell periphery are delivered along microtubulus network by dynein - dependent retrograde trafficking to a juxtanuclear location where they form aggresomes . the development of these aggresomes is part of a cellular defence mechanism against misfolded proteins , and it can be inhibited by drugs that depolymerize microtubules . tubulin undergoes various posttranslational modifications including polyglutamylation , polyglycylation , carboxyterminal cleavage , and acetylation . acetylation is unique among the known tubulin modifications , in that it occurs on the lysine 40 of - tubulin which can be found on stable microtubules in most cell types . the deacetylation of the lysine residue in tubulin is catalyzed by enzymes called histone deacetylases ( hdacs ) . in contrast , histone acetyltransferases ( hats ) transfer acetyl groups to lysine residue to increase acetylation of tubulin . this results in a balance between acetylation and deacetylation states of tubulin , and any shift in this balance results in changes in the regulation of tubulin function . . one interesting role of tubulin and tubulin modifying deacetylases is their influence on aggregation of misfolded proteins . hdac6 contributes to the degradation of aggregated proteins because it is able to bind to both poly - ubiquitinated and dynein motor proteins as an adaptor protein to help transport misfolded proteins along microtubules into aggresomes which are finally degraded by autophagy . hdac6 is able to sense ubiquitinated cellular aggregates and consequently induces the expression of major cellular chaperones by triggering the dissociation of a repressive hdac6 / hsf1 ( heat - shock factor 1 ) / hsp90 ( heat - shock protein 90 ) complex and subsequent hsf1 activation . hdac6 therefore appears as a master regulator of the cell protective response to cytotoxic protein aggregate formation . we have recently shown that proteasome inhibition evoked perinuclear protein accumulation which then leads to the autophagy - mediated removal of the deposits . in the present study , we demonstrate that hsp90 inhibition with geldanamycin can effectively decrease the proteasome inhibitor - induced aggregation . increased tubulin acetylation was observed in response to hsp90 , proteasome , and hdac inhibition , but the acetylation level was not correlated with the amount of the aggregates in the arpe - 19 cells . human retinal pigment epithelial cells ( arpe - 19 , from atcc , ) were used in this study . the cells were grown in dulbecco 's mem / nut mix f - 12 ( 1 : 1 ) medium ( life technologies , paisley , uk ) containing 10 % fetal bovine serum ( hyclone , logan , ut , usa ) , 2 mm l - glutamine ( cambrex , charles city , ia , usa ) , 100 units / ml penicillin ( cambrex ) , and 100 g / ml streptomycin ( cambrex ) . before any exposure , the cells were grown to confluency in a standard incubator ( 10 % co2 , + 37c ) . proteasome inhibition was accomplished with 5 m mg - 132 ( calbiochem , san diego , ca , usa ) . geldanamycin ( ga , calbiochem ) , at 0.25 m concentration , was used to inhibit the function of hsp90 . microtubules were acetylated with 1 m trichostatin a ( tsa ; sigma - aldrich , steinheim , germany ) . taxol ( tax , paclitaxel ; calbiochem ) , at 1 m concentration and nocodazole ( noc ; calbiochem ) , at 5 m concentration , were used to disrupt to function of microtubules . the cells were exposed to the ga , tsa , tax , or noc for 24 h , simultaneously with mg - 132 for 24 h or allowed to recover after 24 h mg - 132 insult in medium with or without chemicals ( ga , tsa , tax or noc ) . phase contrast microscopy photographs were taken from live cells with a nikon eclipse te300 ( nikon , tokyo , japan ) microscope . for transmission electron microscopy ( tem ) , the cell culture samples were prefixed in 2.5 % glutaraldehyde ( in 0.1 m phosphate buffer , ph 7.4 ) for 2 hrs at room temperature , followed by washing ( 15 min in 0.1 m phosphate buffer ) . the samples were postfixed in 1 % osmium tetraoxide ( in 0.1 m phosphate buffer ) for 1subsequently , the samples were infiltrated and embedded in lx - 112 resin ( ladd research industries , burlington , vt , usa ) . polymerization was carried out at 37c for 24 hrs and at 60c for 48 hrs . the sections were examined in a jeol - 1200ex transmission electron microscope ( jeol , tokyo , japan ) at 80 kv . exposed cells were lysed in m - per lysis buffer ( thermo scientific , waltham , ma , usa ) . whole cell extracts ( 20 g of protein ) were run in 10 % or 15 % sds - page gels and then wet blotted to nitrocellulose membranes ( ge healthcare , little chalfont , buckinghamshire , uk ) . the membranes were blocked for 1 hour in 3 % fat - free dry milk in 0.3 % tween 20 / pbs at room temperature ( rt ) . thereafter , the membranes were incubated for 1 hour at rt with rabbit polyclonal ubiquitin antibody ( dakocytomation , glostrup , denmark , cat . rat monoclonal hsp90 antibody ( assay designs , ann arbor , mi , usa , cat . spa - 815 ) or rabbit polyclonal lc3 antibody ( abgent , san diego , ca , usa , cat . primary antibodies were diluted ( 1 : 500 , 1 : 5000 , 1 : 5000 , 1 : 5000 , 1 : 250 or 1 : 8000 resp . ) in 0.5 % bovine serum albumin in 0.3 % tween 20 / pbs except for acetylated tubulin which was diluted in 1 % fat - free dry milk in 0.05 % tween 20 / pbs . after 35 minutes washes with 0.3 % tween 20 / pbs ( for acetylated tubulin 0.05 % tween 20 / pbs ) the membranes were incubated for one hour at rt with horseradish peroxidase - conjugated anti - rabbit igg or anti - mouse igg antibodies or anti - rat igg antibodies ( ge healthcare ) . the secondary antibodies were diluted ( for ubiquitin 1 : 20000 , for hsp901 : 10000 , for hsp701 : 40000 , for hsc701 : 15000 and for lc31 : 5000 , resp . ) in 3 % fat - free dry milk in 0.3 % tween 20 / pbs except for acetylated tubulin ( 1 : 6000 ) which was diluted in 1 % fat - free dry milk in 0.05 % tween 20 / pbs . before detection , all of the membranes were washed as before . protein antibody complexes were detected with an enhanced chemiluminescence method ( millipore , billerica , ma , usa ) . the arpe - 19 cells were either nonstressed , or exposed to drugs , that is , 5 m mg - 132 or 0.25 m geldanamycin , 1 m trichostatin a or 1 m taxol or 5 m nocodazole for 24 hours . in addition , the cells were treated simultaneously with mg - 132 in conjunction with geldanamycin , trichosatin a , taxol or nocodazole up to 24 hours . only a single mg - 132 insult or combination treatment with taxol induced a typical perinuclear aggregation in arpe cells ( figures 1 ( a ) and 2 ( a ) ) . hdac inhibition with trichostatin a or tubulin depolymerization with nocodazole evoked dispersed the mid - peripherical aggregation process during proteasome inhibition . with all of the insults , cytoplasm underwent a similar effective aggregation clearance when exposed to mg - 132 for 24 hours and then allowed to recover for 24 hours in normal cell culture medium ( figures 1 ( b ) and 2 ( b ) ) . a robust elevation of hsp70 protein expression was seen in response to mg - 132 or geldanamycin exposures ( figure 3 ) . abrogation of proteasome - mediated protein degradation caused a clear increase in the amount of hsp70 which has a cytoprotective capacity in the mg - 132 - treated arpe - 19 cells . the classical transcriptional heat - shock gene induction is attributable to the activation of hsf1 transcription factor . in the activation process hsp90 and hsp70 dissociate from hsf1 transcription factor . geldanamycin has been shown to bind hsp90 , to inhibit its function and to elicit the hsp90 client protein degradation in proteasomes . in line with previous studies , the geldanamycin was found to trigger a strong expression of hsp70 , while the hsp90 response remained weaker . the response is likely mediated through hsf1 transcriptional activation . the increase in the amount of inducible hsp70 might be one of the regulators suppressing the proteasome inhibitor - induced aggregation process , when hsp90 is simultaneously inhibited . it has also been documented that a hsp90 inhibitor may prevent the aggregation of protein by regulating client protein posttranslational modifications . since hsp90 inhibition has been reported to trigger autophagy clearance , we wished to analyze the autophagy induction marker lc3 i / ii levels in arpe cells treated with geldanamycin or mg - 132 solely or both together for 6 , 12 , and 24 hours . our findings clearly show that proteasome inhibition mildly induced autophagy , when related to lc3 ii levels , but this was not involved in geldanamycin treatments ( figure 4 ) . this indicates that autophagy clearance is not implicated in the suppression of protein aggregation during hsp90 and proteasome inhibition in the arpe - 19 cells . cellular ubiquitin - protein ( ub ) conjugate levels were analyzed by western blotting from cells treated as described above . the level of ub conjugation was not changed by geldanamycin , trichostatin a , taxol , or nocodazole treatment , but a very intensive induction of ubiquitination was seen in response to mg - 132 exposure whether geldanamycin , trichostatin a , taxol , or nocodazole were present or not ( figure 3 ) . inhibition of hsp90 therefore seems to have only a minor impact on the level of ubiquitination in the arpe - 19 cells , although hsp90 has been shown to regulate both proteasomal and autophagy clearance through its client proteins . the ubiquitin levels were slightly reduced when proteasome inhibition was removed and the cells recovered either with geldanamycin , trichostatin a , taxol , or nocodazole compared to incubations of mg - 132 together with these chemicals . this is apparently explained by the autophagic clearance of proteasome - inhibitor - induced aggregates , as we have recently documented . protein aggregates formed at the cell periphery are delivered along the microtubulus network by dynein - dependent retrograde trafficking to a juxtanuclear location where they form aggresomes . the reversible acetylation of - tubulin has been linked to the regulation of microtubule stability and function . decreased tubulin acetylation has been shown in some reports to reduce microtubule stability , but in other experiments no association was observed . hdac6 deacetylates tubulin , and hsp90 , and forms complexes with many other proteins , including ubiquitinated proteins . hdac6 also interacts with a component in the dynein - dynactin microtubule motor complex and regulates protein aggregation trafficking . trichostatin a is a classical inhibitor of hdac deacetylase activity and thus it also blocks the hdac6 . the phase contrast and transmission electron microscopic analysis revealed dispersed cytoplasmic aggregation in response to simultaneous treatment of trischostatin a or nocodazole and proteasome inhibition ( figures 1 and 2 ) . trichostatin a evoked a clear increase in tubulin acetylation levels , while in the situation of tubulin depolymerizator induced by nocodazole , tubulin acetylation remained at control level ( figure 3 ) . in contrast , a tubulin stabilizer , taxol induced tubulin acetylation that was not , however , as extensive as that evoked by trichostatin a. hsp90 and proteasome inhibition evoked a similar slight increase in the tubulin acetylation levels . the hdac inhibition by trichostatin a probably affects the dynein motor and regulates aggregation localization , but does not prevent the formation of aggregates . moreover , the polymerization state of tubulin regulates the localization of proteasome inhibitor - induced aggregates , but this process can not be estimated by measuring total tubulin acetylation levels . hsp90 inhibition is effectively involved in the regulation of protein aggregation that is independent of hdac inhibition or tubulin acetylation levels in the rpe cells . these findings open new perspectives for understanding the pathogenesis of protein aggregation in retinal cells , and they may be useful in the development of therapeutic treatments to prevent retinal cell deterioration , that is , during aging .\noutput:\n" }, { "from": "agent", "value": "retinal pigment epithelial ( rpe ) cells are continually exposed to oxidative stress that contributes to protein misfolding , aggregation and functional abnormalities during aging . the protein aggregates formed at the cell periphery are delivered along the microtubulus network by dynein - dependent retrograde trafficking to a juxtanuclear location . we demonstrate that hsp90 inhibition by geldanamycin can effectively suppress proteasome inhibitor , mg -132-induced protein aggregation in a way that is independent of hdac inhibition or the tubulin acetylation levels in arpe - 19 cells . however , the tubulin acetylation and polymerization state affects the localization of the proteasome - inhibitor - induced aggregation . these findings open new perspectives for understanding the pathogenesis of protein aggregation in retinal cells and can be useful for the development of therapeutic treatments to prevent retinal cell deterioration ." } ]

[ { "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 , many researchers focused their activity on developing new tools to detect h2o2 , not only as an oxidases reaction byproduct but also as a conservative compound in food and drugs . indeed , hydrogen peroxide finds significant employment in industrial processes as an oxidant : in particular , hydrogen peroxide is released into the environment in either small or large amounts , since it is used as oxidant , whitening , or sterilant tool in packaging materials owing to its sporicidal and bactericidal features . several analytic methods as chemiluminescence , photometry , fluorimetry , titrimetry , spectrophotometry , high - performance liquid chromatography ( hplc ) , and especially electrochemistry are reported in the literature for detection of hydrogen peroxide . the electrochemical techniques provide some interesting advantages in comparison to the other ones mentioned above like fast , specific , and cheap monitoring of hydrogen peroxide . the direct reduction of h2o2 at a bare sensor is not suitable for analytical measures due to its slow kinetics and high potentials required for redox reactions . to overcome these problems , electrochemical biosensors based on the biocatalytic activity of immobilized enzymes towards the substrate h2o2 are helpful because of their high sensitivity , selectivity , and ease of use . some authors , in the recent years , have applied different modified biosensors , based on various redox proteins , to realize interesting tools for the monitoring of h2o2 . catalase ( cat ) belongs to oxidoreductase family class and has a heme prosthetic group at its active site with ferric ion ( fe ( iii ) ) . the catalytic ability of cat to reduce hydrogen peroxide was used in the developing of biosensors . to investigate cat catalytic activity , it is important to study its capacity to perform direct electron transfer ( det ) to the electrode surface . it is usually difficult to observe the det because the heme groups are buried deeply inside in the large structure of the protein . also , denaturation of the redox protein could occur on the sensor surface due to the immobilization method and to the matrix composition . to overcome these problems and promote the det carbon nanotubes ( cnts ) , modified electrodes are widely employed as support for the physical immobilization of biological molecules to promote the det thanks to their high surface / volume ratio and conductivity and also to enhance sensors and biosensors performances . a drawback on the use of cnts to modify electrode surface is their insolubility . however , some authors have obtained good results in the cnts modification of the electrode surface by using polymers as dispersing support . nafion is a perfluorinated polymer resistant to chemical attack and the cnts dispersion in its film has been investigated . in the present study , we report the development of a biosensor for h2o2 monitoring based on the immobilization of catalase in a nafion film containing dispersed functionalized mwcnts - cooh . the det of catalase was investigated either on modified or on bare electrode to identify the optimal conditions for h2o2 detection . in view of the possible practical application , the same modification steps were performed on screen - printed electrodes ( spes ) with a working electrode based on mesoporous graphite ( mg - spe ) . finally , the obtained biosensor was applied for the determination of hydrogen peroxide in beverages samples . catalase from bovine liver ( cat , ec 1.11.1.6 , activity 10,000 u mg protein ) was supplied by sigma - aldrich ( switzerland ) and stored at 20c . in particular , na2hpo4 , nah2po4 , hoc ( cooh ) ( ch2cooh ) 2 , kcl , ( k3 [ fe ( cn ) 6 ] ) , nafion 117 solution ( naf , purum , ~ 5 % solution in a mixture of lower aliphatic alcohols and water ) , ch3ch2oh ( ~ 96 % v / v ) , and h2o2 ( 30 wt . % in h2o ) were purchased from sigma - aldrich ( switzerland ) . high purity deionized water ( resistance : 18.2 m cm at 25c ; toc : 10 g l ) obtained from a millipore direct - q 3 uv system ( france ) was used throughout the experiments . the working solutions were prepared by diluting the stock solution with 0.1 mol l phosphate buffer solution and 0.1 mol l kcl , ph 7.0 ( pbs buffer solution ) , and then deoxygenated by bubbling n2 for about 20 min . multiwalled carbon nanotubes modified with carboxylic groups ( mwcnts - cooh ) were obtained from dropsens ( spain ) . all electrochemical measurements were performed with - autolab type iii potentiostat ( ecochemie , netherlands ) controlled using the gpes manager program ( ecochemie , netherlands ) at room temperature in n2 atmosphere . batch electrochemical experiments were performed in a 5 ml thermostated glass cell ( model 6.1415.150 , metrohm , switzerland ) containing pbs buffer solution , with a conventional three - electrode system . different working electrodes were used , in particular glassy carbon electrode ( gce , cat .6.1204.300 , metrohm , switzerland , = 3 mm ) and a mesoporous graphite screen - printed electrode ( mg - spe , model drp - 110mc , = 4 mm , dropsens , spain ) . a saturated calomel electrode ( sce , cat . 303 / scg / 12 , amel instruments , italy ) as the reference electrode and a carbon rod ( cat .6.1248.040 , metrohm , switzerland ) as the counter one were employed . for spes , all the reported potentials are referred to as saturated calomel electrode ( e = 0.241 v versus nhe ) . all ph measures were performed using a digital ph meter ( 827 ph lab , metrohm , italy ) . the morphology of the samples was observed using high - resolution field emission scanning electron microscopy ( hr fesem , zeiss auriga microscopy ) equipped with microanalysis eds 123 mn - k ev ( bruker ) . the gce surface was polished with 0.3 and 0.05 m alumina slurry on polishing silk cloth ( siem , italy ) and rinsed with deionized water . then , the electrode was sonicated in deionized water to remove trace of alumina from the surface ( sonicator au - 32 , argolab , italy ) . the physical immobilization of the enzyme was realized by dropping onto the working electrode surface 2 l of 0.5 wt . % nafion solution containing 1 mg ml of redox protein either in the presence or in the absence of 1 mg ml of mwcnts - cooh . the electrode surface was finally air - dried for about 20 min at room temperature . the analysis protocol of real beverages is described as follows : 2.5 ml of different beverages sample was diluted to 10 ml with pbs buffer solution . then , a certain amount of h2o2 ( 15 mol l ) was added and the solutions were deoxygenated . then , the samples were analyzed directly by cyclic voltammetry ( cv ) method and finally the recoveries were evaluated . for the study of ph dependance , the mcilvaine buffer was used at different ph values . the effect on the improvement of electrochemical performances by using nanomaterials as mwcnts - cooh was evaluated with cyclic voltammetry measurements of the electroactive area ( ae ) and of the heterogeneous standard rate constant ( k ) of the different electrodes . the cyclic voltammograms ( not shown ) were recorded in a solution of 1 . 1 mmol l potassium ferricyanide in pbs buffer solution . ae was determined from the randles - sevik equation : ip = 2.68610 naedcv , where ip is current in amps ( a ) , n is number of electrons transferred of k3 [ fe ( cn ) 6 ] by cyclic voltammetry ( cv ) in the redox event ( usually 1 ) , ae is electroactive area ( cm ) , d is diffusion coefficient ( 7.610 cm s ) , c is concentration ( mol cm ) , and v is scan rate ( vs ) . k was calculated by an extended method , a combination of nicholson and klingler and kochi treatments , by cv data using the same solution described above , in the scan rate range 5100 mv s. by comparing the results ( see table 1 ) arising from the several modification steps of the sensor , two aspects can be pointed out : ( i ) the parameters obtained for the nafion modified sensor ( naf - gce ) are lower than both the bare sensor ( bare - gce ) and the nanomaterial modified sensor ( naf - mwcnts - cooh - gce ) : presumably , this is due to the nafion film that hinders the charge transfer and slows down the substrate rate towards the sensor surface ; ( ii ) the use of carbon nanotubes enhances hugely the electrochemical signal increasing ae ( about 4 and 8 times compared to the bare - gce and naf - gce , resp . ) and improves k of the ferricyanide ion towards the sensor surface despite the ion exchange polymer presence ( about 1.5 and 2 times compared to the bare - gce and naf - gce , resp . ) : this could be ascribed to their excellent properties of increasing area / volume ratio and high electron conductivity and of facilitating the electron transfer . the association of these nanomaterials with nafion ( as solubilizing agent ) does not impair the electrocatalytic features of carbon nanotubes . this aspect was also observed in our previous work where the use of naf / mwcnts composite film has greatly increased the transfer charge rate . the comparison of electrocatalytic performances was evaluated by using catalase as model redox protein and comparing the voltammetric behavior ( figures 1 ( a ) and 1 ( b ) ) measuring several electrochemical parameters ( see section 3.4 ) . the catalase was immobilized by a nafion film onto the gce surface , in the absence and in the presence of mwcnts - cooh ; the electrochemical behavior of the modified electrodes has been investigated in n2 saturated pbs buffer solution , using cv . the cyclic voltammograms were recorded at naf - gce - cat and naf - mwcnts - cooh - gce - cat modified gces in the potential range from 0.6 v to 0.6 v. in the absence of mwcnts - cooh , catalase immobilized in a nafion film onto gce surface showed a quasi - reversible signal ( see figure 1 ( a ) ) with a midpoint potential of e = 128 mv ; the separation of cathodic and anodic peak potential ep = 80 mv ( at scan rates lower than 100 mv s ) indicated a fast electron transfer reaction according to the literature . for the other modified electrode , when the redox protein is in the presence of carbon nanotubes , cv experiments yielded evidence of a prominent increase ( about 20 times ) of faradic current ( figure 1 ( b ) ) and also an enhancement of electron transfer kinetic was observed at a constant amount of immobilized protein . in particular , e shifted to a more negative potential value ( 140 mv ) and ep was 70 mv , assuming that carbon nanotubes play an important role in the rising of the system reversibility . the effect of ph solution on the modified naf - mwcnts - cooh - gce - cat electrode was also tested . in figure 2 ( a ) , the peak currents at different ph values are shown . this value was consistent with that reported for catalase enzyme . based on these results , ph 7.0 for pbs buffer solution was used as the optimal ph for further experiments . the oxidation peak potential was reported versus solution ph values in the range 3.58.0 ( figure 2 ( b ) ) . the obtained slope ( 0.044 v ) the slope value is slightly smaller than nernst 's value of 0.059 v ph for the reaction of one electron coupled to one proton . this is probably ascribable to the influence of protonation states of trans ligands of the heme iron and amino acids around the heme , or the protonation of h2o molecule coordinated to the coordinated iron . figure 3 ( a ) shows typical cyclic voltammograms of naf - mwcnts - cooh - gce - cat biosensor at different scan rates ( 101400 mv s ) . the dependence of peak currents and peak potentials on the scan rate is also observed in figures 3 ( b ) and 3 ( c ) , respectively . as is obvious from figure 3 ( b ) , the peak currents change linearly with scan rate over a range of 10 to 1400 mv s ( with correlation coefficients of 0.9924 and 0.9914 ) , as expected for thin layer electrochemistry and according to a surface - controlled process . the slope of corresponding log ip versus log v linear plot , with a correlation coefficient of 0.9949 , was found to be 1.115 , very close to the theoretical slope 1 for thin layer voltammetry . the surface concentration of electroactive redox protein ( ) can be estimated using faraday law ( see ( 1 ) ) and calculated from the slope of peak current / scan rate plot : ( 1 ) = 4iprtn2f2av , where v is the scan rate , a is the electrode surface area ( 0.07 cm ) , t is the temperature , n is the number of electrons , and r and f are gas and faraday constants , respectively . thus , the average surface concentration of catalase was found to be 4.7610 mol cm , which indicates that the immobilized enzyme is in the form of an approximate monolayer on the surface of the modified electrode . moreover , the peak - to - peak separation at a scan rate of 10 mv s was approximatively 70 mv , indicating a quasi - reversible electron transfer process . based on the laviron theory , the transfer coefficient ( ) and the electron transfer rate constant ( ks ) for immobilized catalase either in the absence or in the presence of nanomaterials can be estimated by measuring the variation of peak potential separation with scan rate ( at higher scan rates , as shown in figure 3 ( c ) ) and reported in table 2 . besides , by comparing our proposed biosensor to other similar ones in the literature , all based on cat modified gces by using mwcnts , it is evident that the amount of our electroactive catalase is higher , probably due to the simple naf / mwcnts matrix that could increase the exposure extent of the heme group in the catalase enzyme ( see table 3 ) . the formal potential e of our biosensor is much less negative than those proposed by other authors . the formal potential value is dependent on the protein structure , so a change of the heme protein in the naf / mwcnts composite film results in a shift of e to positive potential values . moreover , partial denaturation of the enzyme could cause heme leakage and then a negative shift of the redox peaks ( change in the coordination sphere ) . the voltammetric characterization of the hydrogen peroxide reduction by means of the developed naf - mwcnts - cooh - gce - cat biosensor was performed in pbs buffer solution , at a scan rate of 50 mv s ( figure 4 ( a ) ) . an increase in the cathodic peak with the hydrogen peroxide concentration and a decrease in the anodic peak during the scan reversal have been observed . conversely , in the absence of catalase , no current change has been detected by the naf - mwcnts - cooh - gce electrode . from our experiments , we confirm the ec mechanism previously reported in the literature : ( 2 ) cat - feiii + e + h + cat - feiih + at the electrode surfaceh2o2 + cat - feiih + cat - feiii + h + + h2oin solutionfigure 4 ( b ) reports the catalytic efficiency ( ic / id ) changes versus h2o2 concentration ; ic and i d are the cathodic peak currents in the presence and in the absence of hydrogen peroxide , respectively . as can be observed , the catalytic efficiency increases with the h2o2 concentration up to 298 m , and then a plateau is reached . this is probably due to the denaturing effect of hydrogen peroxide at high concentration values . based on these results obtained using a classical gce electrode and employing a very simple and easy immobilization procedure , the same modification system has been developed on screen - printed electrodes in view of a possible application for determination of hydrogen peroxide in real samples . the surface morphology of the modified screen - printed electrodes ( spes ) was obtained by scanning electronic microscopy ( sem ) . in figure 5 ( a ) , mesoporous graphite spe ( mg - spe bare ) surface , without modification , is shown . figure 5 ( b ) reveals the presence of a cross - linked structure of multiwalled carbon nanotubes modified with carboxylic groups dispersed in a nafion film ( naf - mwcnts - cooh - mg - spe surface ) . moreover , the diameter of the carbon nanotubes ( ~ 14 nm ) is indicated . in the presence of the enzyme , the highly porous architecture that is formed between the mwcnts - cooh and the nafion film is suitable for immobilization of catalase that is confirmed in the following electrochemical measures . also , electrochemical characterization of these spes was carried out and the results are reported in table 4 . also , for these electrodes , the feature of nanomaterials to increase the sensor performances considerably is confirmed , so the following studies were performed using the naf - mwcnts - cooh - mg - spe sensor . successively , the main electrochemical parameters of our proposed biosensor naf - mwcnts - cooh - mg - spe - cat were evaluated ( see table 5 ) . the current - concentration dependence of hydrogen peroxide was modeled by using michaelis - menten nonlinear fitting thus allowing the calculation of the main kinetic parameters ; data obtained are reported in table 6 . it is clear that the biosensor has a good lod of 0.83 mol l and a good sensitivity to determine h2o2 concentrations . moreover , a comparison of analytical and kinetic parameters for h2o2 detection for different redox protein modified electrodes is summarized in table 6 . also , the reproducibility of the developed biosensor was calculated as rsd = 5.0 % by using 500 mol l h2o2 in a series of six experiments . by the data achieved , the following can be assessed : ( i ) the immobilized enzyme retained good biocatalytic activity ; ( ii ) the carbon nanotubes dispersed in the nafion film provided an optimal microenvironment ; ( iii ) the nanocomposite was a good matrix for catalase immobilization and biosensing preparation ; ( iv ) the redox protein maintained active site accessibility and exchanged electrons with the sensor surface . based on the results declared in the previous sections and in order to test the reliability of the proposed biosensor for practical application , different commercial beverages were chosen ( tea , juice , and milk ) . the concentration of 15 mol l was chosen because an fda regulation currently limits residual h2o2 to 0.05 ppm ( corresponding to 15the results show good recoveries , in the range 100.3105.7 % , for our modified naf - mwcnts - cooh - mg - spe - cat biosensor ( table 7 ) . the shelf lifetime of our modified biosensor was tested by measuring its current response obtained for 500 mol l h2o2 concentration during a period of 21 days . during the first week , a 4 % decrease was observed , reaching a 15 % decrease after three weeks . this result can be ascribable to the presence of the nanomaterials , which avoid the fouling phenomena of the surface which could affect the biosensor performances , and also the use of naf / mwcnts composite film provides a strong and biocompatible microenvironment for stabilizing the catalase activity . in this study , an electrochemical biosensor was developed for the determination of hydrogen peroxide concentration in packaged beverages . to this aim , direct electrochemical properties of catalase , confined in a nafion film on the surface of a glassy carbon electrode , were studied . the electron transfer coefficient , , the electron transfer rate constant , ks , and the surface concentration of electroactive redox protein , , were evaluated by cyclic voltammetry studies . the modification of the electrode surface by using nanostructured materials dispersed in nafion polymeric solution resulted in an enhancement of the overall bioelectrochemical properties of the developed biosensor . the biocatalytic activity towards catalase substrate hydrogen peroxide confirmed that the immobilization procedure allowed a good microenvironment for catalase and facilitated the electron exchange to the electrode surface . hence , based on these interesting results obtained , the same modification procedure was applied to screen - printed electrodes . also , this platform of the modified biosensor was entirely characterized and was applied to detect h2o2 in spiked real samples of different commercial beverages obtaining good recoveries .\noutput:\n" }, { "from": "agent", "value": "a catalase - based ( naf / mwcnts ) nanocomposite film modified glassy carbon electrode for hydrogen peroxide ( h2o2 ) detection was developed . the developed biosensor was characterized in terms of its bioelectrochemical properties . cyclic voltammetry ( cv ) technique was employed to study the redox features of the enzyme in the absence and in the presence of nanomaterials dispersed in nafion polymeric solution . the electron transfer coefficient , , and the electron transfer rate constant , ks , were found to be 0.42 and 1.71 s1 , at ph 7.0 , respectively . subsequently , the same modification steps were applied to mesoporous graphite screen - printed electrodes . also , these electrodes were characterized in terms of their main electrochemical and kinetic parameters . the biosensor performances improved considerably after modification with nanomaterials . moreover , the association of nafion with carbon nanotubes retained the biological activity of the redox protein . the enzyme electrode response was linear in the range 2.51150 mol l1 , with lod of 0.83 mol l1 . from the experimental data , we can assess the possibility of using the modified biosensor as a useful tool for h2o2 determination in packaged beverages ." } ]

[ { "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: thyroid carcinoma ( tc ) is the most common endocrine malignancy , with a rapidly rising incidence in recent years worldwide . thyroid malignancies mainly include four histological subtypes : papillary thyroid carcinoma ( ptc ) , which is the most common tc subtype , and follicular thyroid carcinoma ( ftc ) , which are summarized as differentiated thyroid carcinoma ( dtc ) , medullary thyroid carcinoma ( mtc ) and anaplastic thyroid carcinoma ( atc ) . most of dtc have an excellent prognosis with a 5 - year relative survival rate of 98 % in localized disease . generally , dtc can be effectively managed by total thyroidectomy , ablative doses of radioiodine ( rai ) and suppressive treatment . the follow - up is based on measuring serum thyroglobulin ( tg ) levels as a biomarker and imaging with radioiodine ( rai ) therapeutic scans . it has been estimated that about 20 % of patients with ptc will present local or distant persistent or recurrent disease . in 75 % of cases , the disease is located in the neck , most often in the lymph nodes . in 25 % of cases , it is represented by distant metastases that can occur in the lungs ( 50 % ) , bones ( 25 % ) , lungs and bones ( 20 % ) or other sites ( 5 % ) . loco - regional persistence / recurrence is generally treated with further surgery , rai , and , occasionally , external beam radiation therapy . complete biochemical remission has been reported in 2575 % of patients with recurrent disease in lymph nodes , but recurrences in the thyroid bed are often associated with a poorer prognosis . although , the majority of patients are being cured with standard therapy , older patients with metastatic disease at presentation , particularly if the disease is rai - refractory , have poor prognosis , as do patients with anaplastic tc . amiodarone is a widely used drug for the prophylaxis and treatment of cardiac arrhythmias . around 18 % of patients treated with this drugmost of the effects of amiodarone on thyroid function are thought to be due to the iodine load that is related to drug intake . every 200 mg dose of amiodarone contains 75 mg of organic iodine , an amount that exceeds the minimal daily needs of iodine . moreover , it has a very long half - life of approximately 100 days , because it accumulates in the adipose tissue . consequently , effects associated to iodine load due to amiodarone ingestion may persist long after treatment discontinuation . a 65 year - old man was admitted to the endocrinology department of a tertiary academic medical center in october 2013 for the investigation of a left lobe thyroid macro - nodule that was accidentally discovered during a carotid doppler ultrasonography exam . the patient s past medical history includes type 2 diabetes chronically treated with oral anti - diabetic drugs , therapeutically controlled hypertension , extrasystolic arrhythmia and a recent history of two syncopal episodes . in the past 2 years , he had no radiation exposure and his family history was negative for thyroid and neoplastic diseases . his blood pressure was 130/80 mmhg , with a heart rate of 82 beats / minute . cardiac examination revealed extrasystolic arrhythmia and right bundle branch block ; neurological examination established cardiogenic syncope and diabetic polyneuropathy . physical exam was significant for a left - sided thyroid macro - nodule , of woody consistency , without spontaneous tenderness and on palpation measuring approximately 3 cm . thyroid ultrasound showed an asymmetric , isoechoic , homogeneous thyroid gland of normal volume . to the upper pole of the left lobe two , confluent solid nodular formations , of 4.22 ml ( 30.8 / 15.8 / 16.7 mm ) were identified , which were described as hypo - echoic , confluent , inhomogeneous , vascularized and without halo . thyroid function tests revealed normal thyroid function , as shown by a basal tsh level of 2.84 iu / ml and a ft4 concentration of 16.1 pmol / l with normal anti - thyroid peroxidase antibody ( 13 ui / ml ) and anti - thyroglobulin antibody ( 16 ui / ml ) titers and normal calcitoninemia , of 4.84 pg / ml . radioisotope thyroid scan evidenced lack of mtc uptake on the left lobe ( cold macro - nodule ) . subsequently , the percutaneous fine needle aspiration ( fna ) was performed and the result indicated category v in the bethesda system for reporting thyroid cytopathology , i.e. positive for malignant cells . the patient was referred to the surgery department and in december 2013 he underwent total thyroidectomy . the histopathology test revealed well - differentiated papillary cancer of the left lobe with thyroid capsule and peri - thyroidal lymph nodes invasion , t3n1amx . four weeks after thyroidectomy , the patient was referred to the nuclear medicine department and underwent adjuvant radioiodine therapy with 90.65 mci of radioactive iodine ( i ) . the 72 - hours i - whole body scan ( wbs ) failed to indicate uptake , which was in discordance to high thyroglobulin ( tg ) levels of 927.4 ng / ml ( normal 0.1 ng / ml in cured tc ) , low titers of anti - tg antibodies of 26 iu / ml ( normal 115 iu / ml ) , high basal tsh of 72.8 miu / l ) and presence of lateral cervical lymph nodes of below 10 mm diameter , which were noted at ultrasound examination performed by the endocrinologist . the patient started hormone suppression therapy with 150g levothyroxine daily , to maintain the tsh level 0.1 miu / l and ft4 within normal limits . in view of prior use of amiodarone for the past 2 years , which was interrupted 6 weeks before rai therapy and negative wbs , in march 2014l but associated with high serum ( 192 g / l , normal 4670 g / l ) and urinary iodine ( 782 g / l , normal 20299 g / l ) levels , which indicated excessive iodine body load . according to the patients medical records , the tg level decreased to 393.3 ng / ml . thyroid and neck ultrasound were performed and pathological cervical and supraclavicular lymph nodes of below 13 mm diameter were described . thorax computer - tomography ( ct ) scan was negative , and the patient was referred to fluor - 18fdg positron emission computer tomography ( pet - ct ) scan , which exclusively confirmed left latero - cervical and supraclavicular lymphadenopathy ( figure 1 ) as indicated by neck ultrasonography , and no distant metastases . at 6 - months follow - up , at reevaluation in the nuclear medicine department , in july 2014 , serum tg increased to 863 ng / ml and therefore , the patient received an additional dose of 76.4 mcii radioiodine and thyroid hormone suppressive dose was increased to 200 g / d l - thyroxin to maintain full suppression . the post - therapeutic wbs showed rai uptake in the neck . in october 2014 the tg level was still elevated at 1105 ng / ml , so the patient was treated with another completion dose of 118.8 mci i , followed in march 2015 by another dose of 100 mci i , at a tg level of 766 ng / ml . pathological lymph node uptake was confirmed at wbs and no uptake in the thyroid bed or distant secondary disease was evidenced . neck ultrasonography ( figure 2 ) confirmed multiple left latero - cervical and supraclavicular round , hypo - echoic , intensely , vascularized lymph adenopathies with increased stiffness at thyroid elastography and with a diameter of up to 18 mm . in view of lack of adequate response of the disease to radioiodine treatment , and no organic metastases , the patient was proposed for therapeutic lymph node dissection . amiodarone is a widely used , highly efficient anti - arrhythmic drug ; however , treatment puts the patient at risk for a broad thyroid pathology , either hypothyroidism or thyrotoxicosis and , possibly , thyroid malignancy . complex mechanisms are involved in amiodarone - induced thyroid disorders such as autoimmunity , inflammation and unveiling of latent hyperthyroidism by excessive iodine intake . amiodarone therapy was motivated by cardiac disease in our patient , which developed no thyroid dysfunction , and was stopped at the moment the suspicion for thyroid malignancy was set . in recent years , several case reports raised the possibility of an association between amiodarone and cancer . to be mentioned that in rats exposed to amiodarone , the prevalence of tc is increased . in the first large population - based cohort study in that the overall malignancy risk was evaluated in 6418 patients treated with amiodarone , su et al. demonstrated a higher risk of total malignancies in patients , particularly males , treated with amiodarone in comparison to the general population . the use of amiodarone was not found to be associated with tc , but the case number was too small to draw a definite conclusion . previous case reports of cancers developing after regular amiodarone use , for a period of 2 to 5 years suggest that a latency period and high cumulative doses might be prerequisites for the development of amiodarone - associated malignancies . in high amounts , iodine saturates the thyroid gland , blocking further absorption of both non - radioactive and radioactive iodine , thus , a 13 weeks low - iodine diet time interval is recommended in tc patients prior to radioactive iodine treatment . as in the presented case , iodine uptake blockade is prolonged for several months after high iodine exposure by amiodarone intake and may explain lack of rai image on wbs in our patient in spite of biochemical and ultrasonography data . approximately 6 months after discontinuing amiodarone ( as demonstrated by the low serum drug levels ) , both the serum and urinary iodine concentrations were still elevated . although in most thyroid cancer patients treated conventionally by surgery with or without rai , a good disease control is achieved , up to 2030 % may present persistent disease or develop recurrences . prognosis of thyroid cancer may largely vary with the histological type with a 10 - year mortality rate of 510 % for papillary tc and 1520 % for follicular tc , whereas the one - year mortality rate for anaplastic tc approaches 100 % . papillary tc is more frequent in women ( 3:1 ) , but mortality rates are two times higher among men than women . age at diagnosis is a critical predictor of patient outcome as patients aged 60 years commonly present with more aggressive disease , meaning a higher prevalence of lymph nodes and distant metastases , and have an increased mortality rate compared to younger patients ( 31 % vs. 1.2 % ) . lymph node involvement is very common in patients with papillary and follicular tc , ranging from 20 to 90 % during primary surgery , nonetheless the prognostic significance of lymph node metastasis remains controversial . still , the recently published seer ( surveillance , epidemiology and end results program ) national cancer institute data , assessing patient outcomes , have shown that lymphatic metastases are a poor prognostic indicator in older ( 45 years ) ptc patients . routine or prophylactic lymphadenectomy is defined as the removal of lymph nodes in the absence of lymph node metastasis evidenced by preoperative imaging studies or intraoperative inspection . while elective or therapeutic lymphadenectomy involves the removal of regional lymph nodes which are detected pre - or intra - operatively andare suspected to harbor metastases , routine or prophylactic neck dissection defines the removal of lymph nodes in the absence of lymph node metastasis evidenced by preoperative imaging studies or intraoperative inspection . removal of involved lymph nodes has not been systematically demonstrated to reduce local recurrence or to improve long - term survival and central lymph nodes dissection ( clnd ) is recommended according to recent american thyroid association ( ata ) guidelines to papillary tc patients with advanced disease . the european thyroid cancer task force indicates prophylactic clnd in patients with preoperatively suspected and / or intra - operatively proven lymph node metastases . the term central compartment dissection describes removal of lymph nodes and soft tissues in level vi with preservation of the recurrent laryngeal nerves and at least the superior parathyroid glands . the term lateral compartment dissection refers to removal of all soft tissues and lymph nodes in levels iia , iii , iv and v. drawbacks associated with the routine performance of clnd are an increased rate of morbidity , particularly permanent hypoparathyroidism . in the present clinical case , therapeutic lymph node dissection is clearly recommended by persistent lymph node metastases with a diameter of 10 mm , in spite of repeated rai therapy and the patients age . usually , patients with small lymph node metastases undergo i treatment , but abnormalities can still persist after two or three treatment courses . in addition , recurrent disease can develop after incomplete surgical resection of neoplastic tumors , and is not always prevented by postoperative radioiodine treatment . in such cases , surgery should be considered . treatment of disease that is limited to the neck can include extensive surgery and external beam radiotherapy . however , patients over 40 years of age who have poorly differentiated tumors , no rai uptake , a large tumor burden , rapidly progressive disease , soft tissue involvement , and high 18f - fdg uptake do not normally gain disease - free status after treatment of recurrent neck disease . moreover , distant metastases are frequently detected in these patients during the subsequent follow - up period . the most common early side effects of rai treatment include radiation thyroiditis , neck pain and swelling , larynx edema , which may cause compressive symptoms , sialadenitis , and gastritis . cumulative doses of rai are associated with lacrimal and salivary gland dysfunction , pulmonary fibrosis , cancer , and leukemia . these effects are dose - dependent and increase with cumulative activity . over the last decade , a greater risk for secondary malignancies ( leukemia and solid tumors ) after high cumulative therapeutic activities ( 600 mci , 22gbq ) has been reported but there is no international consensus on limiting the rai dose to 600 mci . in fact , the use of rai should be individualized to balance the risks against therapeutic benefit . nearly all patients with distant metastases have high serum tg concentrations and two - thirds of these patients have i uptake in the metastases . despite this , several series have demonstrated that patients with detectable serum tg levels may have a negative whole - body scan . dealing with these patientsis a real challenge . the first negative i wbs of our patient , despite increased tg levels , could be explained , by the interference with the amiodarone treatment . nevertheless , tg was significantly lower at the 3 months post - rai treatment evaluation . occasionally , it is important to exclude false positive tg levels and the presence of thyroid tissue that decreases the sensitivity to detect metastatic disease . the most common cause of a negative iodine scan is tumor de - differentiation , which refers to a tumor , which fails to take up i and is therefore considered rai - refractory . many of these patients also have normal conventional imaging investigations ( ct , mri , neck ultrasonography ) . in these cases , fdg - pet / ct became a useful imaging study as it provides anatomical and prognostic information as patients with differentiated tc with evidence of rai - refractory disease usually have higher glucose metabolism and positive fdg - pet scans . metastases may be observed on the post - therapeutic iodine scan in patients with negative diagnostic wbs . in such patients , rai may still be of some advantage , however a therapeutic effect is not guaranteed and additional therapeutic methods should be considered . in the presented patient surgerythose patients with no uptake even with higher - dose rai have true rai refractory disease , requiring subsequent therapy and a more aggressive approach . for such patients , conventional chemotherapy with doxorubicin yields low response rates of short duration , is often associated with considerable toxicity , and does not prolong survival . in - progress trials investigating novel targeted molecular therapies open new perspectives in rai - refractory tc .\noutput:\n" }, { "from": "agent", "value": "thyroid carcinoma ( tc ) is the most common endocrine malignancy . although the overall prognosis for patients with tc is good , up to 2030 % of patients have recurrent or persistent disease after conventional therapy by surgical resection and radioactive iodine ( rai ) . amiodarone is a highly efficient anti - arrhythmic drug with a very long half - life , so it may interfere with rai many months after the drug withdrawal . this case report mirrors the challenges of thyroid cancer management in an amiodarone - treated patient ." } ]

[ { "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: electronic cigarettes are battery - operated devices that deliver nicotine to the lungs by evaporation of a liquid . chronic idiopathic neutrophilia is a condition characterized by elevated white blood cell and neutrophil counts without any underlying disease ; smoking has been implicated as a potential cause . a male caucasian patient , born in 1977 , presented in september 2005 with asymptomatic elevation of white blood cell and neutrophil count , and mildly - elevated c - reactive protein levels . he was a smoker since 1996 and was treated with 20 mg / day of simvastatin since 2003 due to hyperlipidemia . clinical examination , and laboratory and imaging investigations ruled out any infectious , haematological , rheumatological , or endocrine conditions . he had 2 unsuccessful attempts to quit smoking ; one was unassisted and the second was performed with the use of both varenicline and nicotine replacement therapy ( patches ) . during the subsequent 6.5 years , his leukocyte and c - reactive protein levels were repeatedly elevated ; the condition was consistent with chronic idiopathic neutrophilia . in february 2012 , he started using electronic cigarettes and he managed to quit smoking within 10 days . after 6 months , laboratory examination showed normalized leukocyte count and c - reactive protein levels , confirmed immediately by a second laboratory and by repeated tests after 1 and 2 months . smoking cessation with the use of electronic cigarette led to reversal of chronic idiopathic neutrophilia . the daily use of electronic cigarette may help preserve the beneficial effects of smoking cessation . cigarette smoking is a major cause of disease , affecting several systems in the human body .1,2 although reducing cigarette consumption does not improve prognosis ,3 smoking cessation has important beneficial socioeconomic and health - related implications .4,5 however , quitting smoking is a very difficult task . smokers that try to quit without any medical aid or treatment have extremely low success rate .6 although several pharmaceutical products are available for smoking cessation , long term quit - rates are relatively low .7 therefore , tobacco harm reduction strategies and products have been developed , with the main goal to reduce the amount of harmful substances administered to the human body .8 electronic cigarettes have been introduced to the market in recent years as an alternative to smoking . they are hand - held electronic nicotine - delivery devices consisting of a battery , a cartridge containing liquid , and an electrical resistance that is heated through the battery power and evaporates the liquid . they deal with the chemical addiction by delivering nicotine to the lungs and consequently to the circulation . although millions of people use them all over the world , there is lack of clinical evidence on their efficacy in reversing smoking - related disease and conditions . chronic idiopathic neutrophilia ( cin ) is a condition characterized by asymptomatic elevation of white blood cells ( wbcs ) and neutrophil count that persists for years without any underlying disease .9 smoking has been implicated as a cause of this condition ,9,10 and leukocyte count is a predictor of future cardiovascular events .11,12 to the best of our knowledge , we report for the first time a case study of a subject with cin that was reversed by smoking cessation with the daily use of electronic cigarettes . written informed consent was obtained from the patient for presenting this case report . a male caucasian , born in 1977 , was presented in september 2005 with an elevated wbc count found during a routine check - up . at this time , he had been a smoker since 1996 ( 9 pack - years at the time of presentation ) . he had a positive family history of premature coronary heart disease and hyperlipidemia , which was treated with simvastatin at 20 mg / day since 2003 . complete blood count tests performed 9 and 18 months earlier were normal ( wbc : 89009700 / l , neutrophils : 41834462 / l , lymphocytes : 40054268 / l , eosinophils : 89194 / l , basophils : 623776 / l ) . at presentation , his wbc count was 14,600 / l ( 8614 / l neutrophils , 5256 / l lymphocytes , 292 / l eosinophils and 438 / l basophils ) . he was completely asymptomatic , had no history of recent infections or trauma and reported no fever . he had no changes in body weight or appetite over the past months ; his body mass index ( bmi ) was 27.7 kg / m at presentation . c - reactive protein was elevated at 14 mg / l ( normal range 5 mg / l ) . rheumatologic and infectious disease work - up ( including ana , anti - dsdna , le - test , ra - test , asto , cmv and ebv antibodies , wright test and widal reaction ) were all negative for disease . he was invited for a repeat complete blood count after 2 months , with wbc reaching 21,000 / l ( neutrophils : 14,280 / l , lymphocytes : 5250 / l , eosinophils : 630 / l , basophils : 840 / l ) . once again he was asymptomatic and with no signs of infection or any other inflammatory condition . he was instructed to stop intake of simvastatin and repeat the examination in another 2 months . in january 2006 , leukocytosis was still present ( wbc : 17,900 / l , neutrophils : 11635 / l , lymphocytes : 5012 / l , eosinophils : 537 / l , basophils : 716 / l ) . the diagnosis of cin was suspected and he was offered a bone marrow aspiration biopsy to rule out other conditions . all results were consistent with cin , and mild elevations in c - reactive protein were also noted ( fig .2 ) . he did not receive any other medications during this period besides antipyretics for 2 episodes of common cold ; all laboratory examinations were performed at least 10 weeks far from the common cold episodes . he had two unsuccessful attempts to quit smoking , one without any medical treatment in 2006 and one with varenicline plus nicotine patches in 2010 . a change in statin prescription from atorvastatin ( 20 mg / day ) to rosuvastatin ( 20 mg / day ) was done in may 2010 , but no difference was observed in wbc count in subsequent measurements . in february 2012it should be mentioned that use of electronic cigarettes was a personal choice of the patient ; no advice or recommendation to use it was provided by the physicians , since it has not been approved as a smoking cessation method . one month earlier , his complete blood count was consistent with cin . in august 2012 , routine follow - up showed no leukocytosis ( wbc : 8800 / l , neutrophils : 4400 / l , lymphocytes : 3344 / l , eosinophils : 352 / l , basophils : 704 / l ) . further tests , 1 , 2 and 3 months later revealed no leukocytosis . during this period , he was using the electronic cigarette daily , consuming liquid with nicotine concentration of 9 mg / ml . smoking abstinence was confirmed during his last three visits by measuring carbon monoxide in exhaled breath ; it was within normal limits ( 4 ppm ) . to the best of our knowledge , this is the first study which reports that smoking cessation with the use of electronic cigarette leads to reversal of chronic idiopathic neutrophilia . the most important message is that despite the daily use of electronic cigarette by this patient , the beneficial effects of smoking cessation were maintained . electronic cigarettes were invented in 2003 , with awareness and use increasing significantly over the past 3 years .13 they have been introduced to the market as tobacco harm - reduction products and they may have a unique role in this field . they work by evaporating a nicotine - containing liquid , which is subsequently inhaled by the user . in addition to nicotine , the constituents of liquids used for evaporation are limited to propylene glycol , glycerol , and flavorings . since they deliver nicotine and at the same time resemble the act of smoking by production of visible vapor , they deal with both the chemical ( nicotine delivery ) and behavioral components of cigarette addiction .14 a non - randomized study by polosa et al15 and an internet survey by siegel et al16 suggested that they may be effective as a smoking cessation tool . the absence of tobacco and the lack of combustion are important features in the health - related profile of these products . until recently , research on the composition , toxicology , and clinical effects of electronic cigarettes was scarce . thus , fda and who publicly expressed serious concerns about electronic cigarette use in 2009 , recommending that their use should be avoided . cahn and siegel14 summarized several chemical analyses performed until 2011 , showing that electronic cigarette liquid contents are far less harmful compared to tobacco .14 for nitrosamines they mentioned that , when present , the amount was 500-fold to 1400-fold reduced in electronic compared to tobacco cigarettes .14 substances produced from combustion of tobacco cigarettes , like polycyclic aromatic hydrocarbons , were not present in any of the liquids tested . although still inadequate , research on electronic cigarettes has progressed over the past year . during the 14th annual meeting of the society for research on nicotine and tobacco europe , romagna etal17 presented a cytotoxic study comparing electronic cigarette vapor with tobacco cigarette smoke ; they found that vapor extract from 10 different commercially available liquids were not cytotoxic to cultured mammalian cells compared to significant cytotoxicity observed from tobacco smoke extract .17 only three clinical studies on the effects of electronic cigarettes on human health have been performed . vardavas et al18 found that 5 minute use of electronic cigarette produced a mild but significant elevation in pulmonary resistance .18 however , no comparison with the effects of tobacco cigarettes was performed . flouris et al19 found that no elevation in wbc count was found after electronic cigarette use ; in comparison , wbc and neutrophil counts were significantly elevated immediately after tobacco cigarette smoking .19 farsalinos et al20 studied smokers and electronic cigarette users with echocardiography before and after smoking and electronic cigarette use respectively .20 acute diastolic dysfunction was observed in smokers immediately after smoking 1 cigarette , while diastolic function was preserved after using the electronic cigarette for 7 minutes . interestingly , although electronic cigarette users were previously heavy smokers , it took them on average only 2 days to quit smoking with the use of the device . despite all this data and the fact that no study has found that electronic cigarettes are more harmful when compared to tobacco cigarettes , it must be emphasized that research is still in its infancy . more studies are needed , especially clinical studies , on their long - term effects . it will take several years , however , before such studies are published as awareness and use of electronic cigarettes has increased only recently . delay will also occur as the knowledge that smoking - related disease and the beneficial effects of smoking cessation take several years before becoming clinically evident . until that time , research should focus on the pathophysiological mechanisms by which smoking causes disease and should proceed on both laboratory and clinical level . the crucial scientific question that should be addressed is whether electronic cigarettes are less harmful compared to tobacco cigarettes , since they should be marketed solely as a tobacco harm reduction product and not as a new habit for the general population . in any case , regulation and specific quality standards should be implemented as the use of non - pharmaceutical grade nicotine or other constituents may lead to the presence of toxic tobacco impurities in the liquids , which will be subsequently inhaled by the user .14 although we can not exclude that some constituents of electronic cigarette vapor may have had beneficial effects in reducing wbc count in our patient , the most probable explanation is that reversal of cin was caused by smoking cessation itself . smoking causes diseases by a variety of mechanisms , including inflammation .21 it causes a 20 % 25 % increase in peripheral blood leukocyte count22 in addition to elevated levels of inflammatory markers like c - reactive protein .23 cin is an uncommon condition associated with greater elevation in wbcs and neutrophils than those observed in the majority of smokers . the patient had persistently elevated wbc count and mildly elevated c - reactive protein levels , without any underlying disease . this may represent a state of low - grade inflammation , which is a risk factor for future cardiovascular disease .24 although he was a smoker several years before cin developed , we could not find any specific underlying cause for the development of the condition at the particular time of presentation . we know however that inflammatory markers have a temporal relationship to smoking ,25 and this might explain the delay in cin presentation . cigarette smoking was suggested as a potential cause for this condition in our patient after an extensive diagnostic analysis excluded other possible conditions or intake of medications such as corticosteroids and lithium which are associated with neutrophilia .9 despite the use of medically - approved methods , the patient failed to quit smoking . finally , with the aid of electronic cigarettes , he was able to quit smoking in a timely manner . five months later , cin was reversed , although he was using the electronic cigarette on a daily basis . in conclusion , we presented a case of a young smoker having cin and low - grade inflammation which was reversed after smoking cessation . electronic cigarette use was successful as a smoking - cessation tool , after two failures to quit smoking ( one with the use of currently - approved pharmaceutical methods ) . the daily use of electronic cigarettes did not hinder the beneficial effects of smoking cessation in this patient . undoubtedly , this case report is in no way conclusive about the effects of electronic cigarettes on health . however , it indicates that research on the potential efficacy and health consequences of electronic cigarettes as a tobacco harm reduction product should be intensified . until that time , we can not recommend their use , but physicians will face two important ethical dilemmas in daily practice . should they advise patients who have managed to quit smoking by using electronic cigarettes ( like our patient ) to stop using them , with the risk of smoking relapse ? and should patients who have repeatedly failed to quit smoking by currently approved methods , such as the patient in this study , be denied the possibility , however small it may be , to quit smoking by using electronic cigarettes ?\noutput:\n" }, { "from": "agent", "value": "introduction : smoking is a major risk factor for a variety of diseases . electronic cigarettes are battery - operated devices that deliver nicotine to the lungs by evaporation of a liquid . chronic idiopathic neutrophilia is a condition characterized by elevated white blood cell and neutrophil counts without any underlying disease ; smoking has been implicated as a potential cause.case presentation : a male caucasian patient , born in 1977 , presented in september 2005 with asymptomatic elevation of white blood cell and neutrophil count , and mildly - elevated c - reactive protein levels . he was a smoker since 1996 and was treated with 20 mg / day of simvastatin since 2003 due to hyperlipidemia . clinical examination , and laboratory and imaging investigations ruled out any infectious , haematological , rheumatological , or endocrine conditions . he was followed - up regularly and was advised to stop smoking . he had 2 unsuccessful attempts to quit smoking ; one was unassisted and the second was performed with the use of both varenicline and nicotine replacement therapy ( patches ) . during the subsequent 6.5 years , his leukocyte and c - reactive protein levels were repeatedly elevated ; the condition was consistent with chronic idiopathic neutrophilia . in february 2012 , he started using electronic cigarettes and he managed to quit smoking within 10 days . after 6 months , laboratory examination showed normalized leukocyte count and c - reactive protein levels , confirmed immediately by a second laboratory and by repeated tests after 1 and 2 months.conclusion : smoking cessation with the use of electronic cigarette led to reversal of chronic idiopathic neutrophilia . the daily use of electronic cigarette may help preserve the beneficial effects of smoking cessation ." } ]

[ { "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 human case of sfts was identified in a rural area of the pujiang district ( figure 1 ) . the patient , a 60 - year - old local male subsistence farmer , sought treatment at the zhejiang provincial people s hospital on june 1 , 2012 , after a 6 - day history of fever ( maximum axillary temperature 40c ) , malaise , chills , gingival bleeding , hyperemia of conjunctivae , and diarrhea ( 10 or fewer times per day ) . initial laboratory testing revealed thrombocytopenia ( 1310 platelets / l ; reference range 10030010platelets / l and leukocytopenia ( 0.9310 leukocytes / l ; reference range 41010 / l ) . supportive therapy was provided , and the patient 's condition seemed to improve on the second day : platelet count rose to 3410 platelets / l , and leukocyte count rose to 7.2810 however , on the third day , the patient became weak and died of multiple organ failure . location of zhejiang province in china ( left ) and the location of selected districts ( right ) within the province where serum samples of healthy persons were collected and tested in 2013 for the presence of severe fever with thrombocytopenia syndrome virusserum samples from the patient were tested for the presence of sftsv rna by quantitative real - time reverse transcription pcr as previously described ( 1 ) . the qiaamp viral rna mini kit ( qiagen , hilden , germany ) was used for rna extraction . detection of all 3 viral rna segments by quantitative real - time reverse transcription pcr and isolation of the virus from vero cell culture confirmed the association between the clinical syndrome and sftsv infection . in addition , sftsv - specific igg and low levels of viral rna were detected in a blood sample from a family member of the patient . the family member did not report exposure to potential animal hosts or vectors , so sftsv transmission is believed to have occurred through personal contact when the family member was caring for the patient . signs of illness did not develop in the family member . to investigate if additional mild subclinical infections occurred , we , with the support of the local disease control department , conducted a seroprevalence study in the patient s village in pujiang district . we used an elisa kit provided by the national center for disease control and prevention to prepare and test serum samples for the presence of sftsv - specific igm and igg ( 5,6 ) . all serum samples were negative for sftsv - specific igm , whereas 4 ( 7.4 % ) of the serum samples were positive for sftsv - specific igg ( figure 2 ) . none of the igg - positive participants reported any disease symptoms that are associated with sftsv infections . seroprevalence of igg to severe fever with thrombocytopenia syndrome virus in healthy persons from selected districts in zhejiang province , china , 2013 . to further investigate the occurrence of mild or subclinical sftsv infections , we collected serum samples from healthy volunteers in 5 additional districts in zhejiang province and tested the samples for sftsv - specific igg . tested are shown in parentheses ) : lishui , 10.2 % ( 18/176 ) ; jinhua , 3.5 % ( 7/200 ) ; ningbo , 10.9 ( 28/256 ) ; taizhou , 3 % ( 3/100 ) ; and jiaxing , 5.5 % ( 11/200 ) ( figure 2 ) . results were confirmed by immunofluorescence assay conducted as previously reported ( 1 ) . in brief , sftsv - infected vero cells were fixed with cold acetone , washed with distilled water , air - dried , and then stored at 70c . serum samples were diluted 1:20 in phosphate - buffered saline supplemented with 0.01 % evans blue ( sigma - aldrich co. llc , st . slides were then incubated with the diluted serum samples in a humidified chamber at 37c for 30 min and then washed with phosphate - buffered saline . labeled goat anti human igg conjugate ( boshide , wuhan , china ) , washed , and analyzed by the use of fluorescence microscopy . the results of these experiments confirmed the presence of sftsv - specific igg in 84.5 % ( 60/71 ) of the samples with elisa - positive results . serum samples that were negative for sftsv by elisa were also negative by immunofluorescence assay . the virus also has the limited ability to be transmited from person to person through contact with contaminated blood , but secondary cases are generally less severe and have so far not resulted in fatalities ( 79 ) . nonetheless , there is great public health concern regarding sftsv . our seroprevalence study was prompted by the identification of a subclinical , secondary infection that was most likely caused by person - to - person transmission of the virus from an infected family member with a fatal case of sfts . we found an overall sftsv seroprevalence of 7.2 % among 986 healthy persons who reported no symptoms associated with sfts . because the seropositive participants in our study did not have contact with persons with diagnosed cases of sfts , their infections most likely occurred through natural exposure . from this , we conclude that sftsv infections are widespread in rural areas of zhejiang province , and only a small percentage of the infections result in clinical disease .\noutput:\n" }, { "from": "agent", "value": "in june 2013 , a subclinical infection with severe fever with thrombocytopenia syndrome virus ( sftsv ) was detected in zhejiang province , china , prompting seroprevalence studies in 6 districts within the province . of 986 healthy persons tested , 71 had igg antibodies against sftsv . this finding suggests that most natural infections with sftsv are mild or subclinical ." } ]

[ { "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: ewing sarcoma , peripheral primitive neuroectodermal tumors and askin tumors belong to ewing family of tumors with a variable degree of neuroectoderm differentiation . histologically , they all show small round blue cells . askin tumor is a primitive neuroectodermal tumor of thoracopulmonary region described for the first time in 1979 in 20 children and adolescents with a mean age of presentation of 14.5 months , female preponderance , and median survival of 8 months . askin tumor presents with respiratory problems such as pain , dyspnea , and mass and weight loss . a 14 - year - old girl presented to pediatric emergency with chest pain on the right side of the body , excessive irritability for last 15 days , and difficulty in breathing for 3 days . there was no history of fever , cough , blood mixed vomitus , swelling anywhere , trauma , convulsions , yellowish discoloration of eyes and urine , or blood transfusion . a history of tubercular contact was present in her mother 4 years back . at presentation in emergency : examination revealed sick dyspneic girl with vitals ; respiratory rate ( 32 / min ) , pulse rate ( 88 / min ) , blood pressure ( 102/60 mmhg ) , mild pallor , pedal edema , and normal jugular venous pressure . inspection of respiratory system revealed positive trail sign on left side , fullness of intercostals space on right side , movement decreased on right side , and apical impulse was not visualized . there was decreased movement of right chest wall with tenderness present in right infraaxillary and inframammary area . there was stony dullness sound on percussion of right side of chest in all areas . air entry was decreased / absent in the right side of chest in all areas . blood biochemistry : hemoglobin , total leukocyte count , liver function test , renal function test , viral markers for hepatitis b surface antigen and human immunodeficiency virus were normal . sonography of chest revealed massive fluid in right pleural cavity causing mediastinal shift and displacing abdominal organs downward . right parietal pleura show multiple heteroechoic deposits ( largest measuring 4.7 cm 1.9 cm ) . computed tomography showed well - defined oval heterogeneously enhancing soft tissue dense lesion arising from right lateral chest wall with involvement of pleura and subpleural fat plane and associated permeative erosion of right fifth rib . there was right - sided hydropneumothorax with multiple enhancing nodular pleural deposits with few heterogeneously enhancing nodules in right collapse lung [ figure 2 ] . the child was managed with respiratory support , intravenous antibiotics , intercostal drainage tube , chemotherapy , and radiotherapy . her conditionshe was started on combination of six drugs chemotherapy protocol ( vacac / ie ) : vincristine ( v ; 1.5 mg / m ) , doxorubicin ( a ; 80 mg / m ) , cyclophosphamide ( c ; 1200 mg / m ) , actinomycin d ( ac ; 1.5 mg / m ) , ifosfamide ( i ; 9 g / m ) ; etoposide ( e ; 600 mg / m ) . four cycles ( three weekly ) of above drugs were planned according to italian sarcoma group / scandinavian sarcoma group iii protocol . this was to be followed by radiotherapy with following protocol : total radiation dose was 54 gy , 1.5 gy twice daily , 5 days / week / 36 fractions . radiograph of chest showing radioopaque right side ( a ) well - defined oval heterogeneously enhancing soft tissue dense lesion arising from right lateral chest wall ; and ( b ) erosion of right fifth rib ( a ) round cells having scanty basophilic cytoplasm ; and ( b ) cd 99 marker positivitythe present case presented to us with right side thoracic mass with right side pleural effusion that was straw colored initially , later on became hemorrhagic . malignant lesions included lymphoma , ewing sarcoma , neuroblastoma , rhabdomyosarcoma , and primitive neuroectoderm tumor . diagnosis of askin tumor was established based on the following features : aggressive nature of presentation and biopsy findings ( round cell with basophilic cytoplasm and cd99 positivity ) . rest of the malignant lesions were ruled out based on negative findings : lymphadenopathy and splenomegaly ( lymphoma ) , glycogen granules in cytoplasm ( ewing sarcoma ) , elevated urinary catecholamine ( neuroblastoma ) , spindle - shaped cells with acidophilic cytoplasm ( rhabdomyosarcoma ) . chemotherapy protocol ( vacac / ie ) was started in line with italian sarcoma group / scandinavian sarcoma group iii . local treatment in the form of radiation therapy was planned as parents refused to go for surgery . till now she has completed four cycles of chemotherapy and is able to perform her activities of daily living well . it is a rare disorder mimicking common pediatric conditions such as tuberculosis , lymphoma , neuroblastoma , and rhabdomyosarcoma . so , early diagnosis and timely intervention is critical for favorable outcome of the patients . there are only few case reports from india citing its rarity , clinical presentation , imaging findings , and outcome . recently , a large study by laskar et al . showed the following characteristics in 104 patients : mean age at presentation ( 17.9 years ) , male / female ( 73/31 ) , swelling ( 73/104 ) , pain ( 3/104 ) , swelling and pain ( 33/104 ) , swelling and dyspnea ( 8/104 ) , pain and dyspnea ( 3/104 ) , swelling , pain , and dyspnea ( 6/104 ) , right hemithorax ( 53/104 ) , left hemithorax ( 50/104 ) , sternum ( 1/104 ) , lung metastasis ( 19/104 ) , bone metastasis ( 3/104 ) , liver metastasis ( 2/104 ) , brain metastasis ( 1/104 ) , pleural effusion ( 44/104 ) , lymphadenopathy ( 11/104 ) , and bone marrow involvement ( 6/104 ) . patients were treated with multimodality treatment ( neoadjuvant chemotherapy , chemotherapy , surgical , radiotherapy ) . poor prognostic indicators were age 18 years , poor response to induction chemotherapy , and presence of pleural effusion . in the above study , the overall survival rate was better in nonmetastatic group compared with metastatic group ( 65 % vs 14 % ) at the end of 2 years . there is scarcity of literature highlighting the long - term outcome in such group of patients . subsequently , few reports had been published in english literature citing the presence of extensive disease at presentation as poor prognostic factor . so , there is a need for development of international registry for such rare cancer patients to document problems associated with long - term survival . the late effects of local therapy include scoliosis , restrictive lung disease , hypoplasia of soft tissue , and secondary tumors . our case presented with pain and dyspnea , right hemithorax opacity , and right - sided pleural effusion with lung and pleural metastasis . the presence of pleural effusion was poor prognostic factor , but localized disease , age ( 14 years ) , good response to initial cycle of chemotherapy were favorable factors suggesting good outcome in this patient . this is a rare tumor mimicking tuberculosis , lymphoma , ewing sarcoma , neuroblastoma , and rhabdomyosarcoma .\noutput:\n" }, { "from": "agent", "value": "askin tumor is a rare neoplasm of thoracopulmonary region . but it mimics other common pediatric disorders , such as empyema , lymphoma , and tuberculosis , posing a great diagnostic and therapeutic challenge to the treating clinicians . so it is of utmost importance to make an early diagnosis and proper referral / treatment in such cases . we highlighted diagnostic challenge , treatment , and favorable outcome of a case that presented to us ." } ]

[ { "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: aspirin is easily available across the counter in most countries including the developing countries such as nigeria . when indicated , it is a common practice to maintain patients on long - term , low dose aspirin use without assessing their renal status prior to initiation of treatment . low dose aspirin is increasingly being used as an antiplatelet to prevent thrombosis and other fatal cardiovascular outcomes in at - risk patients .1,2 elderly patients not only form the majority of these at - risk patients ,1,2 but they also readily succumb to the deleterious effects of aspirin on renal function .35 various studies assessing the elderly among caucasian populations have shown that 12 weeks of low dose aspirin use ( 75 mg325 mg / day ) caused significant decreases in both creatinine clearance ( crcl ) and uric acid clearance , as well as elevations in serum creatinine and uric acid .68 these parameters improved upon withdrawal of the drug , but the decline in the glomerular filtration rate persisted 3 weeks posttreatment .68 thus , long - term aspirin administration may have clinically important deleterious effects on renal function .8 this study was therefore undertaken as a pilot study to ascertain whether low dose aspirin compromises renal function amongst nigerians , and if so , to alert practicing physicians on the need to show discretion when prescribing this drug . this study employed a cohort of 30 elderly patients ( age 60 years ) from the ladoke akintola university of technology teaching hospital , southwest nigeria , and was comprised of 16 male and 14 female patients at the commencement of the study . the united nations definition of an elderly person was used .9 ladoke akintola university of technology teaching hospital ethical clearance was obtained , and all of the patients gave informed consent ( verbal and written ) . the patients were those enrolled in long - term care , as well as new patients with various medical conditions necessitating the use of low dose aspirin that were in stable clinical conditions throughout the study . each patient was followed up for a period of 6 weeks with a weekly clinic appointment . excluded from the study were patients with a history of active peptic ulcer , gastrointestinal bleeding , chronic liver diseases , hyperuricemia , serum creatinine 1.5 mg / dl ( 132.6 mol / l ) , a significant history of alcohol consumption , or recent use of anticoagulants , aspirin , or nonsteroidal anti - inflammatory drugs . patients were put on moderate protein intake ( 0.60.8 / kg of body weight ) with the assistance of dieticians a week prior to the commencement of the study ; this was maintained throughout the 6 - week study . the status quo was maintained for all other drugs ( dosages unchanged ) , including diuretics . patients who dropped out of the study were included in the calculations until their exit . the study took place over a period of 12 months from january 2008 to december 2008 . aspirin at a dose of 75 mg / day was administered orally after breakfast for 2 weeks and then stopped . blood and 24 - hour urine were collected at the end of each treatment week , as well as after each of the four consecutive weeks follow - up visits . subjects were taught how to collect their 24 - hour urine prior to their clinic day when the blood would be collected . after an overnight fast , 10 ml of venous blood was collected at the ante cubital fossa in the sitting position without stasis ; 5 ml of the blood was put into lithium heparinized bottle , and the remaining 5 ml were put into a plain bottle . serum was obtained after clotting , centrifuged at 3500 rpm for 10 minutes , and immediately stored at 20c until they were analyzed . sodium and potassium were analyzed using flame emission photometry ( corning 410c photometer ciba corning analytical , halstead essex , uk ) , bicarbonate by method of back titration , and chloride by rapid precision method .10 serum creatinine , blood urea nitrogen , uric acid , and albumin were analyzed by standard methods of jaffes reaction ,11 modified berthelot ,12 enzymatic urease ,13 and bromocresol green ,14 respectively , using the humalyzer 2000 chemistry analyzer ( human gesellschaft fr biochemica und diagnostica mbh , wiesbaden , germany ) . urinary crcl and uric acid clearance were evaluated by 24 - hour urine collection for crcl and uric acid clearances . each patient s baseline samples at enrolment ( before commencing aspirin ) served as the control , and subsequent weekly samples were compared . the weekly mean of the samples was calculated , and the difference of means from the baseline mean were determined and compared for statistical significance ( p 0.05 ) using the statistical package for the social sciences version 16 software ( spss inc , chicago , il , usa ) . s baseline samples at enrolment ( before commencing aspirin ) served as the control , and subsequent weekly samples were compared . the weekly mean of the samples was calculated , and the difference of means from the baseline mean were determined and compared for statistical significance ( p 0.05 ) using the statistical package for the social sciences version 16 software ( spss inc , chicago , il , usa ) . there were 14 ( 46.7 % ) females and 16 ( 53.3 % ) males with age range between 6088 years and mean ages of 68.44 years ( 8.16 ) and 70.43 years ( 9.09 ) for males and females , respectively . systemic hypertension was the most common diagnosis , accounting for 18 ( 60.0 % ) of cases . table 2 shows the stages of renal function based on the national kidney function / doqi guideline : 86.67 % exhibited their basal renal function in stages 1 and 2 based on crcl . figures 18 show the weekly assessment of the effects of low dose aspirin on renal functions among the patients in graphical form . the mean of each weekly parameter was compared with the corresponding baseline parameter , as well as with the p - value displayed on the graph . the p - value for all these weekly parameters did not show statistical significance except for the crcl ( figure 8 ; p = 0.025 ) . the crcl reduced at week 2 , and then increased at week 3 , pleateauing before gradually returning to baseline at the sixth week . the mean hemoglobin was 12.35.6 g / dl with a range of 7.315.0 g / dl . this study did not show any significant deterioration effects in renal function in the geriatric patients studied , during or after a 2 - week administration of low dose ( 75 mg ) aspirin in all of the investigated parameters , as shown in figures 18 . this is not in accordance with previously published studies that were conducted outside nigeria .3,68 previous studies have shown that low dose aspirin ( 75325 mg ) in the elderly , even on a short - term basis , had significant effects on renal tubular function .68 furthermore , one of the studies showed that even at the lowest dose of aspirin ( 75 mg ) per day , administered for 1 week , the uric acid clearance and crcl reduced . only the uric acid clearance returned to the baseline 1 week after the discontinuation of aspirin .6 the disparity from previous studies noticed in this study may be due to the better baseline renal functions of our patients . as shown in table 2 , more than 85 % of the study subjects had their basal renal function ( crcl , 86.7 % ) in stages 1 and 2 of the american national kidney foundation criteria , whereas only about 50 % ( crcl , 57 % ) of the patients in the segal et al8 study had theirs in the later stages . similarly , the study subjects were younger ( age range , 6088 years ; overall mean of 69.408.48 years ) with only four ( 13.33 % ) that were considered to be in the very elderly age group ( 80 years ) . previous studies used older patients with a mean age of 809 years ,8 and an average age of 81 years .7 of note , renal functions depreciate with age ; 15,16 hence , the basal renal functions of the patients in this study were better than those of other studies . anemia in chronic kidney disease becomes progressively pronounced from stage 3 onward .17 similarly , only 14 ( 46.7 % ) of the patients had hypoalbuminemia . previous studies have shown that hypoalbuminemia and anemia potentiate the deleterious effects of low dose aspirin on renal function .6,8 this current study did not conform to this . this may be due to the very small number of our study patients having either hypoalbuminemia or anemia . diuretic combination .18,19 our finding differs from this observation , as 93.3 % of the patients in this study were on this combination , yet there was no significant lowering of the crcl . instead , in figure 8 we observed positive statistical significance ( p = 0.025 ) in the crcl parameter . the crcl at week 2 reduced and increased by the third week , plateauing before gradually returning to baseline at the sixth week . we are of the opinion that the multiple drugs aimed at ameliorating the various comorbid conditions in the patients of our study might have acted in synergy with the low dose aspirin to give this favorable increase in crcl during the study . a larger sample with the application of more advanced statistics is advocated in order to provide a more concrete explanation for this observation . the decision to put an elderly patient on low dose aspirin should be based on the basal renal functions and the age of the patient . caution should be exercised when dealing with those in renal stages 35 , and when dealing with the very elderly ( age 80 years ) . we also suggest that the 75 mg dose of aspirin should be retained as the antiplatelet of choice in the elderly in developing countries . this study did not show any deleterious effects of short - term , low dose aspirin ( 75 mg ) use on the renal function of elderly patients . this 6 - week study was cumbersome for most of the patients , and this precluded the participation of a lot of eligible geriatric patients . not all of the 30 patients completed the study , but their data for the period of participation were included in the analysis . the small sample size combined with the tasking nature of the study that was conducted in a peculiar settingwe suggest that more studies be conducted in our own environment with a larger sample size , and possibly in a center with a predominant geriatric population .\noutput:\n" }, { "from": "agent", "value": "purposeto determine whether low dose aspirin has any deleterious effects on renal function in elderly patients.methodswe conducted a prospective pilot study of 30 nigerians older than 60 years with various chronic ailments necessitating the use of low dose aspirin . patients gave their consent , and institutional ethical clearance was obtained . each patient s baseline samples at enrolment ( before commencing aspirin use ) served as a control , and subsequent weekly samples were compared . the weekly mean of each parameter was calculated , and the differences of means from baseline were determined , and values were compared for statistical differences with the statistical package for the social sciences , version 16 . resultswe found that a majority of patients ( 86.67 % ) had basal renal functions at chronic kidney disease stages 1 and 2 . when compared with the corresponding baseline parameters , the mean weekly serum and urinary electrolytes , urea , creatinine , and uric acid parameters did not change , and the p - value did not show any statistical significance . however , there was positive statistical significance for the creatinine clearance ( p = 0.025 ) . also , unlike in previous studies , anemia and hypoalbuminemia did not affect the renal function parameters.conclusionthis study did not show any deleterious effects with short - term , low dose ( 75 mg daily ) aspirin use on kidney functions in elderly patients . however , caution should be exercised when dealing with patients in renal stages 35 and the very elderly , aged 80 years ." } ]

[ { "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: hematopoietic stem and progenitor cells ( hspcs ) possess the capacity for self - renewal ( mitotic division leading to production of the same stem cells without loss of developmental potential ) and differentiation ( asymmetric division leading to unequal production of daughter cells from the same mother cells ) . though these two opposing forces of self - renewal and differentiation act on hspcs , hematopoietic homeostasis is maintained throughout the lifetime of an individual by carefully orchestrated sequence specific transcription factor networks , genes and signaling pathways ( 1 , 2 ) . transcription factors recruit cofactors to gene regulatory regions , which facilitate or inhibit gene transcription by chromatin modification ( 3 ) . modulation of gene expression by chromatin modification on global and gene - specific level issince the hematopoietic cell lineage development follows a strict hierarchical pattern emanating from a primary single hsc , the hematopoietic system provides an ideal model system to study the correlation between epigenetically directed changes in chromatin structure and gradual restricted cell potential during differentiation . dna organized in loose chromatin ( euchromatin ) is readily available for gene expression and contribute for the maintenance of pluripotency . conversely , dna tightly packed into dense chromatin ( heterochromatin ) has genetic code buried effectively and become inconspicuous for genetic reading and transcription . epigenetic reprogramming describes stable and inheritable alterations in gene expression that occur without permanent changes in dna sequence . such changes include active or repressive histone modifications working in closed concert with dna methylation ( 2 ) . major covalent modifications that occur at histone tails are acetylation / deacetylation by histone acetyltransferases / histone deacetylases and methylation / demethylation by histone methyltransferases / histone demethylases . methylated histone arginine and lysine residuesare considered static modifications because of low levels of methylgroup turnover in chromatin . with the identification of enzymes that counteract , dna methylation is simply binding of a methyl group at carbon - 5 position of cytosine base by dna methyltransferases ( dnmts ) , primarily in cytosine - phosphate - guanine ( cpg ) dinucleotides or cpg islands ( 5 ) . while histone methylation events may be associated with gene activation , certain forms of histone methylation cause a local formation of heterochromatin , which is readily reversible . apparently , dna methylation and histone modifications are dependent on one another , their cross - talk is mediated by biochemical interactions between set histone methyltransferases and dna methyltransferases ( 6 ) . the demethylation process is quite complex and involves proteins , such as the tet ( ten - eleven translocation ) family of proteins . tet1 was found to catalyze the oxidation of 5 - methylcytosine , a well - known epigenetic mark , into 5 - hydroxymethylcytosine in mammalian dna ( 7 ) . interestingly , regulation of promoter demethylation - associated 463 genes is more frequent in the hematopoietic system than in non - hematopoietic tissues ( 241 genes ) , supporting the overall influence of demethylation signals in driving the tight time - and step - controlled hematopoietic cell fate determination . for example , promoter methylation of hematopoietic genes is linked to stemness as demethylation occur during early embryonic development and later on during hematopoietic differentiation . genome wide methylation status of induced pluripotent stem cells ( ipscs ) and somatic cd34 cells further confirm the role of dna methylation in the regulation of hematopoietic gene expression . dna methylation functions during ips cell generation by silencing of genes important in differentiation , and facilitating chromatin remodelling . conversely , dna demethylation appears to play an important role in reactivating pluripotency genes , particularly in the late stages of the reprogramming process . repressive epigenetic modifications , ( h3k9me3 and dna methylation ) at the promoter regions , occasionally observed in partially reprogrammed ips cells , fails to produce the robust reactivation of pluripotency genes ( 8 ) . the primary site of histone acetylation is the addition of acetyl moiety to the - amino terminal of lysine residues , which change the physicochemical properties of histone proteins , interfering with the electrostatic attraction between positively charged histones and negatively charged dna . in contrast , the removal of acetyl groups from the acetylated histones , histone deacetylation , forms the basis of inactive chromatin environment ( heterochromatin ) ( 2 ) . stem cells in the primitive and differentiated stage organize their level by multitude layers of molecular epigenetic events to impose flexible but precise control to establish important regulatory gene expression patterns . in this review , we also delineated the mechanism of aberrant placement of epigenetic marks and mutations in the epigenetic machinery involved in hematopoietic malignancies . stem / progenitor cell differentiation is linked to gradual methylation primarily in cytosine - phosphate - guanine ( cpg ) dinucleotides or cpg islands that reside within dna regulatory sequence by dna methyltransferases . however , whether dna methylation induces transcriptional silencing or preserves silence state of chromatin , remains enigmatic ( 2 ) . dnmt3a and dnmt3b show complementary de novo methylation patterns responsible for silencing of self - renewal genes in hscs ( 9 ) . consistent with this , loss of dnmt3a results in expansion of hsc population by impeding differentiation and upregulation of self - renewal genes ( runx1 and gata3 ) . combined loss of dnmt3a and dnmt3b in hscs result in enhancement of hsc self - renewal by activating - catenin signalling ( 10 ) . dnmt1 is crucial for the progression of stem cells to multipotent progenitors to lineage - restricted myeloid progenitors and regulating cell cycle entry ( 11 ) . dna methylation is known to interplay with other chromatin marks , such as histone modifications ( 12 ) . the dynamic interplay between the epigenetic changes and gender - specific hormone apolipoprotein e ( apoe ) provide insights for the modulation of a reconstituting potential of hspcs . in a study , female mice transplanted with truncated dna methyltransferase 3b isoform , dnmt3b7 , resulted in very high expression levels of apoe . the cpgisland controlling apoe expression had lower levels of modified cytosines in dnmt3b7 transgenic hspcs . dnmt3b7 expression down - regulate hematopoietic number within the female hormonal microenvironment ( 13 ) . stem cell protein , sall4 , recruit dnmts to silence genesto govern - stem cell self - renewal . it has been investigated that dnmts and histone deacetylase repressors interact synergistically to reverse the transcriptional repression effect of sall4 ( 14 ) . overexpression of sall4 leads to increased methylation of silenced genes ( h3k4me3 and h3k79me2 ) in primary hspcs . during normal hematopoiesis and leukemogenesis , sall4 mediated expression up - regulates multiple regulatory genes including hoxb4 , notch1 , runx1 , meis1 and nf - ya , influencing particularly , three important self - renewal pathways involving bmi1 , - catenin and pten . as sall4regulate apoptotic pathways both in normal hscs and leukemic stem cells , gao et al . , deciphered that targeting sall4 combined with bcl2 antagonist ( abt - 737 ) , could lead to leukemic stem cell - specific apoptosis ( 15 ) . the precise combination of genes which on activation / repression control the processes of driving proliferation and suppressing differentiation , have yet to be defined . however , the radix of the aberrant methylation of target genes in the tumorous cell is not fully elucidated . the pml - rar gene translocation and runx1 in acute promyelocyticleukemia recruits dnmts to target promoters that change the active chromatin structure to silence status and contributes to its leukemic transformation ( 16 ) . recently , hypomethylating agents emerged as a standard for treatment in myelodysplastic syndrome as they reprogram methylome and re - establish hematopoiesis ( 17 ) . protein acetylation regulates hsc self - renewal , proliferation , and their differentiation into committed hematopoietic progenitors . histone acetyltransferases ( hats ) acetylate histone proteins by transferring the acetyl group from acetyl - coa to specific lysine residues , resulting in a dispersed structure of chromatin , accessible for transcriptional factors . hats contain p300 / cbp ( cbp and p300 ) , myst ( tip60 , moz , morf , hbo1 and hmof ) , and gnat ( pcaf , gnc5 and elp3 ) family members to regulate normal and malignant hematopoiesis . multiple chromatin factor complexes , such as nua4 / p300 / cbp / hbo1 are required for normal hematopoiesis ( 17 ) . cbp / p300 regulates self - renewal and differentiation in adult hscs through regulating gfi1b , monocyticleukemia zinc finger protein ( moz ) maintains the generation and development of hscs and promote proliferation of progenitors by repressing the transcription of p16 . it has been proposed that the fusion proteins produced upon translocation of the human moz locus with cbp / p300 , support the development of leukemia by altering the regulation of moz transcriptional targets ( 18 ) . histone deacetylase inhibitors result in chromatin remodeling to modulate re - expression of silenced tumor suppressor genes in leukemic stem and progenitor cells which , in turn , result in cellular differentiation , inhibition of their proliferation and self - renewal properties ( 19 ) . histone deacetylase inhibitor , valproic acid ( vpa ) increases self - renewal of hscs by blocking differentiation at multiple regulatory pathways . epigenetically reprogrammed cd34 cells on treatment with vpa generate greater numbers of functional stem cells and multilineage hematopoiesis with capacity for bone marrow reconstitution before clinical transplantation . mechanistically , vpa progress to cell cycle by down - regulating p21 , activating hoxb4 and wnt - signaling pathway ( 20 ) . walasek et al . showed synergistic effects of vpa and lithium to induce self - renewal by blocking differentiation genes and preserve expression of stem cell - related genes ( 21 ) . vpa inhibits proliferation and induces apoptosis in leukemic cells by increasing expression of death receptors and their ligands in acute promyelocyticleukemia and aml - eto dependent leukemia . aberrant formation of fusion proteins through chromosomal translocations of hat and hat - related genes ( e.g. moz , morf , cbp and p300 ) occurs in leukemia . mistargeting of such deleterious fusion proteins contributes to global alterations in histone acetylation patterns in cancer . specific epigenetic gene silencing can occur by aberrant targeting of histone deacetylases to the gene promoter which causes histone hypoacetylation ( 22 ) . epigenetic cross - talk between dna methylation by dna methyltransferases and histone methylation by histone methyltransferases have ramifications for the understanding of gene transcription for normal development and aberrant gene silencing in tumors . it is not yet clear whether dna methylation patterns guide histone modifications ( histone acetylation and methylation ) during gene silencing / or dna methylation take its cues primarily from histone modification status ( 23 ) . histone methylation is a reversible process : methyl marks are established by histone methyltransferases , so - calledthree methylation sites on histones are implicated in activation of transcription : h3k4 , h3k36 , and h3k79 . three lysine methylation sites are connected to transcriptional repression : h3k9 , h3k27 , and h4k20 . methylation at h3k9 is implicated in the silencing of euchromatic genes as well as forming silent heterochromatin . like lysine methylation , . enzymes ( protein arginine methyltransferases , prmt s ) are recruited to promoters by transcription factors ( 24 ) . open chromatin and transcriptionally active regions are most commonly recognized by two different methylation status of h3k4 , h3k4 dimethylation ( h3k4me2 ) and tri - methylation ( h3k4me3 ) . genes associated with silenced dna and heterochromatin are generally associated with methylations at lysine 9 or 27 of histone h3 ( h3k9 and h3k27 ) . coexistence of repressing h3k27me3 and activating h3 - k4me3 epigenetic marks on same dna region , usually at regulatory regions of gene promoters , are calledbivalent domains . this bivalency fine - tunes gene expression during development and contemporarily , keep gene expression in a poised or primed state that allows for either rapid activation or stable silencing upon differentiation of hematopoietic cells ( fig . chromatin - modifying polycomb group ( pcg ) proteins form large multimeric structures distinctly , polycomb repressive complex 1 and 2 ( prc1 and prc2 ) . as observed in knockout mouse lines for ring1b , bmi1 , rae28 , and mel18 , mice harboring mutations in the components of prc1 generate hematopoietic abnormalities . once circumscribed to the chromatin , ring1b and bmi1 ubiquitinate histone h2a at lysine 119 ( h2ak119ub ) ( 26 ) , which is considered to be involved in transcriptional repression by inhibiting transcription initiation or by restraining rna polymerase ii from elongation . it is not yet confirmed that whether prc1 function as a transcriptional repressor is dependent or independent of its h2aub ligase catalytic activity ( 27 ) . prc2stabilize repressive chromatin structure through the function of chromatin modifiers such as enhancer of zeste ( ezh2 ) , embryonic ectoderm development ( eed ) protein and suppressor of zeste 12 ( suz12 ) . prc2 is responsible for di and tri - methylation of lysine 27 of histone h3 ( h3k27me2 / me3 ) to promote transcriptional repression . hscs express high levels of bmi1 , a member of the pcg of transcription repressors . furthermore , prc1 component bmi1 plays an important role in hsc self - renewal and lymphocyte differentiation by transcriptional repression of genes involved in cellular senescence ( p16ink4a , p19arf , and p53 ) ( 28 ) . increased expression of the p53 target gene , wig1 in bmi1 bone marrow suggests that p19arf pathway gets activated in bmi1deficient hematopoietic cells ( 29 ) . bmi1 is critical in preventing ikaros - mediated lymphoid priming , thus , prevents premature lineage specification of hspcs ( 30 ) . it has recently become clear that bmi1 also functions in the protection against oxidative stress . down modulation of bmi1 impairs self - renewal and long - term expansion of leukemic stem cells . bmi1 also functions in an orchestration of the symmetry of hsc divisions and bypassing senescence ( 31 ) . changes in the expression of individual pcg genes cause perturbations in the composition of the prc , which affect overall prc enzymatic activity . ezh2 serve as a tumor - suppressor gene as its inhibition in cancer stem cells offers a potential therapeutic approach to counter the aberrant activation in lymphoma and leukemia ( 33 ) . histone demethylases ( hdms ) reportedly reshape the epigenome of hematopoietic stem cell and thus regulate its fate . there are two families of hdms , the amine oxidase enzyme , known as lysine demethylase ( lsd1 ) and the jumonji c ( jmjc ) domain - containing family . lsd1 forms a core complex with corepressors , including hdac1 / 2 and corest and repress the transcription of target genes . lsd1 specifically removes one or two methyl groups from histone h3 lysine 4 ( h3k4 ) or 9 ( h3k9 ) , depending on the cellular context and the presence of cofactors , thereby repressing or activating transcription . overexpression of the shortest isoform of lsd1 , which is specifically repressed in quiescent hscs , demethylates histone h3k9 more efficiently than other isoforms ( 34 , 35 ) . lsd1 mediates erythroid differentiation via epigenetic modification of the gata - 2 locus and also increase self - renewal potential via upregulation of the hoxa family but retains differentiation ability towards t - cell lineages at transcriptome levels in hscs . the dysregulation of mll in acute myeloid leukemia suggests that lsd1 may also have links to leukemogenesis . lsd1 overexpression seemingly is directly implicated for priming of hscs towards malignant transformation and progression to t - cell leukemogenesis . thus , provides a novel strategy for early diagnosis and effective treatment of the disease ( 36 ) . the second family of hdms includes the jmjc enzymes , which catalyse the removal of mono - , di - and trimethyllysines . several jmjc domain proteins have been identified with different specificities including jhdm1 , jhdm2 , jmjd2 and jumonji at - rich interactive domain 1 ( jarid1 ) . the interaction of the jmjc hdm jarid1d with the polycomb - like protein ring6a / mblr showed that ring6a / mblr enhance jarid1d - mediated h3k4 demethylation , associated with transcriptional repression . jhdm1b has also been shown to interact with pcg proteins in a complex containing ring1b / rnf2 and the bcl6 interacting co - repressor among other proteins ( 37 ) . this co - repressor complex may be implicated in gene repression mediated by bcl6 , a transcription factor frequently dysregulated in b - cell lymphomas . deletion of jarid1b compromises hsc self - renewal capacity , which suggests that jarid1b is a positive regulator of hsc potential ( 38 ) . jarid1b / kdm5b is highly expressed in primitive hematopoietic compartments and is overexpressed in acute myeloid leukemias ( 5 ) . among the histone octamer , h2a is the most abundant ubiquitinated protein and prc1 is the main h2a ubiquitin ( h2aub ) ligase . ubiquitination of histone h2a ( h2a - k119u ) is a common chromatin modification associated with gene silencing , and controlled by the activities of ubiquitin ligating and deubiquitinating enzymes . the ring1 subunit of prc1 monoubiquitinylates histone h2a at lysine 119 ( h2a - k119u ) , which promote transcrition repression and chromatin compaction . another h2a - deubiquitinating enzyme , mysm1 plays a critical role in hsc maintenance , self - renewal , genetic stability in hematopoietic progenitors , and development of lymphoid and erythroid lineages ( 39 , 40 ) . despite its important function and early discovery , histone ubiquitination remains the least understood compared with other histone modifications . stem / progenitor cell differentiation is linked to gradual methylation primarily in cytosine - phosphate - guanine ( cpg ) dinucleotides or cpg islands that reside within dna regulatory sequence by dna methyltransferases . however , whether dna methylation induces transcriptional silencing or preserves silence state of chromatin , remains enigmatic ( 2 ) . dnmt3a and dnmt3b show complementary de novo methylation patterns responsible for silencing of self - renewal genes in hscs ( 9 ) . consistent with this , loss of dnmt3a results in expansion of hsc population by impeding differentiation and upregulation of self - renewal genes ( runx1 and gata3 ) . combined loss of dnmt3a and dnmt3b in hscs result in enhancement of hsc self - renewal by activating - catenin signalling ( 10 ) . dnmt1 is crucial for the progression of stem cells to multipotent progenitors to lineage - restricted myeloid progenitors and regulating cell cycle entry ( 11 ) . dna methylation is known to interplay with other chromatin marks , such as histone modifications ( 12 ) . the dynamic interplay between the epigenetic changes and gender - specific hormone apolipoprotein e ( apoe ) provide insights for the modulation of a reconstituting potential of hspcs . in a study , female mice transplanted with truncated dna methyltransferase 3b isoform , dnmt3b7 , resulted in very high expression levels of apoe . the cpgisland controlling apoe expression had lower levels of modified cytosines in dnmt3b7 transgenic hspcs . dnmt3b7 expression down - regulate hematopoietic number within the female hormonal microenvironment ( 13 ) . stem cell protein , sall4 , recruit dnmts to silence genesto govern - stem cell self - renewal . it has been investigated that dnmts and histone deacetylase repressors interact synergistically to reverse the transcriptional repression effect of sall4 ( 14 ) . overexpression of sall4 leads to increased methylation of silenced genes ( h3k4me3 and h3k79me2 ) in primary hspcs . during normal hematopoiesis and leukemogenesis , sall4 mediated expression up - regulates multiple regulatory genes including hoxb4 , notch1 , runx1 , meis1 and nf - ya , influencing particularly , three important self - renewal pathways involving bmi1 , - catenin and pten . as sall4regulate apoptotic pathways both in normal hscs and leukemic stem cells , gao et al . , deciphered that targeting sall4 combined with bcl2 antagonist ( abt - 737 ) , could lead to leukemic stem cell - specific apoptosis ( 15 ) . the precise combination of genes which on activation / repression control the processes of driving proliferation and suppressing differentiation , have yet to be defined . however , the radix of the aberrant methylation of target genes in the tumorous cell is not fully elucidated . the pml - rar gene translocation and runx1 in acute promyelocyticleukemia recruits dnmts to target promoters that change the active chromatin structure to silence status and contributes to its leukemic transformation ( 16 ) . recently , hypomethylating agents emerged as a standard for treatment in myelodysplastic syndrome as they reprogram methylome and re - establish hematopoiesis ( 17 ) . protein acetylation regulates hsc self - renewal , proliferation , and their differentiation into committed hematopoietic progenitors . histone acetyltransferases ( hats ) acetylate histone proteins by transferring the acetyl group from acetyl - coa to specific lysine residues , resulting in a dispersed structure of chromatin , accessible for transcriptional factors . hats contain p300 / cbp ( cbp and p300 ) , myst ( tip60 , moz , morf , hbo1 and hmof ) , and gnat ( pcaf , gnc5 and elp3 ) family members to regulate normal and malignant hematopoiesis . multiple chromatin factor complexes , such as nua4 / p300 / cbp / hbo1 are required for normal hematopoiesis ( 17 ) . cbp / p300 regulates self - renewal and differentiation in adult hscs through regulating gfi1b , monocyticleukemia zinc finger protein ( moz ) maintains the generation and development of hscs and promote proliferation of progenitors by repressing the transcription of p16 . it has been proposed that the fusion proteins produced upon translocation of the human moz locus with cbp / p300 , support the development of leukemia by altering the regulation of moz transcriptional targets ( 18 ) . histone deacetylase inhibitors result in chromatin remodeling to modulate re - expression of silenced tumor suppressor genes in leukemic stem and progenitor cells which , in turn , result in cellular differentiation , inhibition of their proliferation and self - renewal properties ( 19 ) . histone deacetylase inhibitor , valproic acid ( vpa ) increases self - renewal of hscs by blocking differentiation at multiple regulatory pathways . epigenetically reprogrammed cd34 cells on treatment with vpa generate greater numbers of functional stem cells and multilineage hematopoiesis with capacity for bone marrow reconstitution before clinical transplantation . mechanistically , vpa progress to cell cycle by down - regulating p21 , activating hoxb4 and wnt - signaling pathway ( 20 ) . . showed synergistic effects of vpa and lithium to induce self - renewal by blocking differentiation genes and preserve expression of stem cell - related genes ( 21 ) . vpa inhibits proliferation and induces apoptosis in leukemic cells by increasing expression of death receptors and their ligands in acute promyelocyticleukemia and aml - eto dependent leukemia . aberrant formation of fusion proteins through chromosomal translocations of hat and hat - related genes ( e.g. moz , morf , cbp and p300 ) occurs in leukemia . mistargeting of such deleterious fusion proteins contributes to global alterations in histone acetylation patterns in cancer . specific epigenetic gene silencing can occur by aberrant targeting of histone deacetylases to the gene promoter which causes histone hypoacetylation ( 22 ) . epigenetic cross - talk between dna methylation by dna methyltransferases and histone methylation by histone methyltransferases have ramifications for the understanding of gene transcription for normal development and aberrant gene silencing in tumors . it is not yet clear whether dna methylation patterns guide histone modifications ( histone acetylation and methylation ) during gene silencing / or dna methylation take its cues primarily from histone modification status ( 23 ) . histone methylation is a reversible process : methyl marks are established by histone methyltransferases , so - calledthree methylation sites on histones are implicated in activation of transcription : h3k4 , h3k36 , and h3k79 . three lysine methylation sites are connected to transcriptional repression : h3k9 , h3k27 , and h4k20 . methylation at h3k9 is implicated in the silencing of euchromatic genes as well as forming silent heterochromatin . like lysine methylation , . enzymes ( protein arginine methyltransferases , prmt s ) are recruited to promoters by transcription factors ( 24 ) . open chromatin and transcriptionally active regions are most commonly recognized by two different methylation status of h3k4 , h3k4 dimethylation ( h3k4me2 ) and tri - methylation ( h3k4me3 ) . genes associated with silenced dna and heterochromatin are generally associated with methylations at lysine 9 or 27 of histone h3 ( h3k9 and h3k27 ) . coexistence of repressing h3k27me3 and activating h3 - k4me3 epigenetic marks on same dna region , usually at regulatory regions of gene promoters , are calledbivalent domains . this bivalency fine - tunes gene expression during development and contemporarily , keep gene expression in a poised or primed state that allows for either rapid activation or stable silencing upon differentiation of hematopoietic cells ( fig .2 ) ( 25 ) . chromatin - modifying polycomb group ( pcg ) proteins form large multimeric structures distinctly , polycomb repressive complex 1 and 2 ( prc1 and prc2 ) . prc1 represses genes by mechanisms such as chromatin compaction and decreasing nucleosomal turnover . as observed in knockout mouse lines for ring1b , bmi1 , rae28 , and mel18once circumscribed to the chromatin , ring1b and bmi1 ubiquitinate histone h2a at lysine 119 ( h2ak119ub ) ( 26 ) , which is considered to be involved in transcriptional repression by inhibiting transcription initiation or by restraining rna polymerase ii from elongation . it is not yet confirmed that whether prc1 function as a transcriptional repressor is dependent or independent of its h2aub ligase catalytic activity ( 27 ) . prc2stabilize repressive chromatin structure through the function of chromatin modifiers such as enhancer of zeste ( ezh2 ) , embryonic ectoderm development ( eed ) protein and suppressor of zeste 12 ( suz12 ) . prc2 is responsible for di and tri - methylation of lysine 27 of histone h3 ( h3k27me2 / me3 ) to promote transcriptional repression . hscs express high levels of bmi1 , a member of the pcg of transcription repressors . furthermore , prc1 component bmi1 plays an important role in hsc self - renewal and lymphocyte differentiation by transcriptional repression of genes involved in cellular senescence ( p16ink4a , p19arf , and p53 ) ( 28 ) . increased expression of the p53 target gene , wig1 in bmi1 bone marrow suggests that p19arf pathway gets activated in bmi1deficient hematopoietic cells ( 29 ) . bmi1 is critical in preventing ikaros - mediated lymphoid priming , thus , prevents premature lineage specification of hspcs ( 30 ) . it has recently become clear that bmi1 also functions in the protection against oxidative stress . down modulation of bmi1 impairs self - renewal and long - term expansion of leukemic stem cells . bmi1 also functions in an orchestration of the symmetry of hsc divisions and bypassing senescence ( 31 ) . changes in the expression of individual pcg genes cause perturbations in the composition of the prc , which affect overall prc enzymatic activity . overexpression of bmi1 is associated with malignant hematopoiesis ( 32 ) . ezh2 over - expression direct stem cells toward a cancer stem cell state . ezh2 serve as a tumor - suppressor gene as its inhibition in cancer stem cells offers a potential therapeutic approach to counter the aberrant activation in lymphoma and leukemia ( 33 ) . histone demethylases ( hdms ) reportedly reshape the epigenome of hematopoietic stem cell and thus regulate its fate . there are two families of hdms , the amine oxidase enzyme , known as lysine demethylase ( lsd1 ) and the jumonji c ( jmjc ) domain - containing family . lsd1 forms a core complex with corepressors , including hdac1 / 2 and corest and repress the transcription of target genes . lsd1 specifically removes one or two methyl groups from histone h3 lysine 4 ( h3k4 ) or 9 ( h3k9 ) , depending on the cellular context and the presence of cofactors , thereby repressing or activating transcription . overexpression of the shortest isoform of lsd1 , which is specifically repressed in quiescent hscs , demethylates histone h3k9 more efficiently than other isoforms ( 34 , 35 ) . lsd1 mediates erythroid differentiation via epigenetic modification of the gata - 2 locus and also increase self - renewal potential via upregulation of the hoxa family but retains differentiation ability towards t - cell lineages at transcriptome levels in hscs . the dysregulation of mll in acute myeloid leukemia suggests that lsd1 may also have links to leukemogenesis . lsd1 overexpression seemingly is directly implicated for priming of hscs towards malignant transformation and progression to t - cell leukemogenesis . thus , provides a novel strategy for early diagnosis and effective treatment of the disease ( 36 ) . the second family of hdms includes the jmjc enzymes , which catalyse the removal of mono - , di - and trimethyllysines . several jmjc domain proteins have been identified with different specificities including jhdm1 , jhdm2 , jmjd2 and jumonji at - rich interactive domain 1 ( jarid1 ) . the interaction of the jmjc hdm jarid1d with the polycomb - like protein ring6a / mblr showed that ring6a / mblr enhance jarid1d - mediated h3k4 demethylation , associated with transcriptional repression . jhdm1b has also been shown to interact with pcg proteins in a complex containing ring1b / rnf2 and the bcl6 interacting co - repressor among other proteins ( 37 ) . this co - repressor complex may be implicated in gene repression mediated by bcl6 , a transcription factor frequently dysregulated in b - cell lymphomas . deletion of jarid1b compromises hsc self - renewal capacity , which suggests that jarid1b is a positive regulator of hsc potential ( 38 ) . jarid1b / kdm5b is highly expressed in primitive hematopoietic compartments and is overexpressed in acute myeloid leukemias ( 5 ) . among the histone octamer , h2a is the most abundant ubiquitinated protein and prc1 is the main h2a ubiquitin ( h2aub ) ligase . ubiquitination of histone h2a ( h2a - k119u ) is a common chromatin modification associated with gene silencing , and controlled by the activities of ubiquitin ligating and deubiquitinating enzymes . the ring1 subunit of prc1 monoubiquitinylates histone h2a at lysine 119 ( h2a - k119u ) , which promote transcrition repression and chromatin compaction . another h2a - deubiquitinating enzyme , mysm1 plays a critical role in hsc maintenance , self - renewal , genetic stability in hematopoietic progenitors , and development of lymphoid and erythroid lineages ( 39 , 40 ) . despite its important function and early discovery , the cumulative research data demonstrate the crucial role of epigenetic players in stem cell self - renewal and differentiation gene expression patterns . the startling development of reprogramming technology has catapulted stem cell role in regenerative medicine and disease modeling and offers new hope for personalized regenerative cell therapies . recently developed high - throughput genomic tools greatly facilitate the study of epigenetic regulation in pluripotent stem cells by mapping chromatin - nuclear matrix interactions . elucidating epigenetic landscape will have important implications to expedite manipulation of stem and progenitor cells for regenerative applications and would render novel targets to tackle human diseases prospectively , leading to new therapeutic avenues in regenerative medicine .\noutput:\n" }, { "from": "agent", "value": "hematopoietic stem cells are endowed with a distinct potential to bolster self - renewal and to generate progeny that differentiate into mature cells of myeloid and lymphoid lineages . both hematopoietic stem cells and mature cells have the same genome , but their gene expression is controlled by an additional layer of epigenetics such as dna methylation and post - translational histone modifications , enabling each cell - type to acquire various forms and functions . until recently , several studies have largely focussed on the transcription factors andniche factors for the understanding of the molecular mechanisms by which hematopoietic cells replicate and differentiate . several lines of emerging evidence suggest that epigenetic modifications eventually result in a defined chromatin structure and an individual gene expression pattern , which play an essential role in the regulation of hematopoietic stem cell self - renewal and differentiation . distinct epigenetic marks decide which sets of genes may be expressed and which genes are kept silent . epigenetic mechanisms are interdependent and ensure lifelong production of blood and bone marrow , thereby contributing to stem cell homeostasis . the epigenetic analysis of hematopoiesis raises the exciting possibility that chromatin structure is dynamic enough for regulated expression of genes . though controlled chromatin accessibility plays an essential role in maintaining blood homeostasis ; mutations in chromatin impacts on the regulation of genes critical to the development of leukemia . in this review , we explored the contribution of epigenetic machinery which has implications for the ramification of molecular details of hematopoietic self - renewal for normal development and underlying events that potentially co - operate to induce leukemia ." } ]

[ { "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 18 - year - old boy was admitted to our hospital ( bologna , italy ) due to onset of fatigue and persistent fever , unresponsive to antibacterial therapy . blood analyses showed a white blood cell count of 93,850 / l , with 99 % of lymphoid blast cells , hemoglobin of 11 g / dl , and a platelet count of 70,000 / l . the bone marrow evaluation was diagnostic for a pre - b cell acute lymphoblastic leukemia ( all ) , cd34 , cd19 and cd22 positive at the immunophenotype analysis , with normal karyotype and without central nervous system ( cns ) involvement . according to institutional guidelines andafter informed consent was signed , the patient received a chemotherapeutic program , based on the aieop lal2000 clinical protocol backbone , including a steroid pre - treatment , an induction phase 1a ( vincristine , daunorubicin , l - asparaginase , prednisone and intrathecal cns prophylaxis ) and a phase 1b ( cyclophosphamide , oral 6 - mercaptopurine and cytarabine ) . after this treatment , the patient obtained a complete morphologic remission , with the persistence of positive minimal residual disease , evaluated by polymerase chain reaction rearrangement of immunoglobulin h gene on day 33 , which became negative on day 78 . thus , the patient underwent a third cycle of chemotherapy , which included high dose of methotrexate ( mtx ) ( 3 g / m ) followed by cyclophosphamide ( 400 mg ) , cytarabine ( 3900 mg ) , vincristine ( 2 mg ) and intrathecal mtx ( 10 mg ) . therefore , after hematologic recovery was reached , the second dosage of hd - mtx was administered , followed by vindesine ( 5 mg ) , ifosfamide ( 3200 mg ) and daunorubicin ( 50 mg ) . nine days after mtx infusion , during the iatrogenic aplasia phase , the patient suddenly developed generalized tonic clonic seizures , with loss of consciousness . his blood pressure was 160/100 mmhg ; he was confused , and a detailed neurologic examination showed a strong - force defect involving the left arm . promptly , diazepam and dexametasone were administered , with a momentaneus improvement of his clinical condition . despite the resolution of this event , the patient showed two further episodes of epilepsy during the same day . therefore , a brain computed tomography ( ct ) was immediately performed , revealing the presence of hypodense areas in the bilateral frontal lobes and right parietal parasagittal region , with no intracranial bleeding or venous thrombosis . consistently , mri fluid - attenuated inversion recovery and diffusion - weighted imaging revealed subcortical and cortical hyperintensities in the bilateral frontal lobes and parietal parasagittal region ( figure 1a , b ) . in addiction , the apparent diffusion coefficient ( adc ) map showed elevated signal intensities in the bilateral frontal lobes ( figure 1c ) . these mri observations were suggestive of vasogenic edema rather than cytotoxic edema . in order to exclude cns infective involvement , a lumbar puncture was performed , which resulted negative for microbiological agents and leukemic cells . therefore , based on neuroimaging results and clinical presentation , a diagnosis of posterior reversible encephalopathy syndrome ( pres ) was made . a prophylactic therapy with phenytoin and anti - hypertensive drugs was introduced , and a progressive improvement of clinical conditions , neurological symptoms and cognitive status was observed . the patient reached a complete hematological recovery , but due to the severe neurological complication , his chemotherapeutic program was prematurely stopped . seven months later , a brain mri demonstrated a complete resolution of previous detected lesions ( figure 1d , e ) . unfortunately , the patient relapsed eight months later and died as a consequence of progression disease . posterior reversible encephalopathy syndrome is a clinical - neuroradiological entity , firstly identified by hinchey et al . in 1996 . this condition is often associated with different diseases such as cancer , hypertension , autoimmune abnormalities , eclampsia , sepsis , renal disorders , drugs and bone marrow and solid organ transplant . the clinical presentation is characterized by seizure , which is the most common symptom , headache , confusion , decreased level of consciousness and coma . pres is characterized by transient bilateral lesions , that predominantly affect white matter of the occipital - parietal lobes and can be identified by mri scan , that allows a more accurate etiological diagnosis compared to ct . pres management includes withdrawal of damaging agents , blood pressure control and anticonvulsants in patients with seizures . previously , neurotoxicity has been observed after the administration of high - dose and / or intrathecal mtx in the pediatric population ; conversely , little is known in adult patients . to the best of our knowledge , this is the first report of a pre - b all young adult patient treated with high dose of mtx , who developed a pres . currently , in all , there is a trend towards more intensive treatment of adult patients with pediatric - inspired regimens , based on the high remission rates obtained by this kind of approach . however , an accurate knowledge of potential therapy related toxicities , including neurologic adverse events , is required for the safe and correct management of these patients .\noutput:\n" }, { "from": "agent", "value": "we report here the case of a young adult affected by pre b - cell acute lymphoblastic leukemia ( all ) , who developed , during a pediatric - like chemotherapy consolidation schedule with high dosage of methotrexate , a severe neurological toxicity . clinical presentation and neuroimaging data were diagnostic for posterior reversible encephalopathy syndrome ( pres ) . a complete resolution was quickly obtained with medical blood pressure control and anticonvulsants administration . to the best of our knowledge , this is the first case of pres described in the adult all setting . currently , the clinical management of this aggressive disease is moving towards a pediatric - like approach also in adult patients , due to the better outcome reached with intensive chemotherapeutic regimens in children population . however , therapy - related toxicities have to be taken into account , since their onset may adversely affect patients clinical outcome ." } ]

[ { "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: traumatic subdural hygroma ( sdg ) is an accumulation of cerebrospinal fluid ( csf ) in the subdural space that develops in 46 % of patients with a head injury17 ) . most sdgs are asymptomatic with little mass effect , and do not require surgical intervention at the time of diagnosis . however , studies have reported the subsequent formation of chronic subdural hematoma ( csdh ) following traumatic sdg57121617192227 ) . since yamada et al. 27 ) first reported three cases of traumatic sdg complicated by csdh in 1979 , several studies have reported csdh rates of 458 % following traumatic sdg57121719 ) . despite the considerable rate of transition to csdh in patients with traumatic sdg , the pathomechanism remains unclear . furthermore , no study has investigated the risk factors for developing csdh following traumatic sdg . in the present study , we explored the risk factors that contribute to formation of csdh in patients with traumatic sdg . a total of 2950 patients were admitted to hallym university hospital for traumatic head injury between january 2004 and december 2013 . among them , we identified 89 patients by searching the final imaging analysis program reports ( piviewstar , infinitt , seoul , korea ) with keywords including ' subdural hygroma ' or ' subdural fluid collection ' which developed within 3 months after trauma . of these , patients with a hemostatic disorder ( n = 5 ) , acute subdural hemorrhage ( n = 10 ) , external hydrocephalus ; defined as enlargement of subarachnoid or subdural space in the presence of ventriculomegaly or increased intracranial pressure ( n = 5 ) , and sdg related to craniotomy , infection , and other brain pathology ( n = 15 ) were excluded . to avoid confusion for the differential diagnosis of atrophic brain with a widened csf space , sdg found at the time of initial brain imaging on admissionfinally , we identified 45 patients with traumatic head injury in which traumatic sdg developed during the follow - up period . the diagnosis of traumatic sdg was based on radiological findings showing homogenous subdural fluid collection with low computed tomography ( ct ) density similar to that seen in csf after trauma . regular follow - up ct was performed every week or at the onset of symptom exacerbation . if newly developed sdg was found on follow - up ct , we recommended further evaluation with magnetic resonance imaging ( mri ) . pachymeningeal enhancement was defined as linear enhancement of dura mater on contrast - enhanced t1 - weighted or fluid - attenuated inversion recovery ( flair ) imaging . we performed surgical drainage using a relatively consistent methodology in symptomatic patients with newly developed csdh . initial mental status was evaluated by glasgow coma score ( gcs ) , and the last functional outcome was assessed by the glasgow outcome scale ( gos ) . all patients were divided into two groups based on the presence or absence of csdh . we investigated the associations between csdh development and independent variables , including demographic factors and radiological findings . the chi - square or fisher 's exact test was used to compare categorical variables , and mann - whitney u - test was used to compare continuous data . independent variables with p - values 0.20 were included in binary logistic regression analysis to determine the factors affecting csdh development . the correlation between significant factors and hemorrhage - free survival was analyzed using the kaplan - meier method and the log - rank test . table 1 shows the results of the risk factor analysis for the development of csdh . the most common clinical manifestations were headache ( 86.7 % ) , followed by altered mental status after trauma ( 13.3 % ) . traffic accidents ( 50 % ) and falls ( 50 % ) were the main causes of head trauma . the mean gcs score at admission was 14.221.43 ( range , 815 ) , and 39 of 45 patients ( 86.7 % ) scored 14 . the most common associated injury was traumatic subarachnoid hemorrhage in 21 patients ( 46.7 % ) , followed by cortical contusion in 15 patients ( 33.3 % ) . the mean follow - up period was 143.1130.8 days ( range , 10510 days ) . the mean gos score at the time of the last follow - up visit was 4.820.44 ( range , 35 ) . the mean time for development of sdg from trauma was 8.028.35 days ( range , 140 days ) . thirty - one patients suffered from bilateral sdg , and the remaining 14 patients had unilateral sdg . regular follow - up ct scans were performed in all patients , including those with newly developed clinical deterioration . follow - up ct scans revealed regression of sdg in 25 of 45 patients ( 55.6 % ) , including 13 patients with bilateral sdg and 12 patients with unilateral sdg ( fig . the mean time for sdg regression was 112.1 days ( range , 10365 days ) . the remaining 20 patients ( 44.4 % ) showed transition to csdh during the follow - up period ( fig . the mean time from sdg to development of csdh was 48.3523.8 days ( range , 17120 days ) . the most common clinical manifestations were headache ( 9 of 20 ) , followed by hemiparesis ( 6 of 20 ) , and drowsiness ( 2 of 20 ) . final ct scans after surgery revealed complete regression of csdh in 15 of 17 patients . recurrence of csdh occurred in two patients on the same side and they underwent a re - operation later . the clinical and radiological risk factors for the development of csdh are presented in table 1 . the mean age of patients with csdh development tended to be older than those without csdh development ( 65.15 vs. 60.12 years , p = 0.112 ) . female and male patients showed significantly different transition rates to csdh ( 22.2 % vs. 52.9 % , p = 0.044 ) . however , the clinical presentation and initial gcs were not different between the two groups . neither associated traumatic subarachnoid hemorrhage nor cortical contusion was related with the development of csdh . interval from trauma to sdg was not significantly different between patients with csdh development and patients without csdh development ( 6.5 vs. 9.24 days , p = 0.279 ) . patients with bilateral sdg transitioned to the csdh more frequently than those with unilateral sdg ( 58.1 % vs. 14.3 % , p = 0.006 ) . the multivariate analysis revealed that male ( or , 7.68 ; 95 % ci 1.1849.78 ; p = 0.033 ) and bilateral sdg ( or , 8.04 ; 95 % ci 1.4145.7 ; p = 0.019 ) were significant risk factors for development of csdh ( table 2 ) . hemorrhage - free survival rates were significantly lower in the male and bilateral sdg group ( log - rank test ; p = 0.043 and p = 0.013 , respectively ) ( fig .3 ) . among the 45 patients with newly developed sdg , 15 ( 33 % ) were evaluated with mri . of them , nine patients ( 60 % ) showed diffuse symmetric pachymeningeal enhancement ( fig .1 ) . of the nine patients with pachymeningeal enhancement on contrast - enhanced mri , csdh did not develop in the six patients who did not show pachymeningeal enhancement on mri . the mean time for development of sdg from trauma was 8.028.35 days ( range , 140 days ) . thirty - one patients suffered from bilateral sdg , and the remaining 14 patients had unilateral sdg . regular follow - up ct scans were performed in all patients , including those with newly developed clinical deterioration . follow - up ct scans revealed regression of sdg in 25 of 45 patients ( 55.6 % ) , including 13 patients with bilateral sdg and 12 patients with unilateral sdg ( fig . the mean time for sdg regression was 112.1 days ( range , 10365 days ) . the remaining 20 patients ( 44.4 % ) showed transition to csdh during the follow - up period ( fig . the mean time from sdg to development of csdh was 48.3523.8 days ( range , 17120 days ) . the most common clinical manifestations were headache ( 9 of 20 ) , followed by hemiparesis ( 6 of 20 ) , and drowsiness ( 2 of 20 ) . final ct scans after surgery revealed complete regression of csdh in 15 of 17 patients . recurrence of csdh occurred in two patients on the same side and they underwent a re - operation later . the clinical and radiological risk factors for the development of csdh are presented in table 1 . the mean age of patients with csdh development tended to be older than those without csdh development ( 65.15 vs. 60.12 years , p = 0.112 ) . female and male patients showed significantly different transition rates to csdh ( 22.2 % vs. 52.9 % , p = 0.044 ) . however , the clinical presentation and initial gcs were not different between the two groups . neither associated traumatic subarachnoid hemorrhage nor cortical contusion was related with the development of csdh . interval from trauma to sdg was not significantly different between patients with csdh development and patients without csdh development ( 6.5 vs. 9.24 days , p = 0.279 ) . patients with bilateral sdg transitioned to the csdh more frequently than those with unilateral sdg ( 58.1 % vs. 14.3 % , p = 0.006 ) . the multivariate analysis revealed that male ( or , 7.68 ; 95 % ci 1.1849.78 ; p = 0.033 ) and bilateral sdg ( or , 8.04 ; 95 % ci 1.4145.7 ; p = 0.019 ) were significant risk factors for development of csdh ( table 2 ) . hemorrhage - free survival rates were significantly lower in the male and bilateral sdg group ( log - rank test ; p = 0.043 and p = 0.013 , respectively ) ( fig . among the 45 patients with newly developed sdg , 15 ( 33 % ) were evaluated with mri . of them , nine patients ( 60 % ) showed diffuse symmetric pachymeningeal enhancement ( fig .1 ) . of the nine patients with pachymeningeal enhancement on contrast - enhanced mri , csdh did not develop in the six patients who did not show pachymeningeal enhancement on mri . many studies have described the development of sdg after traumatic brain injury and the transition to csdh . however , no study has investigated risk factors for the development of csdh following traumatic sdg . this is the first study to perform a statistical analysis to elucidate the risk factors associated with transition to csdh . several mechanisms have been suggested with regard to the development of sdg after traumatic brain injury . traumatic separation of the dura - arachnoid interface at the dural border cell layer , and effusion from traumatized vessels can lead to fluid collection1825 ) . an arachnoid tear and csf influx into the subdural space through a flap valve mechanism has also been proposed3410 ) . the possible explanation for the fate of traumatic sdg whether it regresses or evolves into csdh is unclear . some authors have suggested that premorbid conditions , such as cerebral atrophy , which is more common in older patients , may contribute to the development of csdh91214 ) . our results are contrary with this hypothesis . although patients with csdh tended to be older than those without csdh , the difference was not significant . because we excluded patients who had a collection of subdural fluid at the time of initial brain imaging and only included patients with newly developed sdg , we avoided the difficulty distinguishing between traumatic sdg and premorbid cerebral atrophy . delayed resorption of the sdg and tearing of the elongated bridging veins results in hemorrhage into the subdural space . a neomembrane forms if sdg with a bleeding component persists 11326 ) . bleeding in the sdg induces migration or proliferation of inflammatory cells derived from dural border cells , resulting in a layer of fibroblasts along the dura , which develops into the outer membrane of the hematoma6111521 ) . hasegawa et al. 8 ) reported meningeal enhancement on mri with gd - dtpa ( gadolinium diethylene - triamine - pentaacetic acid ) enhancement in five patients with traumatic sdg . in that study , a microscopic examination of the enhanced dura mater revealed a vascularized neomembrane in which the vessel endothelium showed numerous pinocytic vesicles and fenestrations , suggesting that sdg with meningeal enhancement has potential to develop into csdh . although the number of patients evaluated by mri was too small to show statistical significance , the results of our study also support this hypothesis , as seven of nine patients with pachymeningeal enhancement developed csdh . previous studies have shown a marked male preponderance for the development of sdg , as well as transition to csdh2202324 ) . although the significance of bilateral sdg for the development of csdh has not been described , our results show that bilateral sdg was a significant risk factor for the development of csdh . furthermore , persistent bilateral fluid collection could have disturbed expansion of the brain parenchyma and facilitated formation of csdh than that of unilateral sdgfirst , the diagnosis of sdg and csdh was confirmed by radiology report based on visual assessment rather than objective measurement with parameters such as hounsfield units . second , this retrospective study was conducted in a single institute with relatively a small number of cases . further prospective studies are needed to ascertain the role of sex differences and bilateral sdg for the development of csdh . csdhs are common neurosurgical problems associated with significant morbidity in patients with traumatic brain injury . the potential to evolve into csdh should be considered in patients with traumatic sdg , particularly male patients with bilateral sdg . further studies are necessary to elucidate whether pachymeningeal enhancement on mri is a prognostic factor for the development of csdh in patients with sdg .\noutput:\n" }, { "from": "agent", "value": "objectivealthough a high incidence of chronic subdural hematoma ( csdh ) following traumatic subdural hygroma ( sdg ) has been reported , no study has evaluated risk factors for the development of csdh . therefore , we analyzed the risk factors contributing to formation of csdh in patients with traumatic sdg.methodswe retrospectively reviewed patients admitted to hallym university hospital with traumatic head injury from january 2004 through december 2013 . a total of 45 patients with these injuries in which traumatic sdg developed during the follow - up period were analyzed . all patients were divided into two groups based on the development of csdh , and the associations between the development of csdh and independent variables were investigated.resultsthirty - one patients suffered from bilateral sdg , whereas 14 had unilateral sdg . follow - up computed tomography scans revealed regression of sdg in 25 of 45 patients ( 55.6 % ) , but the remaining 20 patients ( 44.4 % ) suffered from transition to csdh . eight patients developed bilateral csdh , and 12 patients developed unilateral csdh . hemorrhage - free survival rates were significantly lower in the male and bilateral sdg group ( log - rank test ; p = 0.043 and p = 0.013 , respectively ) . binary logistic regression analysis revealed male ( or , 7.68 ; 95 % ci 1.1849.78 ; p = 0.033 ) and bilateral sdg ( or , 8.04 ; 95 % ci 1.4145.7 ; p = 0.019 ) were significant risk factors for development of csdh.conclusionthe potential to evolve into csdh should be considered in patients with traumatic sdg , particularly male patients with bilateral sdg ." } ]

[ { "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: pp fae and ve were isolated from 10 week old spf balb / ca mice . briefly , intestinal tissue was soaked in hank 's balanced salt solution containing 30 mm edta for 20 min at 4 c . after incubation , fae and ve were isolated by dissection with 26 g needles using stereomicroscopic monitoring , as shown in fig . total rna was extracted from isolated fae and ve using mirvana kit ( ambion ) according to the manufacturer 's instructions . mirna expression profile was assessed by using mouse mirna microarray release 12.0 ( agilent technologies ) . a hundred nanograms of total rna was labeled with agilent mirna complete labeling reagent and hyb kits ( agilent ) according to the manufacturer 's instructions . the labeled rna was used to probe the array plates via hybridization for 20 h at 55 c . array plates were subsequently washed and then scanned with an agilent g2565ca microarray scanner ( agilent technologies ) . scatter plot of normalized mirna expression profiles showed that 43 mirnas were up - regulated , and nine mirnas were down - regulated , in fae compared with ve by at least two - fold ( fig . ve is dominated by absorptive enterocytes , with scattered goblet cells and enteroendocrine cells . by contrast , fae contains few goblet or enteroendocrine cells and instead is characterized by the presence of antigen - sampling m cells . reflecting the difference in epithelial cell compositions , gene expression is differently regulated between fae and ve . consistent with this , our microarray data showed that mirna profiles between fae and ve were different ( see table 1 , table 2 ) . a unique pattern of mirna expression for fae may reflect important cellular phenotypes as well as functional features in fae . we believe that detailed analysis of fae / m cell - specific mirnas will likely provide new insights related to mechanisms of m - cell development and function .\noutput:\n" }, { "from": "agent", "value": "m cells in follicle - associated epithelium ( fae ) covering intestinal lymphoid follicles serve as a portal of entry for particulate antigens ( kanaya and ohno , 2014 [ 1 ] ) . despite their biological significance , molecular mechanisms that govern m - cell differentiation and function have not been fully elucidated . micrornas ( mirnas ) have a role to control host gene expression profiles that modulate cellular physiology and characteristic . many studies have shown that mirnas regulate diverse biological processes including developmental timing , differentiation and growth control of cells and tissues ( ivey and srivastava , 2010 [ 2 ] ) . mirnas are also relevant to differentiation and function of intestinal epithelium ( mckenna et al . , 2010 [ 3 ] ; runtsch et al . , 2014 [ 4 ] ) . expression profiles and functions of mirnas in the intestinal epithelium have been examined in jejunal and colonic mucosa [ 3 ] . in contrast , those in fae remain uncharacterized . to address this deficiency , we isolated peyer 's patch ( pp ) fae and villous epithelium ( ve ) surrounding the fae , and compared the mirna expression profiles of fae and ve by microarray analysis . this revealed that 43 mirnas were up - regulated , whereas 9 mirnas were down - regulated , in fae compared to ve . a unique pattern of mirna expression by fae may reflect important diversity in cellular phenotypes and / or functional features of fae . all microarray data has been deposited at geo under accession number gse46264 ." } ]

[ { "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 need for earlier and more accurate detection of alzheimer 's disease ( ad ) becomes critical with the much anticipated introduction of disease - modifying agents . the earliest detectable changes in ad may well be in the brain tissue itself , and functional brain imaging provides a noninvasive window directly into the brain 's activity . the utilization of [ f ] - fluorodeoxyglucose ( fdg ) uptake by brain tissue as measured by positron emission tomography ( pet ) is a well - documented method for evaluation of brain function as well as dysfunction . since the earliest examinations of fdg pet studies of brain metabolism , there have been reports of a characteristic pattern of decreased brain metabolic activity that is seen in patients with ad . this pattern is generally distinct from that seen in other types of dementia . other studies have demonstrated a relationship between the magnitude of cognitive impairment in ad and the extent of these metabolic deficits , important in that they demonstrate that progression of neurodegenerative changes is associated with both more cognitive impairment and larger pet metabolic deficits . other reports indicate the potential to detect brain metabolic changes ( in the same distinct pattern seen in patients diagnosed with probable ad ) across groups of premorbid patients , who have not yet developed mci , before symptoms or objective neuropsychological deficits occur . however , detecting the subtle metabolic abnormalities associated with the early neurodegenerative changes that eventually will lead to ad in individual patients ( rather than groups ) using objective evaluation of pet remains less commonly reported . objective analysis of pet brain image data has been available since the origins of pet , but has been chiefly utilized in the research arena . while there are numerous studies that report on pet brain imaging and ad , the numbers of studies that make use of advanced computerized digital image processing tools are fewer , and fewer still are the studies which use this technology to examine brain activity at the single - subject level ( for review see ) . while it is important to our understanding of the disease process to examine brain activity in group studies , the use of objective statistical image analysis enables the comparison of one brain image to a group of control brain images at the single - voxel level . this means of assessment is important to the clinician as it can provide information that may have an impact on early clinical diagnosis and management , particularly if neuroprotective pharmaceutical strategies are achieved . our study examines the usefulness of objective pet brain image analyses compared to standard ( subjective visual ) interpretation of fdg - pet brain image data . this study included a range of subjects , from individuals who were at risk but cognitively normal through the early mild cognitive impairment ( mci ) stage . even in the subjects who met criteria for mci , the average mmse score was 28 ( five patients with probable ad were included as a reference ) . we demonstrate that in this early population , 11 patients had changes apparent on the spm examination consistent with early stages of possible ad , but had pet scans that appeared normal to subjective visual interpretation the standard of care for reading fdg - pet brain scans today . this standard is reviewed further in the discussion , along with the potential implications of adding objective evaluation to this standard . the case is made for objective fdg - pet scan evaluation to improve the current standard for early detection of metabolic changes consistent with possible ad . this research was conducted in accordance with the guidelines and the approval of the institutional review board . subjects were recruited from the community with an emphasis on recruitment of subjects with mci or those in the at - risk cognitively normal state . all subjects were informed of all study procedures and signed informed consent before involvement in the study . in all , a total of 41 subjects were screened . of these , 9 failed to meet the inclusion or exclusion criteria , and 32 subjects were enrolled . ( 31 used , 15 male , 16 female ) , with an age range from 56 to 84 , with a mean age of 718 . this study focused on early detection , specifically with regards to patients with subjective memory loss but still not meeting criteria for mci . to be enrolled in the study , patients must either meet at least mci criteria and have no other neuropsychiatric problems , or must both have a first - degree relative with ad and be apoe4 + . a diagnosis of major depression was not grounds for exclusion , based on the high rate of comorbidity . patients were evaluated with periodic neuropsychological testing ( np ) a total of five times during the study . the criteria for a diagnosis of mild cognitive impairment ( mci ) were : memory complaint with informant corroboration , objective memory impairment with np testing , normal general cognitive function , intact activities of daily living , these criteria were based upon the american academy of neurology 's practice parameters for early detection of dementia . neuropsychological tests used to establish objective cognitive impairment included the folstein mini - mental state examination , clock drawing test , trails a & b , boston naming task , rey - osterrieth complex figure task , and the hopkins verbal learning task . to establish cognitive impairment , subjects must have deficits on at least two scores . if there was only one measure that was abnormal , it was still counted , but denoted as marginal ( in table 2 ) . for amnestic mci , subjects had to have deficits on one test of memory with a score 2 sd outside the age - adjusted normal range , deficits on one test of memory with a score 1.5 sd outside of the normal range if accompanied by a score on a nonmemory test 1 sd , or deficits on at least two memory tests with scores at least 1 sd outside the age - adjusted normal range . to establish cognitive impairment for nonamnestic mci , subjects had to have a nonmemory cognitive test with a score 2 sd outside the normal range , or two or more nonmemory cognitive tests with deficits at least 1 sd outside the age - adjusted normal range . based on the initial np test scores , subjects were either diagnosed as amnestic mci , nonamnestic mci , or combined type mci . four subjects did not initially meet criteria for mci , but were diagnosed at later time points . in addition , five subjects also met clinical criteria for ( and were diagnosed with ) mild to moderate ad . this latter subset had subclinical symptoms and / or were normal but at high risk for development of ad based on the criteria above . the normal control database was collected for general use in comparison with scans from patients referred for pet brain evaluation . this control database was collected with the approval of the institutional review board of the louisiana state university health science center at shreveport . all prospectively identified subjects were recruited by advertisement and fully informed of all risks , and they signed consent forms . only subjects older than 50 that met the criteria ( n = 28 ) were used for the current review . for inclusion in the normal control pet database , subjects had to be physically healthy with no neurological or psychiatric illness , have a normal physical exam , have no memory complaints , and have normal results on basic cognitive screening tests ( folstein mini - mental state exam 27 , and clock drawing test = 4 ) . extensive neuropsychological testing was not completed as a cost / benefit analysis indicated that the yield would be minimal in a normal population with no subjective memory loss . pet scans were also clinically reviewed by the nuclear medicine physicians utilizing subjective criteria and found to be normal or unremarkable . furthermore , individual pet scans were removed from the control group and then compared to the remainder of the control group in a jack - knife fashion , and subjects with pet metabolism changes in a pattern suspicious for the potential of developing dementia ( deficits in medial temporal , lateral temporal , posterior cingulum cortex , and posterior parietal regions ) were excluded . [ 18f ] - fluorodeoxyglucose ( fdg ) positron emission tomography ( pet ) scans were completed at the beginning and at the end of the three - year period . all pet scans were acquired and processed in the same way from the same scanner . all patients were informed to stop any medications potentially affecting brain function 24 hours prior to the study , fast for at least 6 hours prior to the study , and were ensured to have a blood glucose level of less than 200 mg / dl before administering the radiotracer . all patients were injected intravenously with approximately 15 mci ( 555 mbq ) of f - fdg in a room with low ambient noise and light while resting comfortably on a bed . pet images of the brain were obtained 60 minutes later on a ge advance pet scanner ( general electric company , milwaukee , wi ) . emission images of the brain were obtained for 10 minutes per bed position as a static acquisition in 2d mode followed by a 2 minute per bed position transmission scan . images were exported in dicom ( nema , rosslyn , va ) format , and an analyze 7.5 ( mayo clinic , rochester , mn ) compatible image was generated from the dicom slices . this image was imported into the statistical parametric mapping software ( spm , version 8 , wellcome department of imaging neuroscience , university college london ) , where it was spatially normalized into standardized space ( using default settings of 12 - parameter linear affine and nonlinear basis functions ) and filtered with an 8 mm isotropic gaussian filter . the pet brain images obtained from individual patients were reviewed and interpreted in the standard clinical fashion using subjective visual interpretation on the ge advance workstation by one of two experienced nuclear medicine physicians . they were blinded to the diagnosis and to the results of the objective spm analysis . for objective analyses , pet brain images from individual patients were compared to the control database using voxel - by - voxel analysis in spm . since there is a small but significant difference in the mean age of the control group and the subjects in the study , age was entered as a nuisance covariate in the spm analyses . spm generates an spm ( t ) statistic for the entire brain image that is then converted to the normally distributed z - score . this 3d z - score map is then surface rendered or overlaid on axial slices of a canonical image for viewing . an spm ( t ) score of 2 and spatial extent of 100 constituted the statistical threshold . there is an a priori hypothesis inherent in evaluation of patients with memory loss or cognitive decline that deficits in metabolism are expected in certain specific regions . furthermore , the pattern of hypometabolism , if present and consistent with early possible ad , is of significance itself , at any threshold . the specific pattern of metabolic deficits putatively associated with neurodegenerative changes due to early alzheimer 's disease process is described below and discussed later in the paper . fdg - pet scans were evaluated using the spm results in a similar fashion to the clinical readings , except that the spm ( z ) map using the above threshold was used to look for patterns of decreased metabolism consistent with possible ad , rather than the pet scan per se . metabolic deficits in posterior parietal , lateral temporal , posterior cingulum , medial temporal , basal nuclear , and / or posterior hippocampal regions present at this threshold were looked for . pet image maps with smaller ( less than 250 voxels ) , less significant ( z 3 ) , and / or isolated ( 2 regions or less ) metabolic deficits were considered negative , as these findings may occur by chance at the low threshold used . image maps with metabolic deficits that were larger than 250 voxels , had z scores higher than 3 , and / or had two or more regions in the areas being searched were then further evaluated and graded on a score from marginal ( ) to strongly positive ( + + + ) , depending on the spatial extent , z score , number of regions , and presence of a dog - leg pattern . figure 1 shows four example subjects ( s017 : no diagnosis , negative spm evaluation , s003 : no diagnosis with positive spm evaluation , s021 : mci with positive spm evaluation , and s040 : ad ) . there are some features that are common across all three examples with positive findings ( and indeed , across most subjects detected with spm as being consistent with possible early mci / ad ) . this patient has deficits clearly visible on the actual pet scan , which shows up prominently on the spm z - map , both overlaid on cross sections and are surface rendered . with ad , the pattern of brain metabolism deficits observed on fdg pet brain scans is characteristic and well established , with bilateral posterior parietal and lateral temporal deficits forming the dog - leg pattern that is commonly seen and present on this scan as well , more prominently on the left ( all images including surface renderings are in radiological orientation ) . however , all three subjects with positive findings shown ( s003 , s021 , s040 ) have both posterior temporal and posterior parietal deficits in metabolism . also in all three subjects , posterior cingulum hypometabolism is shown . modern techniques involving statistical analyses typically find posterior cingulum cortex metabolic decline , but it is often difficult to see these on the actual pet scan until later in the disease process . medial temporal lobe hypometabolism is not uncommonly seen , especially in earlier stages of the disease process , but has been reported to have more variability . in our present study , we did not examine or consider frontal metabolic deficits . frontal lobe hypometabolism is not uncommonly found in patients with mci / ad , but is nonspecific . one previous study found that patients with mci that did not convert to ad had mainly frontal hypometabolism . furthermore , pet studies of depression can be associated with frontal hypometabolism , and depression is commonly found comorbid with ad . we did not exclude patients with depression from the current study but also did not examine frontal lobe metabolism , specifically because of this factor . initially , subjects were diagnosed based on clinical presentation and criteria for mci or ad . subjects had to meet standard criteria for mci to be diagnosed ( e.g. , subjective memory loss ) . there were 11 subjects that did not initially meet criteria for either mci or ad and 15 who did meet these criteria ( one marginal ) . four of these 15 subjects did not initially meet criteria , but subsequently did meet the criteria for an mci diagnosis ( two marginally so ) later in the study ( in parentheses in table 2 ) . of the 11 subjects who never met mci criteria , there were seven subjects who had np deficits but did not have subjective memory loss criteria for mci and one who had subjective memory loss but never had np deficits . np testing was variable throughout the study in 20 of the 31 subjects . these 20 either had time points where np test scores were normal ( either initially or later in the longitudinal study ) or had time points that met criteria for a different subtype of cognitive impairment . of the 15 subjects diagnosed with mci , 13 had variable np results over the time points measured . of the 11 subjects who did not meet mci or ad criteria , four were consistently negative , and seven had variably positive results . there was variability within subjects with regards to both the presence of and the category of neuropsychological deficit found . for instance , subject 016 was normal , then had a combined deficit , after that became nonamnestic , and finaly , amnestic . these results appear to reveal several factors , particularly evident in individuals with mild or prodromal disease . first , it is very likely that practice effects impacted patient performance across the five assessments , sometimes resulting in normal scores or lack of expected reductions in scores in otherwise affected individuals . furthermore , individual patient variability , including both short - term differences in performance associated with their disease as well as variability attributable to external , nondisease - related factors such as stress or fatigue could have played a role . this may have led to initial misclassification of some subjects , especially because five subjects who met mci criteria had no pet findings consistent with possible early ad . furthermore , the presence of np deficits in those who are at risk but who deny subjective memory loss is not unexpected , as recently published results demonstrate similar findings . binder and others examined variability in np testing in healthy adults and found that deficits were common at low thresholds ( 1 sd ) and still present at higher thresholds ( 2 sd ) . other reports found that subjects diagnosed with mci were sometimes reclassified as either normal or other mci subtype at a follow - up visit . thus , the presence of abnormalities ( especially marginal abnormalities ) in subjects who are at risk are not unexpected , and the intrasubject variability in np results is also consistent with the extant literature . standard ( subjective visual ) fdg - pet scan clinical evaluation initially detected nine of the subjects enrolled in the study . five of these subjects ( all diagnosed with ad ) did not complete the second pet scan . at the second time point , only three of the remaining 25 subjects were detected . while these numbers seem low , the reason for this is that 15 of the subjects were initially preclinical or in fact normal ( although four eventually met criteria for mci ) . in addition , even subjects diagnosed with mci had mild disease , as indicated by the mmse ( mean mmse for patients with mci was 28.4 ) . the spm evaluation initially detected 14 subjects as having changes in brain metabolism consistent with possible early mci or ad that and three subjects as borderline ( total = 17 ) . two of these three subjects were read as positive at the second time point , and one was read as negative ( no findings ) . all subjects that were detected initially were also detected on the second pet scan save for this subject ( s018 ) . one subject who was initially negative did not complete the second scan , and five subjects with more advanced disease also did not complete the latter time - point scan . the five subjects diagnosed with possible ad had spm objective evaluations that were all strongly positive and consistent with possible ad . while it would be expected that subjects with a diagnosis of mci and / or findings on spm objective evaluation would progress , not all subjects would . some subjects progressed , some had no substantial change , and two actually appeared to have spm findings that were smaller on the second scan . bozoki and others recently discovered the presence of cognitive plateaus in 22 % of the patients with ad that they studied ( n = 243 ) . the average length of the plateau was 3.6 years , with the range being 3 to 7 years . metabolic plateau where there is a lack of progression in the deficits in hypometabolism and could help explain the lack of change in some subjects in this present study . another report demonstrated that higher premorbid intellectual function ( a measure of cognitive reserve ) can impact not just cognitive performance but also fdg - pet brain metabolism . it is thus possible that subjects in the preclinical or very early stages of ad might have findings on objective pet evaluation , but have little to no subjective and / or objective memory loss . the diagnosis of mci is made based upon the presence of subjective memory loss with objective cognitive impairment on np testing . in this study , we found that 15 subjects met criteria for a diagnosis of mci either initially or at a subsequent time point . of these , six were consistently negative with respect to metabolic deficits on objective spm evaluation . thus , there were a subset of subjects with no diagnosis who had spm findings and a subset of subjects diagnosed with mci who had no spm findings . in summary , there was little that was consistent with respect to the subjects diagnosed with mci or the at - risk subjects who did not meet criteria . there were some in each category who had no spm findings and some that did . since memory loss and objective impairment are both requirements for a diagnosis of mci , there is of course close association here , but even in this subgroup , nine of the 10 mci subjects did not maintain consistent type of deficit on np scores . the current standard of care for diagnosis of ad is a diagnosis of exclusion made clinically . the gold standard remains a brain biopsy to look for neurofibrillary tangles and amyloid plaques ; however , this is rarely done until autopsy . the use of fdg - pet has been considered for augmentation of the standard of care to improve accuracy and early detection , but cost and accuracy with regard to early detection of mci were problematic . however , previous evaluations in this respect did not include the use of objective statistical evaluation of fdg - pet scans . two current large ongoing studies ( adni : alzheimer 's disease neuroimaging initiative , and nest - dd : network for standardization of dementia diagnosis ) also support the use of objective statistical image analyses for early detection of ad . our research demonstrates a possible advantage with objective spm evaluation over standard ( subjective visual ) clinical interpretation in that clinically relevant patterns of hypometabolism were observed in some subjects not yet diagnosed and were not observed in some subjects who were diagnosed with mci . it is worth mentioning that the former may represent false positive identification and the latter false negatives . while these results presented here are variable and somewhat confusing , it is important to understand the context of a group of subjects consisting mostly of at - risk cognitively normal or very early clinical subjects ( save for five patients with ad , included as positive controls ) . in this population on the borderline of possible development of ad , all three detection algorithms ( np testinghowever , whether either subjects with no spm findings and positive np findings ( and vice - versa ) eventually develop ad must be evaluated at future time points , and so this work must remain preliminary . thus , while the presence of false positives or negatives can not be determined for certain at this time , it is possible that objective statistical evaluation of fdg - pet brain scans could improve the detection rate for nuclear medicine physicians . while these results must be classified as preliminary ( diagnosis of ad is not definitive especially in at - risk cognitively normal subjects ) , it is supported by the extant literature demonstrating fdg pet detection ( via objective statistical evaluation ) in premorbid subjects , both across groups and in other previous studies examining individual subjects . the pattern of deficits in metabolism observed in alzheimer 's disease is consistent : posterior cingulate , posterior parietal , lateral temporal , medial temporal / hippocampus , sometimes basal nuclear and variably frontal hypometabolism . there can be variance within this pattern ( e.g. , some cases are unilateral , some are bilateral ) but the regions themselves are highly consistent . practically , all published articles on fdg - pet imaging of ad spanning 30 years find hypometabolism in these regions ( see e.g. , ) . as early as 1995 , minoshima calls this pattern diagnostic when referring to the pattern of hypometabolism seen in the parietal and temporal regions of fdg - pet brain scans from patients with ad . this pattern is a hallmark feature of ad , and other neurodegenerative diseases have diverse patterns of hypometabolism ( for review see ) . with respect to the frontotemporal lobar dementias ( ftld ) , pick 's disease has a different clinical picture , and the statistical map would demonstrate mostly the frontotemporal pattern of metabolic deficits . the semantic dementia variant of ftld may be a potential diagnostic challenge , but the pattern of memory loss is different ( semantic versus short term ) , and the metabolic pattern is typically restricted to the temporal lobes , especially early in the disease process . in ad , deficits in metabolism may appear in medial temporal regions , but they also quickly appear in the posterior cingulum and / or posterior parietal cortices , and typically appear in these latter regions first . lewy body dementia would be the most problematic differential diagnostic issue , as it has a partially similar pattern of metabolic deficits and a clinical presentation that could be confused . however , the posterior metabolic findings are typically accompanied by a distinctive occipital lobe hypometabolism . vascular dementia has a pattern that depends upon the region of the vascular lesion . it is possible to have vascular lesions and subsequent hypometabolic findings in regions that coincide with those typically seen in ad ; however , this would be atypical as patterns of vascularization in humans do not predispose towards infarcts in medial temporal or posterior cingulum regions . the standard of care in pet brain imaging for detection of ad is subjective visual interpretation of the fdg - pet brain scan . the purpose of this paper was to demonstrate an advantage of objective spm evaluation over the standard clinical ( subjective visual ) pet brain image evaluation , and in this regard was met with a measured degree of success . a key concept is that objective statistical evaluation of pet brain image data has the potential to significantly extend the nuclear medicine physician 's ability to provide pertinent data to the referring physician to improve diagnostic accuracy . previous evaluations of pet imaging as a standard for detection of ad determined that pet imaging for early detection was optionalhowever , these previous examinations did not consider the utility of objective statistical analyses of pet brain imaging data ; they just considered subjective visual interpretation . this is a critical and overlooked detail , and hopefully this and other studies will provide the impetus for re - evaluation ( inclusive of objective analyses ) of fdg - pet in early detection of possible ad . as demonstrated here in this study , objective pet evaluation increased the detection rate in patients diagnosed with early mci from 5/15 to 9/15 subjects ( inclusive of both time points ) . further , the consistent lack of objective pet findings in the other subjects may be indicative of misdiagnosis with mci . spm evaluation also detected changes in four subjects who did not meet criteria for mci ( one was also detected by standard clinical pet evaluation ) , one of whom had no np deficits , indicating the presence of metabolic changes that could herald the eventual onset of ad in these at - risk subjects . however , given the uncertainty in diagnosis at this stage of the disease process , more sensitive detection of hypometabolic regions possibly representing very early ad could be problematic if used in isolation . if used as a tool for the nuclear medicine physician to provide more sensitive answers to referring physicians , it may be of benefit in cases with clinically correlated illness . these results indicate that objective statistical analysis of fdg - pet brain images has the potential to detect changes in brain metabolism that appear consistent with the neurodegenerative changes associated with ad in individual patients diagnosed with mci as well as in the at - risk cognitively normal state at a higher rate than with standard clinical pet brain scan evaluation alone . this is an important finding , as the need for early detection grows as our ability to treat this neurodegenerative disease improves . blood tests that screen for early changes in ad progression may eventually become readily available and sensitive enough for screening purposes ; however , alzheimer 's disease is a brain disorder , and thus examining actual brain activity will always be an optimal means of assessing disease state . given that there are now several fda approved software packages available , objective evaluation of fdg pet brain scans for the early detection of metabolic deficits related to the neurodegenerative changes of alzheimer 's disease in the mci stage is currently available to most pet imaging centers . these objective software packages are specifically designed to function as tools that improve detection capability and thus enable the nuclear medicine physician to aid the referring physician in early diagnosis and subsequent treatment decisions .\noutput:\n" }, { "from": "agent", "value": "the need for early detection of ad becomes critical as disease - modifying agents near the marketplace . here , we present results from a study focused on improvement in detection of metabolic deficits related to neurodegenerative changes consistent with possible early ad with statistical evaluation of fdg - pet brain images . we followed 31 subjects at high risk or diagnosed with mci / ad for 3 years . 15 met criteria for diagnosis of mci , and five met criteria for ad . fdg - pet scans were completed at initiation and termination of the study . pet scans were read clinically and also evaluated objectively using statistical parametric mapping ( spm ) . using standard clinical evaluation of the fdg - pet scans , 11 subjects were detected , while 18 were detected using spm evaluation . these preliminary results indicate that objective analyses may improve detection ; however , early detection in at - risk normal subjects remains tentative . several fda - approved software packages are available that use objective analyses , thus the capacity exists for wider use of this method for mci / ad ." } ]

[ { "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: mucocele is an inflammatory disease caused by the retention of mucoid secretions within a paranasal sinus ; the progressive volume expansion of this lesion can lead to thinning and / or erosion of the bony walls of the sinus . according to the pathogenetic mechanism , mucocele can be considered primary , developing as a retention cyst of degenerated epithelial mucous glands , or secondary , as a result of sinus ostium obstruction or cystic degeneration of inflammatory polyps . frontal sinus mucoceles are the most common , whereas those involving the sphenoid sinus are more unusual , accounting for 1 to 2 % of all mucoceles . although rare , the presence of a vascular lesion inside the sphenoid sinus may determine ostium obstruction , thus causing mucocele development . hence it should be considered among the possible diagnostic hypotheses of masses abutting inside the sphenoid sinus . an 84 - year - old woman with history of hypertension , noninsulin - dependent diabetes , and bilateral cataract , operated on in both eyes , was referred to our institution due to a lesion abutting into the sphenoid sinus . three months before hospital admittance she started complaining of a constrictive frontal headache , progressive worsening of visual acuity in the left eye ; later , sudden homolateral ptosis and diplopia occurred . a postcontrast head computed tomography scan revealed a large nonenhancing lesion within the sphenoid sinus , expanding and remodeling both its medial walls , consistent with the diagnosis of sphenoidal mucocele . at the center of the lesion , a low - density round mass , outlined by a hyperdense rim , suggestive of calcium deposits , a brain magnetic resonance imaging ( mri ) , integrated also by angiographic sequences , confirmed the presence of a homogeneous round mass inside the sphenoid sinus cavity , nonenhancing after intravenous gadolinium injection , markedly and spontaneously hyperintense both in t1 and t2 . the angiographic study showed no flow within this lesion , and , similarly , no flow alteration within the distal vessels of the intracerebral circulation was noted . with regard to these features , suspicion of thrombosed aneurysm of the right intracavernous carotid artery , surrounded by sphenoidal mucocele , was indicated ( fig . ( a ) coronal and ( b ) axial scans showing a homogeneous , spontaneously hyperintense , nonenhancing after contrast injection mucocele filling the sphenoid sinus cavity . the central round mass has a heterogeneous signal with a hypointense rim , consistent with the suspicion of a thrombosed aneurysm of the right intracavernous carotid artery . ( e , f ) postoperative mri showing the complete removal of the mucocele and the unchanged thrombosed aneurysm of the right intracavernous carotid artery . upon admission to our department , the patient 's neurologic examination showed bilateral amaurosis ( patient was already blind in the right eye ) and a complete left ophthalmoplegia . after complete mucocele removal , the aneurysm was clearly identified as a mass arising from the right wall of the sphenoid sinus , occupying mostly the right half of the sphenoid sinus cavity . it appeared to be solid , covered by respiratory mucosa , and not pulsating ( fig . the transmitted pulsation of the uncovered left internal carotid artery , protruding inside the sphenoid cavity at the level of the planum sphenoidale , was observed . ( a ) initial drainage of the mucocele after the opening of the anterior wall of the sphenoid sinus . ( b ) after the complete drainage of the mucocele , the thrombosed aneurysm covered by normal respiratory sinus mucosa is seen in the right part of the sphenoid sinus cavity . the mucocele - eroded bony walls of the sphenoid sinus uncovered the dura of the planum sphenoidale and the left carotid artery in its paraclinoidal tract . ( c ) images of the outpatient clinic endoscopic control at 6 - month follow - up showing the normal pinkish and trophic mucosa of the sphenoid sinus . the mucosa inside the sphenoid sinus appeared normotrophic and normochromic , and no signs or symptoms of systemic inflammation were disclosed preoperatively . as such , we did not suspect any mucosal infection and no culture examination was performed . antibiotic irrigation of the sphenoid cavity was ultimately performed . as already discussed with the patient , according to clinical conditions and radiologic features , no surgical or endovascular treatment of the aneurysm was attempted . a 3 - month postoperative mri confirmed the removal of the sphenoid mucocele , although the aneurysm had not changed ( fig . , the patient was relieved from headaches , but bilateral amaurosis and complete ophthalmoplegia in the left eye had not changed . at this time , the endoscopic endonasal control showed complete healing of the mucosa inside the sphenoid sinus , with normally pinkish mucosa covering the aneurysm mass inside it ( fig . sphenoid mucoceles are rare lesions12 representing only 1 to 2 % of all sinus mucoceles .1345 according to the pathogenetic mechanism , mucocele can be primary , when developed as retention cysts of the sinus epithelium mucous glands , and secondary , caused by sinus ostium obstruction , eventually from masses extending inside the sinus cavities .6 this latter condition corresponds to our case . the increase in volume of the mucocele can lead to erosion and thinning of the bony walls of the sinus . sphenoid sinus mucoceles may present with different symptoms due to compression and / or injury of the surrounding neurovascular structures such as cranial nerves ii , iii , iv , and vi , the carotid arteries , the cavernous sinuses , and the pituitary gland . the symptoms related to cranial nerve involvement ( 50 % of cases ) often lead to the diagnosis and may require timely surgery of decompression . defects of eye motility occur in 30 to 50 % of cases of sphenoid mucoceles with the oculomotor nerve affected more frequently than the abducent and the trochlear nerves .1378 visual acuity worsening is mostly progressive , but sudden blindness may occur .234910 however , the most common symptom is headache , typically supraorbital or retroorbital , occurring in 70 to 80 % of cases .31112 in our case , the mucocele extended in an anterosuperior direction inside the sphenoid sinus , in toward the superior orbital fissure . we could assess that signs and symptoms correlated mostly with the mucocele compressing the left cavernous sinus . the headache ceased after surgery , whereas left ptosis and diplopia remained stable , related to the long - lasting compression of the sphenoidal sinus left medial wall . concerning the amaurosis , the role of previous cataract surgery should not be underestimated . among surgical options for sphenoidal mucocele treatment , transfacial or transcranial approachesthis latter technique is safe and effective , providing a good outcome in terms of sinus opening and mucocele drainage .12457131415 early surgery is strongly recommended in the attempt to achieve cranial nerve function recovery . although visual loss is often irreversible ,7 a few cases of postsurgical improvement have been reported .1516 whereas aneurysms of the intracavernous tract of the internal carotid artery are frequently characterized by partial luminal thrombosis ( 70 % of cases ) , aneurysmal lumen complete occlusion is very rare .17 these aneurysms often present with third , fifth , or sixth cranial nerve palsies ; rarely , they bleed and cause subarachnoid hemorrhage .18 the treatment of thrombosed aneurysms is still a challenge , and some authors suggest surgery in symptomatic patients to relieve the mass effect . lawton et al19 made a morphologic and therapeutic classification of thrombosed intracranial aneurysms , proposing that only totally thrombosed aneurysms ( type 4 ) can be treated with watchful waiting . in our casesimilarly , at follow - up we preferred to adopt a conservative approach , evaluating the possible aneurysm reperfusion by means of an mri integrated by angiographic sequences rather than angiography . we must emphasize that the endoscopic endonasal approach allows a better view of the pathology and anatomy of the cranial base region . in our case , it permitted us to identify the consistency of the carotid thrombosed aneurysm and to recognize its origin from the cavernous sinus . the present case report showed an unusual association of thrombosed aneurysm of internal carotid artery and mucocele within the sphenoid sinus , causing severe neurologic symptoms . the possible presence of a vascular lesion of the internal carotid artery inside the cavernous sinus can be responsible for the development of secondary mucocele and therefore be considered among the different diagnostic hypotheses of space - occupying masses inside the sphenoid sinus cavity .\noutput:\n" }, { "from": "agent", "value": "background mucocele is an inflammatory disease caused by the retention of mucoid secretions within a paranasal sinus . although rare , the presence of a vascular lesion inside the sphenoid sinus could determine ostium obstruction , thus causing mucocele development . clinical presentation an 84 - year - old woman was referred to our institution due to a lesion abutting into the sphenoid sinus ; she was complaining of constrictive frontal headache , progressive worsening of visual acuity in the left eye ; later , sudden homolateral ptosis and diplopia occurred . the radiologic evidence was consistent with the diagnosis of thrombosed aneurysm of the right intracavernous carotid artery , surrounded by sphenoidal mucocele . the patient underwent an endoscopic endonasal transsphenoidal approach exclusively for sphenoid mucocele drainage . conclusion although rare , the presence of a vascular lesion inside the sphenoid sinus has to be considered among the possible diagnostic hypotheses of masses abutting in this cavity ; the association with mucocele is even more rare and , to date , has not been described ." } ]

[ { "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: major depressive disorder ( mdd ) is a mental disorder affecting about 16 % of the us adult population , and is a major cause for concern not only in the united states but the world over . it is a disorder characterized by depressed mood , diminished interest or pleasure , significant weight loss , feelings of guilt or low self - worth , insomnia or hypersomnia , fatigue , poor concentration , or recurrent thoughts of death . the symptoms are widespread , and tend to be quite stable . in 2000 , the world health organization ( who ) estimated depression to be the leading cause of disability as measured by years lived with disability ( yld ) and the fourth leading contributor to the global burden of disease . , a significant amount of research has been dedicated to finding physiological causes of mdd . one such study involved the catecholamine hypothesis that suggested that mdd is caused by decreased levels of the neurotransmitters norepinephrine and serotonin . this finding led to most modern day medication for mdd , which works by preventing the reuptake of these neurotransmitters . neuroimaging research has also shown that enlarged ventricles , sulci , reduced volume of the frontal lobe and basal ganglia are also associated with depressive episodes . such predictors would facilitate the diagnosis of the disorder well before the onset of the symptoms , perhaps allowing measures to prevent the symptoms from ever appearing . a vast amount of research is being conducted in order to find biological predispositions to mdd . there is evidence correlating shape differences of the hippocampus to depression and schizophrenia . in this manuscriptwe analyze interpoint comparisons to investigate the relationship in hippocampus shape space of three populations among twins . the subjects are categorized into three categories : the affected subjects ( clinically depressed , or mdd ) , the nonaffected cotwin of the mdd subjects ( high - risk , or hr ) , and the nonaffected twin pair ( control , or ctrl ) . the dataset includes both monozygotic ( mz ) and dizygotic ( dz ) twin subjects . according to established literature , the concordance rate for monozygotic ( mz ) hr subjects is 40 % , and for dizygotic ( dz ) hr subjects 11 % . this demonstrates that the subjects labeled hr ( due to the fact that their twin is mdd ) are in fact high riskour data set includes n = 114 subjects ( 57 twin pairs ) : 29 ctrl - ctrl pairs , 22 hr - mdd pairs , and 6 mdd - mdd pairs . the subjects are young female twins recruited through an epidemiological sample based on missouri birth records . to ensure that hippocampus shape space is the only independent variable , other factors had to be controlled ; all of the subjects were right handed and were screened for factors that may cause structural changes of the brain such as loss of consciousness greater than 5 minutes , chronic medical or neurological illnesses , or pregnancy . to obtain images of the hippocampus , very high resolution magnetic resonance imaging ( mri ) 1.5 t scanner was used to acquire three mprage scans ( 160 slices at 256x256 fov , 1.0 mm isotropic voxels ) . using analyze , the images were registered and averaged , converted to 8 - bits while optimizing the intensity range , and interpolated to 0.5 mm isotropic voxels . the image protocol implemented above allows for optimal comparative analysis . for each of left andright hemispheres separately , 22 three - dimensional landmarks were identified for each hippocampus and were used to generate and align hippocampal subcubes to a standardized orientation . using the landmark data , for each pair of subjects and for each of left and right hippocampus , we produce an interpoint shape comparison , as described below . for two subjects x and y ( for the left hemisphere , say ) , let x1 , , xn and y1 , , yn be the corresponding landmarks , where n = 22 . finding the shape comparison involves a landmark matching ( lm ) transformation . the transformation is nonparametric , and this flexibility implies that overfitting must be guarded against via regularization . lm finds a diffeomorphism that minimizes an error criterion which includes both landmark mismatch and transformation complexity . that is , ( 1 ) * = arg inf d ( identity , ) 2 + i = 1n ( xi ) yi2 , where d is a geodesic distance in a group of diffeomorphisms and 0 is a regularization parameter which controls the relative contribution of transformation complexity versus landmark mismatch to the optimization objective . the algorithm solves the nonlinear euler equation by a newton method combined with a shooting procedure . we use lm ( x , y ) = * , the energy of the minimizing diffeomorphism , as the shape comparison between two subjects x and y ( for the left hemisphere , say ) . applying lm to the left or right hippocampus data for each pair of subjectsyields an interpoint comparison matrix d. however , d is nn , hollow ( zeros on the diagonal ) and is asymmetric . the nature of the hippocampus shape space is such that under ideal conditions , it should yield a symmetric distance matrix . the asymmetry of the matrix d does not reflect the true nature of the hippocampus shape space , and is in fact a result of the limitations in the lm matching method . hence , before further investigation , d must be symmetrized to d , using an appropriate symmetrization technique . in this workwe symmetrize via dij = min { dij , dji } . figure 1 depicts the structure of the interpoint comparison matrices for the 114 subjects . figure 2 depicts the actual interpoint comparison matrix dlm - left ( after symmetrization ) for the 114 subjects . our task is to begin describing the relationship of the three populations ( mdd , hr , ctrl ) amongst one another in the hippocampus shape space elicited by the lm interpoint comparisons . first , we present a multidimensional scaling ( mds ) scatter plot ; unfortunately , we see in figure 3 that no significant relationship can be discerned from this plot . employing linear discriminant analysis ( lda ) after mds for all possible mds target dimensionalities analysis via lda mds lm ( ) a la miller et al . nevertheless , we will see in figures 4 and 5 a suggestion that perhaps progress can be made on our task , given a sufficiently clever methodology . figure 4 depicts kernel probability density estimates for the lm - left comparisons to show that the entries of the interpoint comparisons matrix dlm - left that correspond to comparisons between hr and ctrl ( the solid line in figure 4 ) are , overall , smaller than the entries which correspond to comparisons between hr and mdd . that is , figure 4 suggests a stochastic ordering relationship : d ( hr , ctrl ) std ( hr , mdd ) . again , dependencies amongst the entries of d make it difficult to assess the statistical significance of the result depicted in figure 4 . each row of the interpoint comparisons matrix d , corresponding to a single hr subject , gives rise to two samples : { d ( hr , ctrli ) } and { d ( hr , mddj ) } . that is , we have the vector of comparisons from that hr subject to every ctrl subject , and we have the vector of comparisons from that hr subject to every mdd subject . ( we do not include in these vectors the twin of the particular hr subject under consideration ; ignoring twinnedness in the analysis proves beneficial that we eliminate bias in similarity status between a subject and her twin that is not due to condition ( mdd , hr , ctrl ) . ) for this individual hr subject 's two sample data , a wilcoxon - mann - whitney test of the null hypothesis that the distribution of comparisons d ( hr , ctrl ) is the same as the distribution of comparisons d ( hr , mdd ) , against the alternative of stochastic ordering , yields a p - value . figure 5 provides a quantile - quantile plot of these p - values for dlm - left . under the null hypothesis , the plot demonstrates a clear deviation from a uniform distribution , again suggesting a stochastic ordering relationship d ( hr , ctrl ) std ( hr , mdd ) . again , dependencies amongst the entries of d make it difficult to assess the statistical significance of the result depicted in figure 5 . the quantile - quantile plot independently reiterates the suggestion of a stochastic ordering relationship that was first seen using the kernel probability density estimates . thus , while figures 4 and 5 give an inkling of the type of information that can be gleaned regarding the relationship in hippocampus shape space of the three populations ( mdd , hr , ctrl ) amongst one another , it remains henceforth to accurately assess the figures ' suggestion . to further uncover the characteristics of hippocampus shape space , we consider the task of classifying each hr subject as either mdd or ctrl . asbefore , we consider the two samples , { d ( hr , ctrli ) } and { d ( hr , mddj ) } , associated with each individual hr subject . we classify the hr subject as belonging to mdd or ctrl based on the wilcoxon - mann - whitney test statistic p - value , as described in ; ( see also [ 15 , page 183 ] ) . once we have classified each of the hr subjects in this way , we assess the relative similarity of hr to ctrl versus mdd based on the classifier 's performance based on the collection of hr subjects ' classifier - assigned class labels , taken as a whole . this procedure can be employed with lm interpoint comparisons obtained on left , right , or both left and right hippocampuses , and with any of the three populations ( hr , ctrl , mdd ) as the population of interest the role of hr in the description above . classifying the 22 hr subjects as either mdd or ctrl using dlm - left results in 19 classified as ctrl versus 3 classified as mdd . the probability of obtaining a result this extreme or more extreme ( the p - value ) under the least favorable null hypothesis h0 : hr are equally likely to be classified as mdd as ctrl is p .01 against each one - sided alternative . lm - right yields 16 classified as ctrl versus 6 classified as mdd classification performance not statistically significantly distinguishable from chance . combining left and right , the shape comparisons lm ( lm - left and right ) yields 20 classified as ctrl versus 2 classified as mddp .0005 for each one - sided alternative and strong statistical evidence that hr is more like ctrl than mdd in hippocampus shape space . an analogous analysis classifying the 33 mdd subjects as either hr or ctrl using lm - left shows that mdd is more like ctrl than it is like hr ( p .00002 for each one - sided alternative ) , and that the left carries more information than does the rightthe results obtained from classifying the 59 ctrl subjects as either hr or mdd are more nuanced : in this case , using lm - left indicates that ctrl is more like hr than it is like mdd ( p .0005 ) while using lm - right indicates that ctrl is more like mdd than it is like hr ( p .0005 ) . finally , we note that in the last two columns of table 1 we consider classifying the 22 hr subjects ( via leave - one - out crossvalidation ) as hr or mdd and as hr or ctrl . these results are consistent with our other findings hr is more difficult to distinguish from ctrl than from mdd , and the information extracted via lm - left is more powerful for this task than is lm - right . our analysis indicates that hr is more like ctrl than it is like mdd , mdd is more like ctrl than it is like hr , and ctrl is not obviously more like one or the other . also , we discern that the left hippocampus carries more information than does the right . if hippocampus shape space were one - dimensional if the population shapes could be accurately represented in 1then the joint relationship described by these three results could be depicted as in figure 6 , with the ctrl population between the hr and mdd populations in terms of shape . however , it must be noted that this depiction ( figure 6 ) offers only a simplified view of the true infinite dimensional nature of the shape space configuration , as suggested by the fact that the 2 - dimensional mds embedding depicted in figure 3 presents little or no class separation . our stated task is in terms of populations to begin describing the relationship in hippocampus shape space of the three populations ( mdd , hr , ctrl ) amongst one another . however , our results are conditional using lm - left we classify , for example , the 22 hr subjects representing the hr population as belonging to either the mdd or the ctrl class , conditionally on training data from mdd and ctrl . this , in fact , is the standard approach in probabilistic pattern recognition ; see , for example , . the difference between a focus on populations versus conditionals is indicative of a difference betweenpolicy science and laboratory science . a justification for the conditional approach in laboratory sciencewould be unnatural , because in a given application , one has to live with the [ training ] data at hand . in policy science , however , knowledge about the populations themselves may be the focus . by performing our analysis thrice , for each of the three populations in turn conditionally on the training data from the other two , we obtain three conditionals . letting nj denote the class - conditional sample sizes for each of the three classes , we see that the joint distribution for our sample is ( n1 + n2 + n3 ) d - dimensional ( where d is the presumed shape space dimensionality of each observation ) . the overall joint distribution of interest the three populations in shape space \" is of course not simply the product of our three conditionals . however , some population inferences regarding stochastic ordering can be performed via the ( multiple ) conditionals , and in particular the conditional approach justifies the simplistic view of our three populations in shape - space given by figure 6 .\noutput:\n" }, { "from": "agent", "value": "by analyzing interpoint comparisons , we obtain significant results describing the relationship in hippocampus shape space of clinically depressed , high - risk , and control populations . in particular , our analysis demonstrates that the high - risk population is closer in shape space to the control population than to the clinically depressed population ." } ]

[ { "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: conventional x - rays have presented limitations for the evaluation of the condyle due to the overlapping of anatomical structures in its region and the distortion of images9 . computed tomography ( ct ) and magnetic resonance imaging ( mri ) have been the methods of choice for evaluation of the tmj structures5 ,6,9,12 . in addition , ct has been the first option for diagnosis , surgical planning , and treatment of osseous trauma injuries due to their high specificity and sensitivity2 ,4,11,13 . it has been demonstrated that multislice detector ct ( mdct ) is an accurate technique for evaluating bone changes in the condyle . this study evaluated ct images of simulated osseous lesions in the condyle in parasagittal slices and compared the validity of the images acquired using different mdct protocols . fifteen dry mandibles in which condyle lesions were produced involving only the cortical or cortical and medullar portions of the bone were evaluated . spherical lesions were produced with high - speed and spherical drills sizes 1 , 3 , and 6 . the sites of the head of the mandible were classified by pole in : 1 - anterior , 2 - lateral , 3 - posterior , 4 - medial , and 5 - superior ( figure 1 ) . induced lesions simulated sizes that were very similar to the diameter of a used dental burr ( 1.0 mm ) and depth equal to half the diameter of the burr ( approximately 0.5 mm ) ( figure 2 ) . subsequently , mandibles underwent mdct scans ( 64 rows , aquilion , toshiba medical inc . , tustin , ca , usa ) with the following parameters : 0.5 mm of slice thickness , with 0.3 mm reconstruction interval by 0.5 s , with 120 kv , 300 ma and matrix 1024x1024 using a bone tissue filter . the original data were transferred to an independent workstation ( dell precision 420 hardware , windows xp ) , using radiostudio ( version 1.7 - anne solutions company ) to generate automatic and simultaneous multiplanar reconstructed images . analysis was performed using two protocols : ( 1 ) multiplanar reconstruction ( mpr ) : coronal , axial and sagittal images ( figure 3 ) ; ( 2 ) parasagittal reconstructions ( figure 4a , 4b , and figure 5 ) . axial images corresponded to original images and axial / mpr consisted of the association of axial and mpr images . two previously calibrated observers interpreted the images with protocols in random order , in two different sessions , separated by an interval of , at least , 1 week . the observers evaluated the absence or the presence of bone destruction and its localization according to each protocol . statistical analyses included estimation of kappa statistics , validity test ( sensitivity - specificity ) and chi - square test using spss software version 15.0 ( statistical package will be social science , chicago , il , usa ) . observer 1 , in the first measurement , had the highest agreement with the gold standard in the lateral polar region ( 0.75 ) and the lowest in the medial polar region ( 0.42 ) . observer 2 had the highest agreement with the gold standard in the lateral polar region ( 0.84 ) and the lowest in the medial polar region ( 0.57 ) . observer 1 , in the second measurement , presented the highest agreement with the gold standard in the superior polar region ( 0.90 ) and the lowest in the medial polar region ( 0.52 ) . both observers had the lowest agreement with the goldstandard in the medial polar region of the axial , coronal and sagittal images . in the analysis of parasagittal images ( table 2 ) , observer 1 showed higher agreement with the gold standard in the superior polar region for parasagittal images for both first ( 0.79 ) and second ( 0.90 ) measurements . observer 2 had higher agreement with the gold standard in anterior polar region ( 0.85 ) . observer 1 had the lowest agreement in medial ( 0.37 ) and observer 2 in the posterior ( 0.63 ) polar region . obs 1 - second analysis of observer 1 . in a total of 30 mandible heads evaluated and related to 5 poles , a total of 25 perforations was found in the medial pole ( drill 1 = 10 , drill 3 = 7 , and drill 6 = 8 ) , 22 perforations in the lateral pole ( drill 1 = 8 , drill 3 = 7 , and drill 6 = 7 ) , 21 perforations in the anterior pole ( drill 1 = 7 , drill 3 = 7 , and drill 6 = 7 ) , 23 perforations in the posterior pole ( drill 1 = 6 , drill 3 = 9 , and drill 6 = 8 ) , 23 perforations in the superior pole ( drill 1 = 7 , drill 3 = 8 , and drill 6 = 8 ) . sensitivity and specificity are shown in table 3 . highest sensitivity was observed for superior poles for both methods and observers ( table 3 ) . highest values for specificity were observed for medial , lateral , and anterior poles for both observers and methods . imaging of the tmj region is limited with conventional radiography due to the overlap of anatomical structures , making visualization of the area of interest very difficult1 ,3,5,14,18 . recent studies have demonstrated that ct is one of the best methods to evaluate abnormalities of the tmj and adjacent structures , since it provides better visualization of soft and hard tissues without overlapping of images3 ,9,10,13,15,16,19 . ct scanning has been the best option to the present date for the diagnosis of oral - and maxillofacial diseases , surgical planning and treatment of bone lesions9 ,15,19 . ludlow , et al. 12 ( 1995 ) published a comparative study in vitro for detection of bone alterations in the tmj region . this study compared biplanar ( sagittal and coronal ) temporomandibular images produced by multidirectional tomographic and panoramic techniques . series of dentin chips were placed at four locations on the head of the tmj of a dried human skull . biplanar tomography provided significantly more accurate assessment of condylar lesions than panoramic images ( p = 0.007 ) . the effects of observer and repeated observations were marginally significant at p = 0.046 and p = 0.030 , respectively . in comparison to the study of ludlow , et al. 12 ( 1995 ) , the present investigation demonstrated statistically significant differences in relation to the position of the simulated lesions at the head of the mandible , influenced by the diameter of the drills and the number of perforations in each polar region . the types of images did not show significant differences regarding the percentages of agreement in polar regions . in the lateral , posterior and superior polar regions , the p value for the chi - square test was 1.0 . in the medial and anterior polar regions , the p values were p = 0.530 and p = 0.718 , respectively . those authors observed that the combination of axial ct with coronal and sagittal images provided more accurate images than conventional ct . in their study ,100 % of the pathological bone alterations were observed . using software that could easily be installed in a personal computer , they showed that it is possible to reconstruct original images coming from any source with dicom ( digital imaging communication in medicine ) images . perrella , et al. 13 ( 2007 ) reported that values of sensitivity and specificity were 100 % for both single - slice and multislice protocols for the detection of simulated lesion in the mandible 's body . however , the acquisition method utilized limited the ability to detect the correct number of loci in multilocular lesions and the location of medullar invasion . the use of thinner slices when scanning a lesion was responsible for more effective results in the detection of medullar invasion and characterization of loci . in the present studythe values were not influenced by the acquisition method used by perrella , et al . ( 2007 ) ; they were influenced by the size of drill 1 , which made the evaluation of different regions more difficult . cara , et al. 3 ( 2007 ) evaluated and compared the validity of different single and multislice methods for analyses of simulated lesions in the head of the mandible . sensitivity results were : axial single - slice method 1 ( 62.7 % ) , axial multislice method 2 ( 66.2 % ) , axial / multiplanar reconstruction single - slice protocol 3 ( 72.7 % ) , axial multi - slice / multiplanar reconstruction protocol 4 ( 93.1 % ) . association of axial images with multiplanar reconstruction ( mpr ) using multislice ct scan demonstrated high accuracy in relation to single - slice method . the present study determined the validity of images acquired by using multi - slice ct scans with different protocols in multiplanar reconstructions and parasagittal slices . specificity was higher for both observers in both protocols for medial , lateral , and anterior . the association of ct protocols for visualization of the region of the head of the jaw was established in intention to improve the visualization of the presence of alterations of each region of the head of the jaw . the validity of multislice ct was established for the detection of mandibular lesions using both protocols . valid protocols are important to improve the visualization of structures of the mandibular polar region . anterior and posterior poles were better visualized from a latero - medial perspective using parasagittal images . lateral , medial , and the superior poles were better visualized from an anterior posterior perspective .\noutput:\n" }, { "from": "agent", "value": "conventional radiography has shown limitation in acquiring image of the atm region , thus , computed tomography ( ct ) scanning has been the best option to the present date for diagnosis , surgical planning and treatment of bone lesions , owing to its specific properties . objective : the aim of the study was to evaluate images of simulated bone lesions at the head of the mandible by multislice ct . material and methods : spherical lesions were made with dental spherical drills ( sizes 1 , 3 , and 6 ) and were evaluated by using multislice ct ( 64 rows ) , by two observers in two different occasions , deploying two protocols : axial , coronal , and sagittal images , and parasagittal images for pole visualization ( anterior , lateral , posterior , medial and superior ) . acquired images were then compared with those lesions in the dry mandible ( gold standard ) to evaluate the specificity and sensibility of both protocols . statistical methods included : kappa statistics , validity test and chi - square test . results demonstrated the advantage of associating axial , coronal , and sagittal slices with parasagittal slices for lesion detection at the head of the mandible . results : there was no statistically significant difference between the types of protocols regarding a particular localization of lesions at the poles . conclusions : protocols for the assessment of the head of the mandible were established to improve the visualization of alterations of each of the poles of the mandible 's head . the anterior and posterior poles were better visualized in lateral - medial planes while lateral , medial and superior poles were better visualized in the anterior - posterior plane ." } ]

[ { "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: raccoons ( procyon lotor ) are the host of b. procyonis roundworms , intestinal parasites ( 3 ) . up to 82 % of adult raccoons and 90 % of juvenile raccoonsthese eggs are eliminated through raccoon feces and accumulate at raccoon latrines ( 4 ) . b. procyonis roundworm eggs remain infective for many years and can infect juvenile raccoons and intermediate hosts such as rodents and birds that ingest them ( 3 ) . transmission often occurs at raccoon latrines when eggs are ingested with seeds found in fecal material ( 4 ) . larvae migrate through intermediate host tissues and can enter the central nervous system , resulting in death ( 3 ) . raccoon population densities have increased in response to increased anthropogenic resources that are available in agricultural and urban ecosystems ( 5 ) . thus , raccoon latrines often exist near human habitats , increasing the risk for zoonoses ( 4 ) . reported cases of human b. procyonis roundworm infections are rare ( n = 18 ) , and all have occurred in north america ; however , prevention is a public health priority because of the severity of the resulting neurologic disease ( 610 ) . our objective was to develop a management technique that could interrupt transmission of b. procyonis roundworm eggs between raccoons and intermediate hosts , ultimately decreasing the environmental levels of eggs and potential for reinfection . we examined the effects of latrine removal and treatment of raccoons by using randomly distributed anthelmintic baits on the basis of b. procyonis roundworm prevalence at latrines and among intermediate hosts . by implementing a specific , protocol - based approach to disease prevention , supported by experimentally derived data , we hope to provide public health officials with an effective , spatially explicit , prophylactic method for reducing infection risk . we conducted this study in grant , miami , and wabash counties in north - central indiana in portions of the upper wabash basin . this area is 88 % agricultural ; only 8 % of the landscape remains forested ( 11 ) . some contiguous riparian forest remains ; however , most patches are 5 hectares ( ha ; 1 ha = 10,000 m ) ( 11 ) . the range of patch sizes , levels of patch isolation , and raccoon densities in treatment and control patches were representative of the landscape ( figure ) . study area of raccoon latrines showing locations of treatment and control patches , upper wabash basin , north - central indiana , 20072008 . dominant land use is represented by degree of shading . in march 2007 ( spring 07 ) , we removed all visible latrines ( n = 559 ) in the treatment patches . we located latrines by systematically searching all appropriate horizontal substrate and area at the bases of large trees throughout each forest patch ( 3 ) . after manual removal , we used a torch to sterilize the substrate and surrounding soil associated with each latrine ( technical appendix ) . at control sites , we sampled a minimum of 20 latrines ( n = 198 ) by removing 2 g fecal material per fecal deposit at each latrine ( 12 ) . we returned to our study sites 3 additional times for fecal sampling in october and november 2007 ( fall 07 ) , june 2008 ( summer 08 ) , and november 2008 ( fall 08 ) . during these subsequent visits , we sampled 2 g of fecal material per fecal deposit at a minimum of 20 latrines in all treatment and control patches . all samples were stored at 20c until they were examined for b. procyonis roundworm eggs . eggs were identified by microscopic examination following centrifugal fecal flotation in sheather sugar solution ( 3 ) . we identified b. procyonis roundworm eggs on the basis of size and morphologic appearance and designated each sample as positive or negative . prevalence was measured as the proportion of positive samples at each study patch during each sampling period . differences between pretreatment and posttreatment prevalence and between treatment and control patches were determined by using log linear analyses performed with proc catmod sas version 9.1 ( sas institute inc . , cary , nc , usa ) ( goodness - of - fit tests ) . in spring 07 , after the initial latrine removal from treatment patches , baits were distributed throughout treatment patches once a month for the duration of the study . baiting densities were determined on the basis of average abundance of raccoons in each study patch ( technical appendix ) . prevalence of b. procyonis roundworm larvae within an intermediate host , white - footed mice ( peromyscus leucopus ) , was determined . a minimum of 10 mice were captured from each of the 16 study patches during each of 3 sampling periods : 1 pretreatment ( summer 07 ) , and 2 posttreatment ( fall 07 and summer 08 ) . after capture , mice were euthanized with carbon dioxide and refrigerated until examination for b. procyonis roundworm larvae . brains were removed and examined separately by pressing them between glass plates , and larvae were examined under a dissecting microscope . prevalence of infection was determined for mice within each study patch for each sampling period . differences between treatment and control patches were determined by fisher exact test ( 12 ) . pretreatment sampling of latrines in spring 07 detected b. procyonis roundworm eggs at 757 ( 33 % ) of latrines sampled across all patches ( table ) . however , prevalence of eggs in treatment patches declined by 3-fold after baiting in all sampling periods ( p 0.04 ) . our baseline pretreatment estimate of prevalence of infection among intermediate hosts did not differ ( p = 0.426 ) between treatment patches ( 32 % ) and control patches ( 37 % ) . approximately 1 year after baiting activities began , we detected a significant decline in the prevalence of b. procyonis roundworm larvae in mice between treatment and control patches ( 27 % vs. 38 % ; p = 0.05 ; table ) . * the effect of treatment on prevalence by patch is represented by the proportional change between pretreatment and final sampling . ha , hectare ( 10,000 m ) ; spring 07 , march 2007 ; fall 07 , october and november 2007 ; summer 08 , june 2008 ; fall 08 , november 2008 ; nc , no change . current public health initiatives to prevent human infections with b. procyonis roundworms focus on education of human health care and veterinary professionals ( 6 ) . our practical approach decreased prevalence of the parasite , suggesting decreased transmission and possibly reduced risk for humans . baiting strategies have effectively controlled rabies ( 13 ) and decreased prevalence of zoonotic parasites , including echinococcus multilocularis tapeworms ( 14 ) . our baiting strategy combined with latrine removal effectively decreased egg levels at latrines and ultimately decreased prevalence among mice . hegglin and deplazes ( 14 ) demonstrated a long - term decrease in prevalence of e. multilocularis tapeworms among foxes ( definitive hosts ) after monthly baiting for 4 years and conjectured that this decrease was caused by decreased infections among intermediate hosts . our study supports their hypothesis because we measured decreases in prevalence among intermediate hosts after baiting . the reduction of prevalence at latrines and among intermediate hosts suggests that our low - cost approach ( technical appendix ) could have a lasting effect on transmission dynamics ; however , further study to assess frequency of distribution and type and dose of baits for sustained prevalence is needed . raccoon latrines are commonly found near homes ( 4 ) , and implementation of baiting strategies , in conjunction with traditional raccoon management on public lands , could reduce the risk for transmission on nearby private properties .\noutput:\n" }, { "from": "agent", "value": "baylisascaris procyonis roundworms , a parasite of raccoons , can infect humans , sometimes fatally . parasite eggs can remain viable in raccoon latrines for years . to develop a management technique for parasite eggs , we tested anthelmintic baiting . the prevalence of eggs decreased at latrines , and larval infections decreased among intermediate hosts , indicating that baiting is effective ." } ]

[ { "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: . these injuries can occur in a fashion similar to those of the biliary system , resulting in laceration , transection or occlusion of the hepatic arterial . this case report describes a patient who presented with acute bleeding from a pseudoaneurysm of the replaced right hepatic artery and the left main hepatic artery following a laparoscopic cholecystectomy . a 64 - year - old male referred to our hospital 4 weeks after having a laparoscopic cholecystectomy complicated by a common bile duct injury . he had undergone a difficult laparoscopic cholecystectomy with intraoperative bile duct injury suspected at the end of the procedure at a peripheral hospital . the surgeon inserted a drain in the surgical bed at the time of the surgery . postoperatively , the patient was started on piperacillin and tazobactam , and underwent an endoscopic retrograde cholangiopancreatography ( ercp ) , which confirmed the presence of a common bile duct injury . a biliary stent was placed . the patient continued to have daily bile drainage ranging from 100 to 350 ml per day . upon presentation to our center , the patient was febrile ( 38.9 c ) and complained of a left upper limb pain and swelling . hematology was consulted , and a diagnosis of acute upper limb venous thrombosis was established . owing to the presence of blood in the drain , he was kept on the maximum prophylactic dose of unfractionated heparin . a ct angiography of the abdomen showed two collections , one at the surgical bed near the drain , and the other was subcapsular below the left lateral lobe of the liver , as well as an aneurysm of the replaced right hepatic artery with an active bleeding blush ( fig . 1 ) . the patient was immediately referred for an angiography , which confirmed the ct scan findings ( fig . an ercp was also performed , which revealed a strasberg class d injury , and a plastic biliary stent was inserted . after the angio - stent insertion and stabilization of the patient , five days later he developed hematemesis and melena with a significant drop in his hb to 2g / l , and his total bilirubin became 183 mol / l of which 91 mol / l is direct . a gastroscopy was performed and showed hemobilia ( bleeding from the ampulla of vater ) . subsequent angiography demonstrated a leak of contrast just above the arterial stent ; hence , a further stent was placed to cover that area of the aneurysm . similar symptoms reoccurred a week later , and a new angiography showed a new aneurysm from the left proper hepatic artery . a percutaneous thrombin injection of the aneurysm was performed as the bleeding branch was unreached via direct angiography and was filling in retrograde perfusion . during recovery a chest spiral ctfigure 1 : a ct scan showed replaced right hap inside the collection ( straight arrow ) . figure 2 : an angiographic scan showed superior mesenteric artery ( straight arrow ) and replaced right hap ( angulated arrow ) . an angiographic scan showed superior mesenteric artery ( straight arrow ) and replaced right hap ( angulated arrow ) . an angiographic scan showed stent in the replaced right hepatic artery . on day 7 , the patient bled again from the same aneurysm of the left hepatic artery . a repeated angiography revealed the bleeding with a reduced flow in the stented , replaced right hepatic artery ( fig . the active bleeding was stopped using gel - foam embolization of the two branches of the left hepatic artery ( fig .5 ) with a decision to embolize the whole left hepatic artery if bleeding did not stop while holding the heparin infusion . the patient 's liver function was preserved , and the bleeding stopped despite anticoagulation . figure 4 : an angiographic scan showed reduced flow in the stented replaced right hepatic artery . figure 5 : an angiographic scan showed left hap after a gel foam . a laparoscopic cholecystectomy is reportedly associated with an increased incidence of biliary and vascular injuries . specifically , biliary injuries are reported in 0.21 % of procedures with a 10-fold increase when compared with open surgery , whereas vascular injuries occur in 0.250.5 % of procedures . the symptoms may appear in the early postoperative period or as late as 120 days after operation . a pseudoaneurysm of the hepatic artery or its branches can lead to bleeding through the drain or in the form of hemobilia in 20 % of cases . however , the classical clinical triad described by quinke of right upper quadrant pain , jaundice and hemobilia has been reported in 32 % of patients with laparoscopic cholecystectomy - related hepatic artery pseudoaneurysms ( haps ) . the clinical presentation of hap is bleeding , which might be intermittent bleeding if discovered early . if it is not identified , a massive hemorrhage may occur with a rupture , and the mortality rate could be as high as 50 % . in our patient , direct vascular injury , erosion due to clip encroachment and diathermy shorting on clip - associated infections are likely to be precipitating factors . bile is cytotoxic and the amphipathic properties of bile acids make them powerful solubilizers of membrane lipids , causing cell death . a canine study by sandblom et al . showed that bile delays the healing of a liver wound , attributable to the fibrolytic or cytotoxic effects of bile . bile can therefore cause a weakening of suture lines or sites of surgical clips in vessels . the presence of an infection is another contributing factor for the development of the hepatic artery aneurysm . the most likely cause in our patient was a combination of an infection and a traumatic injury . the treatment of a hepatic artery aneurysm is an emergency because the patient may exsanguinate from a rupture at any time . patients with hematemesis or melena following the laparoscopic cholecystectomy should have an urgent endoscopy , and if no cause is identified , an abdominal ct and hepatic angiography should be performed . definitive treatment with radiologic embolization is the treatment of choice for hap , although some reports of conservative management have been recorded . in our case , the stenting of the replaced right hepatic artery and gel - foam embolization of the left hepatic artery were performed . when a patient presents with massive gi bleeding , a climbing total bilirubin level and recent hepatobiliary manipulation or intervention , a high index of suspicion is always needed . the added complexity in our patient was the presence of deep vein thrombosis and pulmonary embolism , the development of a left hap in the presence of a thrombosed replaced right hepatic artery that was stented and finally , bleeding from the left hap , which stopped with gel - foam embolization .\noutput:\n" }, { "from": "agent", "value": "hepatic artery pseudoaneurysm is a rare complication of laparoscopic cholecystectomy . a high index of suspicion and early identification and therapy are important points needed to prevent rupture . we report a case of complex biliary and vascular injuries 4 weeks after a laparoscopic cholecystectomy . the patient had recurrent bleeding from a hepatic artery pseudoaneurysm that has been treated successfully with angiographic stenting and embolization ." } ]

[ { "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 important task in molecular biology is the accurate classification of biological specimens on the base of their gene expression profiles . methods for accurate and reproducible classification are increasingly required for the potential biomedical applications of expression profiles , such as disease classification , diagnosis and monitoring . in this paperwe describe scudo , a web server implementing an original signature identification method . given a set of expression profiles from control and affected subjects , scudo verifies the existence of a signature ( actually , a set of signatures , as explained below ) that can be used to classify the profiles according to a phenotype of interest , such as the control / affected status . the method is composed of a sequence of simple processing steps , none of which is original ; however their combination results in a robust and novel model of profile data analysis , that corresponds to a different way of exploiting similarities and differences among biological samples for classification purposes . specifically , the originality of the method is that it introduces a new concept of subject - specific signatures , as opposed to disease - specific signatures , that also includes the benefits of rank - based classification , data dimensionality reduction and the power of network analysis in its design . our method was tested against a selection of the best current approaches in the course of the sbv improver diagnostic signature challenge , an open competition designed to assess and verify computational approaches for classifying clinical samples based on gene expression ( 1 ) . in an effort to increase robustness of the outcome with respect to chance and disease specificity , the sbv challenge required a diagnosis for all of four diseases , namely psoriasis , multiple sclerosis ( ms ) , chronic obstructive pulmonary disease ( copd ) and lung cancer . for each disease , the organizers ( a team of researchers from ibm research and philip morris international ) suggested a list of publicly available mrna expression datasets to use as possible training sets and then solicited a healthy / affected diagnosis for a previously unpublished set of profiles ( test set ) . the submitted predictions were scored by the organizers according to a combination of three previously selected metrics : the area under the precision - recall curve ( aupr ) , the belief confusion metric ( bcm ) and the correct class enrichment metric ( ccem ) . the method implemented in scudo ranked second overall , and first in the ms sub - challenge , out of 54 submissions . interestingly , the ms diagnostic appeared to be the most difficult of the four , according to the plots of the distribution of random versus observed scores prepared by the organizers . the overall first placement was achieved by the winning team through a skillful application of linear discriminant analysis ( lda ) ; the third place was obtained by a team that applied lasso regression ( 2 ) . ( see ( 3 ) and ( 4 ) , respectively , for the details of the winning methods and of the scoring algorithm and score distribution plots . ) the method on which scudo is based represents a completely new way of addressing the expression profile classification problem . contrary to current practices , instead of evaluating a set of profiles by means of a common yardstick ( a single list of highly discriminating mrna / mirna species ) , our method first seeks to summarize the characteristics of each profile by means of a rank - based signature and then it performs a systematic , all - to - all signature comparison . the comparison consists in the measurement of a distance that quantifies the degree of similarity between any two signatures using a simplified version of the enrichment score ( es ) ( 5 ) . the result of the comparison is a distance matrix , which is then visualized in the form of a map of individual signatures . in such a map , the spontaneous emergence of groups ( i.e. clusters of closely connected nodes ) of transcriptionally similar subjects is typically observed . in a diagnostic application , a diagnostic classification for an unseen individual can subsequently be performed by determining the position of the individual 's transcriptional signature relative to the control / affected groups . the map is in the form of a graph where the nodes correspond to signatures / subjects and the length of a connecting edge encodes the level of similarity between the connected nodes ( short edge = high similarity ; no edge = negligible similarity ) . scudo accepts two separate datasets as input , respectively a testing and a training dataset , but it can also be used with a single ( training ) dataset . if a testing set is specified , scudo runs the same rank - based classification algorithm on it , but it skips the feature selection step , using instead the list of features ( genes or mirnas ) already selected for the training dataset . the optimization of the signature length is left to the user and is performed by trial and error ; in practice the user needs to try and select the n1 and n2 values that provide the clearest separation between the affected and the control subjects ( n1 = number of up - regulated genes to consider , n2 = number of down - regulated genes , n1 + n2 being the total signature length ) . crucially , we have shown that our method is robust to variations of its input parameter values , therefore the selection process is not critical and satisfactory values can be found with only a few iterations ( 6 ) . the expected result is the emergence of a partitioning of the set of samples in separate , clearly visible groups on the basis of signature similarity . while for the training set the sample classificationis known in advance and thus the correctness of the partitioning is immediately verified by the appearance of homogeneously colored groups , for the test set in general the sample classification is the desired final output and needs to be deduced from the graph . the classification problem for the test set is then reduced to the simpler task of identifying the control / affected phenotype associated to each of the emerging groups in the test graph , in what we call the labeling step . this relatively simple labeling step can be carried out by means of empirical methods that rely on some form of previous knowledge . one form of previous knowledge consists of a small number of samples for which the classification is known ; by adding these samples to the test set , one can deduce the labeling of the groups based on the membership of the known samples . another form of previous knowledge is represented by a list of literature - derived disease genes ; by computing the average expression values of these genes across all the members of a group , one can deduce the labeling of the groups by comparing averages and taking a majority vote . we used both these methods for the labeling of samples in the sbv improver competition . our rank - based signature method is quite general and we have tested it successfully with a large assortment of data types : mrna and mirna profiles for various diseases / treatments / experiments , obtained from biopsies , blood and urine and even some non - biological multidimensional datasets ( i.e. engineering data ) . with scudowe are making available an online implementation of our new method to encourage experimentation and discovery of novel applications . scudo accepts a testing and a training dataset as input ( figure 1 ) , but it can also be used with a single ( training ) dataset , in case the user is not interested in the testing step . if a testing set is specified , scudo produces a map of the profiles using the same list of features ( genes or mirnas ) that were used in producing the training profiles map . in a sense , the testing set is used to validate the quality of the feature list , obtained examining the training set , as a starting point in producing discriminating signatures for a different set of profiles . the input data fields for the training set are on the left , the ones for the testing set on the right . a microarray expression dataset to be analyzed needs to have been previously normalized ; the choice of the algorithm is not critical ( i.e. either mas5 or rma can be used for affymetrix platforms ; either calibrated or uncalibrated data can be used for rt - pcr profiles ) , the data does not need to be log transformed . the data must be in a tab - separated text format , with one gene or probeset per row , and one sample ( i.e. a patient profile ) per column ; the testing and training datasets must have the same number of rows and the same gene / probeset on corresponding rows . the first column of the file is reserved for a gene / probeset identifier while the first row of the file is used for sample identifiers . both set of identifiers must be unique character strings without spaces ; the leftmost field of the first row , corresponding to the probeset i d column , needs to be filled with a placeholder character string . assuming that the user is using both a training and a testing dataset , the typical analysis workflow is as follows : upload the two data files , specify the algorithm parameters , launch the analysis , examine the two resulting maps ( one for the training profiles , the other for the testing profiles ) . after inspecting the maps , the user can repeat the same process with different parameter values , for example with a different signature size . the input parameters to be specified on the start page are : column ranges corresponding to the two classes of profiles ( i.e. control , affected ) in the training datasetn1 = number of genes from top ranked genes to include in signaturen2 = number of genes from bottom ranked genes to include in signaturepval = p - value to be used for the initial feature selectionn = percentage of all of the signature - to - signature distances that will be used for drawing the map of subjects . column ranges corresponding to the two classes of profiles ( i.e. control , affected ) in the training dataset n1 = number of genes from top ranked genes to include in signature n2 = number of genes from bottom ranked genes to include in signature pval = p - value to be used for the initial feature selection n = percentage of all of the signature - to - signature distances that will be used for drawing the map of subjects . the user has the option to use the same file for the training and testing dataset , presumably selecting different ranges of columns as the training and the testing sets . the column ranges specified by the user for the testing set are also used to assign different colors to the two groups of samples . only the specified columns for both sets are used for the analysis . in the current version of scudo , the optimization of input parameters such as the signature length and the p - value of the feature selection step is left to the user and is performed by trial and error . in a typical session , the user needs to try and select the n1 and n2 values that provide the clearest separation between the affected and the control subjects in the output maps , starting with the suggested value of p - value ( 0.01 for mrna , 0.1 for mirna profiles ) . based on our experience with a large number of representative datasets , good starting values for n1 and n2are 250/250 for mrna , 25/25 for mirna and these values can be repeatedly doubled or halved until good separation is achieved ; if unsuccessful , a more stringent p - value can be tried . the p - value is not critical because it does not represent a threshold for inclusion of crucial features in a signature ; rather , the main purpose of the initial feature selection step is to prevent pollution of signature composition by non - informative features ( i.e. to remove the probesets / genes that are stuck high or low ) . the value of n is finally adjusted to improve clarity of the map by either reducing the clutter ( smaller n ) or increasing the number of connecting edges ( larger n ) as needed . the output of the tool is a map for each of the input dataset ( see figure 2 ) . the nodes in the map correspond to subjects and the length of a connecting edge encodes the level of similarity between the connected nodes ( short edge = high similarity ; no edge = negligible similarity ) . the map is in the form of a network drawn using cytoscape web , which allows manipulation and setting of display attributes . the desired outcome of the analysis is a map of the testing set in which the profiles are clearly divided in two groups composed of nodes of the same color ; such result would give high confidence in the fact that using the selected feature list the user will be able to satisfactorily classify a new set of profiles using signatures composed of the n1 + n2 most differentially expressed genes of each profile . snapshot of the scudo result page ; the map for the training data is on the left , the one for the testing data on the right . once the user is satisfied with the result , he / she can download the maps as graphical files , or as network files ( edge list ) ready to be imported in cytoscape ( 7 ) or similar tools . a cytoscape plugin such as clustermaker ( 8 ) can be useful in identifying clusters in those maps in which the boundaries between groups are not immediately apparent ( as in the right map of figure 2 ) ; see reference ( 6 ) for an example of use of such plugin . the user can also download a file containing the subject specific signatures ( one column per subject ) plus two consensus signaturesthe consensus signature for each group is computed as follows : the rank of each gene in a profile is computed separately for each subject by sorting expression values from the most expressed to the least expressed , then the columns of gene ranks corresponding only to the subjects included in the group are summed row - wise and the resulting rank sums are sorted to provide a new set ofconsensus ranks ; the signature for the group is then composed by the first n1 and the last n2 gene ids ordered according to the new consensus rank list . the consensus signature is reminiscent of a disease gene list although derived using our unconventional approach and can be used to study the underlying molecular mechanism of a disease ( for an instance of such an application see ( 9 ) ) . a sample set of expression profiles and corresponding suggested parameter values are available in the initial page . the two datasets comprise profiles of circulating mirna in patient with early breast cancer and matching controls published by two different research groups ( geo accession numbers gse22981 and gse41526 , including 40 and 70 profiles respectively ) . gse41256 was used as the training set and gse22981 as the testing set , because the larger size of the former improves the performance of the feature selection step . the two datasets were used as downloaded from geo ( gse series matrix format ) except for the required changes in the formatting ; also , in the first set we had to remove six rows corresponding to mirna species that were missing from the other set ( both set use the same platform , illumina human v2 microrna expression beadchip ) . the recommended signatures sizes are 20/20 for both sets ; the recommended p - value of 0.001 , empirically found to work best , is uncharacteristically small for scudo , probably reflecting the existence of high noise levels or confounding signals in the two datasets . in the two resulting maps ( figure 2 ) it can be observed that ( i ) in the training set map , scudo is able to group together control and affected patients with good accuracy and ( ii ) in the testing set , scudo is able to separate control and affected subjects reasonably well as long as the analysis is restricted to the subset of caucasian american individuals . these results are of particular interest in view of the fact that the authors of the first set were not able to identify a reproducible diagnostic signature ( 10 ) and that the authors of the second set reported differences in terms of differentially expressed circulating mirnas between caucasian american and african american subjects ( 11 ) . scudo implements a new expression profile classification based on the degree of similarity between profile - specific signatures . as a consequence of being rank - based , scudo is quite robust to differences in lab protocols , data processing and batch effects , because it relies only on the relative ordering of the gene expression values within each profile , and not on the values themselves ( for more details on this point see ( 6 ) ) . this robustness can be appreciated in the analysis of the provided sample data files , which are from the same affymetrix platform but have been produced by different research groups and have undergone different normalizations . additionally , we have shown that our method is robust to wide variations of its parameter values therefore the choice of the values is not overly critical . our rank - based signature method is quite general and we have tested it successfully with a large assortment of data types : mrna and mirna profiles for various diseases / treatments / experiments , obtained from biopsies , blood and urine , and even some non - biological multidimensional datasets ( i.e. engineering data ) . using publicly available data , we have obtained promising results on the stratification of patients with respect to treatment response ( 12 ) and early diagnosis of cancer based on blood mirna ( 13 ) ; we have preliminary results for sample classification in toxicity studies . the reasons for this generality are that being completely data driven , our method is agnostic about the details of the mechanisms producing the transcriptional response . by making available an online implementation of our new method we want to encourage experimentation with new data types and discovery of novel applications . scudo has been used as part of a class project by the students of a graduate course held at the university of trento during the spring 2014 semester , whose feedback we gratefully acknowledge . funding for open access charge : the microsoft research university of trento centre for computational and systems biology ( cosbi ) .\noutput:\n" }, { "from": "agent", "value": "scudo ( signature - based clustering for diagnostic purposes ) is an online tool for the analysis of gene expression profiles for diagnostic and classification purposes . the tool is based on a new method for the clustering of profiles based on a subject - specific , as opposed to disease - specific , signature . our approach relies on construction of a reference map of transcriptional signatures , from both healthy and affected subjects , derived from their respective mrna or mirna profiles . a diagnosis for a new individual can then be performed by determining the position of the individual 's transcriptional signature on the map . the diagnostic power of our method has been convincingly demonstrated in an open scientific competition ( sbv improver diagnostic signature challenge ) , scoring second place overall and first place in one of the sub - challenges ." } ]

[ { "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: most often it is seen in children of five to twelve years of age because of its unique ossification and vascularity . immuno compromised states like hiv , tuberculosis , intravenous drug abuse and trauma have been predisposing factors for adult patellar osteomyelitis . we report two cases of patellar osteomyelitis in adult diabetic women with uncontrolled glycemic levels and having no previous history of any trauma or systemic infection . a 43 - year - old diabetic woman presented with complaints of left knee pain and swelling with no history of trauma . on examination , pointed tenderness was present over anterior aspect of patella with patellar grind test positive . culture and sensitivity revealed no growth and the patient was prescribed antibiotics for 6 weeks . knee arthrotomy and curettage of patellar sinus tracts was done with evacuation of intramuscular abscess . patella osteomyelitis in adults is very rare . in patients with uncontrolled diabetes , vague anterior knee pain , elevated esr and crp , one should keep patellar subacute osteomyelitis as a differential diagnosis which can be further confirmed by x - ray , mri or bone scan . an appropriate early treatment with antibiotics and surgical interventionit appears as a cartilaginous structure at birth and starts to ossify at the age of five years . patella osteomyelitis is a rare condition , with highest incidence found in children between ages of five to twelve years . in 1829 , thirion from belgium was first to report a case of patella osteomyelitis . primary hematogenous osteomyelitis of patella in adults is a rare entity often seen in immunocompromised patients with predisposing factors like hiv , intravenous drug abuse , disseminated tuberculosis and trauma . with recent surge in incidence of diabetes mellitus which also produces an immunocompromised state , may predispose to a similar condition . here , we report two cases of patellar osteomyelitis in adult diabetic women . a 43 - year - old lady presented to us with complaints of severe left anterior knee pain and swelling with no history of any trauma . patient has been taking treatment with her family physician for past six weeks with no relief of symptoms but aggravation of symptoms for past few days . onno history of any other joint involvement , activities of daily living were affected and because of the knee pain , unable to squat and walk pain free . local examination revealed local rise of temperature , minimal effusion , no discoloration of skin or any signs of trauma , point tenderness over the anterior aspect of patella , patella grind test positive and knee range of movements painful and restricted , no instability present . investigations revealed uncontrolled sugars ( fasting & postprandial and glycosylatedhemoglobin ) , elevated esr 82 mm at 1sthour and crp2 .9 mg / l . x - ray showed solitary localized , well circumscribed patellar cyst ( fig . 1 , 2 ) and mri ( fig . patient was subjected to knee arthroscopy where chondral blister was present on lateral facet of patella ( fig . culture reports had no growth but few pus cells were noted . intravenous clindamycin and amikacinpatient has excellent relief of symptoms and on further physiotherapy regained complete pain free range of movements in next four weeks . arthroscopic pictures of the case 1 . a 46 - year - old diabetic lady with knee pain on and off for past few months , presented with severe anterior knee pain , swelling over knee and distal thigh , inability to walk , squat and complete restriction of knee movements . patient was having high grade fever with chills and rigor . on examination , local warmth , tenderness over patella , patella grind test positive , rom was painful and restricted terminally ( 501000 ) and no instability was noted . blood test revealed uncontrolled sugars , elevated esr ( 82 mm at the end of 1 hour ) , crp ( 12.8 mg / dl ) . mri showed an abscess involving intermuscular plains of quadriceps encircling the distal femur and posterior compartmental muscles of leg with osteomyelitis of patella ( fig . patient was started on intravenous antibiotics , but had no relief of pain , so subjected to surgical intervention , knee arthrotomy with incision and drainage of abscess in quadriceps muscle was done . tissue sent for histopathological examination revealed necrotic and granulation tissue consistent with osteomyelitis , tuberculosis was ruled out but no specific organism was identified . patient had significant relief of symptoms with intravenous antibiotics for two weeks and oral antibiotics for four weeks . a 43 - year - old lady presented to us with complaints of severe left anterior knee pain and swelling with no history of any trauma . patient has been taking treatment with her family physician for past six weeks with no relief of symptoms but aggravation of symptoms for past few days . onno history of any other joint involvement , activities of daily living were affected and because of the knee pain , unable to squat and walk pain free . local examination revealed local rise of temperature , minimal effusion , no discoloration of skin or any signs of trauma , point tenderness over the anterior aspect of patella , patella grind test positive and knee range of movements painful and restricted , no instability present . investigations revealed uncontrolled sugars ( fasting & postprandial and glycosylatedhemoglobin ) , elevated esr 82 mm at 1sthour and crp2 .9 mg / l . x - ray showed solitary localized , well circumscribed patellar cyst ( fig . 1 , 2 ) and mri ( fig . patient was subjected to knee arthroscopy where chondral blister was present on lateral facet of patella ( fig . culture reports had no growth but few pus cells were noted . intravenous clindamycin and amikacinpatient has excellent relief of symptoms and on further physiotherapy regained complete pain free range of movements in next four weeks . a 46 - year - old diabetic lady with knee pain on and off for past few months , presented with severe anterior knee pain , swelling over knee and distal thigh , inability to walk , squat and complete restriction of knee movements . patient was having high grade fever with chills and rigor . on examination , local warmth , tenderness over patella , patella grind test positive , rom was painful and restricted terminally ( 501000 ) and no instability was noted . blood test revealed uncontrolled sugars , elevated esr ( 82 mm at the end of 1 hour ) , crp ( 12.8 mg / dl ) . mri showed an abscess involving intermuscular plains of quadriceps encircling the distal femur and posterior compartmental muscles of leg with osteomyelitis of patella ( fig . patient was started on intravenous antibiotics , but had no relief of pain , so subjected to surgical intervention , knee arthrotomy with incision and drainage of abscess in quadriceps muscle was done . tissue sent for histopathological examination revealed necrotic and granulation tissue consistent with osteomyelitis , tuberculosis was ruled out but no specific organism was identified . patient had significant relief of symptoms with intravenous antibiotics for two weeks and oral antibiotics for four weeks . the literature search revealed patellar osteomyelitis is a rare condition and is predominantly seen in the age group of 5 to 12 year . patella is a cartilaginous structure with limited blood supply till the age of 5 year . ossification begins from the age of 5 year with rich vascularisation till the age of 12 and is completed by the age of 15 , beyond which the vascularity again diminishes and hence explains higher incidence of osteomyelitis between 5 to 12 year of age and decreased incidence in adults . the cartilage layer which is resistant to infection is thick in children and hence infection remains confined to patella without extending into the knee joint . whereas in adults cartilage gets thinned out and may lead to septic arthritis of knee . also lack of periosteum over patella explains absence of periosteal reaction which is typical of osteomyelitis at any other site . rocher s ( 1923 ) series most of the patients were between five and fifteen years , only one of his patients was infant and none adult . moore ( 1938 ) suggested that the rarity of the disease under the age of five was explained by the fact that before that age the patella is cartilaginous . ropke ( 1904 ) showed by injection experiments that until the age of about four years the patella is largely a cartilaginous mass , the very little blood supply . vascularisation then proceeds with ossification , small vessel passing into the patella from a plexus on its anterior surface . history of trauma can predispose to it , can also be as a sequalae to infected prepatellar bursitis . staphylococcusaureus is found to be most common organism in hematogenous osteomyelitis followed by tubercular etiology . immunocompromised states like hiv , intravenous drug abuse , patient on chemotherapy for malignancies are more prone for patellar infections [ 6 - 8 ] . pseudomonas osteomyelitis was reported in intravenous drug abuse by munddj et al in 1981 . in our casesstudy even though no organisms were identified , tuberculosiswas ruled out and so non - specific organism should have been an etiology and in our patients gradual onset and progressive symptoms were again suggestive of subacute nature of the infection which is more common in diabetic patient . but till now no cases of patellar osteomyelitis in diabetes have been reported in literature . the author believes that immune compromised states which exist in patient with uncontrolled diabetes mellitus are also prone to develop such infections . few studies have been conducted on immunological function in relation to increased susceptibility to infections in diabetes mellitus . bybee and rogers additionally had shown that phagocyte functional defect was not confined to ketoacidosisbut also occurred in poorly controlled diabetics . another interesting observation , which suggests the possibility of genetic determination of the phagocyte defect , by molenaar . serum factors played an important role in the phagocyte function of the diabetics ; certain serum factors may competitively bind neutrophil receptors thereby preventing complement mediated phagocytosis . chemotaxis of neurophils was found to be less in diabetics in a well controlled study of mowat and baum . assessment of lymphocyte transformation in response to phytohaemagglutinin showed a decrease in diabetics with poor control . supportive blood investigations , x - rays , mri and bone scan confirm the diagnosis . when diagnosed early an arthroscopic evaluation can be diagnostic and therapeutic but incases where there is a well set infection with abscess extending into quadriceps muscle an open procedure in indicated . needle aspiration and lavage technique has been reported in a paper with satisfactory outcome most of the time cultures remain sterile , particularly in diabetic patients . adults with risk factors like intravenous drug abuse , hiv infection , and trauma have been common cause mentioned in the literature . recent surge of diabetes mellitus which also produce an immuno compromised state and more prone for such infections which may have an atypical presentation , so one should have an high index of suspicion to reach the diagnosis and intervene early to have a satisfactory outcome . atypical anterior knee pain with poor glycemic control in a diabetic patient , a high index of suspicion toward subacute patellar osteomyelitis will enable early diagnosis and treatment and avoid complications .\noutput:\n" }, { "from": "agent", "value": "introduction : patella osteomyelitis is a rare entity in adults . most often it is seen in children of five to twelve years of age because of its unique ossification and vascularity . immuno compromised states like hiv , tuberculosis , intravenous drug abuse and trauma have been predisposing factors for adult patellar osteomyelitis . we report two cases of patellar osteomyelitis in adult diabetic women with uncontrolled glycemic levels and having no previous history of any trauma or systemic infection.case report : a 43 - year - old diabetic woman presented with complaints of left knee pain and swelling with no history of trauma . on examination , pointed tenderness was present over anterior aspect of patella with patellar grind test positive . radiography and mri revealed solitary well circumscribed patellar cyst . lateral chondral blisters were noted while doing arthroscopy and secretions oozed out on puncturing . curettage was carried out for the same . culture and sensitivity revealed no growth and the patient was prescribed antibiotics for 6 weeks . second case was a 46 - year - old diabetic lady with similar presentation . mri additionally showed abscess in intermuscular plains around knee joint . an aspirated fluid was negative for growth of organisms . knee arthrotomy and curettage of patellar sinus tracts was done with evacuation of intramuscular abscess . antibiotics were given for 6 weeks . both patients had complete relief of symptoms.conclusion : patella osteomyelitis in adults is very rare . in patients with uncontrolled diabetes , vague anterior knee pain , elevated esr and crp , one should keep patellar subacute osteomyelitis as a differential diagnosis which can be further confirmed by x - ray , mri or bone scan . an appropriate early treatment with antibiotics and surgical intervention can give a satisfactory result ." } ]

[ { "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 52 - year - old man came to medical attention in 1993 with fever , confusion , lethargy , and leg weakness . the patient was obtunded , with a stiff neck , leg spasticity , hyperreflexia , babinski signs , and a skin lesion . a punch biopsy of the lesion showed multinucleated giant cells and spherules with endospores consistent with c. immitis . cranial computed tomography showed obstructive hydrocephalus , and a ventriculo - peritoneal shunt was placed . ventricular cerebrospinal fluid ( csf ) had four leukocytes ( wbc ) / mm , 40 mg / dl glucose , and 70 mg / dl protein . both serum ( 1:128 ) and csf ( 1:32 ) had positive microcomplement fixation antibody titers to c. immitis . coccidioidal meningitis was diagnosed , and the patient received amphotericin b intravenously and intrathecally for 6 weeks , until elevated serum creatinine levels prevented further administration of the drug . over the first 8 months , the patient slowly improved ; his mental status returned to near normal , and he could walk and care for himself . four years later , the patient had recurring headaches , fevers , and declining mental status . ventricular csf obtained from the shunt tubing contained 42 wbc / mm ( 68 % lymphocytes , 14 % mononuclear cells , 17 % atypical lymphocytes , 15 % neutrophils , and 3 % eosinophils ) , 51 mg / dl glucose , and 11 mg / dl protein and grew c. immitis . lumbar csf and csf obtained directly from the ventricle at the time of shunt replacement did not grow fungi . the patient was treated with fluconazole ( 1,200 mg per day ) for several weeks , clinically improved over several months , and was discharged on fluconazole ( 800 mg per day ) . c. immitis was isolated on sabouraud dextrose agar at 30c from the tip of the ventriculo - peritoneal shunt tubing . the initial growth of colonies was moist and gray and had a white , cottony , aerial appearance . the shunt tubing was then fixed in formalin , and a small scraping was taken from the tip of the tubing , stained with calcofluor , and examined under a dissecting microscope . coarse , septate , branched hyphae , which had thick - walled , barrel - shaped arthroconia along with empty - appearing cells , were seen , consistent with the hyphae of c. immitis ( 6 ) ( figure 1 ) . the c. immitis isolate had a fluconazole mic of 8 g / ml obtained by the macrobroth dilution technique . at the fungal reference laboratory , c. immitis strains with a mic # 8 g / ml are considered fluconazole sensitive . material from the tip of the shunt tubing was stained with molecular probes sytox green nucleic acid stain ( part # : s - 7020 , molecular probes , eugene , or ) , which is an impermeable , high - affinity , dead - cell stain . after brief incubation with sytox green stain , the nucleic acids of dead cells fluoresce bright green when excited with the 488 - nm spectral line of the argon - ion laser . the stain was prepared at 0.1 % ( v / v ) in autoclaved double - filtered nanopure water . the material was directly stained with 0.4 ml of sytox green and allowed to react for 5 minutes . next , the sample was mildly washed with autoclaved nanopure water to remove excess stain and minimize background fluorescence . the sample was then sectioned at each centimeter from the distal portion to the proximal portion . coccidioides immitis hyphae dislodged from the tip of the ventriculo - peritoneal catheter tip , fixed in formalin and stained with calcofluor . stained barrel - shaped arthroconidia ( arrows ) are seen , along with empty cells ( x400 ) . the upper left image shows a section from the tip of the shunt tubing stained with sytox green nucleic acid stain and examined by scanning confocal microscopy with argon - ion laser light source . this specific staining for nucleic acids clearly shows the presence of a biofilm and some 4 - to 6 - m cells . the upper right image shows an unstained , transmitted light microscopic image of the same area of the edge of the tubing . the bottom right image shows a recombined image with the nucleic acid stain colocalized with the transmitted light image . the recombined image shows that a substantial ( ~ 30 m ) biofilm composed of 4 - to 6 - m cells has colonized the scalloped ( x630 total magnification mosaic ) scanning confocal microscopy was performed with a leica tcs - nt confocal microscope ( heidelberg , germany ) a 63x 1.2 n.a water immersion plan apo lens objective was used for confocal laser microscope imaging . the confocal microscope was optimally configured for sytox green analysis by using the 488 - nm excitation laser with a 488 - nm dichroic mirror and relative short pass filter of 580 nm in the first beam - splitter position . a band filter allowing wavelengths of 525 nm to 550 nm to pass to the first photo multiplier tube was used for imaging of the sytox green stain . clsm analysis showed a layer of stained coccoid cells , 20 to 39 in depth , on the tip of the ventriculo - peritoneal shunt tubing ( figure 2 ) . the depth of the colonization was indicative of a biofilm and is consistent with previous studies showing biofilm growth on explanted medical devices ( 3 ) . the observed cocci were consistent with c. immitis spherule morphology and clearly formed a biofilm on the surface of the tubing . a. scanning electron microscopy shows the presence of leukocytes and red blood cells on the tip of the ventriculo - peritoneal mass , within which coccoid cells can be visualized . the enclosing matrix material has condensed by dehydration , but the outline of the 4 - to 6 - m coccoid cells ( arrow ) , similar to those of c. immitis , can be resolved within the mass ( x4 ,000 ) . b. scanning electron microscopy of the surface of the ventriculo - peritoneal shunt , showing complete colonization of the surface by a matrix - enclosed biofilm formed by the cells of c. immitis . within the dehydration - condensed matrix of this biofilm , a hyphal element ( arrow ) and coccoid cells ( 4 - 6 m ) of the pathogen can be discerned ( x5 ,000 ) . electron microscopy was performed on a jeol 6100 scanning electron microscope ( sundbyberg , sweden ) . analysis by electron microscopy revealed colonization of the tip of the ventriculo - peritoneal shunt tubing by unidentified cocci encapsulated in an exopolysaccharide matrix ( figure 3a ) . the amorphous mass was formed as the exopolysaccharide matrix material was condensed by dehydration , but the 4 - to 6 - m spherical profiles of the c. immitis cells are clearly visible . figure 3b shows a confluent biofilm formed on the tubing by c. immitis - containing hyphal elements as well as coccoid cells of c. immitis in the dehydration - condensed biofilm . the c. immitis biofilm was similar in structure to candida sp . biofilms that also demonstrated hyphae and yeast organisms enveloped by an extracellular matrix ( 7 ) . a. scanning electron microscopy shows the presence of leukocytes and red blood cells on the tip of the ventriculo - peritoneal mass , within which coccoid cells can be visualized . the enclosing matrix material has condensed by dehydration , but the outline of the 4 - to 6 - m coccoid cells ( arrow ) , similar to those of c. immitis , can be resolved within the mass ( x4 ,000 ) . b. scanning electron microscopy of the surface of the ventriculo - peritoneal shunt , showing complete colonization of the surface by a matrix - enclosed biofilm formed by the cells of c. immitis . within the dehydration - condensed matrix of this biofilm , a hyphal element ( arrow ) and coccoid cells ( 4 - 6 m ) of the pathogen can be discerned ( x5 ,000 ) . first , the c. immitis in the ventricular shunt tubing was present in the hyphal phase . c. immitis is a dimorphic fungus that in nature is usually found in the mycelial phase ( 6 ) . when the fungus infects humans , it is normally present in tissues in the yeast phase ( 6,8 ) . with rare exceptions ( 911 ) , autopsy studies have demonstrated c. immitis to be in the yeast phase in the csf and meninges of patients with coccidioidal meningitis ( 8 ) . the biofilm infection on the shunt tubing may have been responsible for reversal of the normal human yeast phase . second , in spite of the 4 - year duration of the infection , c. immitis organisms recovered from the patient demonstrated an antimicrobial sensitivity to fluconazole . however , this possibility was precluded since the mycology reference laboratory routinely used the mycelial form of fungi in their antimicrobial testing . third , fungal persistence continued in spite of the patient s taking fluconazole in a dosage that usually , but not always , produces clinical improvement ( 12 ) . since our patient did not have a fungal peritonitis or evidence of systemic coccidioidal infection from csf containing c. immitis that would have normally exited the shunt tubing into the peritoneal cavity , we thought that noncompliance in taking the fluconazole could not account for the treatment failure . instead , we concluded that the fungal biofilm was the most likely explanation for the fluconazole failure . antimicrobial - drug resistance is known to develop when fungi or bacteria form a biofilm ( 2,13,14 ) . in vitro studies with strains of pathogenic candida spp . that were sensitive to fluconazole and amphotericin b in the planktonic state developed marked resistant to these antifungal drugs when the fungi were within a biofilm ( 13,15 ) . cryptococcus neoformans have been shown to produce biofilms on catheters ( 4,5 ) ; our case demonstrates that c. immitis can also produce a biofilm on indwelling catheters . fungal biofilms should be considered as a potential cause for treatment failure of systemic fungal infections , especially if catheters or other artificial prostheses are indwelling in the patient .\noutput:\n" }, { "from": "agent", "value": "we describe a case of recurrent coccidioidal meningitis in which a fungal biofilm on the tip of ventriculo - peritoneal shunt tubing was likely responsible for a 4 - year persistence of coccidioides immitis , despite the patient s taking an adequate dosage of fluconazole . fungal biofilms should be considered as a cause for treatment failure and fungal persistence , especially when artificial prostheses or indwelling catheters are present ." } ]

[ { "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 has been proposed that in the yeast saccharomyces cerevisiae , interactions between homologous dna sequences with dna double - strand breaks ( dsb ) and the consequent recombination are involved in homology searching for pairing . however , this issue remains debatable as it has been reported that pairing can be achieved through dsb - dependent or - independent pathways in other organisms . we recently demonstrated that the sme2 locus , which is located on chromosome ii , shows robust pairing in the early stage of the horsetail movement and that the robust pairing occurs independently of dsb formation and , hence , independently of recombination . the sme2 gene encodes a meiosis - specific polyadenylated non - coding rna , named meirna , that is essential for entry into meiosis in s. pombe . we reported that the sme2 rna mediates robust pairing of homologous chromosomes in meiosis : deletion of the sme2 sequence eliminates this robust pairing and transposition to other chromosomal sites confers the robust pairing at those sites ( fig . 2 ) . remarkably , the sme2 rna transcripts accumulate at their respective gene loci and their retention at the homozygous sme2 loci is essential for robust pairing at the sme2 locus . thus , the chromosomally - retained sme2 rna seems to act as an identifier of homologous chromosomes . ( a ) pairing frequency at the sme2 locus during progression through the horsetail stage decreases with deletion of the sme2 sequence ( sme2 ) compared with the wild - type ( wt ) . ( b ) pairing frequency at the ade8 locus increases with insertion of the sme2 sequence ( + sme2 ) compared with the wild - type ( wt ) . meirna was initially identified as a 0.5 kb sme2 transcript that complements the defect of meiosis progression in the sme2 mutant . on the other hand , we identified a longer transcript ( 1.5 kb ) , extended at the 3 end , as a major transcript during meiosis . this discrepancy was explained by the finding that meirna is a major target of mmi1 , which selectively eliminates meiosis - specific transcripts in vegetative cells . in an mmi1 temperature - sensitive mutant background , both the 1.5 kb and the 0.5 kb transcriptthus , the short ( 0.5 kb ) and the long ( 1.5 kb ) transcripts were named meirna - s and meirna - l , respectively . the mei2 protein , a key regulator of meiosis in s. pombe , binds to the sme2 transcript to form a distinct dot at the sme2 locus in the horsetail nucleus . the 5 - region of the sme2 transcript , corresponding to meirna - s , is necessary for mei2 binding , but unnecessary for robust pairing . in contrast , meirna - l is essential for robust pairing of the sme2 loci . deletion of polyadenylation sites at the 3 - end of meirna - l results in the loss of meirna retention at the sme2 locus and of robust pairing . the 3 - extended region specific to meirna - l ( that is meirna - l with the meirna - s sequence deleted ) is sufficient for its chromosomal retention and for robust pairing . thus , we expect that chromosomal retention of meirna - l through its 3 - region has a role in robust pairing , as described below . figure 3 . distinct functional domains of the sme2 transcript . the sme2 rna transcript can be divided into two distinct domains : the 5 - portion of meirna - l , corresponding to meirna - s , and the 3 - extended region specific to meirna - l . mei2 protein binds to the 5 - portion of meirna - l ( meirna - s ) . mmi1protein binds to dsr motifs , which are concentrated in the 3 - extended region of meirna - l . we speculate that as yet unknown proteins may bind to meirna - l and play a role in pairing . chromosomally - accumulated meirna - l at the sme2 locus may play a role in recruiting specific rna - binding proteins essential for pairing or recognition . on the other hand , even when the sme2 locus was removed from chromosome ii , no obvious defects in chromosome segregation or spore formation were detected . these observations raise the possibility that other as yet undiscovered pairing sites may also exist on chromosome ii . an array of recognition complexes at multiple sites on each chromosome might act as chromosome - specific identifiers . such recognition complexes could be arrays of rna - protein complexes , transcription factories or specialized chromatin structures . although mei2 forms a dot at the sme2 locus in the horsetail stage , it has been demonstrated that mei2 is unnecessary for robust pairing ( fig . mmi1 also binds to meirna - l and forms a dot at the sme2 locus . however , in a hypomorphic mmi1 - 48 mutant , the robust pairing was enhanced , suggesting that mmi1 negatively regulates robust pairing by degrading meirna - l . protein components that interact with the 3 - extended region specific to meirna - l may be involved in the robust pairing ( fig . alternatively , specific components may not be involved at all . instead , rna bodies formed at defined loci along the chromosome may act as a barcode for agglutination of homologous chromosomes . recent reports demonstrate that rna transcripts function as a scaffold in the assembly of many nuclear bodies at their respective gene loci . the most striking example of rna bodies is in the nucleolus formed around the rrna genes . s. pombe rrna gene clusters locate on both ends of chromosome iii , and occupy a defined position within the nucleolus . these findings provide an insight into the role of rna nuclear bodies in the functional organization of chromosomes within the nucleus . a previous model also proposed a role for transcription in homologous chromosome recognition and pairing : this model depicts a chromosome as a linear array of transcription factories , providing a possible mechanism for how transcription results in recognition and pairing of homologous chromosomes when chromosomes are pre - aligned in a chromosome bouquet . a similar model , in which meiosis - specific polyadenylated rna transcripts initiate the pairing process , has been previously proposed in the lily . other studies have reported a similar link between pairing and transcription : in drosophila embryos , somatic pairing is initiated at the histone gene cluster at the time when zygotic expression begins ; in drosophila male meiosis , the pairing sites correspond to the highly transcribed rdna loci and histone genes . another more direct link has been reported : in mammals non - coding rna accumulated at their respective gene loci has been shown to mediate transient x - chromosome pairing and to mark the onset of x inactivation . these findings imply that rna transcripts retained at gene loci may act as chromosome identifiers for their homologous partner . recognition can be achieved by an active mechanism based on dna - rna , rna - rna or protein - protein interactions , or by a passive mechanism based on agglutination of transcription factories , as discussed in recent literatures . these questions can be answered once critical factors for recognition are identified in the sme2 rna body or similar pairing mechanisms are identified in other chromosomal loci of s. pombe or in other organisms .\noutput:\n" }, { "from": "agent", "value": "pairing and recombination of homologous chromosomes are essential for ensuring correct segregation of chromosomes in meiosis . in s. pombe , chromosomes are first bundled at the telomeres ( forming a telomere bouquet ) and then aligned by oscillatory movement of the elongated horsetail nucleus ( fig . 1 ) .1,2 telomere clustering and subsequent chromosome alignment promote pairing of homologous chromosomes .3 - 5 however , this telomere - bundled alignment of chromosomes can not be responsible for the specificity of chromosome pairing . thus , there must be some mechanism to facilitate recognition of homologous partners after telomere clustering . recent studies in s. pombe have shown that rna transcripts retained on the chromosome , or rna bodies , may play a role in recognition of homologous chromosomes for pairing ( fig . 1 ) .6 acting as fiducial markers of homologous loci they would abrogate the need for direct dna sequence homology searching ." } ]

[ { "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: patients undergoing cardiopulmonary bypass ( cpb ) surgery frequently develop systematic inflammatory response syndrome , ranging from mild to severe complications such as pericardial , pleural and / or abdominal effusion , liver enlargement and edema . these complications are characterized by increased capillary permeability , a shift of fluid and protein from the intravascular to the interstitial space and may further progress into hypovolemia , massive generalized edema , acute respiratory distress syndrome , or even capillary leak syndrome ( cls ) or multiple organ dysfunction ( mod ) or failure , with a substantial morbidity and mortality . although the incidence of postoperative effusion in children is substantial ( 25 % ) nearly 97,000 ( germany 1998 ) and 800,000 ( usa 1996 , american heart association , ) patients undergo cpb surgery annually ( ~ 10 % for congenital heart disease ) , hence postoperative complications constitute a significant clinical problem . the extensive contact between heparin anticoagulated blood and foreign surfaces of the extracorporal circuit during cpb , in combination with anesthetics and other medication used during and after surgery stimulates the immune system . tumor necrosis factor - ( tnf - ) , interleukin ( il ) - 6 and il - 8 ( proinflammatory cytokines ) may contribute to myocardial dysfunction and increased apoptosis and increased neutrophil activation , and il - 10 may contribute to immune depression and increased susceptibility to infection . there is some evidence that patients who later develop postoperative complications may be identified in the early perioperative or even in the preoperative period . several scoring systems use clinical and / or laboratory data acquired during or after therapy to predict cardiac patients outcome with informative serum parameters like soluble endothelial ( se ) - selectin for restenosis or perioperative c - reactive protein ( crp ) , lactate , il - 6 or altered blood coagulation after open heart surgery . the prediction of patients at risk for postoperative complications is important for the individual preoperative prophylactic treatment . preoperative prediction is based on the hypothesis that the primed immune system amplifies the immune response to cardiosurgical trauma ; for example , tnf - or fibronectin primed neutrophils respond more strongly to stimulation in vitro . priming in the patients may be caused by an allergic / atopic predisposition but can also be a result of fresh or reactivated viral infection . a recent study in this journal indicates gender as a predisposing factor for mod in children . in a recent study we showed that children who suffered from postoperative effusions and edema ( poee ) are , 24 hours before surgery , already exhibiting altered antigen expression on leukocytes , by which risk assessment would be possible using discriminant analysis . based on these results we hypothesized that children at risk of poee have an altered preoperative level of markers of immunoactivation , allergic / atopic predisposition or t - helper type 2 ( th2 ) phenotype , which may be used as predictors for risk assessment . in addition , we also included readily available standard laboratory parameters in order to test predictive strength . the advantage of a serological classifier over that based on antigen expression data by flow cytometry is that these data and methods are accessible for virtually all clinical facilities and are easily standardized . in the present studywe show that children at risk of poee are already predisposed to the condition and can be predicted from these data . this prospective non - randomized study was conducted between november 1995 and may 2001 following approval by the ethical committee of the medical faculty at the university of leipzig , germany . a total of 75 patients who underwent cardiac surgery with cpb were analyzed [ inclusion criteria : aged 318 years , body weight 12 kg ; exclusion criteria : missing informed consent of parents , palliative cardiac surgery ( e.g. if single ventricle circulation was the aim of surgery , ( glenn , fontan or total cavopulmonary connection [ tcpc ] ) . the surgical procedures included were : closure of atrial septal defect ( n = 39 ) or ventricular septal defect ( n = 11 ) ; replacement of pulmonary valve by an allogeneic heart valve ( n = 18 ) ; resection of an aortic subvalvular stenosis resulting from a subaortic membrane or fibrous cap ( n = 6 ) ; correction of tetralogy of fallot ( n = 1 ) . all children received similar anesthesia , medication and intraoperative and postoperative care and cpb as detailed elsewhere . after delivery to the intensive care unit postoperatively , the incidence of pericardial - , pleural - and / or abdominal - effusion was monitored by echocardiography , chest x - ray or sonogra - phy . if patients developed detectable effusions after removal of the thoracic drainage ( which was usually one day after surgery ) until discharge they were allocated into the poee group ( n = 29 ) , or into the non - poee group ( no effusion , n = 46 ) . as evaluated visually , all poee patients had edema of the face and / or hands and / or feet . incidence of edema was not used for poee discrimination because quantitative measures of extravascular body fluid volume ( such as scintigraphy following labelling of the extravascular fluid by radiolabelled sulphide or bromide ) were ethically not feasible in children . massive generalized edema , cls or mod as defined by seghaye et al . was not observed in any of the patients . however , 65 % of the poee patients fulfilled at least one mod criterion as defined by trotter et al . . postpericar - diotomy syndrome with effusions and fever of non - infectious origin within a week , or later , of surgery was not present in any of the patients . blood was obtained one day ( median : 20 hours ) before surgery in untreated tubes as well as in ethylenediamine - tetracetic acid ( edta ) and heparin tubes , centrifuged at 2800 g for 10 min at 4c and the supernatant was collected . urine was sampled in untreated tubes . within 1 hour after collection , serum , edta - plasma and urine samples were stored in aliquots at -80 c . the concentration of the complement components ( c3 , c4 , c5 , c1 - inhibitor , c3d ) and immunoglobulin ( ig ) g2 was determined by radial immune diffusion ( the binding site , heidelberg , germany ) with serum or edta - plasma ( c3d ) and total hemolytic complement ch100 by lysis of antibody - coated sheep erythrocytes ( the binding site ) . all other parameters were quantified using enzyme - linked immunosorbent assay [ ige , interleukin ( il ) - 1 , tnf - , interferon - , rantes , histamine : beckman - coulter , krefeld , germany ; il - 4 , il - 10 , il - 13 , soluble intracellular adhesion molecule - 1 ( sicam - 1 ) , platelet endothelial cell adhesion molecule - 1 ( pecam ) : bender medsystems , vienna , austria ; il - 5 , il - 6 high sensitivity , il - 10 high sensitivity , il - 12 p40 / p70 , soluble leukocytic ( sl ) - selectin , se - selectin : r & d systems gmbh , wiesbaden , germany ; il - 2 , il -2-receptor , serum and urine neopterin : dpc biermann gmbh , bad nauheim , germany ; il - 4 high sensitivity , il - 11 : natutec , frankfurt , germany ; il - 12 p70 , il - 13 : biozol diagnostica ver - trieb gmbh , eching , germany ; c5a : behringwerke ag , marburg , germany ] . the complement fragment ratios c3d / c3 , c5a / c5 and immunoglobulin ratio ige / igg2 , were calculated as measures for complement activation and th2 / th1 imbalance , respectively . additionally , routine laboratory and clinical chemistry parameters were determined ( cell count , differential blood count , crp , creatinine , electrolytes , protein , hematocrit , blood coagulation parameters ) . in total 56 parameters were analyzed per patient including age , gender and body weight . data are displayed as mean standard deviation ( sd ) . between - group comparisonwas undertaken by unpaired student 's t - test or mann - whitney u - test as appropriate [ statistical program for social sciences version 8.0 ( spss ) , knowledge dynamics , canyon lake , tx ] . discrimination of patients into the poee and control group was tested by data pattern analysis using two different methods as detailed . this classifier was optimized by increasing the f - probability followed by determination of the unstandardized canonical discriminant function . , the triple matrix data pattern analyzer classif1 was used as an algorithmic data mining approach . with classif1 no replacement of missing data values and no mathematical assumptions on parameter distributions are required . this prospective non - randomized study was conducted between november 1995 and may 2001 following approval by the ethical committee of the medical faculty at the university of leipzig , germany . a total of 75 patients who underwent cardiac surgery with cpb were analyzed [ inclusion criteria : aged 318 years , body weight 12 kg ; exclusion criteria : missing informed consent of parents , palliative cardiac surgery ( e.g. if single ventricle circulation was the aim of surgery , ( glenn , fontan or total cavopulmonary connection [ tcpc ] ) . the surgical procedures included were : closure of atrial septal defect ( n = 39 ) or ventricular septal defect ( n = 11 ) ; replacement of pulmonary valve by an allogeneic heart valve ( n = 18 ) ; resection of an aortic subvalvular stenosis resulting from a subaortic membrane or fibrous cap ( n = 6 ) ; correction of tetralogy of fallot ( n = 1 ) . all children received similar anesthesia , medication and intraoperative and postoperative care and cpb as detailed elsewhere . after delivery to the intensive care unit postoperatively , the incidence of pericardial - , pleural - and / or abdominal - effusion was monitored by echocardiography , chest x - ray or sonogra - phy . if patients developed detectable effusions after removal of the thoracic drainage ( which was usually one day after surgery ) until discharge they were allocated into the poee group ( n = 29 ) , or into the non - poee group ( no effusion , n = 46 ) . as evaluated visually , all poee patients had edema of the face and / or hands and / or feet . incidence of edema was not used for poee discrimination because quantitative measures of extravascular body fluid volume ( such as scintigraphy following labelling of the extravascular fluid by radiolabelled sulphide or bromide ) were ethically not feasible in children . massive generalized edema , cls or mod as defined by seghaye et al . was not observed in any of the patients . however , 65 % of the poee patients fulfilled at least one mod criterion as defined by trotter et al . . postpericar - diotomy syndrome with effusions and fever of non - infectious origin within a week , or later , of surgery was not present in any of the patients . blood was obtained one day ( median : 20 hours ) before surgery in untreated tubes as well as in ethylenediamine - tetracetic acid ( edta ) and heparin tubes , centrifuged at 2800 g for 10 min at 4c and the supernatant was collected . urine was sampled in untreated tubes . within 1 hour after collection , serum , edta - plasma and urine samples were stored in aliquots at -80 c . the concentration of the complement components ( c3 , c4 , c5 , c1 - inhibitor , c3d ) and immunoglobulin ( ig ) g2 was determined by radial immune diffusion ( the binding site , heidelberg , germany ) with serum or edta - plasma ( c3d ) and total hemolytic complement ch100 by lysis of antibody - coated sheep erythrocytes ( the binding site ) . all other parameters were quantified using enzyme - linked immunosorbent assay [ ige , interleukin ( il ) - 1 , tnf - , interferon - , rantes , histamine : beckman - coulter , krefeld , germany ; il - 4 , il - 10 , il - 13 , soluble intracellular adhesion molecule - 1 ( sicam - 1 ) , platelet endothelial cell adhesion molecule - 1 ( pecam ) : bender medsystems , vienna , austria ; il - 5 , il - 6 high sensitivity , il - 10 high sensitivity , il - 12 p40 / p70 , soluble leukocytic ( sl ) - selectin , se - selectin : r & d systems gmbh , wiesbaden , germany ; il - 2 , il -2-receptor , serum and urine neopterin : dpc biermann gmbh , bad nauheim , germany ; il - 4 high sensitivity , il - 11 : natutec , frankfurt , germany ; il - 12 p70 , il - 13 : biozol diagnostica ver - trieb gmbh , eching , germany ; c5a : behringwerke ag , marburg , germany ] . the complement fragment ratios c3d / c3 , c5a / c5 and immunoglobulin ratio ige / igg2 , were calculated as measures for complement activation and th2 / th1 imbalance , respectively . additionally , routine laboratory and clinical chemistry parameters were determined ( cell count , differential blood count , crp , creatinine , electrolytes , protein , hematocrit , blood coagulation parameters ) . in total 56 parameters were analyzed per patient including age , gender and body weight . data are displayed as mean standard deviation ( sd ) . between - group comparisonwas undertaken by unpaired student 's t - test or mann - whitney u - test as appropriate [ statistical program for social sciences version 8.0 ( spss ) , knowledge dynamics , canyon lake , tx ] . discrimination of patients into the poee and control group was tested by data pattern analysis using two different methods as detailed . this classifier was optimized by increasing the f - probability followed by determination of the unstandardized canonical discriminant function . the triple matrix data pattern analyzer classif1 was used as an algorithmic data mining approach . with classif1 no replacement of missing data values and no mathematical assumptions on parameter distributionsclinical data are comparable in the control group and among those patients at risk for poee . data on patients and surgical parameters were grouped according to the clinical outcome in non - poee and poee groups ( table 1 ) . patients with poee were of similar age and gender , while duration of surgery + anesthesia and extracorporal circulation were longer . other parameters , including priming and infusion volume , duration of hypothermia and hemofiltration volume ( i.e. volume of fluid that has been removed from the blood to accomplish normal hematocrit values at the end of surgery ) were not significantly different ( not shown ) . poee patients had a higher body weight ( table 2 ) and stayed in hospital one day longer after surgery . clinical and surgical data of poee and non - poee patients ( means sd ) chi - squared test , ns = not significant , two - tailed student 's t - test , mann - whitney u - test . cpb , cardiopulmonary bypass ; icu , intensive care unit ; poee , postoperative effusions and edema . patients at risk of poee exhibited signs of inflammation . children with poee had preoperatively significantly higher levels of several complement components , tnf - , neutrophilic granulocyte count and percentage ( table 2 ) . these data indicate increased immune activation / alteration of at risk patients . at risk patientsthe use of single parameters for individual risk assessment is insufficient , as most data for the poee patients ( 75 % ) showed significant overlap with non - poee patients . the highest discrimination by a single parameter was obtained withc3 ( specificity : 55 % ; sensitivity : 67 % ) . on multivariate analysis , however , the majority of patients from both groups were correctly classified irrespective of the classification program applied ( spss / classif1 ; specificity : 80.4 % / 97.8 % ; sensitivity : 86.2 % / 72.4 % ; and negative : 90.2 % / 84.9 % ; and positive : 73.5 % / 91.3 % predictive values ) ( table 3 ) . only nine of the 56 parameters were required for these classifications ( table 4 ) . five parameters were unique to each classifier , while increased c5 and sl - selectin serum concentration , increased neutrophil percentage or count and elevated hematocrit were selected by both classification methods as discriminant factors . misclassifications were not assigned to a certain type of cardiac defect ( chi - squared test ; see also table 3 , classification of subgroups ) , indicating that poee prediction is independent of the surgery performed . this interpretation is also supported by the result that atrial septal defect patients and the patients who underwent other types of surgeries were both classified with nearly identical sensitivity , specificity and negative and positive predictive values ( table 3 ) . first , that cardiac surgery patients with problematic postoperative disease already exhibit elevated serum concentration of complement components c3 and c5 , tnf - and neutrophils ( count and percentage ) one day preoperatively . second , that preopera - tive risk assessment based on serological and clinical chemistry data is possible , with high levels of accuracy . the preoperative predictive risk assessment represents a clear advantage over assays relying on data acquired during or after cardiac intervention . preoperative differences , as selected by our explorative data analysis , indicate a preopera - tive activation of the immune system , for example , by a subclinical inflammatory response , an atopic / allergic predisposition or a condition resulting from the congenital heart disease . in contrast to the recent report that mod in children is gender related , gender was not a predisposing factor in our study . twenty - four hour preoperative serum parameters in post operative non - poee and poee patients ( means sd ) . from the 56 determined parameters , those selected by one of the classification programs or exhibiting significant differencesare shown two - tailed student 's t - test , mann - whitney u - test . parameter used by s = spss classifier , c = classif1 classifier or s , c = both classifiers . il , interleukin ; poee , postoperative effusions and edema ; sl - selectin , soluble leukocytic - selectin ; tnf - , tumor necrosis factor - alpha . classification of poee and non - poee patients ( confusion matrices ) of 24 h preoperative serological parameters by the spss and the classif1 classifiers ( see table 4 ) classification result shown separately for asd patients or the residual patients applying the identical classification algorithms as for the total group of patients . simultaneous classification non - poee / poee for one patient increases line sum above 100 % . preoperative parameters and coefficients for prediction of postoperative cardiac surgery outcome by the spss and classif1 classifiers formula of the discriminant function : constant + , resulting value 0 , non - poee risk , if 0 , poee risk . parameter on average above ( + ) or below ( - ) the 2575 % percentile thresholds for c1 - inhibitor : 300/377 mg / l ( 25 % / 75 % ) ; c3 : 1181/1456 mg / l ; c5 : 100/131 mg / l ; sl - selection : 1102 / 1501g / l , neutrophil count : 3900 / 5520cells / l ; eosinophil count : 85 / 269cells / l ; hematocrit : 34.0 / 39.8 % ; partial thrombin time : 33.3 / 37.9 s ; k : non - poee patients have , on average , all parameters unchanged ( 0 ) between the 2575 % percentile thresholds . unknown patients are classified according to the highest number of positional coincidences , with the poee or the non - poee patients classification mask . the parameters selected by the two classifiers in this study indicate increased poee risk for patients with elevated inflammatory response by increased complement and neutrophil activation and coagulation ( see table 4 ) . in different cardiac situations , crp , se - selectin , sicam - 1 and neutrophil adhesion molecule expressionhave been discussed as risk factors . as already suggested by others , preoperatively altered blood coagulation values such as partial thrombin time were found to be prognostic for postoperative blood loss . fibrinogen and fibrin are ligands for mac - 1 , inducing neutrophil , monocyte or resting platelet activation . our study indicates this activation by elevated sl - selectin level as an important discriminant parameter . cpb is associated with major qualitative and quantitative alterations of humoral pathways and changes in leukocyte subsets , generating a systemic inflammatory response with interactions between vascular endothelium , platelets and leukocytes including signal exchanges , adhesion molecule expression and secretion of cytokines or chemokines in a multi - step process . patients with an altered immune profile before surgery might show a more pronounced or sustained immune response after surgery . in an unstimulated immune system , cpb exposure constitutes the initial stimulus that might prime the system for postoperative complications . in patients with a primed or predisposed immune profile , cpb as the second stimulus may facilitate an enhanced immune response , which , in turn , may lead to poee , cls or multiple organ failure . the main discriminators of at risk patients ( elevated levels of complement and activated complement components , tnf - and il - 10 ) indicate the significance of complement system and monocyte activation . il - 10 release is specific to cpb surgery and patients with poee or mod release higher quantities of il - 10 . increased il - 10 release as an indicator of mod or effusions is also supported by the finding that perioperative methyl - prednisolone administration , that enhances il - 10 release during cpb surgery in adults , aggravates postoperative effusions and bleeding in children with postcardiotomy syndrome . an observation that contrasts with the finding that children with mod had reduced il - 10 serum levels prior to cpb . patients from our study had no gender - related differences in any of the analyzed laboratory parameters . we have no explanation for this discrepancy , but differences in the age distribution and the congenital heart diseases of patients included in our study , as compared to trotter et al . severe allergic reactions with cardiac surgery and allergic predisposition in adults at risk for cardiovascular death have been reported . the interpretation of allergic / atopic predisposition in poee risk was indicated by our recent observation of elevated leukocyte function asscoiated molecule - 1 ( lfa - 1 ) expression on leukocytes of at risk patients , as lfa - 1 expression is increased on leukocytes of atopic children . we reported earlier that patients at risk for poee also had increased preoperative histamine and eosinophil counts , among others . the results from the present study do not clearly support the hypothesis of risk prevalence for atopic / allergic patients because only few of the selected markers could indicate an atopic / allergic predisposition ( e.g. tnf - and il - 10 ) . we conclude from these differences that both increased inflammatory status and allergic / atopic predisposition are predictors of increased poee in children . taken together , risk patients might have : ( i ) latent infection ; ( ii ) atopic / allergic predisposition ; or ( iii ) immune alterations as a result of the congenital heart disease . these hypotheses have to be further scrutinized by future studies . because children with postoperative complications usually have a longer stay on the icu , a longer period of mechanical ventilation and stay longer in hospital , preoperative risk assessment is of clear therapeutic advantage and can be cost - effective by reducing any stay in intensive care . by prospective classification , up to 86 % of the patients at risk were correctly identified preoperatively . in view of the fact that such predictions were not possible at all until now , these predictive values are promising . however , the classifier will be optimized by increasing the number of patients enrolled in studies and by combining this serological classifier with additional parameters such as flow - cytometric data . individual risk assessment before cardiac surgery of this type might open new ways to develop individual treatment strategies with two possible clinical consequences : first , postponement of surgery until the normalization of clinical parameters ( e.g. elimination of stress or a latent infection ) ; and , second , application of individual prophylaxis in the case of endogenous reasons for immune system alterations . the hypothesis that postponement or individual prophylaxis will reduce poee has to be scrutinized in additional studies . the proposed serological classifier should permit individual risk assessment in hospitals with lower patient numbers . it is planned to set up and optimize an on - line classifier for poee risk assessment on the internet . one of the practical consequences of this would be that diseases could be categorized at institutions where no sufficient database can be generated in a reasonable time period . risk assessments for patients at other institutions can be calculated for test purposes using the indicated spss classifier formula ( table 4 ) . the local data correction factor is obtained as a ratio between the parameter mean from non - poee patients from table 2 of this study and the mean of the respective parameter from the local non - poee group of 20 to 40 complication - free patients . the local data correction factor for the establishment of the individual patient 's triple matrix for the classif1 classificationthe parameters selected by the two classifiers in this study indicate increased poee risk for patients with elevated inflammatory response by increased complement and neutrophil activation and coagulation ( see table 4 ) . in different cardiac situations , crp , se - selectin , sicam - 1 and neutrophil adhesion molecule expressionpreoperatively altered blood coagulation values such as partial thrombin time were found to be prognostic for postoperative blood loss . fibrinogen and fibrin are ligands for mac - 1 , inducing neutrophil , monocyte or resting platelet activation . our study indicates this activation by elevated sl - selectin level as an important discriminant parameter . cpb is associated with major qualitative and quantitative alterations of humoral pathways and changes in leukocyte subsets , generating a systemic inflammatory response with interactions between vascular endothelium , platelets and leukocytes including signal exchanges , adhesion molecule expression and secretion of cytokines or chemokines in a multi - step process . patients with an altered immune profile before surgery might show a more pronounced or sustained immune response after surgery . in an unstimulated immune system , cpb exposure constitutes the initial stimulus that might prime the system for postoperative complications . in patients with a primed or predisposed immune profile , cpb as the second stimulus may facilitate an enhanced immune response , which , in turn , may lead to poee , cls or multiple organ failure . the main discriminators of at risk patients ( elevated levels of complement and activated complement components , tnf - and il - 10 ) indicate the significance of complement system and monocyte activation . il - 10 release is specific to cpb surgery and patients with poee or mod release higher quantities of il - 10 . increased il - 10 release as an indicator of mod or effusions is also supported by the finding that perioperative methyl - prednisolone administration , that enhances il - 10 release during cpb surgery in adults , aggravates postoperative effusions and bleeding in children with postcardiotomy syndrome . an observation that contrasts with the finding that children with mod had reduced il - 10 serum levels prior to cpb . patients from our study had no gender - related differences in any of the analyzed laboratory parameters . we have no explanation for this discrepancy , but differences in the age distribution and the congenital heart diseases of patients included in our study , as compared to trotter et al . severe allergic reactions with cardiac surgery and allergic predisposition in adults at risk for cardiovascular death have been reported . the interpretation of allergic / atopic predisposition in poee risk was indicated by our recent observation of elevated leukocyte function asscoiated molecule - 1 ( lfa - 1 ) expression on leukocytes of at risk patients , as lfa - 1 expression is increased on leukocytes of atopic children . we reported earlier that patients at risk for poee also had increased preoperative histamine and eosinophil counts , among others . the results from the present study do not clearly support the hypothesis of risk prevalence for atopic / allergic patients because only few of the selected markers could indicate an atopic / allergic predisposition ( e.g. tnf - and il - 10 ) . we conclude from these differences that both increased inflammatory status and allergic / atopic predisposition are predictors of increased poee in children . risk patients might have : ( i ) latent infection ; ( ii ) atopic / allergic predisposition ; or ( iii ) immune alterations as a result of the congenital heart disease . because children with postoperative complications usually have a longer stay on the icu , a longer period of mechanical ventilation and stay longer in hospital , preoperative risk assessment is of clear therapeutic advantage and can be cost - effective by reducing any stay in intensive care . by prospective classification , up to 86 % of the patients at risk were correctly identified preoperatively . in view of the fact that such predictions were not possible at all until nowhowever , the classifier will be optimized by increasing the number of patients enrolled in studies and by combining this serological classifier with additional parameters such as flow - cytometric data . individual risk assessment before cardiac surgery of this type might open new ways to develop individual treatment strategies with two possible clinical consequences : first , postponement of surgery until the normalization of clinical parameters ( e.g. elimination of stress or a latent infection ) ; and , second , application of individual prophylaxis in the case of endogenous reasons for immune system alterations . the hypothesis that postponement or individual prophylaxis will reduce poee has to be scrutinized in additional studies . the proposed serological classifier should permit individual risk assessment in hospitals with lower patient numbers . it is planned to set up and optimize an on - line classifier for poee risk assessment on the internet . one of the practical consequences of this would be that diseases could be categorized at institutions where no sufficient database can be generated in a reasonable time period . risk assessments for patients at other institutions can be calculated for test purposes using the indicated spss classifier formula ( table 4 ) . the local data correction factor is obtained as a ratio between the parameter mean from non - poee patients from table 2 of this study and the mean of the respective parameter from the local non - poee group of 20 to 40 complication - free patients . the local data correction factor for the establishment of the individual patient 's triple matrix for the classif1 classificationthe development of postoperative edema and effusion ( poee ) in children after cardiopulmonary bypass surgery can be predicted preoperatively . the immune activation has cellular ( neutrophil , eosinophil , monocyte counts , hematocrit ) and humoral ( c1 - inhibitor , c3 , c5a / c5 , il - 10 , sl - selectin , partial thrombin time , serum potassium ) components . preoperative normalization of the immune activation status has the potential of decreasing the intensive care treatment and the overall level of postoperative complications . cls , capillary leak syndrome ; cpb , cardiopulmonary bypass ; crp , c - reactive protein ; edta , ethylenediaminetetracetic acid ; ig , immunoglobulin ; il , interleukin ; lfa - 1 , leukocyte function associated molecule - 1 ; mod , multiple organ dysfunction ; poee , postoperative effusions and edema ; se - selectin , soluble endothelial - selectin ; sl - selectin , soluble leukocytic - selectin ; th1 / 2 , t - helper type 1/2 ; tnf , tumor necrosis factor . the authors thank mrs jacqueline richter for excellent technical help . a grant to undertake this studywas provided by the schsisches minis - terium fr wissenschaft und kunst ( smwk , research grant p.o . ) , dresden , and deutsche stiftung fr herzforschung , frankfurt , germany .\noutput:\n" }, { "from": "agent", "value": "aimpostoperative effusions and edema and capillary leak syndrome in children after cardiac surgery with cardiopulmonary bypass constitute considerable clinical problems . overshooting immune response is held to be the cause . in a prospective study we investigated whether preoperative immune status differences exist in patients at risk for postsurgical effusions and edema , and to what extent these differences permit prediction of the postoperative outcome.methodone - day preoperative serum levels of immunoglobulins , complement , cytokines and chemokines , soluble adhesion molecules and receptors as well as clinical chemistry parameters such as differential counts , creatinine , blood coagulation status ( altogether 56 parameters ) were analyzed in peripheral blood samples of 75 children ( aged 318 years ) undergoing cardiopulmonary bypass surgery ( 29 with postoperative effusions and edema within the first postoperative week ) . resultspreoperative elevation of the serum level of c3 and c5 complement components , tumor necrosis factor - , percentage of leukocytes that are neutrophils , body weight and decreased percentage of lymphocytes ( all p < 0.03 ) occurred in children developing postoperative effusions and edema . while single parameters did not predict individual outcome , > 86 % of the patients with postoperative effusions and oedema were correctly predicted using two different classification algorithms . data mining by both methods selected nine partially overlapping parameters . the prediction quality was independent of the congenital heart defect.conclusionindicators of inflammation were selected as risk indicators by explorative data analysis . this suggests that preoperative differences in the immune system and capillary permeability status exist in patients at risk for postoperative effusions . these differences are suitable for preoperative risk assessment and may be used for the benefit of the patient and to improve cost effectiveness ." } ]

[ { "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: about a decade ago most healthcare professionals had never heard the term human factors . even todayit is still not as familiar to many clinicians as most human factors experts would like to think . nevertheless significant progress has been made in human factors science as well as in applications of human factors concepts aimed at healthcare improvement . but , as russ and colleagues suggest in a recent article , this may be based on widely held misconceptions of human factors concepts and approaches . russ and colleagues discuss a number of fictions about human factors some of which may arise from the channels through which human factors science was introduced to healthcare ( e.g. frequently using experts working in an environment heavily influenced by human factors research such as aviation to teach healthcare providers about human factors concepts rather than human factors scientists ) . stepping back , these misconceptions may also signal some of the specific challenges that will have to be addressed in taking human factors expertise forward in healthcare and they may provide learning opportunities for human factors experts . in his editorial to the article by russ and colleagues , catchpole puts his finger on a sore spot for many human factors experts by stating : if we wish healthcare to be fundamentally changed by hf ( human factors ) , we must also expect hf to be changed by healthcare . collaboration between clinicians and hf professionals , with each shaping the views of the other , will develop and extend the use of hf for the unique demands of healthcare . following up on this thought of how key characteristics of healthcare might inspire change in human factors science this paper discusses the challenges of overcoming fragmentation of care . research and intervention efforts aiming to understand and mitigate the effects of fragmentation of care on patient safety frequently focus on patient handover . using examples of recent handover research we argue that the predominant research strategy is to focus on isolated handover episodes . this approach may actually hinder the development of an integrative framework that is urgently needed to effectively manage the risks associated with today s fragmentation of care . instead it is a call to start a discussion of current areas of healthcare human factors that might benefit from a critical reflection of the predominant approach to research and improvement . because the examples used to illustrate the need for such a discussion are drawn from handover research , the discussion will only cover selected aspects of fragmentation and additional or different challenges may be present in other areas of healthcare human factors . nevertheless , we believe that this paper may inspire critical reflections of the blind spots inherent in certain research approaches used when addressing patient safety problems . in the future , these reflections might make a unique contribution to moving the field forward . healthcare organisations around the world manifest striking fragmentation and turbulence that impede their capacity to provide high quality care , to assure and improve patient safety , and retain the skilled professionals critical to both . within hospitals , where the most acutely ill patients are treated and the greatest portion of healthcare costs are accrued , communication issues are among the most frequent contributory factors of adverse events . it has consistently been shown that communication is particularly vulnerable at organisational interfaces where handover occurs . handovers permeate the healthcare system and can occur at shift changes , when clinicians take breaks , when patients are transferred within or between hospitals , and during admission , referral or discharge ( figure 1 ) . one study estimated that approximately 1.6 million handovers occur per year in a typical teaching hospital . thus , handover communication at different levels of the organisation presents a major challenge for human factors research and interventions aiming at improved patient safety . in terms of the organisational interfaces wherehandovers have been studied , most studies have investigated care transitions between healthcare organisations ( admission and discharge ) , handovers during shift changes of nurses or physicians handovers in hospital settings where multiple patients are handed over within the same profession . , intra - hospital transitions , or handovers of single patients between departments / units frequently involving different specialties and / or professions , have received far less research attention . however , these interfaces also contribute significantly to the fragmentation of care because the responsibility for the patient and for the continuity of care is shared by many healthcare providers . handover is defined as the transfer of professional responsibility and accountability for some or all aspects of care for a patient , or groups of patients , to another person or professional group on a temporary or permanent basis aiming at informational , relational and management continuity in patient care . with an increasing number of studies tracing the causes of adverse events and delays in treatment to inadequate handover and coordination of care , , thus , handover has repeatedly been identified as a priority area for patient safety research and improvement . , this has led to an increase in initiatives aimed at raising awareness and political commitment to improve handover . for example , effective handover is a patient safety goal that has recently been included in hospital accreditation in australia . also , prevention of handover error is one of the five solution areas of the high 5s initiative , a mechanism established in 2006 through collaboration between the commonwealth fund , the who world alliance for patient safety and the who collaborating centre for patient safety , to implement innovative patient safety solutions over five years . as a consequence , handover research in healthcarein fact , the claim that healthcare is lagging behind other high - risk industries in which handover has received considerable attention from human factors research for many years can no longer be made . recent research in healthcare has highlighted the complexities of handover that have not yet been acknowledged by other industries . now may be the time to pause and consider if the approaches applied by human factors researchers may have missed a critical element . the goal of any handover is the transfer of primary responsibility for the patient and of information necessary for continuing safe patient care across organisational interfaces . , this may include information that is not needed immediately but at a later stage in the care process and thus needs to be remembered and transmitted when required . the handover can occur written , verbally or both and should ideally be a moment of shared cognition between clinicians providing opportunities for collaborative cross - checking . , handover research usually focuses on the information transfer aspect and investigates a single type of handover occurring at a specific interface within the care process . in so doing , studies mostly use idiosyncratic measures limiting the comparability of findings and the generalizability of recommendations for improvement . thus , while the research activity on handover has increased significantly in healthcare , it seems that the methodological approaches taken so far replicate the problem of fragmentation of care rather than solve it . in reviewing the handover literature for research methods , six frequently used approaches can be identified across various clinical settings and sometimes combined in a single study : general clinician self - assessment of handover practice using surveys , interviews or focus groups , clinician self - assessment after a specific handover episode , behavioural observation during handover , , including ethnographic field - study approaches , retrospective adverse event studies and observational and experimental effect studies . while the studies using this rather broad range of methodological approaches have significantly contributed to an improved understanding of factors impacting on safe handover , there is a lack of a common framework integrating these approaches into a coherent set of analytical techniques . firstly , studies using different methods for investigating handovers at the same organisational interface have often generated contradictory results . a common framework would facilitate the detection and interpretation of such contradictions and potentially allow for choosing the analytical techniques most appropriate for a particular type of handover occurring at a particular organisational interface . secondly , handover occurs many different forms at many different times during a patient s journey through the hospital ( figure 1 ) . therefore , measurement approaches need to reflect the interrelatedness of handover episodes throughout the continuum of care . in recent years , first studies have attempted to incorporate a more process - oriented approach to handover . , these attempts can be broken down into a clinician centred approach and a process - or patient - oriented approach . the clinician centred approach was used in a study of clinician workflow surrounding the handover in a medical intensive care unit . the focus here was on the preparatory tasks by the outgoing staff before the handover and the tasks to be done by the receiving staff after the handover . focusing on the continuum of surgical care , another study followed patients throughout the perioperative setting and recorded all handovers during that period . although this study covered only a limited period of the care process and was narrowly focused on completeness and accuracy of information transmission , it can serve as a basic model for a more comprehensive analysis of safe handover along the care path . based on the evidence of information loss and idiosyncratic handover practices at many organisational interfaces within healthcare , handover improvements have been suggested that focus on a standardisation of handover content and sometimes provide procedural support using a basic handover structure. ,21 , despite the widespread use and the intuitive plausibility of standardised handover protocols , for example , the empirical evidence on their effects beyond mere adherence to the protocol ( i.e. effects on subsequent patient care ) is scarce . while medical research relies heavily on randomized controlled trials to establish scientific evidence , it is surprisingly uncommon to test and refine organisational interventions systematically before implementing them in the clinical setting . few studies have tried to link process characteristics such as handover structure with outcome measures such as retention of patient care information , uncertainty during patient care decisions , a need to obtain information from other sources and repetition of clinical tasks . overall , the available evidence is not sufficient to draw reliable , valid conclusions because of the heterogeneity of organisational interfaces and handover protocols used in these studies . more specifically , it is unknown which component of standardisation efforts ( e.g. clear distribution of roles , separation of clinical tasks and handover communication , checklist of items to be discussed , general structure of the handover communication ) has which effect . moreover , dismissing other interventions that have not been studied extensively prematurely may be a missed opportunity for patient safety improvement . the scientific discipline of human factors strives for a holistic approach to understanding and solving problems that highlights relationships and interactions and thus departs from the out - dated reductionism that decomposes wholes into individual elements . butdo we really walk the talk ? while there is much rhetoric about the importance of handover for the continuity of care , handover research has mainly focused on isolated handover episodes at single organisational interfaces . the limited consideration of the embeddedness of handover in the overall process of patient care has led to problems concerning : i ) idiosyncratic measurement approaches , i.e. measures that are tailored towards a specific handover episode and do not necessarily allow for comparison across different organisational interfaces that may involve handover of individual or multiple patients ; ii ) fragmented research evidence , i.e. descriptions of a heterogeneous spectrum of handover episodes without systematic characterisation of the handover context that could provide a frame of reference for comparing and integrating research evidence , and iii ) narrowly focused intervention strategies , i.e. strong push towards standardisation of handover communication without convincing evidence or scientific understanding of the contribution of the individual components of a standardisation effort . in summary , the focus of current handover research on isolated handover episodes is too narrow to truly understand the impact of handover on the continuation of safe patient care while the patient transitions a series of organisational interfaces . thus , the current research strategy may even reinforce a fragmented view of patient care instead of providing scientific evidence to effectively bridge the potential gaps along the care path . if we design handover episodes based on studies that did not consider the embeddedness of this specific handover in the process of care and in the associated succession of handovers , the impact of this intervention is bound to be very limited . there are several ways in which a patient - centred research strategy might change the study of patient handover . for example , extending the focus of analysis beyond the actual handover meeting can provide additional information on factors contributing to safe care . currently , the evaluation of handover quality defined as complete and accurate transfer of information occurs immediately after the handover is complete . but two hours later or at the end of the shift the evaluation of that very handover might generate different evaluations . also , if the handover and the corresponding evaluation of handover quality was tailored to the goal of transferring the information required by the next care provider for effectively and safely carrying out their tasks , it may not address the needs of the clinicians involved in later stages of the care process . one possible way to overcome this fragmentation is to develop a patient - centred research strategy focussing on the interdependencies of handover episodes during a series of transitions occurring along the typical care path . such a framework would facilitate an exploration of issues concerning the timing and synchronisation of various handover channels at interfaces . it could also serve as a foundation for a methodological approach for assessing handover systematically along the care path as well as for an integrative strategy to develop and test interventions spanning across organisational boundaries . if we consider the simplified overview of handers occurring along typical care paths in figure 1 , a multitude of methodological and practical challenges come to mind . collecting information on a series of handovers related to a single patient using a combination of methods such as chart reviews , observations , clinician self - and peer - assessments will generate huge amounts of data that need to be interpreted within a common framework . moreover , designing the instruments for data collection and deciding on the timing of data collection and the allocation of researchers for collecting data requires a high level of pre - existing understanding of each handover episode . last but not least , the feasibility of such a study design will depend on balancing researcher availability at the time and location of a given handover and the need for knowledge about previous handovers ( e.g. to detect omissions of previously discussed items ) . despite the challenges associated with developing and implementing such a framework , the development of a patient - centred research strategy has the potential to significantly influence future handover research . in addition to large scale projects aiming at understanding the interdependencies of handover episodes along the care path , an overarching framework can also be applied when isolating research questions for small scale projects and allows for acknowledging the wider system when interpreting the results of these more focused studies and when designing interventions . an integrative framework of handover episodes along the care path is urgently needed to effectively manage the risks associated with today s fragmentation of care and to develop scientific methods for systematically assessing the needs for , and the effects of , patient safety solutions . this will result in novel insights into safe handover that will lay the foundation for optimising the continuum of care across the multiple organisational interfaces patients encounter , as part of their journey through a hospital .\noutput:\n" }, { "from": "agent", "value": "the integration of human factors science in research and interventions aimed at increased patient safety has led to considerable improvements . however , some challenges to patient safety persist and may require human factors experts to critically reflect upon their predominant approaches to research and improvement . this paper is a call to start a discussion of these issues in the area of patient handover . briefly reviewing recent handover research shows that while these studies have provided valuable insights into the communication practices for a range of handover situations , the predominant research strategy of studying isolated handover episodes replicates the very problem of fragmentation of care that the studies aim to overcome . thus , there seems to be a need for a patient - centred approach to handover research that aims to investigate the interdependencies of handover episodes during a series of transitions occurring along the care path . such an approach may contribute to novel insights and help to increase the effectiveness and sustainability of interventions to improve handover.significance for public healthwhile much of public health research has a preventive focus , health services research is generally concerned with the ways in which care is provided to those requiring treatment . this paper calls for a patient - centred approach to research on patient handover ; a significant contributor to adverse events in healthcare . it is argued that this approach has the potential to improve our understanding of handover processes along the continuum of care . thus , it can provide a scientific foundation for effective improvements in handover that are likely to reduce patient harm and help to maintain patient safety ." } ]

[ { "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: breast cancer is the most prevalent cancer in the world , and ovarian cancer is the sixth most common cancer in the world . inherited mutations in the breast cancer susceptibility gene 1 ( brca1 ) [ mim 113705 ] and breast cancer susceptibility gene 2 ( brca2 ) [ mim 600185 ] are associated with a high risk of developing breast and ovarian cancers in females of different age and ethnic groups . these well - defined high - penetrance genes show loss - of - full function germ line mutations in hereditary cases and decreased expression in sporadic tumors . approximately , 5 to 10 percent of breast cancer and at least 10 percent of ovarian cancers are hereditary . sequence variation in the brca1 gene accounts for 45 percent of inherited breast cancer and more than 90 percent of inherited breast and ovarian cancer , and both genes combined account for only 25 percent of familial risk . the spectrum of mutations in these genes varies between populations , with some showing a high frequency of unique mutations . many such alterations may be recurrent , often being identified in isolated populations as the results of a founder effect and may be the basis of differences in cancer risk between populations . ashkenazi jewish , norwegian , dutch , and icelandic people have a higher rate of certain genetic alterations in brca1 . most of brca1 and brca2 research has been focused on the caucasian populations ; however , the allelic frequency of higher penetrance genes in the asian population may be higher than that in caucasian population . immigrant asian women especially from south asia who are settled in the west show high rates of these cancers . risch et al . reported greater frequencies of mutations among cases of ovarian cancer that were of indo - pakistani descent than among british or mixed northern - or western - european ethnicity in ontario , canada . although 60 percent of the world 's population resides in the asian continent , and the fact that the chinese , malays , and indians are three major asian haplogroups , genetic predisposition to hereditary diseases and the applicability of genetic testing in these diverse ethnic groups is still unclear . these regions have high rates of both these cancers especially the developing south asian countries . amongst the asian countries , pakistan has one of the highest rates of breast and ovarian cancer with breast cancer being the most common and ovarian the third most common malignancy amongst pakistani women and the most common cancer of gynecological origin in pakistan . a nine - year study period at a tertiary care cancer institution in karachi , pakistan showed that breast cancer was the most common cancer in females accounting for 38.2 percent of total cancer cases , at rates almost highest in asia and ovarian cancer accounting for 4.9 percent . incidence rates in this region are on such a rapid rise that it is necessary to check the contributory factors , genetic and nongenetic . an insight into the above data emphasizes the formulation of a brca1 and brca2 database for the pakistani population . study conducted by authors was carried out at the centre for research in applied and experimental medicine , national university of science and technology , rawalpindi . this study focused on mutational screening of brca1 gene in diagnosed cases of both hereditary and sporadic breast and ovarian cancer . in course of brca1 gene screening , all exon - intron boundaries were sequenced . questionnaire was filled out containing information of their personal , family , and disease history . ethnicity of each candidate was noted with the aim of finding founder effect mutations clustered to a specific ethnic group . amplification of all the exon - intron boundaries of brca1 gene by polymerase chain reaction ( pcr ) was performed using the oligonucleotide primers designed from the intronic sequences of the gene . purified products were subjected to dna sequencing by automated genetic analyzer , beckman coulter ceq8000 , genetic analysis system . the sequencing chromatograms of the affected individuals were compared with the corresponding control full length gene sequences from ucsc genome browser database to identify the aberrant nucleotide base pair change . ensembl database was used to recheck the gene sequence for cdna and mrna information . two major pioneering investigations were accomplished by liede et al . at the national cancer institute , karachi and jinnah hospital , lahore and by rashid et al . at the shaukat khanum memorial hospital , lahore . a comparatively small study focusing on mutational analysis of brca1 gene was performed by malik et al . at the comsats institute of information technology , islamabad . liede et al . conducted a case - control study of 341 case subjects with breast cancer , 120 case subjects with ovarian cancer , and 200 female control subjects . rashid et al . selected patients from 176 breast and / or ovarian cancer families who were diagnosed with invasive breast or epithelial ovarian cancer . the entire coding regions of the brca1 and brca2 genes were screened using single strand conformational polymorphism ( sscp ) analysis , denaturing high pressure liquid chromatography ( dhplc ) analysis , and the protein truncation ( ptt ) assay . automated dna sequencing was performed for each sample revealing variants by sscp , dhplc , or ptt . after dna extraction , single strand conformational polymorphism ( sscp ) was done for exons of brca1 , and sequence analysis was performed for putative sequence variant . the results of samples recorded on biorad gel documentation system showed good yield and amplification of the dna with the primers . the chromatograms of brca1 gene from affected patients ( figure 1 ) after mutational screening of the exons in all the samples of our study group revealed no pathogenic sequence variant correlating with breast or ovarian cancer pathogenesis . this is suggestive of the need to focus on the role of other high - or low - penetrance genes in breast and ovarian cancer predisposition in pakistani population . by adding present and previous results regarding both brca1 and brca2 genes , a database with new percentage prevalence was formed . the role of brca1 and brca2 in the pathogenesis of breast and ovarian cancer in pakistan was noted , and the most prevalent pakistani mutations were highlighted . identified 42 sequence variants harboring 31 brca1 mutations and 11 brca2 variants in their study group of 341 women with breast cancer and 120 women with ovarian cancer . rashid et al . studied 176 pakistani breast and ovarian cancer patients selected on family history and on age of diagnosis and identified a total of 30 sequence variants and among them 23 deleterious mutations in brca1 and 7 mutations brca2 gene . detected a total of 6 variants in their samples ( tables 1 and 2 ) . mutations in brca1 and brca2 were found , respectively , in nine and three percent of breast and ovarian cancer patients ( figure 2 ) . these results are authenticated by risch et al . who reported a high frequency of brca1 mutations among cases of ovarian cancer that were of indo - pakistani descent ( 14 % ) along with jewish ( 21 % ) and italian ( 17 % ) ancestry in a population - based study of 649 cases of ovarian cancer in ontario , canada . the remaining 88 percent of breast and ovarian cancers can be attributed to the involvement of other genes such as tumor protein ( tp53 ) [ mim 191170 ] , phosphatase and tension homolog ( pten ) [ mim 601728 ] , checkpoint kinase 2 ( chek2 ) [ mim 604373 ] , and estrogen receptor 1 ( esr ) [ mim 133430 ] . twenty one distinct brca1 mutations were observed by liede et al . which are mostly insertions , deletions , or point mutations and exon 11 , the largest exon of the gene , was mainly found to be the disease causing region . one intronic variant in exon 14 ( ivs14 - 1ga ) ten distinct types of brca2 variants were detected by these researchers , 9 in exon 11 , and only one in exon 22 , the 9140dela mutation in a muhajir breast cancer patient ( table 2 ) . five brca1 mutations ( 2080insa , 3889delag , 4184del4 , 4284delga , and ivs14 - 1arg ) and one brca2 mutation ( 3337ct ) were identified in multiple unrelated case subjects and represented candidate founder mutations . rashid et al . reported a total of twenty - two distinct mutations , 15 distinct variants in brca1 , and 7 distinct variants in brca2 . among thesewere 12 frame shift mutations , 8 nonsense mutations , and 2 splice - site mutations ( tables 1 and 2 ) . the most commonly observed brca1 mutation was the 4627ca , nonsense mutation identified in 5 families . four mutations , 185delag , 185insa , 4627ca , and 5622 ct , were recurrent ; these accounted for 52 percent of all identified brca1 mutations . observed two types of mutations in brca1 , one insertion and one nonsense variant ( tables 1 and 2 ) . mutational analysis of all these studies emphasizes the justification of genetic testing for predisposing brca1 germ line mutations for any pakistani family with multiple female breast and / or ovarian cancer cases . in total , brca1 variant 4627ca was observed in 22 percent of the probands showing recurrent mutations and features as the most prevalent brca1 mutation in pakistani population ( figure 3 ) , while 15 percent of these patients showed the 4184del4 brca1 variant which appears to be the second most prevalent mutation in pakistani population ( figure 4 ) . brca2 mutational analysis revealed 3337ct and 5057deltg to be equally prevalent ( 50 percent each ) in the study participants showing recurrent brca2 variants . pakistan has a pivotal location on the map of asia , being at the crossroads of south asia , the middle east , and central asia . pakistani population has a very rich anthrogeneological background owing to successive waves of invasions and adaptation of different haplogroups including persians , aryans , mongols , sikhs , arabs , greeks , turks , and the british . massive migrations from india in 1947 and more recently from afghanistan have contributed to further diversifying the pakistani population . punjabis comprise the largest ethnic group in the country at 44.15 percent , while other important ethnic groups include pashtuns ( 15.42 percent ) , sindhis ( 14.1 percent ) , seraikis ( 10.53 percent ) , muhajirs ( 7.57 percent ) , balouchis ( 3.57 percent ) , and others ( 4.66 percent ) . the diverse ethnic blend concentrated in this region , especially in urban regions , contributes greatly to the genetic variability for inheritance of breast and ovarian cancer . the two major studies of liede et al . and rashid et al . in the 54 brca1 mutations of both of these studies , 31 ( 57 % ) were found in the punjabi ethnic group . amongst the 18 brca2 variants of both these studies , 6 ( 33 % ) hence , the punjabi ethnic group showed maximum sequence variants in the brca gene variants ( table 3 ) . twelve of the 21 brca1 mutations ( 57 percent ) and 8 of the 10 brca2 mutations ( 80 percent ) detected by liede et al . detected ten mutations ( 33 percent ) which were unique to the pakistani population , which is comprised of 5 brca1 mutations ( 33 percent ) and 5 brca2 mutations ( 71 percent ) . the finding of thirteen recurrent brca1 and two recurrent brca2 mutations in some members of the pakistani population could allow very economical screening for such mutations in specific ethnic groups in the country which could be of great benefit to public health measures . the most prevalent brca1 mutation of both studies combined , 4627ca , was found in six punjabi patients increasing the likelihood of finding this variant in punjabi ethnicity . four probands showed the 4184del4 brca1 variant out of which three were punjabi and one sindhi . all the four carriers of the brca1185insa and the two carriers of the brca15622 ct were also of punjabi ethnicity . this predisposition of the punjabis to maximum brca variants can lead to focusing on the specific sequence variants of this ethnic group . rashid et al . also found 185delag in two non - jewish unrelated pakistani carriers of pathan ethnicity , whose ancestors originated from the same geographic region in the north - west frontier province of pakistan . these two mutations can be the focus of candidate founder mutations in this ethnic group . the two cases with the brca14284delag mutation belonged to the muhajir ethnic group , again signifying the importance of focusing on this mutation in this particular ethnic group . in brca2 screening , liede et al. found the recurrent 3337ct variant in two memon breast cancer patients pointing towards the significance of finding this mutation in other memon patients as well .5057 deltg brca2 mutation was a finding of both studies ; rashid et al . detected this mutation in a punjabi patient , while liede et al . detected it in a minority ethnic group , a parsi ovarian cancer patient . ever since the discovery of breast and ovarian cancer genes , many advances in clinical research have been made which provide the rationale for moving genetic testing of these genes into clinical practice . brca1 and brca2 , like other genes , have not only served as molecular markers for hereditary breast cancer risk screening but also become important indicators for breast cancer prevention , treatment , and prognosis . genetic testing is gaining acceptance worldwide and has been established throughout north america and much of europe . genetic counseling , especially in country like pakistan having one of the highest rates of consanguinity , is practiced by many health professionals ; however , its expansion into the health policy and training regimes of health care providers is needed . the awareness , however , of genetic testing as a tool for preventive and treatment - oriented management of these tumors is limited . formulation of brca mutational database can serve as a cost - effective tool to identify individuals at high risk such as unaffected carrier relatives who have a defective allele that can be transferred to offspring . such tests are strategized on the basis of most prevalent mutations in a particular population / ethnic group that can save both time and money . tillthen the most effective options for breast cancer risk reduction include prophylactic bilateral mastectomy prophylactic oophorectomy , and oral administration of tamoxifen in some countries . if genetic testing for these genes becomes streamlined , these prophylactic procedures and other preventive strategies will be warranted to become routine for mutation carriers along with vigilant medical checkups , especially in an economically challenged country like pakistan . the need for larger collaborative studies between medical professionals and molecular biologists can not be emphasized enough . this is necessary for gaining further insight into mutational spectra and ethnic distribution of different types of mutations , in a search for founder effect mutations , which can become a part of cancer screening policies in pakistan . the high prevalence of these cancers and the presence of recurrent mutations of these genes in the pakistani population , especially the observation of a high percentage of brca1 variants in ovarian cancer cases , emphasize the need for improving genetic counseling strategies and make genetic testing a part of screening policies . the more work done on the genomics of this disease with relevance to the pakistani population , the closer a genetic cure targeted for this specific population can be found . a. farooq contributed in the design of study experimentation ; a. k. naveed is the supervisor of study ; z. azeem assisted in experimentation and data compilation ; t. ahmed assisted in data compilation .\noutput:\n" }, { "from": "agent", "value": "introduction . pakistani population has a very rich anthrogeneological background with waves of migration from neighboring regions . incidence rates of breast and ovarian cancer in pakistan are on such a rapid rise that it is necessary to check the contributory factors , genetic and nongenetic . an insight into the prevalence data emphasizes the formulation of a brca1 and brca2 database for the pakistani population . method . in this study conducted by authors , data from diagnosed cases of both sporadic and inherited female breast and ovarian cancer cases was gathered after performing molecular genetic analysis by screening for alterations in the coding sequence of the brca gene . the region of interest was analyzed by the aid of various molecular biology tools such as automated dna sequencer . bioinformatics software was used to interpret the results , and database was prepared . results . mutational screening of the exons in all the samples of our study group did not reveal any pathogenic mutation . these results along with the results of the previous pakistani studies for both brca1 and brca2 genes were summed up to prepare a pakistani database . percentage involvement of these genes was estimated . nine percent of these cancers show alterations in brca1 gene while 3 percent have shown brca2 variants . the remaining 88 percent of breast and ovarian cancers can be attributed to the involvement of other genes ." } ]

[ { "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: salivary glands are composed of acinar cells , either serous or mucous , and ductal cells of several varieties . the primary saliva is formed in the lumen of the acinar cells , where the accumulation of ions generates a transepithelial osmotic gradient driving water movement . in the second stage of secretiontherefore , alterations of sodium transporters and water channels may affect the formation and the ductal modification of the saliva . immunofluorescence labelling and confocal microscopy revealed a polarized distribution of na , k - atpase , the secretory isoform of na / k / 2 cl cotransporter ( nkcc2 ) , and type 1 na / h exchanger ( nhe1 ) in the basolateral membranes of acinar and intralobular duct cells1 ) . na , k - atpase produces an inward - directed sodium chemical gradient in the acinar cell2 ) . although sodium influx is negligible in resting cells , it is rapidly increased by activation of nkcc2 , nhe1 , and nonselective cation channels in the acinar cell3 ) . blockade of nkcc2 causes significant reduction of acetylcholine - stimulated secretion4 ) , in which the residual secretion is attributed to the operation of na / h and cl / hco3 antiport5 , 6 ) . the amiloride - sensitive epithelial sodium channels ( enac ) are localized to the surface epithelial cells of the secretory duct . among their three homologous subunits , only - subunit can produce an amiloride - sensitive current7 ) , while - and - subunits are not functional on their own8 ) . on the other hand , there have been known multiple isoforms of aquaporin ( aqp ) water channels in the salivary gland . among them , aqp5 may be the only isoform of aqp playing a major role in the salivary secretion process . strong aqp5 labelling is located in the apical membrane of serous - type acinar cells from the rat submandibular gland9 ) . the transepithelial water movement occurs through the apical aqp5 channels and paracellular pathways10 ) , leading to the secretion of isotonic primary saliva . although the presence of aqp1 and aqp8 has been also generally accepted , their role in the salivary secretion remains controversial11 ) . over the last two decades , nitric oxide ( no ) has been found to play a role in the regulation of various physiological functions . it has been also implicated in mediating the nerve - evoked vasodilator and secretory responses in the salivary gland . parasympathetic nerve activity increases the submandibular blood flow , and elicits the flow of saliva and output of protein by mechanisms that involve in situ generation of no in the ferret12 ) . a previous study revealed that no synthase ( nos ) is not present in the acinar cells , but in neural terminals within the gland and in the apical membrane of the excretory and striated ducts , the cytoplasm of granular convoluted tubules , and , to a lesser extent , in the cytoplasm of excretory and striated ducts13 ) . furthermore , the salivation induced by cholinergic agonists or that produced by the chorda stimulation was decreased by inhibition of no synthesis by n - nitro - l - arginine methyl ester ( l - name ) in the rat submandibular gland11 , 15 ) . nevertheless , the role of no in the regulation of sodium transporters and aqp channels in the salivary gland has not been established . therefore , the present study was aimed to explore the role of no in the regulation of sodium transporters and aqp channels in the salivary gland . rats were inhibited of endogenous generation of no by treatment with l - name , and the expression of sodium transporters and water channels was determined in the submandibular gland . the experimental group was treated with l - name ( 100 mg / l drinking water ) for 1 week . they were thawed and homogenized with polytron homogenizer at 3,000 rpm in a solution containing sucrose ( 250 mmol / l ) , edta ( 1 mmol / l ) , phenylmethylsulfonyl fluoride ( 0.1 mmol / l ) , and potassium phosphate buffer ( 20 mmol / l ) , at ph 7.6 . the homogenate was centrifuged at 1,000 g for 15 min to remove the whole cells , nuclei , and mitochondria . the supernatant was then ultracentrifuged at 100,000 g for 1 h to produce a pellet containing membrane fractions enriched for both plasma membranes and intracellular vesicles . protein samples were loaded and electrophoretically size - separated with a discontinuous system consisting of 8 - 12.5 % polyacrylamide resolving gel and 5 % polyacrylamide stacking gel . the proteins were then transferred to a nitrocellulose membrane at 40 v for 3 h. the membrane was washed in tris - based saline buffer ( ph 7.4 ) containing 0.1 % tween - 20 ( tbst ) , blocked with 5 % nonfat milk in tbst for 1 h , and incubated with antibodies in 2 % nonfat milk / tbst for 1 h at room temperature . the antibodies used were polyclonal anti - rabbit -1 and -1 subunits of na , k - atpase ( 1:2,500 , upstate biotechnology , lake placid , ny , usa ) , nkcc2 ( 1:1,000 , chemicon , temecula , ca , usa ) , nhe1 ( 1:500 , alpha diagnostic , san antonio , tx , usa ) , - subunit of enac ( 1:500 , alpha diagnostic , san antonio , tx , usa ) , aqp1 ( 1:1,000 , alomone , jerusalem , israel ) , aqp5 ( 1:1000 , alpha diagnostic , san antonio , tx , usa ) , endothelial nos ( enos ) and neuronal nos ( nnos ) ( 1:750 , transduction ; lexington , ky , usa ) . the membrane was then incubated with horseradish peroxidase - labeled goat anti - rabbit igg ( 1:1,200 ) in 2 % nonfat milk in tbst for 2 h. the bound secondary antibody was detected by enhanced chemiluminescence ( amersham , buckinghamshire , england ) . the protein levels were determined , using the transmitter scanning videodensitometer ( biomed instruments , fullerton , ca , usa ) . the statistical significance of values between groups was determined by the unpaired t - test . the experimental group was treated with l - name ( 100 mg / l drinking water ) for 1 week . the submandibular glands were rapidly isolated under ketamine anesthesia . they were rapidly frozen and kept at -70 until analyzed . for protein preparation , they were thawed and homogenized with polytron homogenizer at 3,000 rpm in a solution containing sucrose ( 250 mmol / l ) , edta ( 1 mmol / l ) , phenylmethylsulfonyl fluoride ( 0.1 mmol / l ) , and potassium phosphate buffer ( 20 mmol / l ) , at ph 7.6 . the homogenate was centrifuged at 1,000 g for 15 min to remove the whole cells , nuclei , and mitochondria . the supernatant was then ultracentrifuged at 100,000 g for 1 h to produce a pellet containing membrane fractions enriched for both plasma membranes and intracellular vesicles . protein samples were loaded and electrophoretically size - separated with a discontinuous system consisting of 8 - 12.5 % polyacrylamide resolving gel and 5 % polyacrylamide stacking gel . the proteins were then transferred to a nitrocellulose membrane at 40 v for 3 h. the membrane was washed in tris - based saline buffer ( ph 7.4 ) containing 0.1 % tween - 20 ( tbst ) , blocked with 5 % nonfat milk in tbst for 1 h , and incubated with antibodies in 2 % nonfat milk / tbst for 1 h at room temperature . the antibodies used were polyclonal anti - rabbit -1 and -1 subunits of na , k - atpase ( 1:2,500 , upstate biotechnology , lake placid , ny , usa ) , nkcc2 ( 1:1,000 , chemicon , temecula , ca , usa ) , nhe1 ( 1:500 , alpha diagnostic , san antonio , tx , usa ) , - subunit of enac ( 1:500 , alpha diagnostic , san antonio , tx , usa ) , aqp1 ( 1:1,000 , alomone , jerusalem , israel ) , aqp5 ( 1:1000 , alpha diagnostic , san antonio , tx , usa ) , endothelial nos ( enos ) and neuronal nos ( nnos ) ( 1:750 , transduction ; lexington , ky , usa ) . the membrane was then incubated with horseradish peroxidase - labeled goat anti - rabbit igg ( 1:1,200 ) in 2 % nonfat milk in tbst for 2 h. the bound secondary antibody was detected by enhanced chemiluminescence ( amersham , buckinghamshire , england ) . the protein levels were determined , using the transmitter scanning videodensitometer ( biomed instruments , fullerton , ca , usa ) . the statistical significance of values between groups was determined by the unpaired t - test . in the l - name - treated group , the systolic blood pressure measured indirectly by the tail cuff method in a conscious state was significantly higher in the experimental group than in the control ( 1469 vs 1216 mmhg , p 0.05 , n = 6 each ) . accordingly , the expression of enos and nnos in the submandibular gland was decreased significantly ( fig . the expression of 1 - subunit of na , k - atpase was significantly increased , although that of 1 - subunit remained unchanged ( fig . the expression of nkcc2 , nhe1 , and - subunit of enac was increased significantly ( fig . the expression of aqp5 was significantly decreased , while that of aqp1 was not significantly altered ( fig . no has been implicated in mechanisms mediating nerve - evoked vasodilator and secretory responses in salivary glands . the salivation induced by cholinergic agonists or chorda stimulation was decreased by no synthesis inhibition in the submandibular gland12 , 13 , 15 ) . therefore , it is plausible to hypothesize that no plays a role in regulating the sodium transporters and aqp channels in the salivary gland . previous studies have shown that l - name treatment decreases the gene and protein expression of enos16 , 17 ) . the present study also demonstrated a decreased expression of both enos and nnos in the submandibular gland following the treatment with l - name , which may have resulted in a decreased formation of no . the down - regulation of nos was associated with an increased expression of a1 - subunit of na , k - atpase , nkcc2 , nhe1 , and a - subunit of enac , suggesting that these sodium transporters should be under tonic inhibitory influence of no in the submandibular gland . the up - regulation of these transporters may then , at least in part , account for the decreased salivation following inhibition of no synthesis in rat submandibular gland13 , 15 ) , possibly through an enhancement of the ductal reabsorption of sodium . on the other hand , this finding suggests that aqp5 is under tonic excitatory influence of no in the submandibular gland . transgenic mice lacking aqp5 display reduced pilocarpine - stimulated saliva secretion ( 60 % ) , in which the secreted saliva is more hypertonic and viscous18 ) . in sjgren 's syndrome , an abnormal distribution of aqp5 has been demonstrated in the acini , which is likely to contribute to the deficiency of fluid secretion19 ) . a down - regulation of aqp5 may result in a decrease of water flux in the acinar cell and hence the formation of primary saliva . in this context , the l - name - induced reduction of secretory responses12 , 13 , 15 ) may be attributed in part to the down - regulation of aqp5 . the expression of aqp1 has been demonstrated to be continuously distributed to microvasculature during embryonic and postnatal development in the rat submandibular gland20 , 21 ) . however , the expression of aqp1 proteins was not significantly altered by the l - name - treatment . in transgenic mice lacking aqp1 , pilocarpine - induced salivary secretion showed no defects in volume or composition of saliva18 , 22 ) . finally , it is worth to note that the systolic blood pressure was significantly increased , indicating that the animals were in a state of systemic withdrawal of tonic influences of endogenous no . furthermore , the alteration of sodium transporters and water channels can not be attributed to the increased blood pressure , perse , since an attenuated salivation has not been documented in other models of hypertension . in summary , these results indicate that sodium transporters and water channels are under tonic regulatory influence of no in the submandibular gland . an altered no synthesis may affect the expression of these transporters and channels , and hence the formation and secretion of saliva . further studies will be needed to directly measure the sodium and water flux in the ductal epithelia to determine the actual contribution of each transporter .\noutput:\n" }, { "from": "agent", "value": "a role of nitric oxide ( no ) in the regulation of sodium transporters and water channels in the salivary gland was investigated . male sprague - dawley rats were treated with ng - nitro - l - arginine methyl ester ( l - name , 100 mg / l drinking water ) for 1 week . the control group was supplied with normal tap water . the expression of na + , k + - atpase , type 2 na + / k + / 2 cl - cotransporter ( nkcc2 ) , type 1 na + / h + exchanger ( nhe1 ) , - subunit of epithelial sodium transporter ( enac ) , and aquaporin - 5 ( aqp5 ) and aquaporin - 1 ( aqp1 ) proteins were determined in the submandibular gland by western blot analysis . following the treatment with l - name , the expression of na + , k + - atpase 1 - subunit , nkcc2 , nhe1 , and enac - subunit increased significantly . on the contrary , the expression of aqp5 was significantly decreased , while that of aqp1 was not significantly altered . these findings indicate that the sodium transporters and water channels may be under a tonic regulatory influence of no in the salivary gland ." } ]

[ { "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: acquired immunodeficiency syndrome ( aids ) is an infectious disease caused by the human immunodeficiency virus ( hiv ) . reverse transcriptase ( rt ) , protease ( pr ) , and integrase ( in ) are the three viral enzymes that are required for viral replication and all three have been targeted by anti - aids therapeutics . in catalyzesthe insertion of viral dna into the host genome in two sequential steps , termed 3 - processingthe 3 - p reaction cleaves two nucleotides from the 3 end of the viral dna , exposing a deoxycytosine residue that is used in a nucleophilic attack on the host dna in the st reaction . both of these reactions involve two mg ions held in place by three acidic residues asp64 , asp116 , and glu152 that collectively constitute the dde motif . in inhibitorsmerck s raltegravir ( ral , 1 , figure 1 ) ( october 2007 ) and gilead s elvitegravir ( evg ) ( august 2012 ) were the first two in inhibitors to be approved by the fda . the approved in inhibitors selectively block the st step , and members of this class of drugs are called in strand transfer inhibitors ( instis ) because of their ability to preferentially block the enzyme s st reaction relative to the 3 - p reaction . all of the known instis share important structural features , which include a coplanar arrangement of three heteroatoms that chelate the two catalytic mg ions , and a halobenzyl ring that binds to the penultimate base ( a deoxycytidine ) adjacent to the deoxyadenosine that lies at the 3 end of the viral dna after the 3 - p reaction . binding of instis blocks the st reaction by displacing the viral 3 - terminal deoxyadenosine from the catalytic mg ions . treatment with 1 and evg selects for resistant forms of hiv , and there is considerable cross - resistance to these two drugs . glaxosmithkline s dolutegravir ( dtg , 2 , figure 1 ) is a recently fda - approved second - generation insti ( august 2013 ) , which shows improved efficacies against ral and evg - resistant strains of hiv . however , 2 also selects for resistant strains of hiv . this emphasizes the need to develop agents that can overcome resistant strains of in , including the emerging strains resistant to 2 . we recently reported that 1 - hydroxy -1,8-naphthyridin-2h - one -3-carboxamides , which include both 4 - unsubstituted and 4 - hydroxyl - containing analogues ( 3 and 4 , respectively , figure 1 ) , potently inhibit wild - type ( wt ) in in biochemical assays and show good antiviral efficacies in single - round infection assays of hiv - 1 infectivity ( figure 1 ) . importantly , members of this series retain good antiviral potency against a set of mutants resistant to 1 in these latter assays . herewe describe structural variation at the 4 - position of compound 3 , which yielded agents of type 5 ( figure 1 ) that enhance their efficacy against additional mutant forms of in that are resistant to 1 . mg - chelating heteroatoms are shown in red , with the 4 - position of the 1 - hydroxy -1,8-naphthyridin-2 ( 1h ) - one ring being indicated in blue . in is a member of the polynucleotidyl transferase class of enzymes that share similar catalytic mechanisms . there is also a large body of data that describes the known instis , their efficacy against wt and drug - resistant forms of hiv , and their interactions with prototype foamy virus ( pfv ) in . accordingly , the structures of previously described inhibitors can be used to aid the design of new anti - in compounds . this is exemplified by the development of 1 by merck , which can be traced to dihydroxypyrimidine carboxamide inhibitors of the hepatitis c virus ns5b rna polymerase ( rnap ) . inhibitors of hiv - 1 ribonuclease h ( rnase h ) have been reported , which , like instis , inhibit their target enzyme by chelating two mg ions in the enzyme active site . in rnase h , the mg ions are held in place by a dedd motif ( d443 , e478 , d498 , and d549 ) . compounds that inhibit both in and rnase h have been reported . by analogy to the rnap example , the known rnase h inhibitors might provide insights that can be used to design improved insti inhibitors . accordingly , the design of our bicyclic 1 - hydroxy -1,8-naphthyridin-2h - one instis ( 3 and 4 ) was guided by the report that compounds such as the biaryl - containing 6 ( figure 2 ) , which have submicromolar inhibitory potency against rnase h ( ic50 = 0.64 m ) , also have low micromolar inhibitory potency against hiv - 1 in ( st ic50 = 2.4 m ) . in the case of 6 , the reported ec50 value ( half - maximal concentration providing protection against viral - induced cell death ) in a hiv - 1 hxb2 single - cycle viral replication assay in hela p4 - 2 cells was 34 m . ribonuclease h ( rnase h ) inhibitors 6 and integrase inhibitor 5a with the core metal - chelating 1 - hydroxy -1,8-naphthyridin-2 ( 1h ) - one system shown in red and the key 4 - amino group indicated in blue . metal chelation by the 1 - hydroxy -1,8-naphthyridin-2h - one nucleus , which is common to 3 , 4 , and 6 , can theoretically be achieved via the heteroatom triad formed by the n - hydroxyl group , the 2 - oxo group , and the 8 - naphthyridine nitrogen . however , an important component of 3 and 4 , not found in 6 , is a halobenzyl group , which is known to be important for binding to in by interacting with the penultimate deoxycytosine in the 3 - end of enzyme - bound viral dna . in the case of 3 and 4 , this binding functionis served by a 2,4 - difluorobenzyl carboxamide group , which is appended at the 3 - position of the bicyclic nucleus . previous work has shown that the nature and pattern of halogen phenyl substitution can significantly affect the potency of instis . in developing 3 and 4 , we found that a 2,4 - difluorobenzyl moiety , which is present in 2 , was superior to the other halobenzyl rings we tested . an important feature of 3 and 4 is that the carbonyl oxygen of the 2,4 - difluorobenzyl amide group may not be an obligatory component of the metal - chelating triad . as a consequence , there may be greater flexibility in this region of the molecule than is found with inhibitors , such as 1 , where the halobenzyl amide carbonyl participates in mg chelation . this flexibility is reminiscent of what is seen with 2 , where the flexibility of the haloamide component is thought to contribute to the ability of 2 to maintain efficacy against certain forms of in that are resistant to 1 . in our current work , we further modified the 1 - hydroxy -1,8-naphthyridin-2h - one nucleus by incorporating new functionalities at the 4 - position . in undertaking these efforts , we noted that for rnase h inhibitors such as 6 , an extended aryl functionality increased their inhibitory potency . in contrast to 6 , where the aryl functionality is attached through a methylene unit , for reasons of synthetic simplicity , we employed a 4 - amine group in 5a . subsequently , we prepared a series of analogues ( 5a5v ) using an iterative process of design , synthesis , biological evaluation , and redesign . amidation of methyl ester 7 ( obtained in three steps from commercially available methyl 2 - fluoronicotinate ) using 2,4 - difluorobenzylamine gave the known amide 8 in 70 % yield ( scheme 1 ) . subsequent reaction with toluenesulfonyl chloride produced the tosylated analogue 9 ( 93 % yield ) , which was treated with a variety of amines to provide 10a10v ( scheme 1 ) . a subset of these amines ( 10a10u ) was converted to final products ( 5a5u ) by hydrogenolysis of the n - benzyloxy group ( h2 / 10 % pdc ) . in the case of final product 5p , acetylation of intermediate 10o to yield 10p was done prior to debenzylation . for final product 5v , treatment of intermediate 10v with tfa yielded the free amine 11 prior to debenzylation ( scheme 1 ) . reagents and conditions : ( i ) 2,4 - difbnnh2 ; ( ii ) tscl , tea , mecn ; ( iii ) rrnh or rrnh - hcl , diea , dmf ; ( iv ) ac2o , tea , dcm ; ( v ) tfa , dcm ; ( vi ) h2 , 10 % pdc , meoh . compounds were evaluated in biochemical assays using radiolabeled oligonucleotides to measure their inhibitory potential in the 3 - p and st reactions . the initial series of compounds was designed to examine the role of aromatic functionality at the 4 - position . the in st inhibitory potency of 5a ( ic50 = 0.340.08 m , table 1 ) was approximately 10-fold better than the value previously reported for 6 , which contains a similar 1,4 - phenyl group . in contrast , introducing a 4 - nitrile or a 4 - amino group onto 5a ( giving 5c and 5d , respectively ) slightly increased the potency of the compound in the st reaction relative to 5a . importantly , shortening the 4 - substituent by removal of one phenyl ring gave an approximate 19-fold enhancement in potency relative to 5a ( 5e , st ic50 = 0.0180.006 m , table 1 ) . assays were performed using a gel - based protocol with mg cofactor as describe in ref ( 22 ) . antiviral potencies were evaluated in a cell - based assay using lentiviral vectors carrying wt in as well as mutant forms of in that are resistant to 1 , y143r , n155h , and the double mutant , g140s / q148h . in these assays , amine 5a was approximately two orders - of - magnitude more potent against the wt enzyme ( ec50 = 37263 nm , table 2 ) than what has been reported for 6 ( 32 m ) . all members of the series ( 5a5e ) showed nanomolar st inhibitory potencies against wt enzyme , with 5d and 5e being significantly more potent ( ec50 = 6.32.4 and 141.9 nm , respectively ) than other members of the series ( ec50 values 100 nm ) . because all compounds showed no cytotoxicity up to 250 m ) , selectivity indices ( si = cc50 / ec50 ) were from at least 500 to greater than approximately 40000 ( table 2 ) . of particular note , while compound 5e was only slightly less potent against the wt vector than what has been reported for 1 ( ec50 = 42 nm ) , it was significantly less susceptible to loss of efficacy against the mutants : y143r ( 2-fold loss versus a reported 54-fold loss for 1 ) , n155h ( 8-fold loss versus a reported 39-fold loss for 1 ) , and g140s / q148h ( 32-fold versus a reported 425-fold loss for 1 ) . the large loss of potency incurred by 1 against the y143r mutant derives from a loss of stacking of the inhibitor with the y143 phenyl ring . the ability of compounds in the current series to retain good efficacy against the y143r mutant indicates that they do not have a similar interaction as 1 with the aryl ring of y143 . cytotoxic concentration resulting in 50 % reduction in the level of atp in human osteosarcoma ( hos ) cells . cells were infected with viral constructs carrying in mutations and indicated values correspond to the fold - change ( fc ) in ec50 relative to wt . we prepared an additional series of analogues ( 5f5v ) in which several alkylamines were introduced at the 4 - position ( table 3 ) . in biochemical assays in vitro , most of these analogues exhibited low nanomolar inhibitory potencies in the st reaction . however , compounds 5i and 5k , which contained cycloheptyl and n - butylphenyl substituents , respectively , had st ic50 values of 0.460.18 and 0.280.11 m , respectively , which were markedly elevated relative to other members of the series . a third member of the series , having an ( s ) - ethyl n - prolinate group , was also significantly less potent [ ( s ) - 5u , st ic50 = 0.310.04 m ] ( table 3 ) . assays were performed using a gel - based protocol with mg cofactor as describe in refs ( 9 ) and ( 22 ) . antiviral potencies were determined for 5f5v in cells infected with viral vectors harboring wt and mutant forms of in ( table 4 ) . most compounds of the series displayed ec50 values in the low nanomolar range against the wt vector , with a majority of the compounds showing single - digit nanomolar potencies . these compounds also showed low cytotoxicity , which resulted in good si values , with several compounds showing si 10000 . noteworthy exceptions were compounds 5 g , 5h , and ( s ) - 5u , which not only had significantly reduced antiviral potencies ( ec50 values of 2688 , 1200260 , and 59072 nm , respectively ) but also showed greater cytotoxicity ( cc50 values of 131.8 , 8.43.2 , and 187 m , respectively ) ( table 4 ) . these latter compounds are the only members of the series having tertiary amines at the 4 - position . as such , these analogues would not be able to form internal hydrogen bonds between their 4 - amino groups and the 3 - carboxamide carbonyl oxygen . in spite of their poor antiviral efficacies , the in vitro st ic50 values for 5 g and 5h ( 87 and 79 nm , respectively , table 3 ) were only modestly elevated relative to most other members of the series ( typically 30 nm or lower ) . in some cases , the in vitro ic50 values for 5 g and 5h were better than compounds such as 5i and 5k ( 460 and 280 nm , respectively , table 3 ) , which paradoxically exhibited good ec50 values against the wt vector ( 123 and 5013 nm , respectively , table 4 ) . these data could indicate that being able to form an intramolecular hydrogen bond between the 4 - amino group and the 3 - carboxamide carbonyl oxygen has a more important role for the activity of the compounds in an antiviral assay done in cultured cells than in the biochemical assay done in vitro . cytotoxic concentration resulting in 50 % reduction in the level of atp in human osteosarcoma ( hos ) cells . cells were infected with viral constructs carrying in mutations and indicated values correspond to the fold - change ( fc ) in ec50 relative to wt . selectivity index ( si ) calculated as the ratio of cc50 to ec50 . the main objective of the current study was to derive minimally cytotoxic inhibitors having good antiviral potency against cells infected with wt virus , which also retained their efficacy against viruses harboring mutant forms of in that are resistant to 1 . as shown in table 4 , relative to their potencies against wt , almost all members of the current series maintained complete or nearly complete efficacy against virus having the y143r mutant . in addition , most members of the series showed good retention of efficacy against virus having the n155h and g140s / q148h mutants ( with a few exceptions , 10-fold or less loss of potency ) ( table 4 ) . members of the series also commonly exhibited high si values , in the range of four orders - of - magnitude . on the basis of these data , we examined selected members of the series ( 5o5q and 5v ) against a more extensive panel of insti - resistant mutants that included r263 k and g118r mutants , which have recently been identified through in vitro selection studies with second - generation instis . for reference , we also included 1 and 2 as well as the parent 1 - hydroxy -1,8-naphthyridin-2h - ones ( 3 and 4 ) , which formed the starting points for the current series . although 1 is potent against viral vectors that carry wt in ( ec50 = 42 nm ) , it shows extensive loss of antiviral efficacy against the mutants , y143r ( ec50 = 16216 nm ; 41-fold loss ) , n155h ( ec50 = 15433 nm ; 38-fold loss ) , and g140s / q148h ( ec50 = 1900300 nm ; 475-fold loss ) . compound 1 is more tolerant of the g118r mutant ( ec50 = 365 nm ; 9-fold loss ) and even less affected by the r263 k mutant ( ec50 = 94 nm ; 2-fold loss ) ( table 5 ) . in contrast , the recently fda - approved second - generation inhibitor 2 , while showing similar potency to 1 against wt vector ( ec50 = 1.60.9 nm ) , exhibits a significantly smaller loss of potency against vectors having the mutants y143r ( ec50 = 4.31.2 nm ; 3-fold loss ) , n155h ( ec50 = 3.61.3 nm ; 2-fold loss ) , and g140s / q148h ( ec50 = 5.80.5 nm ; 4-fold loss ) ( table 5 ) . however , as expected , 2 shows some loss of potency against virus having the r263 k ( ec50 = 113 nm ; 7-fold loss ) and g118r ( ec50 = 135 nm ; 8-fold loss ) mutants . cells were infected with viral constructs carrying in mutations and indicated values correspond to the fold - change ( fc ) in ec50 relative to wt . among the current series , the antiviral potencies of 5o5q are approximately equivalent to 1 against wt enzyme , with 5v being slightly more potent ( equivalent to 2 ) ( table 5 ) . compounds 5p , 5q , and 5v also show fold - loss of potencies that are approximately equivalent to 2 against the panel of mutants , with the exception of 5v , which shows greater fold - loss of potency against the mutant g140s / q138h ( 32-fold ) . however , because 5v has greater potency against the wt virus than either 5p or 5q , the effective antiviral potencies against virus having the g140s / q138h mutant are approximately equal for the three compounds ( ec50 = 35 nm ) . a summary analysis of table 5 shows that 5p exhibits a profile against the panel of mutants that is similar to 2 . because of its slightly better potency against wt in , compound 5v exhibits the best overall performance among the new inhibitors , with both absolute potencies and fold - loss of potencies against the various mutant vectors that are similar to 2 . the sole exception is the g140s / q148h mutant , where 5v suffers an approximate 7-fold loss of potency relative to 2 . importantly , 5v shows from 5 - to 10-fold enhanced performance across the entire panel relative to the starting compound 4 . the standard assays are performed in the presence of 5 % fetal bovine serum ( fbs ) . to examine the potential effects of serum protein binding on their antiviral potencies , compounds 5p , 5q , and 5vwere evaluated against the wt vector in the presence of increasing amounts fbs ( 5 % , 10 % , and 15 % ) . these experiments showed that the antiviral potencies of the compounds were essentially unchanged relative to values shown in tables 4 and 5 , which were obtained in the presence of 5 % fetal bovine serum protein ( data not shown ) . the title compounds were originally designed to chelate the two mg ions at the in active site . however , hiv - 1 reverse transcriptase ( rt ) also contains two active sites , the polymerase active site and the rnase h active site , each of which has two bound mg ions . to examine whether representative compounds of the series could also bind mg ions at one or both of the active sites in rt , we tested 5p , 5q , and 5v , to see whether they inhibited either the rnase h or the polymerase activity of rt . nevirapine , a well - known nonnucleoside reverse transcriptase inhibitor ( nnrti ) , was included as a positive control in the polymerase inhibition assays . the polymerase inhibition assays show that all three compounds are able to inhibit the dna - dependent dna polymerase activity of hiv - 1 rt ( figure 3a ) . all of the compounds are less potent than nevirapine in the polymerase assay , compound 5v the most potent , followed by 5p , then 5q . it is not clear at this point whether the compounds are binding the mg ions at the polymerase active site or binding within the nnrti - binding pocket near the polymerase active site , similar to nevirapine . it is also possible that they may be binding at some other site in hiv - 1 rt . polymerase and rnase h inhibition assays ( a ) : the effects of 5p , 5q , and 5v on the dna - dependent dna polymerase activity of rt are shown . reactions were performed with wt rt in the presence of various concentrations of compounds ( 0 , 0.02 , 0.1 , 0.5 , 1 , or 10 m ) . samples were precipitated with etoh and then fractionated on a 15 % polyacrylamide sequencing gel . rnase h inhibition assay ( b , c , d ) : the effects of 5p , 5q , and 5v on the rnase h activity of rt are shown . the reactions were incubated for the amount of time indicated ( 1 , 5 , 10 , and 15 min ) in the presence of the indicated concentration of the individual compounds ( 0 , 0.1 , 0.5 , 1 , and 10 m ) . the size of intact rna ( full length ) is 60 nt , as shown in the no - rt lane . the rna fragments derived from the 17 and 8 families of cleavages are shown . the compounds were also tested for their ability to inhibit the rnase h activity of rt . dna template / primer ( t / p ) , the 3 end of the dna primer is preferentially located at the polymerase active site ; the rnase h active site contacts the rna template approximately 17 to 18 nucleotides ( nt ) from the polymerase active site . the initial rnase h cleavage occurs approximately 17 nt from the polymerase active site . the rt then alters its interactions with the t / p , so that rnase h can make additional secondary cleavages approximately 8 nt from the 3 end of the primer ( 8 cleavages ) . we found that 5p , 5q , and 5v varied in their abilities to inhibit rnase h activity ( figure 3b d ) . however , the ranking of the potencies of the compounds in the rnase h assay is different from the polymerase assay ( figure 3a ) , which suggests that the compounds are interacting with the rt in different places in the two assays . the data show that 5q is the most potent inhibitor of rnase h ( it was the least potent compound in the polymerase assay ) . compound 5q did not completely block rnase h activity , even at the highest concentration ; a large amount of full length rna was present in the reaction that contained 5q at the 10 m concentration . it is also apparent that more of the product of the 17 cleavages remained after 10 and 15 min as compared to the no compound controls . similar results were obtained with 5v , while 5p had very little effect on rnase h activity . at the highest concentration , there were subtle effects on the 8 cleavages , but the compound is obviously less potent , in the rnase h assay , than the other two . it is quite difficult to use the results of the in vitro assays to estimate ic50 values . in the polymerase assay , it is clear that all of the compounds are less potent than nevirapine . we did not have a potent rnase h inhibitor that would allow us to make a similar comparison in the rnase h inhibitor assay . although it is clear that the current compounds are primarily in inhibitors , because these compounds can inhibit both the rnase h and polymerase activity of hiv - 1 rt , they could serve as the starting point for the synthesis of additional compounds that would be specifically designed to inhibit these alternate targets . in that regard , because there are no potent rnase h inhibitors , and because many of the known rnase h inhibitors are relatively toxic , using these compounds as leads to develop new rnase h inhibitors is a potentially attractive option . our current study examines the effects of introducing an amine functionality at the 4 - position of our previously reported 1 - hydroxy -1,8-naphthyridin-2h - ones ( 3 and 4 ) . the focus of the work was to enhance antiviral potency , with particular emphasis on retaining efficacy against viruses harboring mutant forms of in that have been shown to be resistant to the first - generation insti , 1 . for reference we employed 2 , which is a recently fda - approved second - generation insti with improved performance against the known resistant mutants . most members of the series of new inhibitors ( 5 ) show single - digit nanomolar antiviral potency against wt enzyme , with si values greater than 10000 . as a whole , the family of new inhibitors exhibited a smaller fold - change than 1 in antiviral assays that employed in mutants y143r , n155h , and the double mutant g140s / q148h . among the new inhibitors , compound 5p showed a profile against the panel of mutants that was comparable to 2 , with 5v exhibiting the best overall absolute performance among the new inhibitors , approximately 5 - to 10-fold enhancement relative to the starting compound 4 . although 2 is more effective than first - generation instis in its ability to retain efficacy against resistant forms of in , it has been shown that 2 can select for resistant forms of the enzyme . therefore , there is a continuing need for the development of new agents as potential alternatives to the currently approved panel of three fda - approved instis . the structural class of agents presented herein may represent an attractive platform for developing such next - generation instis . h and c nmr data were obtained on a varian 400 mhz spectrometer or a varian 500 mhz spectrometer and are reported in ppm relative to tms and referenced to the solvent in which the spectra were collected . solvent was removed by rotary evaporation under reduced pressure , and anhydrous solvents were obtained commercially and used without further drying . purification by silica gel chromatography was performed using combiflash rf 200i with etoac hexanes solvent systems . preparative high pressure liquid chromatography ( hplc ) was conducted using a waters prep lc4000 system having photodiode array detection and phenomenex c18 columns ( catalogue no .00 g -4436-p0-ax , 250 mm 21.2 mm 10 m particle size , 110 pore ) at a flow rate of 10 ml / min . binary solvent systems consisting of a = 0.1 % aqueous tfa and b = 0.1 % tfa in acetonitrile were employed with gradients as indicated . electrospray ionization mass spectra ( esi - ms ) were acquired with an agilent lc / msd system equipped with a multimode ion source . purities of samples subjected to biological testing were assessed using this system and shown to be 95 % . high - resolution mass spectra ( hrms ) were acquired by lc / ms - esi using an ltq - orbitrap - xl at 30k resolution . a solution of p - methylbenzenesulfonate ( 9 ) ( 1.0 mmol ) , n - ethyl - n - isopropylpropan -2-amine ( 10 mmol ) and amines rrnh or rrnhhcl ( 5.0 mmol ) in dmf ( 2.0 ml ) was heated to 50 c ( 1 h ) . the crude mixture was purified by combiflash silica gel chromatography ( hexanes and ethyl acetate ) to provide amides ( 10a10v ) . amides ( 10a10u or 11 ; 0.2 mmol ) were dissolved in meoh ( 15 ml ) and etoac ( 5 ml ) and the solution degassed and stirred at room temperature under h2 over pdc ( 10 % , 0.2 mmol ) ( 1 h ) . the mixture was filtered and the filtrate was concentrated , and the resulting residue was purified by hplc to provide amides ( 5a5v ) . a solution of methyl 1 - ( benzyloxy ) -4-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxylate ( 7 ) ( 1.0 g , 3.17 mmol ) and ( 2,4 - difluorophenyl ) methanamine ( 2.0 ml , 15.86 mmol ) in dmf ( 3.0 ml ) was subjected to microwave irradiation with stirring ( 140 c ; 2 h ) . the resulting product mixture was purified by combiflash silica gel chromatography to provide 8 as a white solid ( 964 mg , 70 % yield ) . h nmr ( 400 mhz , cdcl3 ) 10.35 ( t , j = 5.5 hz , 1h ) , 8.80 ( dd , j = 4.7 , 1.8 hz , 1h ) , 8.49 ( dd , j = 7.9 , 1.8 hz , 1h ) , 7.67 ( dd , j = 7.6 , 1.8 hz , 2h ) , 7.427.36 ( m , 4h ) , 7.31 ( dd , j = 7.9 , 4.7 hz , 1h ) , 6.896.82 ( m , 2h ) , 5.28 ( s , 2h ) , 4.66 ( d , j = 6.0 hz , 2h ) . esi - ms m / z : 438.1 ( mh ) . to a suspension of 8 ( 967 mg , 2.21 mmol ) in ch3cn ( 10 ml ) and ch2cl2 ( 2.0 ml ) were added n - ethyl - n - isobutyl -2-methylpropan-1-amine ( 2.81 ml , 13.27 mmol ) and 4 - methylbenzene -1-sulfonyl chloride ( 1.27 g , 6.63 mmol ) , and the mixture was stirred at room temperature ( overnight ) . the resulting mixture was purified by combiflash silica gel chromatography using solid loading to provide 9 as a colorless oil ( 1.21 g , 93 % yield ) . h nmr ( 400 mhz , cdcl3 ) 8.76 ( dd , j = 4.7 , 1.7 hz , 1h ) , 8.28 ( t , j = 5.8 hz , 1h ) , 8.23 ( dd , j = 8.1 , 1.7 hz , 1h ) , 7.907.88 ( m , 2h ) , 7.667.64 ( m , 2h ) , 7.477.45 ( m , 1h ) , 7.407.35 ( m , 5h ) , 7.97.26 ( m , 1h ) , 6.866.78 ( m , 2h ) , 5.30 ( s , 2h ) , 4.50 ( d , j = 5.9 hz , 2h ) . treatment of 9 with [ 1,1 - biphenyl ] -4-amine as outlined in general procedure a , provided 10a as a colorless oil in 97 % yield . h nmr ( 400 mhz , cdcl3 ) 13.23 ( s , 1h ) , 10.86 ( t , j = 5.5 hz , 1h ) , 8.62 ( dd , j = 4.5 , 1.5 hz , 1h ) , 7.91 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.717.69 ( m , 2h ) , 7.587.34 ( m , 7h ) , 7.287.23 ( m , 5h ) , 7.09 ( d , j = 8.5 hz , 2h ) , 6.88 ( dd , j = 8.3 , 4.5 hz , 1h ) , 6.84 ( d , j = 8.8 hz , 1h ) , 5.32 ( s , 2h ) , 4.65 ( d , j = 5.8 hz , 2h ) . treatment of 9 with 9h - fluoren -2-amine as outlined in general procedure a , provided 10b as a colorless oil in 99 % yield . h nmr ( 400 mhz , cdcl3 ) 13.31 ( s , 1h ) , 10.87 ( t , j = 5.7 hz , 1h ) , 8.59 ( ddd , j = 4.6 , 1.7 , 0.7 hz , 1h ) , 7.85 ( ddd , j = 8.3 , 1.6 , 0.7 hz , 1h ) , 7.767.15 ( m , 8h ) , 7.05 ( dd , j = 8.1 , 2.0 hz , 1h ) , 6.886.84 ( m , 3h ) , 6.836.78 ( m , 2h ) , 6.726.66 ( m , 2h ) , 5.33 ( s , 2h ) , 4.65 ( d , j = 5.8 hz , 2h ) , 3.84 ( s , 2h ) . esi - ms m / z : 601.2 ( mh ) . treatment of 9 with 4 - amino - [ 1,1 - biphenyl ] -4-carbonitrile as outlined in general procedure a provided 10c as a yellow solid in 98 % yield . h nmr ( 400 mhz , cdcl3 ) 13.21 ( s , 1h ) , 10.84 ( t , j = 5.7 hz , 1h ) , 8.66 ( dd , j = 4.5 , 1.6 hz , 1h ) , 7.91 ( dd , j = 8.2 , 1.7 hz , 1h ) , 7.747.60 ( m , 4h ) , 7.557.53 ( m , 2h ) , 7.447.38 ( m , 4h ) , 7.13 ( d , j = 8.5 hz , 2h ) , 6.94 ( dd , j = 8.3 , 4.6 hz , 1h ) , 6.886.80 ( m , 2h ) , 6.786.75 ( m , 2h ) , 5.33 ( s , 2h ) , 4.65 ( d , j = 5.8 hz , 2h ) . treatment of 9 with benzidine as outlined in general procedure a , provided 10d as a colorless oil in 97 % yield . h nmr ( 400 mhz , cdcl3 ) 13.20 ( s , 1h ) , 10.83 ( t , j = 5.8 hz , 1h ) , 8.668.50 ( m , 1h ) , 7.88 ( dd , j = 8.4 , 1.5 hz , 1h ) , 7.697.67 ( m , 2h ) , 7.44 ( d , j = 8.4 hz , 2h ) , 7.397.34 ( m , 3h ) , 7.327.287 ( m , 4h ) , 7.02 ( d , j = 8.6 hz , 2h ) , 6.866.80 ( m , 2h ) , 6.726.67 ( m , 2h ) , 5.29 ( s , 2h ) , 4.62 ( d , j = 5.8 hz , 2h ) . esi - ms m / z : 604.2 ( mh ) . treatment of 9 with aniline as outlined in general procedure a , provided 10e as a yellow solid in 65 % yield . h nmr ( 400 mhz , cdcl3 ) 13.19 ( s , 1h ) , 10.85 ( t , j = 5.7 hz , 1h ) , 8.61 ( dd , j = 4.5 , 1.7 hz , 1h ) , 7.81 ( dd , j = 8.3 , 1.6 hz , 1h ) , 7.69 ( dd , j = 7.8 , 1.6 hz , 2h ) , 7.437.36 ( m , 4h ) , 7.31 ( dd , j = 10.7 , 4.9 hz , 2h ) , 7.18 ( t , j = 7.4 hz , 1h ) , 7.067.041 ( m , 2h ) , 6.876.79 ( m , 3h ) , 5.32 ( s , 2h ) , 4.64 ( d , j = 5.8 hz , 2h ) . treatment of 9 with methanamine ( 2.0 m in thf ) as outlined in general procedure a , provided 10f as a white solid in 72 % yield . h nmr ( 400 mhz , cdcl3 ) 12.09 ( d , j = 4.9 hz , 1h ) , 10.83 ( t , j = 5.6 hz , 1h ) , 8.70 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.47 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.69 ( dd , j = 7.7 , 1.6 hz , 2h ) , 7.417.35 ( m , 4h ) , 7.207.17 ( m , 1h ) , 6.866.78 ( m , 2h ) , 5.26 ( s , 2h ) , 4.61 ( d , j = 5.8 hz , 2h ) , 3.41 ( d , j = 5.6 hz , 3h ) . treatment of 9 with dimethylamine hydrochloride as outlined in general procedure a , provided 10 g as a white solid in 91 % yield . h nmr ( 400 mhz , cdcl3 ) 8.61 ( dd , j = 4.6 , 1.7 hz , 1h ) , 8.20 ( dd , j = 8.1 , 1.7 hz , 1h ) , 8.05 ( t , j = 5.9 hz , 1h ) , 7.67 ( dd , j = 7.5 , 1.8 hz , 2h ) , 7.55 ( dd , j = 15.1 , 8.5 hz , 1h ) , 7.417.36 ( m , 3h ) , 7.19 ( dd , j = 8.1 , 4.6 hz , 1h ) , 6.886.78 ( m , 2h ) , 5.22 ( s , 2h ) , 4.66 ( d , j = 6.0 hz , 2h ) , 2.95 ( s , 6h ) . esi - ms m / z : 465.2 ( mh ) . treatment of 9 with morpholine as outlined in general procedure a , provided 10h as a colorless oil in 99 % yield . h nmr ( 400 mhz , cdcl3 ) 8.48 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.078.03 ( m , 2h ) , 7.687.60 ( m , 3h ) , 7.39 ( dd , j = 4.2 , 2.2 hz , 3h ) , 7.13 ( dd , j = 8.0 , 4.6 hz , 1h ) , 6.896.80 ( m , 2h ) , 5.08 ( s , 2h ) , 4.64 ( d , j = 5.9 hz , 2h ) , 3.613.59 ( m , 4h ) , 3.053.03 ( m , 4h ) . treatment of 9 with cycloheptanamine as outlined in general procedure a , provided 10i as a colorless oil in 96 % yield . h nmr ( 400 mhz , cdcl3 ) 11.77 ( d , j = 9.1 hz , 1h ) , 10.77 ( t , j = 5.7 hz , 1h ) , 8.69 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.24 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.68 ( dd , j = 7.8 , 1.6 hz , 2h ) , 7.417.34 ( m , 4h ) , 7.19 ( dd , j = 8.2 , 4.5 hz , 1h ) , 6.866.78 ( m , 2h ) , 5.26 ( s , 2h ) , 4.63 ( d , j = 5.7 hz , 2h ) , 4.01 ( dq , j = 13.2 , 4.4 hz , 1h ) , 2.132.05 ( m , 2h ) , 1.821.74 ( m , 4h ) , 1.621.60 ( m , 4h ) , 1.521.42 ( m , 2h ) . treatment of 9 with 2 - phenylethanamine as outlined in general procedure a , provided 10j as a colorless oil in 78 % yield . h nmr ( 400 mhz , cdcl3 ) 12.06 ( t , j = 4.7 hz , 1h ) , 10.77 ( t , j = 5.7 hz , 1h ) , 8.678.66 ( m , 1h ) , 8.30 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.697.66 ( m , 2h ) , 7.387.36 ( m , 4h ) , 7.297.21 ( m , 6h ) , 7.12 ( dd , j = 8.2 , 4.5 hz , 1h ) , 6.886.79 ( m , 2h ) , 5.24 ( s , 2h ) , 4.63 ( d , j = 5.8 hz , 2h ) , 3.963.91 ( m , 2h ) , 3.083.05 ( m , 2h ) . treatment of 9 with 4 - phenylbutan -1-amine as outlined in general procedure a , provided 10k as a colorless oil in 93 % yield . h nmr ( 400 mhz , cdcl3 ) 11.99 ( t , j = 4.6 hz , 1h ) , 10.79 ( t , j = 5.7 hz , 1h ) , 8.688.66 ( m , 1h ) , 8.31 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.68 ( dd , j = 7.5 , 1.5 hz , 2h ) , 7.397.33 ( m , 3h ) , 7.26 ( dd , j = 10.9 , 3.9 hz , 3h ) , 7.187.12 ( m , 4h ) , 6.836.78 ( m , 2h ) , 5.24 ( s , 2h ) , 4.62 ( d , j = 5.7 hz , 2h ) , 3.68 ( q , j = 6.3 hz , 2h ) , 2.65 ( t , j = 7.0 hz , 2h ) , 1.81 ( qd , j = 6.9 , 3.5 hz , 4h ) . esi - ms m / z : 569.2 ( mh ) . treatment of 9 with pentan -1-amine as outlined in general procedure a , provided 10l as a colorless oil in 95 % yield . h nmr ( 400 mhz , cdcl3 ) 11.99 ( t , j = 4.6 hz , 1h ) , 10.79 ( t , j = 5.7 hz , 1h ) , 8.68 ( dd , j = 4.5 , 1.2 hz , 1h ) , 8.39 ( dd , j = 8.2 , 1.4 hz , 1h ) , 7.68 ( dd , j = 7.5 , 1.5 hz , 2h ) , 7.427.35 ( m , 4h ) , 7.17 ( dd , j = 8.2 , 4.6 hz , 1h ) , 6.866.78 ( m , 2h ) , 5.25 ( s , 2h ) , 4.63 ( d , j = 5.7 hz , 2h ) , 3.70 ( td , j = 7.0 , 5.1 hz , 2h ) , 1.831.75 ( m , 2h ) , 1.531.26 ( m , 4h ) , 0.92 ( t , j = 6.9 hz , 3h ) . treatment of 9 with propan -2-amine as outlined in general procedure a , provided 10 m as a colorless oil in 73 % yield . h nmr ( 400 mhz , cdcl3 ) 11.66 ( d , j = 8.9 hz , 1h ) , 10.78 ( t , j = 5.6 hz , 1h ) , 8.718.67 ( m , 1h ) , 8.28 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.697.67 ( m , 2h ) , 7.407.34 ( m , 4h ) , 7.197.16 ( m , 1h ) , 6.866.78 ( m , 2h ) , 5.26 ( s , 2h ) , 4.63 ( d , j = 5.7 hz , 2h ) , 4.244.17 ( m , 1h ) , 1.40 ( d , j = 6.3 hz , 6h ) . treatment of 9 with tert - butyl ( 2 - aminoethyl ) carbamate as outlined in general procedure a , provided 10n as a white solid in 37 % yield . h nmr ( 400 mhz , cdcl3 ) 11.74 ( s , 1h ) , 10.75 ( t , j = 5.5 hz , 1h ) , 8.698.56 ( m , 1h ) , 8.34 ( d , j = 7.9 hz , 1h ) , 7.64 ( dd , j = 7.4 , 1.6 hz , 2h ) , 7.367.31 ( m , 4h ) , 7.177.13 ( m , 1h ) , 6.826.74 ( m , 2h ) , 5.20 ( s , 2h ) , 5.09 ( d , j = 18.3 hz , 1h ) , 4.57 ( d , j = 5.7 hz , 2h ) , 3.77 ( dd , j = 10.8 , 5.4 hz , 2h ) , 3.39 ( dd , j = 11.4 , 5.5 hz , 2h ) , 1.36 ( s , 9h ) . treatment of 9 with 2 - aminoethanol as outlined in general procedure a , provided 10o as a white solid in 71 % yield . h nmr ( 400 mhz , cdcl3 ) 11.74 ( t , j = 4.8 hz , 1h ) , 10.80 ( t , j = 5.7 hz , 1h ) , 8.698.68 ( m , 1h ) , 8.41 ( dd , j = 8.2 , 1.0 hz , 1h ) , 7.68 ( dd , j = 7.3 , 1.5 hz , 2h ) , 7.417.35 ( m , 4h ) , 7.197.15 ( m , 1h ) , 6.866.78 ( m , 2h ) , 5.24 ( s , 2h ) , 4.61 ( d , j = 5.7 hz , 2h ) , 3.903.80 ( m , 2h ) , 3.82 ( dd , j = 10.0 , 5.1 hz , 2h ) , 2.88 ( bs , 1h ) . to a solution of 10o ( 46 mg , 0.10 mmol ) in ch2cl2 ( 3 ml ) was added triethylamine ( 32 l , 0.23 mmol ) and acetic anhydride ( 11 l , 0.12 mmol ) and the solution was stirred at room temperature ( 1.5 h ) . purification by combiflash silica gel chromatography provided 10p as a white solid ( 26 mg , 52 % yield ) . h nmr ( 400 mhz , cdcl3 ) 11.93 ( t , j = 5.2 hz , 1h ) , 10.70 ( t , j = 5.7 hz , 1h ) , 8.67 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.29 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.64 ( dt , j = 4.1 , 2.2 hz , 2h ) , 7.377.29 ( m , 4h ) , 7.16 ( dd , j = 8.2 , 4.5 hz , 1h ) , 6.836.75 ( m , 2h ) , 5.22 ( s , 2h ) , 4.58 ( d , j = 5.8 hz , 2h ) , 4.29 ( t , j = 5.6 hz , 2h ) , 3.89 ( q , j = 5.5 hz , 2h ) , 2.05 ( s , 3h ) . treatment of 9 with methyl 2 - aminoacetate hydrochloride as outlined in general procedure a , provided 10q as a white solid in 95 % yield . h nmr ( 400 mhz , cdcl3 ) 12.27 ( t , j = 5.5 hz , 1h ) , 10.70 ( t , j = 5.6 hz , 1h ) , 8.71 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.22 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.67 ( dd , j = 7.8 , 1.7 hz , 2h ) , 7.447.35 ( m , 4h ) , 7.20 ( dd , j = 8.2 , 4.6 hz , 1h ) , 6.876.78 ( m , 2h ) , 5.26 ( s , 2h ) , 4.66 ( d , j = 5.7 hz , 2h ) , 4.44 ( d , j = 5.6 hz , 2h ) , 3.81 ( s , 3h ) . esi - ms m / z : 509.1 ( mh ) . treatment of 9 with methyl ( s ) -2-aminopropanoate hydrochloride as outlined in general procedure a , provided ( s ) - 10r as a white solid in 93 % yield . h nmr ( 400 mhz , cdcl3 ) 11.85 ( d , j = 8.8 hz , 1h ) , 10.67 ( t , j = 5.6 hz , 1h ) , 8.678.66 ( m , 1h ) , 8.15 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.63 ( dd , j = 7.4 , 1.6 hz , 2h ) , 7.377.31 ( m , 4h ) , 7.177.14 ( m , 1h ) , 6.836.75 ( m , 2h ) , 5.23 ( s , 2h ) , 4.644.58 ( m , 1h ) , 4.61 ( d , j = 6.3 hz , 2h ) , 3.70 ( s , 3h ) , 1.61 ( d , j = 6.9 hz , 3h ) . esi - ms m / z : 523.2 ( mh ) . treatment of 9 with methyl ( r ) -2-zminopropanoate hydrochloride as outlined in general procedure a , provided ( r ) - 10r as a white solid in 95 % yield . h nmr ( 400 mhz , cdcl3 ) 11.85 ( d , j = 8.8 hz , 1h ) , 10.67 ( t , j = 5.6 hz , 1h ) , 8.678.66 ( m , 1h ) , 8.15 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.63 ( dd , j = 7.4 , 1.6 hz , 2h ) , 7.377.317 ( m , 4h ) , 7.177.14 ( m , 1h ) , 6.836.75 ( m , 2h ) , 5.23 ( s , 2h ) , 4.644.58 ( m , 1h ) , 4.61 ( d , j = 6.3 hz , 3h ) , 3.70 ( s , 3h ) , 1.61 ( d , j = 6.9 hz , 3h ) . treatment of 9 with methyl ( s ) -2-amino-2-phenylacetate hydrochloride as outlined in general procedure a , provided ( s ) - 10s as a white solid in 91 % yield . h nmr ( 400 mhz , cdcl3 ) 12.76 ( d , j = 8.3 hz , 1h ) , 10.65 ( t , j = 5.7 hz , 1h ) , 8.61 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.01 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.62 ( dd , j = 7.6 , 1.8 hz , 2h ) , 7.51 ( dd , j = 7.9 , 1.2 hz , 2h ) , 7.397.31 ( m , 7h ) , 7.01 ( dd , j = 8.2 , 4.6 hz , 1h ) , 6.836.75 ( m , 2h ) , 5.53 ( d , j = 8.3 hz , 1h ) , 5.20 ( s , 2h ) , 4.67 ( qd , j = 15.3 , 5.8 hz , 2h ) , 3.69 ( s , 3h ) . treatment of 9 with methyl ( r ) -2-amino-2-phenylacetate hydrochloride as outlined in general procedure a , provided ( r ) - 10s as a white solid in 91 % yield . h nmr ( 400 mhz , cdcl3 ) 12.76 ( d , j = 8.3 hz , 1h ) , 10.64 ( t , j = 5.6 hz , 1h ) , 8.628.60 ( m , 1h ) , 8.027.96 ( m , 2h ) , 7.61 ( dd , j = 7.3 , 1.8 hz , 2h ) , 7.50 ( d , j = 7.4 hz , 2h ) , 7.437.24 ( m , 7h ) , 7.01 ( dd , j = 8.2 , 4.5 hz , 1h ) , 6.836.75 ( m , 2h ) , 5.53 ( d , j = 8.3 hz , 1h ) , 5.20 ( s , 2h ) , 4.66 ( qd , j = 15.3 , 5.7 hz , 2h ) , 3.68 ( s , 3h ) , 3.65 ( d , j = 0.8 hz , 4h ) . esi - ms m / z : 585.2 ( mh ) . treatment of 9 with methyl ( s ) -2-amino-3-hydroxypropanoate hydrochloride as outlined in general procedure a , provided ( s ) - 10ts as a white solid in 83 % yield . h nmr ( 400 mhz , cdcl3 ) 11.21 ( d , j = 9.7 hz , 1h ) , 10.66 ( t , j = 5.6 hz , 1h ) , 8.67 ( dd , j = 4.5 , 1.6 hz , 1h ) , 8.30 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.63 ( dd , j = 7.6 , 1.8 hz , 2h ) , 7.367.31 ( m , 4h ) , 7.17 ( dd , j = 8.2 , 4.6 hz , 1h ) , 6.836.75 ( m , 2h ) , 5.22 ( s , 2h ) , 4.604.57 ( m , 3h ) , 3.99 ( t , j = 4.8 hz , 2h ) , 3.75 ( s , 3h ) . esi - ms m / z : 539.2 ( mh ) . treatment of 9 with methyl ( r ) -2-amino-3-hydroxypropanoate hydrochloride as outlined in general procedure a , provided ( r ) - 10 t as a white solid in 97 % yield . h nmr ( 400 mhz , cdcl3 ) 11.19 ( d , j = 9.4 hz , 1h ) , 10.67 ( s , 1h ) , 8.68 ( d , j = 4.2 hz , 1h ) , 8.29 ( d , j = 8.1 hz , 1h ) , 7.63 ( d , j = 6.0 hz , 2h ) , 7.357.32 ( m , 4h ) , 7.17 ( dd , j = 8.1 , 4.5 hz , 1h ) , 6.826.76 ( m , 2h ) , 5.22 ( s , 2h ) , 4.604.58 ( m , 3h ) , 3.99 ( t , j = 5.4 hz , 2h ) , 3.75 ( s , 3h ) . treatment of 9 with ethyl ( s ) - pyrrolidine -2-carboxylate hydrochloride as outlined in general procedure a , provided 10u as a white solid in 73 % yield . h nmr ( 400 mhz , cdcl3 ) 8.64 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.34 ( dd , j = 8.0 , 1.6 hz , 1h ) , 8.16 ( t , j = 5.8 hz , 1h ) , 7.66 ( dd , j = 7.5 , 1.6 hz , 2h ) , 7.49 ( dd , j = 15.0 , 8.5 hz , 1h ) , 7.377.32 ( m , 3h ) , 7.237.19 ( m , 1h ) , 6.866.75 ( m , 2h ) , 5.24 ( q , j = 8.7 hz , 2h ) , 4.62 ( d , j = 3.4 hz , 2h ) , 4.37 ( dd , j = 8.5 , 3.8 hz , 1h ) , 4.013.94 ( m , 2h ) , 3.763.73 ( m , 1h ) , 3.503.45 ( m , 1h ) , 2.402.34 ( m , 1h ) , 2.021.98 ( m , 3h ) , 1.07 ( t , j = 7.1 hz , 3h ) . treatment of 9 with ( 2,4 - dimethoxyphenyl ) methanamine as outlined in general procedure a , provided 10u as a colorless oil in 89 % yield . h nmr ( 400 mhz , cdcl3 ) 12.00 ( t , j = 6.0 hz , 1h ) , 10.76 ( t , j = 5.7 hz , 1h ) , 8.65 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.28 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.707.68 ( m , 2h ) , 7.407.33 ( m , 4h ) , 7.267.24 ( m , 1h ) , 7.08 ( dd , j = 8.2 , 4.6 hz , 1h ) , 6.846.76 ( m , 2h ) , 6.476.45 ( m , 2h ) , 5.26 ( s , 2h ) , 4.73 ( d , j = 6.1 hz , 2h ) , 4.59 ( d , j = 5.7 hz , 2h ) , 3.79 ( s , 3h ) , 3.76 ( s , 3h ) . esi - ms m / z : 587.2 ( mh ) , 609.2 ( mna ) . to a solution of 10v ( 93 mg , 0.16 mmol ) in ch2cl2 ( 2.0 ml ) was added tfa ( 1.0 ml ) , and the mixture was stirred at room temperature ( 5 min ) then concentrated by rotary evaporation under reduced pressure . purification of the resulting residue by combiflash silica gel chromatography provided 11 as a white solid ( 69 mg , 100 % yield ) . h nmr ( 400 mhz , cdcl3 ) 10.62 ( t , j = 5.7 hz , 1h ) , 8.75 ( dd , j = 4.6 , 1.6 hz , 1h ) , 8.04 ( dd , j = 8.1 , 1.6 hz , 1h ) , 7.67 ( dd , j = 7.7 , 1.7 hz , 2h ) , 7.387.35 ( m , 4h ) , 7.24 ( dd , j = 8.1 , 4.6 hz , 1h ) , 6.876.78 ( m , 2h ) , 5.26 ( s , 2h ) , 4.63 ( d , j = 5.8 hz , 2h ) . treatment of 10a as described under general procedure b and purification by preparative hplc ( linear gradient of 50 % b to 90 % b over 30 min ; retention time = 22.8 min ) provided 5a as a white powder in 70 % yield . h nmr ( 400 mhz , dmso - d6 ) 12.31 ( s , 1h ) , 10.60 ( t , j = 5.8 hz , 1h ) , 8.61 ( dd , j = 4.5 , 1.7 hz , 1h ) , 7.86 ( dd , j = 8.2 , 1.7 hz , 1h ) , 7.617.55 ( m , 4h ) , 7.447.36 ( m , 3h ) , 7.27 ( t , j = 7.3 hz , 1h ) , 7.207.15 ( m , 1h ) , 7.13 ( d , j = 8.5 hz , 2h ) , 7.07 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.026.97 ( m , 1h ) , 4.46 ( d , j = 5.7 hz , 2h ) . treatment of 10b as described under general procedure b and purification by preparative hplc ( linear gradient of 60 % b to 80 % b over 30 min ; retention time = 21.3 min ) provided 5b as a white powder in 65 % yield . h nmr ( 400 mhz , dmso - d6 ) 12.54 ( s , 1h ) , 10.68 ( t , j = 5.7 hz , 1h ) , 8.59 ( dd , j = 4.5 , 1.6 hz , 1h ) , 7.82 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.79 ( d , j = 7.5 hz , 1h ) , 7.76 ( d , j = 8.1 hz , 1h ) , 7.49 ( d , j = 7.5 hz , 1h ) , 7.41 ( dd , j = 15.3 , 8.7 hz , 1h ) , 7.317.29 ( m , 2h ) , 7.247.20 ( m , 1h ) , 7.207.17 ( m , 1h ) , 7.07 ( dd , j = 8.1 , 1.8 hz , 1h ) , 7.026.97 ( m , 2h ) , 4.47 ( d , j = 5.8 hz , 2h ) , 3.79 ( s , 2h ) . treatment of 10c as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 80 % b over 30 min ; retention time = 22.3 min ) provided 5c as a white powder in 39 % yield . h nmr ( 400 mhz , dmso - d6 ) 12.13 ( s , 1h ) , 10.53 ( t , j = 6.2 hz , 1h ) , 8.64 ( d , j = 4.4 hz , 1h ) , 7.88 ( d , j = 8.2 hz , 1h ) , 7.83 ( bs , 4h ) , 7.67 ( d , j = 8.4 hz , 2h ) , 7.43 ( dd , j = 15.6 , 8.3 hz , 1h ) , 7.217.16 ( m , 3h ) , 7.11 ( dd , j = 9.0 , 3.8 hz , 1h ) , 7.00 ( t , j = 8.9 hz , 1h ) , 4.46 ( d , j = 6.1 hz , 2h ) . treatment of 10d as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 70 % b over 30 min ; retention time = 15.6 min ) provided 5d as a white powder in 51 % yield . h nmr ( 400 mhz , dmso - d6 ) 12.42 ( s , 1h ) , 10.89 ( bs , 1h ) , 10.67 ( t , j = 5.8 hz , 1h ) , 8.62 ( dd , j = 4.5 , 1.6 hz , 1h ) , 7.85 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.47 ( t , j = 7.9 hz , 2h ) , 7.437.40 ( m , 3h ) , 7.237.18 ( m , 1h ) , 7.09 ( d , j = 8.6 hz , 2h ) , 7.027.00 ( m , 2h ) , 6.76 ( d , j = 8.4 hz , 2h ) , 4.48 ( d , j = 5.9 hz , 2h ) . treatment of 10e as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 90 % b over 30 min ; retention time = 20.2 min ) provided 5e as a white powder in 86 % yield . h nmr ( 400 mhz , dmso - d6 ) 12.39 ( s , 1h ) , 10.86 ( s , 1h ) , 10.65 ( t , j = 5.7 hz , 1h ) , 8.61 ( dd , j = 4.5 , 1.6 hz , 1h ) , 7.75 ( dd , j = 8.2 , 1.7 hz , 1h ) , 7.42 ( dd , j = 15.4 , 8.7 hz , 1h ) , 7.27 ( t , j = 7.8 hz , 2h ) , 7.227.17 ( m , 1h ) , 7.137.00 ( m , 5h ) , 4.47 ( d , j = 5.8 hz , 2h ) . treatment of 10f as described under general procedure b and purification by preparative hplc ( linear gradient of 20 % b to 50 % b over 30 min ; retention time = 26.4 min ) provided 5f as a white powder in 63 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.19 ( bs , 1h ) , 10.08 ( bs , 1h ) , 8.59 ( d , j = 3.8 hz , 1h ) , 8.55 ( d , j = 8.1 hz , 1h ) , 7.48 ( dd , j = 15.4 , 8.5 hz , 1h ) , 7.22 ( dd , j = 8.0 , 4.5 hz , 1h ) , 7.187.13 ( m , 1h ) , 7.00 ( dd , j = 9.7 , 7.6 hz , 1h ) , 4.42 ( d , j = 5.6 hz , 2h ) , 3.12 ( s , 3h ) . esi - ms m / z : 361.1 ( mh ) . treatment of 10 g as described under general procedure b and purification by preparative hplc ( linear gradient of 20 % b to 45 % b over 30 min ; retention time = 21.6 min ) provided 5 g as a yellow solid in 89 % yield . h nmr ( 400 mhz , dmso - d6 ) 8.79 ( t , j = 5.9 hz , 1h ) , 8.57 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.19 ( dd , j = 8.0 , 1.6 hz , 1h ) , 7.70 ( dd , j = 15.5 , 8.7 hz , 1h ) , 7.25 ( dd , j = 8.0 , 4.6 hz , 1h ) , 7.187.13 ( m , 1h ) , 7.02 ( td , j = 8.5 , 2.6 hz , 1h ) , 4.38 ( d , j = 5.8 hz , 2h ) , 2.76 ( s , 6h ) . treatment of 10h as described under general procedure b and purification by preparative hplc ( linear gradient of 20 % b to 45 % b over 30 min ; retention time = 20.5 min ) provided 5h as a yellow solid in 82 % yield . h nmr ( 400 mhz , dmso - d6 ) 8.91 ( t , j = 5.8 hz , 1h ) , 8.628.61 ( m , 1h ) , 8.23 ( dd , j = 8.0 , 1.6 hz , 1h ) , 7.70 ( dd , j = 15.4 , 8.7 hz , 1h ) , 7.30 ( dd , j = 8.0 , 4.6 hz , 1h ) , 7.217.16 ( m , 1h ) , 7.05 ( td , j = 8.5 , 2.2 hz , 1h ) , 4.41 ( d , j = 5.8 hz , 2h ) , 3.673.65 ( m , 4h ) , 2.982.96 ( m , 4h ) . treatment of 10i as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 80 % b over 30 min ; retention time = 25.8 min ) provided 5i as a yellow solid in 87 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.68 ( bs , 1h ) , 10.45 ( t , j = 5.7 hz , 1h ) , 8.62 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.35 ( dd , j = 8.3 , 1.5 hz , 1h ) , 7.457.39 ( m , 1h ) , 7.26 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.17 ( ddd , j = 10.5 , 9.4 , 2.6 hz , 1h ) , 7.036.98 ( m , 1h ) , 4.44 ( d , j = 5.7 hz , 2h ) , 4.02 ( bs , 1h ) , 1.931.88 ( m , 2h ) , 1.581.50 ( m , 4h ) , 1.471.45 ( m , 4h ) , 1.311.38 ( s , 2h ) . treatment of 10j as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 80 % b over 30 min ; retention time = 22.0 min ) provided 5j as a yellow solid in 93 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.80 ( bs , 1h ) , 10.36 ( t , j = 5.8 hz , 1h ) , 8.59 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.48 ( dd , j = 8.3 , 1.6 hz , 1h ) , 7.42 ( dd , j = 15.3 , 8.6 hz , 1h ) , 7.227.18 ( m , 6h ) , 7.187.14 ( m , 1h ) , 7.036.98 ( m , 1h ) , 4.43 ( d , j = 5.8 hz , 2h ) , 3.823.78 ( m , 2h ) , 2.87 ( t , j = 7.3 hz , 2h ) . treatment of 10k as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 80 % b over 30 min ; retention time = 26.7 min ) provided 5k as a yellow solid in 78 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.96 ( bs , 1h ) , 10.48 ( t , j = 5.5 hz , 1h ) , 8.62 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.51 ( dd , j = 8.3 , 1.6 hz , 1h ) , 7.42 ( dd , j = 15.4 , 8.7 hz , 1h ) , 7.257.16 ( m , 4h ) , 7.127.07 ( m , 3h ) , 7.07 ( d , j = 7.0 hz , 1h ) , 7.016.97 ( m , 1h ) , 4.46 ( d , j = 5.7 hz , 2h ) , 3.61 ( bs , 2h ) , 2.54 ( t , j = 6.9 hz , 2h ) , 1.611.60 ( m , 4h ) . treatment of 10l as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 80 % b over 30 min ; retention time = 23.7 min ) provided 5l as a yellow solid in 72 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.95 ( bs , 1h ) , 10.47 ( t , j = 5.7 hz , 1h ) , 8.63 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.54 ( dd , j = 8.3 , 1.5 hz , 1h ) , 7.467.40 ( m , 1h ) , 7.24 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.19 ( ddd , j = 10.5 , 9.4 , 2.6 hz , 1h ) , 7.046.99 ( m , 1h ) , 4.46 ( d , j = 5.8 hz , 2h ) , 3.603.57 ( m , 2h ) , 1.57 ( dd , j = 14.0 , 7.0 hz , 2h ) , 1.291.21 ( m , 4h ) , 0.81 ( t , j = 7.1 hz , 3h ) . treatment of 10 m as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 80 % b over 30 min ; retention time = 17.0 min ) provided 5 m as a white solid in 80 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.47 ( bs , 1h ) , 10.42 ( t , j = 5.9 hz , 1h ) , 8.64 ( dd , j = 4.5 , 1.6 hz , 1h ) , 8.41 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.44 ( dd , j = 15.4 , 8.6 hz , 1h ) , 7.27 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.227.17 ( m , 1h ) , 7.02 ( td , j = 8.6 , 2.6 hz , 1h ) , 4.46 ( d , j = 5.8 hz , 2h ) , 4.174.09 ( m , 1h ) , 1.20 ( s , 3h ) , 1.18 ( s , 3h ) . treatment of 10n as described under general procedure b and removal of tert - butyl protection [ tfa ch2cl2 ( 1:1 , 2 ml ) , room temperature ] followed by purification using preparative hplc ( linear gradient of 0 % b to 40 % b over 30 min ; retention time = 25.9 min ) provided 5n as a white solid in 61 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.65 ( s , 1h ) , 9.88 ( t , j = 5.9 hz , 1h ) , 9.09 ( s , 1h ) , 8.69 ( dd , j = 4.5 , 1.3 hz , 1h ) , 8.48 ( dd , j = 8.1 , 1.4 hz , 1h ) , 7.83 ( bs , 2h ) , 7.65 ( dd , j = 15.6 , 8.8 hz , 1h ) , 7.34 ( dd , j = 8.1 , 4.6 hz , 1h ) , 7.277.21 ( m , 1h ) , 7.08 ( dd , j = 9.9 , 7.3 hz , 1h ) , 4.50 ( d , j = 5.5 hz , 2h ) , 3.68 ( q , j = 5.9 hz , 2h ) , 3.10 ( bs , 2h ) . treatment of 10o as described under general procedure b and purification by preparative hplc ( linear gradient of 20 % b to 50 % b over 30 min ; retention time = 21.6 min ) provided 5o as a yellow solid in 70 % yield . h nmr ( 400 mhz , dmso - d6 ) 11.13 ( bs , 1h ) , 10.49 ( t , j = 5.5 hz , 1h ) , 8.62 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.55 ( dd , j = 8.2 , 1.6 hz , 1h ) , 7.42 ( dd , j = 15.3 , 8.6 hz , 1h ) , 7.23 ( dd , j = 8.2 , 4.5 hz , 1h ) , 7.227.16 ( m , 1h ) , 7.02 ( dd , j = 9.3 , 7.7 hz , 1h ) , 4.46 ( d , j = 5.6 hz , 2h ) , 3.683.65 ( m , 2h ) , 3.56 ( t , j = 5.2 hz , 2h ) . treatment of 10p as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 50 % b over 30 min ; retention time = 23.6 min ) provided 5p as a white powder in 79 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.55 ( bs , 1h ) , 10.34 ( t , j = 5.5 hz , 1h ) , 8.69 ( d , j = 4.5 hz , 1h ) , 8.55 ( d , j = 8.2 hz , 1h ) , 7.52 ( dd , j = 15.4 , 8.6 hz , 1h ) , 7.32 ( dd , j = 8.1 , 4.3 hz , 1h ) , 7.277.22 ( m , 1h ) , 7.07 ( t , j = 7.4 hz , 1h ) , 4.51 ( d , j = 5.7 hz , 2h ) , 4.19 ( t , j = 5.1 hz , 2h ) , 3.84 ( d , j = 4.9 hz , 2h ) , 2.00 ( s , 3h ) . treatment of 10q as described under general procedure b and purification by preparative hplc ( linear gradient of 20 % b to 50 % b over 30 min ; retention time = 28.4 min ) provided 5q as a white solid in 44 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.43 ( brs , 1h ) , 10.09 ( t , j = 5.7 hz , 1h ) , 8.62 ( dd , j = 4.5 , 1.3 hz , 1h ) , 8.43 ( dd , j = 8.2 , 1.4 hz , 1h ) , 7.50 ( dd , j = 15.5 , 8.7 hz , 1h ) , 7.25 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.207.12 ( m , 1h ) , 7.00 ( td , j = 8.2 , 2.4 hz , 1h ) , 4.42 ( s , 2h ) , 4.41 ( s , 2h ) , 3.60 ( s , 3h ) . treatment of ( s ) - 10r as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 50 % b over 30 min ; retention time = 26.4 min ) provided ( s ) - 5r as a white solid in 40 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.18 ( t , j = 5.8 hz , 1h ) , 10.02 ( d , j = 8.4 hz , 1h ) , 8.70 ( dd , j = 4.5 , 0.9 hz , 1h ) , 8.46 ( d , j = 8.2 hz , 1h ) , 7.57 ( dd , j = 15.4 , 8.5 hz , 1h ) , 7.347.31 ( m , 1h ) , 7.23 ( dd , j = 13.8 , 6.1 hz , 1h ) , 7.07 ( td , j = 8.6 , 2.7 hz , 1h ) , 4.784.71 ( m , 1h ) , 4.49 ( qd , j = 15.5 , 6.0 hz , 2h ) , 3.61 ( d , j = 0.5 hz , 3h ) , 1.47 ( d , j = 6.9 hz , 3h ) . treatment of ( r ) - 10r as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 50 % b over 30 min ; retention time = 26.4 min ) provided ( r ) - 5r as a white solid in 40 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.18 ( t , j = 5.8 hz , 1h ) , 10.02 ( d , j = 9.6 hz , 1h ) , 8.70 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.46 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.57 ( dd , j = 15.5 , 8.8 hz , 1h ) , 7.33 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.24 ( ddd , j = 10.6 , 9.4 , 2.6 hz , 1h ) , 7.107.05 ( m , 1h ) , 4.74 ( dq , j = 13.9 , 6.9 hz , 1h ) , 4.49 ( qd , j = 15.2 , 5.7 hz , 2h ) , 3.61 ( s , 3h ) , 1.47 ( d , j = 6.9 hz , 3h ) . treatment of ( s ) - 10s as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 70 % b over 30 min ; retention time = 22.6 min ) provided ( s ) - 5r as a white solid in 51 % yield . h nmr ( 400 mhz , dmso - d6 ) 11.72 ( d , j = 8.0 hz , 1h ) , 10.57 ( t , j = 5.9 hz , 1h ) , 8.67 ( dd , j = 4.5 , 1.2 hz , 1h ) , 8.46 ( dd , j = 8.2 , 1.4 hz , 1h ) , 7.49 ( dd , j = 15.4 , 8.6 hz , 1h ) , 7.37 ( d , j = 4.2 hz , 3h ) , 7.357.31 ( m , 1h ) , 7.297.24 ( m , 2h ) , 7.09 ( dd , j = 9.8 , 7.3 hz , 1h ) , 6.01 ( d , j = 8.1 hz , 1h ) , 4.55 ( d , j = 5.7 hz , 2h ) , 3.61 ( s , 3h ) . treatment of ( r ) - 10s as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 60 % b over 30 min ; retention time = 26.3 min ) provided ( r ) - 5s as a white solid in 31 % yield . h nmr ( 400 mhz , dmso - d6 ) 11.72 ( d , j = 8.3 hz , 1h ) , 10.57 ( t , j = 5.4 hz , 1h ) , 8.67 ( d , j = 4.5 hz , 1h ) , 8.46 ( d , j = 8.2 hz , 1h ) , 7.49 ( dd , j = 15.2 , 8.6 hz , 1h ) , 7.377.36 ( m , 2h ) , 7.33 ( dd , j = 8.1 , 4.1 hz , 1h ) , 7.297.24 ( m , 2h ) , 7.09 ( dd , j = 9.8 , 7.1 hz , 1h ) , 6.01 ( d , j = 8.1 hz , 1h ) , 4.55 ( d , j = 5.6 hz , 2h ) , 3.61 ( s , 3h ) . treatment of ( s ) - 10 t as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 50 % b over 30 min ; retention time = 15.9 min ) provided ( s ) - 5 t as a white solid in 44 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.72 ( bs , 1h ) , 10.62 ( bs , 1h ) , 10.37 ( t , j = 5.9 hz , 1h ) , 8.70 ( dd , j = 4.5 , 1.5 hz , 1h ) , 8.38 ( dd , j = 8.2 , 1.5 hz , 1h ) , 7.52 ( dd , j = 15.4 , 8.7 hz , 1h ) , 7.31 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.25 ( ddd , j = 10.5 , 9.4 , 2.6 hz , 1h ) , 7.107.06 ( m , 1h ) , 4.774.72 ( m , 1h ) , 4.51 ( qd , j = 15.3 , 5.6 hz , 2h ) , 3.81 ( qd , j = 11.1 , 4.3 hz , 2h ) , 3.63 ( s , 3h ) . treatment of ( r ) - 10 t as described under general procedure b and purification by preparative hplc ( linear gradient of 25 % b to 50 % b over 30 min ; retention time = 20.5 min ) provided ( r ) - 5 t as a white solid in 42 % yield . h nmr ( 400 mhz , dmso - d6 ) 10.61 ( d , j = 8.7 hz , 1h ) , 10.37 ( t , j = 5.6 hz , 1h ) , 8.70 ( dd , j = 4.5 , 1.4 hz , 1h ) , 8.38 ( dd , j = 8.2 , 1.4 hz , 1h ) , 7.52 ( dd , j = 15.6 , 8.7 hz , 1h ) , 7.32 ( dd , j = 8.2 , 4.6 hz , 1h ) , 7.25 ( ddd , j = 11.2 , 10.6 , 6.4 hz , 1h ) , 7.07 ( dd , j = 9.7 , 7.3 hz , 1h ) , 4.75 ( dt , j = 8.8 , 4.3 hz , 1h ) , 4.51 ( qd , j = 15.4 , 5.8 hz , 2h ) , 3.81 ( qd , j = 11.0 , 4.4 hz , 2h ) , 3.63 ( s , 3h ) . treatment of ( s ) - 10u as described under general procedure b and purification by preparative hplc ( linear gradient of 40 % b to 70 % b over 30 min ; retention time = 12.5 min ) provided ( s ) - 5u as a yellow solid in 48 % yield . h nmr ( 400 mhz , dmso - d6 ) 8.91 ( t , j = 5.9 hz , 1h ) , 8.65 ( dd , j = 4.6 , 1.5 hz , 1h ) , 8.39 ( dd , j = 8.0 , 1.6 hz , 1h ) , 7.73 ( dd , j = 15.4 , 8.7 hz , 1h ) , 7.34 ( dd , j = 8.0 , 4.6 hz , 1h ) , 7.267.20 ( m , 1h ) , 7.09 ( td , j = 8.6 , 2.4 hz , 1h ) , 4.51 ( dd , j = 15.1 , 6.3 hz , 1h ) , 4.384.30 ( m , 2h ) , 3.95 ( q , j = 7.1 hz , 2h ) , 3.64 ( dd , j = 15.2 , 6.4 hz , 1h ) , 3.18 ( dd , j = 12.8 , 8.1 hz , 1h ) , 2.111.93 ( m , 1h ) , 1.921.87 ( m , 2h ) , 1.801.76 ( m , 1h ) , 1.03 ( q , j = 7.0 hz , 3h ) . treatment of 10v as described under general procedure b and purification by preparative hplc ( linear gradient of 30 % b to 50 % b over 30 min ; retention time = 19.5 min ) provided 5v as a white solid in 47 % yield . h nmr ( 400 mhz , dmso - d ) 10.59 ( t , j = 5.8 hz , 1h ) , 8.66 ( dd , j = 4.5 , 1.4 hz , 1h ) , 8.61 ( dd , j = 8.1 , 1.6 hz , 1h ) , 7.36 ( d , j = 6.6 hz , 1h ) , 7.30 ( dd , j = 8.1 , 4.6 hz , 1h ) , 7.18 ( d , j = 9.2 hz , 1h ) , 7.00 ( d , j = 2.4 hz , 1h ) , 4.46 ( d , j = 5.8 hz , 2h ) . esi - ms m / z : 347.1 ( mh ) . hrms calcd c16h13f2n4o3 [ mh ] , 347.0950 ; found , 347.0953 . determination of in 3 - p and st inhibitory values using an in vitro assay in reactions were carried out using [ - p ] - labeled dna as previously described . cytotoxicity was measured using the human osteosarcoma cell line , hos ( dr . richard schwartz , michigan state university , east lansing , mi ) , by monitoring atp levels using a luciferase reporter assay as previously reported . aspreviously described , the human embryonic kidney cell line 293 t was transfected with the pnlngomivrluc vector , which was made from pnlngomivrenv.hsa by removing the hsa reporter gene and replacing it with a luciferase reporter gene between the noti and xhoi restriction sites . vsv - g - pseudotyped hiv was produced transfecting 293 t cells as described previously . on the day prior to transfection , 293 t cells were plated on 100 mm diameter dishes at a density of 1.510 cells per plate .293 t cells were transfected with 16 g of pnlngomivrluc and 4 g of phcmv - g ( obtained from dr . jane burns , university of california , san diego ) using the calcium phosphate method . at approximately 6 hafter the calcium phosphate precipitate was added , the 293 t cells were washed twice with phosphate - buffered saline ( pbs ) and incubated with fresh media ( 48 h ) . the virus - containing supernatants were then harvested , clarified by low - speed centrifugation , filtered , and diluted for preparation in infection assays . on the day prior to the screen , hos cells were seeded in a 96 - well luminescence cell culture plate at a density of 4000 cells in 100 l per well . on the day of the screen , cells were treated with the compounds from a concentration range of 10 m to 0.0005 m using 11 serial dilutions and then incubated at 37 c ( 3 h ) . after this incubation , 100 l of virus stock diluted to achieve a maximum luciferase signal between 0.2 and 1.5 rlus was added to each well and the plates were incubated at 37 c ( 48 h ) . infectivity was measured by using the steady - lite plus luminescence reporter gene assay system ( perkinelmer , waltham , ma ) . luciferase activity was measured by adding 100 l of steady - lite plus buffer ( perkinelmer ) to the cells , incubating at room temperature ( 20 min ) , and measuring luminescence using a microplate reader . kaleidagraph ( synergy software , reading , pa ) was used to perform regression analysis on the data . the in coding region was removed from pnlngomivrenv.luc ( between kpni and sali sites ) and inserted between the kpni and sali sites of pbluescript ii ks + . using thisconstruct as the wild - type template , the following in - resistant mutants were prepared via the quikchange ii xl ( stratagene , la jolla , ca ) site - directed mutagenesis protocol : g118r , y143r , q148h , q148 k , n155h , g140s + q148h , g140a + q148 k , and e138 k + q148 k. the following sense with cognate antisense ( not shown ) oligonucleotides ( integrated dna technologies , coralville , ia ) were used in the mutagenesis : g118r , 5 - gtacatacagacaatcgcagcaatttcaccagtac - 3 ; e138 k , 5 - ggcggggatcaagcagaaatttggcattcccta - 3 ; g140a , 5 - ggggatcaagcaggaatttgccattccctacaatc - 3 ; g140s , 5 - ggggatcaagcaggaatttagcattccctacaatc - 3 ; y143r , 5 - gcaggaatttggcattccccgcaatccccaaagtcaagga - 3 ; q148h , 5 - cattccctacaatccccaaagtcatggagtaatagaatcta - 3 ; q148 k , 5 - cattccctacaatccccaaagtaaaggagtaatagaatctatgaa - 3 ; n155h , 5 - ccaaagtcaaggagtaatagaatctatgcataaagaattaaagaaaattataggaca - 3 . the double mutation g140s + q148h was constructed by using the previously generated q148h mutant and the appropriate oligonucleotide for the second mutation , g140s . the double mutation g140a + q148 k was made by using the q148 k mutant and the appropriate oligonucleotide for the second mutation , g140a . the double mutation e138 k + q148 k was made by using the q148 k mutant and the appropriate oligonucleotide for the second mutation , e138 k. the dna sequence of each construct was verified independently by dna sequence determination . the mutant in coding sequences from pbluescript ii ks + were then subcloned into pnlngomivrenv.luc ( between the kpni and sali sites ) to produce the full - length mutant hiv - 1 in constructs . the assay used to determine whether the compounds inhibit the of polymerase activity of rt has been previously described . briefly , the 47 sequencing primer ( 5 - cgccagggttttcccagtcacgac - 3 ; new england biolabs ) was 5 end - labeled with [ - p ] atp and t4 polynucleotide kinase . after purification , the labeled primer was annealed to single - stranded m13mp18 dna ( 1 g of dna for each sample to be assayed ) by heating and slow cooling . for each sample ,0.1 g of wild - type rt ( approximately 17 nm final ) added to the labeled primer template ( approximately 9.0 nm ) in 25 mm tris hcl ( ph 8.0 ) , 75 mm kcl , 10 mm mgcl2 , 100 g of bsa per ml , and 10 mm chaps . the reaction mixture was supplemented with 0.5 m ( each ) of datp , dctp , dgtp , and ttp . the compounds were added to give final concentrations of 0 , 0.02 , 0.1 , 0.5 , 1 , or 10 m . the reactions were allowed to proceed at 37 c for 60 min and were stopped by the addition of edta . the samples were precipitated by the addition of two volumes of etoh , fractionated by electrophoresis on a 6.0 % polyacrylamide gel , and the gel was autoradiographed . briefly , rna oligonucleotide ( 5 - ggggccacuuuuuaaaagaaaaggggggacuggaagggcuaauucacucac - 3 ) was obtained from dharmacon research , inc . the rna oligonucleotide was 5 - end labeled and was then annealed to a dna oligonucleotide ( 5 - gagtgaattagcccttccagtccc - 3 ) by heating and slow cooling . a 0.2 m concentration of the rna / dna hybrid was suspended in 25 mm tris ( ph 8.0 ) , 50 mm nacl , 5.0 mm mgcl2 , 100 g of bovine serum albumin / ml , 10 mm chaps , and 1 u of superasin ( ambion ) . the compounds were added to the reactions to give the following final concentrations ( 0 , 0.1 , 0.5 , 1 , and 10 m ) . the reactions were initiated by the addition of 50.0 ng of rt and were incubated at 37 c . aliquots were removed at the indicated time points , and the reactions halted by addition of 2 gel loading buffer ( ambion ) .\noutput:\n" }, { "from": "agent", "value": "there are currently three hiv - 1 integrase ( in ) strand transfer inhibitors ( instis ) approved by the fda for the treatment of aids . however , the emergence of drug - resistant mutants emphasizes the need to develop additional agents that have improved efficacies against the existent resistant mutants . as reported herein , we modified our recently disclosed 1 - hydroxy -2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides in inhibitors to develop compounds that have improved efficacies against recombinant in in biochemical assays . these new compounds show single - digit nanomolar antiviral potencies against hiv vectors that carry wild - type ( wt ) in in a single round replication assay and have improved potency against vectors harboring the major forms of drug resistant in mutants . these compounds also have low toxicity for cultured cells , which in several cases , results in selectivity indices ( cc50 / ec50 ) of greater than 10000 . the compounds have the potential , with additional structural modifications , to yield clinical agents that are effective against the known strains of resistant viruses ." } ]

[ { "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: myxoma is a benign tumor that originates from the mesenchymal tissue , often from the heart , skin , subcutaneous and aponeurotic tissue . primary intracranial myxomas are rare and only few cases have been reported in the literature . though metastatic brain myxomas from atrial myxomas are known but primary intracranial myxomas are very rare . a 12 - year - old male had 2 - month history of mild occipital headache which was unnoticed . local hairdresser noticed a slight bulge in the occipital region while doing haircut . his mri and ct brain showed evidence of a 5.34.64.9 cm expansile lytic sclerotic lesion arising from the right occipital bone showing prominent trabecular pattern . there was no edema but it was producing erosion of the right half of occipital bone extending up to c1 vertebra [ figure 1 ] . the diagnosis suggested was a malignant bone neoplasm ( ewing sarcoma ) or intraosseus hemangioma . a craniotomy with near total excision of the mass was done leaving residual mass near the vertebral artery . pre - op ct scan showing expansile lytic sclerotic lesion arising from the right occipital bone multiple small bony and soft tissue pieces with a slimy surface were submitted for histopathology . stellate cells with abundant myxoid matrix with few cells showing pleomorphic nuclei and few tumor giant cells were also seen . histological diagnosis of fibromyxoid tumor [ figure 2 ] was made and immunohistochemical markers were advised . sections from the tumor show bony trabeculae with stellate tumor cells with myxoid matrix ( h and e , 40 ) on immunohistochemistry the tumor cells expressed vimentin [ figure 3 ] . they were immunonegative for sma , desmin , cd34 , s - 100 , ema , ck , cd31 , and gfap .2 d - echocardiography was done to search for primary but there was no mass lesion in the cardiac muscles . postoperative radiotherapy for the residual lesion was started two weeks after wound healing and a total of 50.4 gy in 28 fractions to tumor bed was given on linear accelerator . post - radiotherapy ct scan showed minimal edema and no residual disease [ figure 4 ] . vimentin - positive stellate cells ( vimentin , 40 ) ct scan ( postoperative ) showing no residual diseasethey usually occur in the cardiac muscles which are known to cause neurological symptoms due to thromboembolic events and metastasis to the brain . primary intracranial myxomas are extremely rare . only few reports [ table 1 ] in literature exists on cerebral tumors that histopathologically resemble myxoma . myxoma may occur in any part of the cranial base but mainly occurs at the joints , such as sphenopetrosal suture and the petrooccipital suture . it has been reported that tumors were located behind the sigmoid sinus of the posterior fossa , hypophyseal fossa , cerebellopontine angle area , and the mastoideum of temporal bone . our patient had mass in the occipital region near occipito parietal joint indenting the right cerebellar hemisphere and was asymptomatic . summary of cases of primary intracranial myxoma none of the patients including ours had a cardiac focus and there was no familial inheritance . . this might not be feasible when the tumor invades into or derives from the skull base or vital structures prohibit a radical resection which may lead to recurrence . in our casehe was asymptomatic after removal of the tumor but received radiotherapy for the residual lesion . myxomas are most prevalent in patients in the third and fourth decade but can occur at any age and both sexes . they may arise from the meninges mimicking a meningioma or other forms of meningeal tumor . those appearing intracranially with no meningeal or dural attachment arise probably from the small vessels supplying the brain parenchyma . those arising from the bone develop in the marrow , expand the cortex , and destroy bone by aseptic necrosis . in this case , mri showed a well - defined soft tissue mass , extra - axial in location , in the posteroinferior aspect of right cerebellar hemisphere , producing erosion of the right half of occipital bone extending upto c1 vertebral level . an echocardiography is mandatory in all cases to differentiate a primary intracranial myxoma from atrial myxoma with embolisation . zhang et al . , delivered postoperative radiotherapy to eight patients in his series of 23 patients . hence for full appraisal of radiotherapy , further studies are required , although in our case we gave post - operative radiotherapy in view of the residual disease left by the surgeon . the differential diagnosis for myxoid intracranial tumors includes myxomatous meningioma , intracranial neurothekeoma , epithelioid hemangiothelioma , sarcoma with myxoid degeneration and metastatic myxoma . epithelial membrane antigen ( ema ) positivity is seen in patients who have meningioma with myxoid components . sarcoma stains positive for smooth muscle actin and desmin and neurothekeoma stains positive for s - 100 protein . true myxomas will stain positive for vimentin only and other markers are negative suggesting its mesenchymal origin . myxomas occur rarely as part of familial and inherited disorders such as carney 's complex or marfan 's syndrome ; however , such associations were absent in this patient . primary intracranial myxoma should be distinguished from other myxoid intracranial tumors such as myxomatous meningioma , epitheloid hemangioendothelioma or sarcoma through appropriate pathological and immunohistochemical analysis . the distinction between primary intracranial myxoma and neurothekeoma of the meninges also needs to be reassessed . surgery remains the main treatment and role of radiotherapy is not established but may be given for residual disease .\noutput:\n" }, { "from": "agent", "value": "myxomas are benign tumors arising from mesenchymal tissues throughout the body . these tumors are usually seen in the atrium of heart and the jaw bone . only a few cases of primary intracranial myxomas have been described in the literature . a rare case of primary myxoma of the occipital region is presented . a 12 - year - old boy had mild occipital headache for the past 2 months which was unnoticed . local hairdresser noticed a bulge in the occipital region while doing haircut and informed the parents and medical opinion was taken . he was seen by a neurosurgeon and after investigations he underwent craniotomy . near total resection of the tumor was achieved . histopathology and immunohistochemistry confirmed it to be a myxoma with no underlying cardiac focus . following surgery the patient had rapid recovery ." } ]

[ { "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: dermoid and epidermoid cysts are the developmental cysts encountered throughout the body , with 7 % occurring in the head and neck and only 1.6 % in the oral cavitythese cysts occur most often in patients in their 2 and 3 decade of life . clinically the lesion presents as a slow growing asymptomatic mass , usually located in the midline , above or below the mylohyoid muscle . when located above the muscle , the cyst manifests as a sublingual swelling ; when below the muscle the clinical aspect will be a submental swelling . in 1955 , meyer updated the concept of dermoid cyst to describe three histological variants , that is , the true dermoid , epidermoid and teratoid cyst . true dermoid cysts are cavities lined with epithelium with keratinization and skin appendages in cyst wall . the lining of teratoid cyst varies from stratified squamous to a ciliated respiratory epithelium containing derivatives of ectoderm , mesoderm and endoderm . teratoid cyst rarely arises in the head and neck region , in the oral cavity ; these cysts occur in the area of the floor of the mouth and may also occur on the tongue , lips , buccal mucosa or the interior of the bone . they are asymptomatic but their slow enlargement can cause obstruction with consequent dysplasia , dysphonia and dyspnea . a 2 - year - old female child was brought to our institute with swelling beneath the tongue . the swelling was present since birth , which was of peanut size and increased to the present size in the last 2 months [ figure 1 ] . clinical photograph showing swelling in the floor of the mouth on examination , a single swelling was seen in the floor of the mouth , measuring approximately 432 cm . the ct scan findings revealed a well - defined cystic lesion of approximately 4.93.13 cm in floor of the mouth with a small locule extending posteriorly and compromising anterior pharyngeal space [ figure 2 ] . there was no evidence of cervical lymphadenopathy nor did the swelling show any relation with the thyroid gland . based on the above findings , a clinical diagnosis of ranula was given and surgical excision was planned . computed tomography ( ct ) showing well - defined cystic lesion in the floor of the mouth the swelling was excised completely and sent for histopathological examination . on gross examination , the lesional tissue was creamish brown in color and measured 431.8 cm in size , it was soft in consistency , with smooth borders and surface [ figure 3 ] . on sectioning of the specimen , a cystic cavity was seen containing a thick creamish brown cheesy material with a foul odor . the hematoxylin and eosin ( h and e ) stained sections of the specimen showed ciliated pseudostratified columnar and stratified squamous orthokeratinized epithelial cystic lining over the fibrovascular connective tissue [ figure 4 and 5 ] . mucous cells and goblet cells were seen in the cystic epithelium . connective tissue capsule showed dermal appendages like sweat glands , sebaceous glands and hair follicle . adipose tissue and muscle tissue were also seen [ figure 6 ] . with observed histopathological picture a diagnosis of teratoid cystphotograph of the gross specimen after excision photomicrograph showing respiratory epithelium along with sweat glands and muscles in the connective tissue capsule ( h & e stain , 40 ) high power view showing keratinized stratified squamous and ciliated pseudostratified columnar epithelial lining ( h & e stain , 100 ) photomicrograph showing skin appendages along with muscles and adipose tissue ( h & e stain , 100 ) developmental cysts are the most common cause of cystic masses affecting the head and neck region in children . of these , thyroglossal cysts are the most common , accounting for 70 % of the cases , followed by branchial cleft cyst . epidermoid and dermoid cysts occur throughout the body , with 7 % occurring in the head and neck region and 1.6 % within the oral cavity . the origin of dermoid and epidermoid cysts of the floor of the mouth , like other developmental cysts , is controversial . the congenital theory postulates that these cysts are derived from the cell rests , entrapped during the midline closure of the bilateral first and second brachial arches . other possible theories of origin include : ( a ) ectodermal differentiation of multipotential cells pinched off at the time of anterior neuropore closure , ( b ) failure of separation of surface ectoderm from underlying neural tube , ( c ) they may arise from tuberculum impar of his ( d ) it has been proposed that it is a variant of thryroglossal cyst . the acquired theory proposes that the cysts are derived from traumatic or iatrogenic inclusion of epithelial cells or from occlusion of sebaceous gland duct . majority of the case occur between the ages 15 and 35 years with a slight male predilection . for oral lesions , lesions have also been reported in the buccal mucosa , tongue , lips , intraosseously in the mandible and maxilla . anatomically the cysts in the floor of the mouth can be further categorized as sublingual ( located above geniohyoid muscle ) , submental ( located between geniohyoid and mylohyoid ) and submandibular ( located in lateral aspect of floor of the mouth ) . it presents as painless , slow growing swelling which lifts the tongue and may lead to difficulty in eating , breathing or closing the mouth . deeper lesions between geniohyoid and mylohyoid muscles produces a swelling in the neck giving rise toit is generally seen that the cyst is well - encapsulated and the cystic cavity contains keratinous cheesy material . cystic lumen containing caseous , sebaceous , purulent material with hair , nail and fat globules have also been reported . histologically , the cysts were divided into the following types by meyer in 1955 : epidermoid cyst : they are lined by simple squamous epithelium , with fibrous wall and no dermal appendages . these cysts develop from the upper part of pilosebaceous unittrue dermoid cyst : they are lined by keratinizing stratified squamous epithelium with dermal appendages in the connective tissue wall . the lumen contains keratin , sebum and varying amounts of hair and fatteratoid cyst : they are lined by epithelium ranging from keratinizing squamous to pseudostratified columnar respiratory epithelium with dermal appendages in the connective tissue wall along with derivatives of all three germ layers ( ectoderm , mesoderm and endoderm ) . epidermoid cyst : they are lined by simple squamous epithelium , with fibrous wall and no dermal appendages . the cystic cavity lacks sebum or hair . these cysts develop from the upper part of pilosebaceous unit true dermoid cyst : they are lined by keratinizing stratified squamous epithelium with dermal appendages in the connective tissue wall . the lumen contains keratin , sebum and varying amounts of hair and fat teratoid cyst : they are lined by epithelium ranging from keratinizing squamous to pseudostratified columnar respiratory epithelium with dermal appendages in the connective tissue wall along with derivatives of all three germ layers ( ectoderm , mesoderm and endoderm ) . the differential diagnosis for this cyst includes ranula , sialolithiasis of submandibular gland ducts , thyroglossal duct cyst , cystic hygroma , brachial cleft cyst , cellulitis of floor of mouth , schwannoma , lipoma , etc . the lesion is usually treated by excision . based on the location of the cyst either an intra - or extraoral surgical approach is followed . teratoid cysts are uncommon lesions of the oral cavity and are usually not present since birth . in the present case , the lesion was present since birth in a 2 - year - old female child and histopathologically showed derivatives of all the three germ layers , hence the diagnosis of teratoid cyst was confirmed .\noutput:\n" }, { "from": "agent", "value": "the teratoid cyst is a rare variant of the dermoid cyst which seldom occurs in the oral cavity . if seen , they generally present as slow growing cysts of the floor of mouth , reported commonly in the 2nd and 3rd decade of life in males . histopathologically , dermoid cyst is classified as epidermoid cyst , true dermoid cyst and teratoid cyst depending on the presence of adnexal structures and derivatives of all three germ layers . herewith we report a rare case of teratoid cyst of the floor of the mouth , in a 2 - year - old female child , which was present since birth ." } ]

[ { "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: injuries occurring during skiing involve not only the lower but also the upper extremities1 . epidemiological data suggest that upper - body injuries account for 3050 % of all skiing injuries , and upper - extremity injuries for 2035 % 1 . the most common fracture among skiers is that of the clavicle , and the most common dislocation is that of the glenohumeral joint2 . the upper extremities engage in defensive mechanisms , protecting the trunk when the body falls2 . some studies have suggested that the proportion of upper - extremity injuries increases over time1 , 2 . , many shoulder muscles are subjected to continuous stress4 , which , if continuous , triggers responses such as protective muscle spasms3 , 4 . excessive spasms can limit the range of motion ( rom ) and cause serious muscle pain5 . in this study , the tester prescribed pain - free range exercises to a female amateur skier who complained of shoulder limitations in range of motion and pain caused by protective spasms . a 23 - year - old female who complained of pain in the right glenohumoral and scapulothoracic joints , developing 3 weeks prior , was enrolled . the study purpose and methodswere explained to the subject , who provided informed consent according to the principles of the declaration of helsinki before participating . the subject was a female amateur skier aged 23 years , and was radiographically free of shoulder bone fractures or ligament injuries . however , she complained of pain ( corresponding to a visual analog scale [ vas ] score of 9 ) in the posterior deltoid area , and exhibited shoulder rom limitations on initial evaluation ; shoulder flexion and abduction were 40 and 70 , respectively . because of her severe pain , she felt that massage and manipulation therapy were inappropriate . also , she could not perform rom exercises . during the first 2 - week session , pain control featured application of hot packs , electrical therapy , and ultrasound . as a result , the vas score fell to 8 , but no significant changes were observed in rom ; shoulder flexion and abduction were 45 and 75 , respectively . thus , the earlier treatment was discontinued and pain - free range exercises newly prescribed for 3 weeks . the subject attached a 3 - kg sandbag to each wrist , and performed shoulder flexion and abduction within the range 045 , and semi - wall push - ups 90 in terms of elbow flexion and 45 in terms of shoulder flexion . each sub - exercise was performed 20 times , and three sets of each sub - exercise were required over a 3 - week period . both shoulder flexion ( 175 ) and abduction ( 180 ) improved compared to the initial values . more skiiers complain of pain in excessively tense muscles caused by overloading of those muscles , or by exercise of defensive mechanisms associated with skiing , than of pain caused by serious skiing injuries ( bone fractures and ligament problems ) 1,2,3 . this study considered that our patient should not be treated , initially , with massage or manipulation therapy because of her severe pain , and because she could not perform rom exercises5 . after these exercises , the vas score was 2 , and both shoulder flexion and abduction improved compared to the initial values . as the subject could exercise without pain , the treatment may have been rapidly effective . in addition , muscle - strengthening exercise within the pain - free range may have rapidly reduced hypertonus , maintained muscle strength around the affected region ( which could have become weakened during recovery ) , and played a role in minimizing the decline in shoulder rom ( which could have occurred during recovery ) . in addition , the semi - wall push - up exercises may have strengthened the serratus anterior muscle and improved scapular stability . therefore , this study recommends that muscle - strengthening exercises within the pain - free range , rather than simple pain treatments , should be used to treat acute muscle injuries in skiers . in addition , future studies should consider relationships between shoulder injuries and skiier ability , physical strength , the equipment used , and environmental elements .\noutput:\n" }, { "from": "agent", "value": "[ purpose ] this study prescribed pain - free range exercises for a female amateur skier who complained of limitations in her shoulder range of motion , and pain caused by protective spasms ; the tester evaluated the effects of such exercise on pain . [ subject and methods ] a 23 - year - old female who complained of pain of 3 weeks in duration in the right glenohumoral and scapulothoracic joints was enrolled . [ results ] after pain - free range exercises , the visual analog pain score was 2 and the shoulder flexion and abduction angles improved compared to the initial values . [ conclusion ] thus , this study suggests muscle - strengthening exercises within the pain - free range , rather than simple pain treatments , as therapy for acute muscle injuries in skiers ." } ]

[ { "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: total joint arthroplasty is performed with objectives of providing pain relief and better quality of life to the patients suffering from arthritis of the hip and knee joints .1 rarely , serious complications including vascular injury can occur during the procedure , which may affect the outcome of surgery .123 the incidence of vascular injury in primary total hip arthroplasty ( tha ) is approximately 0.04 % .4 we report an unusual case of vascular injury during preparation of the acetabulum in primary tha . a 72 - year - old male presented with severe arthritis of left hip secondary to avascular necrosis of the femoral head . preoperative radiograph showed presence of a large osteophyte at the floor of the acetabulum [ figure 1a ] . a cementless total hip replacement with modified hardinge 's approach was performed using large head metal on metal articulation with articular surface replacement cup ( voluntary recall since august 2010 ) , unipolar metal head and corail femoral stem ( depuy orthopaedics , inc . , intraoperatively , a 3.2 mm drill was used to identify the floor of the acetabulum and the depth of reaming . two hours later , the patient developed unexplained hypotension with tachycardia , which was treated with colloids and 2 units of blood . abdomen and pelvis ultrasound examination conducted for investigating the cause of pain revealed a large ( 18 cm 10 cm 7 cm ) retroperitoneal hematoma . four units of fresh frozen plasma ( ffp ) and 6 units of platelets were administered for the management of hematoma . a lobulated pseudoaneurysm of 2.2 cm 1.2 cm size , arising from one of the branches of the left internal iliac artery [ figure 2a ] was reported in an emergency ct angiography . subsequently , the patient developed acute renal failure , which required hemodialysis and inotrope support for 10 days . on 19 day , the patient was discharged from the hospital with complete recovery and full weight bearing . a total of 16 units of blood , 4 units of ffp and 6 units of platelets were required for the treatment during his hospital stay . atsimilarly , no evidence of pseudoaneurysm was detected on repeat computed tomography ( ct ) angiography [ figure 2c ] . ( a ) preoperative radiograph of pelvis with both hips showing a large osteophyte at the floor of the acetabulum in the left hip ( b ) postoperative anteroposterior radiograph showing left hip arthroplasty ( a ) computed tomography angiography showing pseudoaneurysm of a tributary of left internal iliac artery ( b ) computed tomography angiography arrow showing post coil - embolisation of the pseudoaneurysm ( c ) six years followup of computed tomography angiography showing no pseudoaneurysmmodern total joint arthroplasty is a successful and safe surgery ; however there are chances of limb or life threatening vascular complications .1 vascular injury is relatively uncommon during primary tha compared to total knee arthroplasty and revision tha . indirect vessel injury can be the result of various causes including mechanical stretching , maneuvering of the limb and thermal injury from bone cement .1567 the common causes of vascular injury in tha are inadvertent placement of acetabular screws ,891011 thermal injury due to bone cement as well as fixation of intraoperative periprosthetic fractures , embolization or injury to the vessel wall during surgical approach or maneuvering of the limb .48 in our case , vascular injury was not caused by any of the above mentioned mechanisms , but occurred during preparation of the acetabulum by a depth assessment from a drill hole . medial acetabular osteophytes can result in lateralization of the cup which may affect abductor mechanics . these range from medial reaming to identify the pulvinar or using a power drill to make a small hole through the medial wall gradually and use a depth gauge to assess the bone thickness .12 we used a 3.2 mm drill bit to assist in placing the acetabular component in the optimum position . we believe that the vascular injury to the branch of internal iliac artery was probably caused by this technique which might explain the late presentation of symptoms of blood loss and formation of pseudoaneurysm [ figure 3 ] . the internal iliac artery is 4 cm long , begins at the common iliac bifurcation , level with the lumbosacral intervertebral disc and anterior to the sacroiliac joint . it descends posteriorly to the superior margin of the greater sciatic foramen where it divides into an anterior trunk , which continues in the same line towards the ischial spine and a posterior trunk , which passes back to the greater sciatic foramen . common iliac artery is most commonly involved ( 70 % ) , next the internal iliac artery is involved ( 25 % ) . iliac artery aneurysms are bilateral in approximately 30 % cases .1314 line diagram of the iliac vessels showing how the drill bit may have injured the branch of the internal iliac artery in the previous case series on vascular injury during tha , the injury is reported to affect the external iliac vein and artery or profunda femoris artery , which was treated by open surgery and vascular repair .14 however , in our case , injury occurred to internal iliac artery . we advice surgeons to be extremely careful while drilling medial wall of the acetabulum or use some other technique to identify the true acetabular floor . similarly , close postoperative surveillance is required for diagnosing the vascular injury which can be successfully managed with aggressive multidisciplinary approach .\noutput:\n" }, { "from": "agent", "value": "vascular injury is one of the rare complications of primary total hip arthroplasty ( tha ) . we report an unusual case of lobulated pseudoaneurysm arising from one of the branches of the left internal iliac artery during acetabulum preparation in tha , which was successfully treated with coil embolization and multidisciplinary care . after 6 years follow up , patient did not have any symptoms related to the hip replacement . we recommend that surgeons should be extremely cautious while drilling medial wall of the acetabulum for depth assessment . aggressive multidisciplinary approach , including possible support from an interventional radiologist is required for the treatment of such vascular injuries ." } ]

[ { "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: peripheral artery disease ( pad ) is an important marker of cardiovascular morbidity and mortality , with prevalence that increases progressively with age . the prevalence of pad ranges from 1 % 3 % , in the fourth or fifth decade of life , to greater than 20 % in the eighth decade .1,2 the ankle - brachial index ( abi ) , which is a noninvasive and inexpensive measurement used to identify pad in the elderly population , has remarkably high sensitivity and specificity ( 90 % , for each ) , compared against invasive angiography .3 abi , as a marker of pad , has been widely used to predict coronary artery disease ( cad ) .1,48 moreover , obstructive atherosclerotic lesions in at least one coronary artery have been reported in 60 % 80 % of patients with pad who had undergone cardiac catheterization .9 these patients had more extensive and calcified lesions , suggesting a more aggressive form of atherosclerosis .1012 the anatomical complexity of cad , and the number of vessels affected , influence the type of treatment that is offered to patients , and have an impact on short - and long - term prognosis . in recent years , the need for objective measurements to identify cad has spurred the development of several angiographic scores .1315 over the last few years , the syntax score ( ss ) has become the most widely used angiographic score , because it can guide the most appropriate type of revascularization ( percutaneous or surgical ) for each individual , and it also provides prognostic information for mid - term follow - up after revascularization .16 this study aimed to report a detailed description of coronary anatomical markers in older patients , with and without pad , and to compare the results with published data on general populations . the study recruited patients 65 years old who had been admitted to the federal university of so paulo consecutively between september 2011 and july 2012 for coronary angiography for ischemic coronary disease ( silent ischemia , stable angina , or acute coronary syndromes [ acs ] without st segment elevation ) . patients were excluded if they had acs with st elevation , creatinine clearance of 30 ml per minute , or if blood pressure could not be measured in one limb , for any reason . this study was approved by the institutional review board of the federal university of so paulo , brazil ( study number : cep 1299/11 ) . after the patient had rested for at least 5 minutes in a supine position , measurement was performed using a portable ultrasound doppler ( dv 610b ; medmega , so paulo , brazil ) and an innova aneroid sphygmomanometer ( bic , so paulo , brazil ) , with cuff inflators appropriate for brachial circumference . systolic blood pressure measurements of the brachial , tibial posterior , and dorsalis pedis arteries were taken on both sides of the limb . abi was calculated as the ratio between the lowest ankle systolic pressure and the highest brachial systolic pressure .17,18 abi was determined for each leg , and the lowest value was considered for analysis . the patients were divided into two groups , according to abi ( group 1 : abi 0.9 ; group 2 [ normal ] : abi 0.9 ) . although abi 1.3 is considered abnormal , none of our patients reached this value . coronary angiography was performed using conventional techniques , and analyzed by three experienced interventional cardiologists , who were blinded to clinical data . cad was defined as single vessel or multivessel disease , according to the number of epicardial arteries with at least one lesion measuring 50 % diameter stenosis . each coronary lesion measuring 50 % diameter stenosis was classified according to its complexity into types a , b1 ( one type b characteristic ) , b2 ( two or more type b characteristics ) , or c , according to the criteria of the american heart association . this classification is based on success rates for the percutaneous approach , with lower success rates reported for b2 and c type lesions .19 the ss evaluates stenosis that has caused a reduction of more than 50 % in luminal diameter , in vessels of 1.5 mm or larger diameter . the number and extent of lesions , the tortuosity of the affected segments , the presence of thrombus or calcification , total occlusion , and involvement of bifurcation or trifurcation were evaluated . the ss is the sum of the individual scores for each lesion , and was calculated using syntax score calculator software version 2.11 ( syntax score working group , www.syntaxscore.com ) . in the syntaxtrial ,16 the study which was responsible for development of the ss , only patients with three - vessel or left main cad were included , resulting in terciles with high values , compared with all comers studies . nevertheless , these values are widely used as a tool to choose between surgical ( ss 33 ) or percutaneous ( ss 22 ) revascularization . studies that include patients with one - and two - vessel disease provide a more appropriate , real world sample population , and yield terciles that compare appropriately to our group . at least two large trials included patients with stable and unstable coronary syndromes , allowing for proper comparison ; both yielded similar tercile levels , with patients in the highest level having ss 16.20,21 one study , which included only patients with non - st elevation acs , yielded slightly lower tercile and average values .22 these studies have demonstrated the value of the ss , as a prognostic tool for mid - term follow - up ; the higher the syntax score , the greater the risk for late events after revascularization .16,2022 next , we compared the rates for ss 33 , and ss 16 , in our population , and whether there was accordance with abi results . continuous variables were expressed as means with standard deviations , or as medians with 25th and 75th percentiles , according to the presence or absence of a normal distribution , as determined by the kolmogorovwhitney test and student s t - test were used for analyzing continuous variables , in accordance with the distribution . fisher s exact test , or the chi - square test , was used for categorical variables . a multivariable logistic regression model was used to identify potential independent predictors of cad , multivessel disease , and the presence of b2 or c type lesions in the overall population . odds ratios ( or ) and their respective 95 % confidence intervals ( ci ) were used to quantify the analyses . the variables included in the model were : age , sex , hypertension , dyslipidemia , diabetes mellitus , smoking status , and abi measurement . spss version 20.0 statistical software ( ibm corp , armonk , ny , usa ) was used for all analyses . a total of 204 patients were recruited , with a median age of 72.5 years ( interquartile range : 6877 years ) . we observed a higher number of female patients , and patients with acs , in group 1 ( patients with abnormal abi of 0.9 ) . abi had a sensitivity of 76.7 % , and a specificity of 55 % , for predicting obstructive cad , with an efficacy similar to the treadmill test .23 in the overall study population , abi of 0.9 was strongly associated with the presence of cad ( or = 2.43 ; ci : 1.474.03 ; p = 0.0001 ) . patients in group 1 more often exhibited multivessel disease ( or = 2.63 ; ci : 1.484.67 ; p = 0.001 ) and b2 or c type lesions ( or = 3.28 ; ci : 1.845.85 ; p = 0.0001 ) , compared with those in group 2 . the median ss in the general population was 7 ; it was significantly higher in group 1 than in group 2 ( 12 versus 3 ; p 0.001 ) ( table 2 ) . the number of patients with multivessel disease was slightly greater ( 66 % versus 50 % ; p = 0.05 ) , and rates of complex lesions ( b2 or c type ) were significantly higher ( 70.9 % versus 53.8 % ;p = 0.039 ) in group 1 , compared with group 2 . considering only patients with obstructive coronary disease , median ss values and rates of ss 16 were similar in both groups ( table 3 ) . considering only patients with multivessel disease , the proportion of patients with ss 33 was only 8 % among group 1 , and was zero in group 2 ( p = 0.1 ) . the risk of cad can be estimated on the basis of multiple markers of atherosclerotic disease . carotid intimal media thickening and high calcium scores , for example , have been associated with higher prevalence of cad .2426 more appropriate use of abi to diagnose pad has been well established in the literature . it has the benefit that it can be performed quickly by health care professionals , sparing advanced diagnostic methods .1,46 in a prospective study of 165 patients undergoing elective cardiac catheterization , abi was correlated with the number of coronary vessels with obstructive lesions , and with the angiographic gensini score .11 this relation also exists in patients undergoing cardiac catheterization on an urgent or emergency basis . in a multivariate analysis , pathological abi was significantly associated with the risk of multivessel disease in patients with acs ( or = 1.58 ; ci : 1.162.15 ; p 0.05 ) .12 our study investigated the anatomic characteristics in a high - risk group ( older than 65 years , and referred for coronary angiography ) and included the abi as a further indicator of atherosclerotic involvement . our use of a more sensitive method for calculating abi resulted in superior detection of cad prevalence in group 1 ; hence , abi is a good discriminator for the presence and severity of disease in the older general population . other trials have shown similar incidences of pad in patients with cad .27,28 patients with and without abnormal abi had similar demographic characteristics . however , the frequency of acs was higher in patients with abnormal abi ( 68 % versus 32 % ; p = 0.0001 ) . the presence of pad , irrespective of the diagnostic criteria used , is related to an increased risk of developing acs . the relative risk of myocardial infarction varies from 1.2 to 4.7 in several series .2932 pad is a powerful predictor of cardiovascular events , even compared to the prior existence of cad as a predictor .33 moreover , the association of pad and acs increases by 60 % the probability of progression to congestive heart failure .6 suitable characterization of coronary anatomy is essential in the selection of a revascularization strategy ( percutaneous or surgical ) , especially in high surgical risk groups . evaluation of coronary complexity by the number of vessels involved ( single or multivessel disease ) is flawed ; a patient may present various complex lesions in a single vessel , or have several lesions of low complexity , or without clinical significance , in multiple vessels . with the development of percutaneous intervention , which has allowed complex lesions to be treated with high success rates , the ss was created as a tool to quantify anatomical complexity , when percutaneous or surgical myocardial revascularization is being considered . in general , patients with high ss ( 33 in multivessel disease , or 16 in non-3-vessel disease patients ) have a greater risk of cardiovascular events after angioplasty , in comparison to events after surgery .16,22,34 aside from evaluating the angiographic characteristics of each lesion , the ss also considers the proportion of ischemic myocardium that is at risk from stenosis . this is one reason that may explain the prognostic suitability of the ss , as higher scores correspond to larger ischemic areas . korkmaz et al , after evaluating 150 patients with acs , irrespective of age , showed that patients with abi 0.9 had a higher ss , compared with patients with abi of 1.01.09 ( 17.89.1 versus 12.55.9 ; p 0.001 ) .35 in a recent study , ikeda et al selected 496 asian coronary angiography patients , with a mean age of 69.211.4 years , and compared abi against ss . they reported mean values of ss similar to ours for the abnormal abi group .36 however , an analysis was not performed for patients with cad only . benyakorn et al also demonstrated a significant negative correlation between abi and ss , but theirs was a different population , which included a large proportion of patients with valvular disease , and included all age groups .37 because of the higher surgical risk and the high frequency of comorbidities in elderly patients , percutaneous treatment is favored over surgical treatment . therefore , the ability to closely predict coronary anatomy is important . in this series , with the first record of a correlation between abi and the complexity of cad in elderly patients , the use of the ss as a quantitation tool for the disease has also helped us to understand the context of medical practice by which angioplasty has been used more often in elderly patients .38 once low rates ( only 8 % ) of high anatomic risk patients among those with multivessel disease are observed , the percutaneus intervention may be a good choice in a vast portion of this population . in the present study , the statistical correlation between abi and ss was lost when analyzing only patients with obstructive cad ( 13 versus 9 ; p = 0.148 ) , probably reflecting more extensive disease in the elderly in both groups . the similar frequencies , between groups , of patients with ss 16 , and ss 17 ( the last terciles of the limus eluted from a durable versus erodable stent coating ( leaders ) 20 and resolute21 trials , respectively ) may indicate a need to establish specific values for predict cardiac events in the elderly . within the realms of modern percutaneous intervention , abi did not identify in this population a subpopulation in which percutaneous revascularization could not be considered particularly if we contemplate a scenario in which functional revascularization is accessible , and would reduce the number of vessels to be treated .39 this small exploratory study has many limitations , including the small number of patients and the lack of clinical follow - up . the inclusion of patients who had been referred for coronary angiography selected a population with a higher incidence of coronary heart disease and pad . therefore , these results , in a population of asymptomatic elderly patients , should be interpreted with caution . the finding that ss was consistent with the proper indication for percutaneous intervention , in a large proportion of patients , confirms previous clinical observations . however , its significance can only be affirmed in randomized studies specifically designed for this purpose . abnormal abi is a marker of coronary complexity , even in high risk elderly patients . similar frequencies of patients with cad , in the highest terciles of the ss , between those with , and without , abnormal abi , are unexpected data , which should be explored in appropriately - sized studies .\noutput:\n" }, { "from": "agent", "value": "backgroundin the elderly , the ankle - brachial index ( abi ) has greater than 90 % sensitivity and specificity for peripheral artery disease identification . a well - known relation exists between peripheral artery disease and the number of diseased coronary vessels . yet , other anatomical characteristics have important impacts on the type of treatment and prognosis.purposeto determine the relation between abi and the complexity of coronary artery disease , by different anatomical classifications.methodsthis study was a prospective analysis of patients 65 years old who were undergoing elective coronary angiography for ischemic coronary disease . the abi was calculated for each leg , as the ratio between the lowest ankle pressure and the highest brachial pressure . the analysis of coronary anatomy was performed by three interventional cardiologists ; it included classification of each lesion with > 50 % diameter stenosis , according to the american heart association criteria , and calculation of the syntax score.resultsthe study recruited 204 consecutive patients ( median age : 72.5 years ) . stable angina was present in 51 % of patients . although only 1 % of patients reported peripheral artery disease , 45 % exhibited an abnormal abi . the number of lesions per patient , the number of patients with complex lesions , and the median syntax scores were greater in the group with abnormal abi . however , among 144 patients with obstructive coronary artery disease , despite abnormal abi being able to identify a higher rate of patients with b2 or c type lesions ( 70.9 % versus 53.8 % ; p = 0.039 ) , the mean syntax scores ( 13 versus 9 ; p = 0.14 ) , and the proportion of patients with syntax score > 16 ( 34.2 % versus 27.7 % ; p = 0.47 ) , were similar , irrespective of abi.conclusionin patients 65 years old the presence of peripheral artery disease could discriminate a group of patients with greater occurrence of b2 and c type lesions , but similar median syntax score ." } ]

[ { "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: neuroblastoma is the most common extracranial solid tumor in childhood and accounts for 7 % of malignancies in patients younger than 15 years . it originates from the sympathetic nervous system , and in particular from a developing and incompletely committed precursor cell derived from neural - crest tissues . neuroblastoma occurs sporadically in 98 % of cases ; a genetic defect is involved in the rare familial neuroblastoma . in the subset of cases of neuroblastoma presenting in the context of other congenital abnormalities of the neural crest , the association with a germline loss - of - function mutation of homeobox gene phox2b has been demonstrated ; on the other hand , familial neuroblastoma not associated with other congenital disorders of the neural crest arises from activating mutations of the anaplastic lymphoma kinase ( alk ) oncogene , whose somatic mutations are , however , observed in sporadic cases of the disease . due to the widespread presence of the sympathetic nervous tissue in various body organs and apparatus , the presenting features of neuroblastoma may be variable , depending not only on the location of the primary tumor but also on the frequent metastases . furthermore , in young children , neuroblastoma exceptionally manifests with paraneoplastic opsoclonus - myoclonus - ataxia ( poma ) due to antineuronal nuclear ( anti - hu ) antibodies which have also been associated with gastrointestinal disturbances , such as constipation , gut dismotility and paralytic ileus . on the contrary , watery diarrhea due to aberrant vasoactive intestinal peptide secretionproteinuria is not part of the presenting features of childhood cancer . in patients with neuroblastomawe report a case where proteinuria was the initial reason for medical evaluation in a child with neuroblastoma . a 10 - month - old girl was admitted to our hospital for investigations for nephrotic - range proteinuria . she was born to unrelated , italian , healthy parents , by spontaneous delivery at the 38th week of an uncomplicated pregnancy ; her birth weight was 3,110 g. her growth and development were normal until the age of nine months , when she began vomiting , feeding poorly , sweating copiously , and losing weight . on admission , her weight was 7,220 g ( 3th percentile ) , reduced from having previously reached 8,450 g ; her length was 68 cm ; her body temperature was 37.5 c with a heart rate of 150 beats / min and respiratory rate of 46 breaths / min ; blood pressure was normal on repeated measurements ( 82/43 mm hg ) . complete blood cell count showed leukocytes 12,800 / mm , red cell count 7,160,000 / mm , hemoglobin 15.7 g / dl , platelets 501,000 / mm . blood urea nitrogen was 28 mg / dl ( 10.23 mmol / l ) , creatinine 1.5 mg / dl ( 132.60 mol / l ) , glucose 92 mg / dl ( 5.1 mmol / l ) , ast 25 iu / l , alt 42iu / l ; total plasma protein level was 7.9 g / dl , with albumin 56.9 % ( 4.2 g / dl ) , a17 .3 % , a221 .3 % , 16.3 % , 23.4 % , 4.8 % ; uric acid was 8.5 mg / dl , sodium 138 mmol / l , potassium 3.2 mmol / l , chloride 88 mmol / l , venous ph 7.55 with a partial pressure of carbon dioxide of 29.2 mm hg ( probably due to crying and hyperventilation ) , bicarbonate 27.8 mmol / l and be + 4 . the at iii activity was 100 % , prothrombin activity 100 % and aptt 29 s , serum lactate dehydrogenase was 376iu / l and ferritin 5.9 mol / l ( normal value for age 7140 mol / l ) . she had polyuria and hypostenuria ( diuresis 125 ml / kg / 24 h ) ; urinalysis revealed nephrotic - range proteinuria ( 6,100 mg / 24 h ) with albuminuria 4,540 mg / 24 h , urinary loss of igg 107 mg / 24 h , and a1 microglobulin 29.4 mg / 24 h ; mild glucosuria ( 39 mg / dl ) and aminoaciduria were also found , without hematuria or casts ; urinary ph was 7.5 and urinary density 1,005 . electrocardiogram revealed sinus tachycardia 180 beats / min ; echocardiogram showed very mild concentric left ventricular hypertrophy , however , without pathological features . an endocrinologic evaluation revealed increased plasma renin ( 8 g / l / h ; reference range 1.0 - 4.5 g / l / h ) and aldosterone ( 4.83 nmol / l ; reference range 0.1 - 0.8 nmol / l ) levels , while cortisol and thyroid hormones were within the normal range ; plasma erythropoietin was 42.6 mu / ml ( reference range 3.7 - 37.5 mu / ml ) . urinary excretion of vanillylmandelic acid was increased to 11 mg / 24 h ( 1.57 mg / kg / 24 h ; reference range 0.1 - 0.18 mg / kg / 24 h ) , while catecholamines were in the normal range , except for the normetanephrine and noradrenaline , which were also elevated ( normetanephrine 1,537 g / 24 h , reference range 88 - 440 g / 24 h ; noradrenaline 120 g / 24 h , reference range 010 g / 24 h ) . the ultrasound abdomen examination revealed a solid , suprarenal mass on the left side , sized 22 cm ; the right kidney showed slightly increased echogenicity on the upper side . high - resolution ct showed an abdominal mass sized 55.810.7 cm , localized between the vertebral bodies d9 and l3 and the aorta , enveloping the celiac tripod , the superior mesenteric artery and bilaterally the renal vessels . the upper half of the right kidney showed an area of reduced perfusion , while the left kidney showed abnormal tissue density . adrenal glands were not identifiable in the context of the tumor mass , in which some calcifications were recognizable . histopathology showed a tumor with a low grade of neuroblastic differentiation , with mitosis - karyorrhexis index ( 2 % ) and elevated mitotic activity . in this patient , the presenting signs and symptoms of neuroblastoma included severe dehydration , polyglobulia , tubulointerstitial damage with acute kidney injury and renal insufficiency , electrolyte and acid - base unbalancing and heavy glomerular proteinuria . although diarrhea and dehydration may be observed at presentation of neuroblastoma , tubular alterations are definitely unusual . we have been able to identify only one case previously : a 4 - year - old boy affected by neuroblastoma presenting with nephrotic syndrome has been described in 1979 and renal histology demonstrated membranous glomerulonephritis due to immune complex . on the other hand , poma syndrome and gastrointestinal disturbances are associated with anti - hu antibodies , and furthermore , the development of immune complex has been demonstrated in mice with c1300 neuroblastoma tumors confirming the tendency of neuroblastoma to produce immunologic paraneoplastic diseases . nevertheless , in a recent study performed on a broad series of adults with solid tumors , the prevalence of rheumatic syndromes was only 2.65 % , and none of them manifested nephropathy , which shows the exceptionality of those manifestations also in adult patients . in our opinion , the physiopathology of the complex clinical picture of the case we describe herein is not ascribable to autoimmune pathogenesis , but rather to a hemodynamic mechanism , subsequently complicated by a series of other physiopathologic phenomena . the initial event was the development of the tumor mass from the adrenal glands and its extension upwards to envelope the great abdominal blood vessels and bilaterally the renal vessels . the meaningful feature is that the disruption of renal blood supply and the hemodynamic consequences have been different in the various areas of renal tissue , as revealed by sonography and ct findings . so , local increased intraglomerular pressure could prime the development of the hyponatremic - hypertensive syndrome , characterized by glomerular hyperfiltration with proteinuria , polyuria , acid - base and electrolyte unbalancing , as rarely described in children with renovascular systemic hypertension . although in those circumstances , as expected , the consequence of the proteinuria is the development of nephrotic syndrome , in other cases the plasma albumin inexplicably remains at a normal level , even in case of lasting and massive albuminuria , as in our patient . we could speculate that the severe dehydration , following copious sweating , vomiting and polyuria , caused such hypovolemia with hemoconcentration that plasma albumin concentration persisted beyond the threshold of edema . also the polyglobulia could be explained by the same mechanism , even if another factor could have been the increased production of erythropoietin , probably stimulated by local renal parenchyma hypoxia . hypovolemia was also responsible for the mild activation of the renin - angiotensin - aldosterone system and perhaps for metabolic alkalosis with hypochloremia and hypokalemia , but the loss of chloride through sweating was likely the most important cause of this phenomenon . hypovolemia and the disruption of local renal blood circulation caused acute kidney injury and the signs and symptoms of proximal tubular damage , as glucosuria and aminoaciduria . on the other hand , the profound hypochloremia was the cause of the metabolic alkalosis , instead of metabolic acidosis typically associated with proximal tubular damage . increased vasoactive amine secretion from neuroblastoma is not infrequent , and may cause elevated , although usually not severe , hypertension . in conclusion , in our 10 - month - old child , alteration of the renal function , at both the glomerular and tubular levels , were the presenting features of neuroblastoma , resulting from multiple pathogenic mechanisms . our report furthermore emphasizes the high variability and various facets of the clinical manifestations of neuroblastoma .\noutput:\n" }, { "from": "agent", "value": "neuroblastoma is the most common extracranial solid tumor in childhood . its presenting signs and symptoms may be highly variable , depending on the location of the primary tumor and its local or metastatic diffusion and , rarely , with paraneoplastic syndrome such as opsoclonus - myoclonus - ataxia syndrome and gastrointestinal disturbances , due to autoantibodies or to aberrant secretion of vasoactive intestinal peptide . herein we describe a 10 - month - old child with neuroblastoma presenting with a complex clinical picture characterized by acute kidney injury manifested by renal insufficiency and signs and symptoms of tubulointerstitial damage , with polyuria , polydipsia , glucosuria , aminoaciduria and hypochloremic metabolic alkalosis , and of glomerular damage with heavy proteinuria . imaging study documented a suprarenal mass enveloping the aorta and its abdominal and renal ramifications and bilaterally renal veins . this clinical picture shows some analogies with the hyponatremic - hypertensive syndrome concerning the renovascular disease ; however , in absence of systemic arterial hypertension , the heavy proteinuria and the polyuria could be explained by sectional increased intraglomerular pressure , due to local renal blood vessels constriction . hypochloremic metabolic alkalosis probably developed because of local production of renin , responsible of renin - angiotensin - aldosterone system activation , but above all because of chloride loss through sweating . the long lasting dehydration , due to vomiting , sweating and polyuria , caused prolonged prerenal failure evolving in proximal tubular damage manifestations ." } ]

[ { "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: our current lifestyle has led to an important increase in the demand for laxatives , medicinal products that induce or contribute to defecation . their high demand is clearly established : in 1995 , it was estimated that 25 % of women and 10 % of men in germany considered they had difficulty to defecate and suffered constipation . along with analgesics , laxatives are the most commonly obtained medicines by patients without consulting a doctor . therefore , they could be easily used inadequately and abusively . in germany sales figures of around 39 million units per year , with a value of dm 400 million , and in the united states around usd 600 million of laxatives are sold every year . the commercialization of laxatives is greater every year and covers broad sectors of modern society , where its use is observed in different economic strata and different age groups . this is a cause for concern and leads to a permanent analysis of risks which could be associated to the massive use of these types of medicines . among the most used laxativesbeing self - administed or prescribed by a physician , we find that senna infusions , bisacodyl , sodium picosulphate , sodium docusate , stimulating laxatives , and lactulose are considered osmotic - type laxatives . from its introduction by the arabs in the xix century , the anthranoid laxatives have been widely used around the world . among the plants that contain anthranoid laxatives , senna ( senna alexandrina or cassia angustifolia ) is the most used . due to their natural origin , apparent low oral toxicity , effectiveness , and accessibility without a medical prescription , there is an important need , therefore , to characterize the potential harmful and / or toxic effects of the anthranoid laxatives . the derivatives are obtained from leaves and / or dried pods of senna alexandrina , or from the direct use of the plant parts , separately or mixed . the anthranoid compounds are classified in anthrones ( rhein anthrone ) , anthraquinones ( aloe - emodin , chrysophanol rhein ) and dianthrones ( sennosides ) , and are present in plants mainly as sugar derivatives . since the - glycosidic bond is resistant to acid digestion and to - glycosidase activity in the small intestine , the anthranoid glycosides are not absorbed in the small intestine . instead , they are maintained as prodrugs until they reach the large intestine where they are metabolized to the active drug , the aglicone rhein anthrone for the - glycosidase and reductase activity of the intestinal flora . senna contains various anthranoids , where the most important are sennosides a and b ; followed by aloe - emodin , emodin , and chrysophanol . the sennosides , main active metabolite of senna , show a very low toxicity in rats and their genotoxic activity in bacterial strains as well as mammal cells , in the cases where it was significant , was classified as weak . the toxicological and mutagenic status of the senna crude extract , however , is less characterized . in a study by hietala et al . , the laxative effect and the acute toxicity of certain fractions of senna extracts in rats were investigated . results showed that the laxative and toxic components could be separated from pods and senna extracts . the most powerful laxative components , sennosides a + b and the v fraction ( with relative potentials of 1 and 0.9 , resp . ) have the lowest toxicity ( intravenous toxicity relative to 1 and less than 1 ) while the fractions with very low laxative activity ( rhein -8-glucoside and fraction iv with relative potentials of 0.56 and 0.05 ) have the highest acute toxicity ( relative toxicities of 10 and 32 , resp . ) . this suggests that there are other active molecules in the senna extract that could be responsible for its toxicity . anthranoids such as chrysantine , hidroxyanthraquinones , presenting in trace concentrations in the extract , show a different and highly controversial toxicological status to the sennosides . the hydroxyanthraquinones emodin and aloe - emodin gave positive results in genotoxic assays in salmonella typhimurium , v79 - hgprt , rat hepatocytes , and mouse fibroblasts , however , in another study , such genotoxicity was not observed . in a study by mori , the induction of neoplasms in the intestine , stomach , and rat liver , subjected to a diet containing 1 % hidroxyanthraquinones for 480 days , was induced . it is worth mentioning that these effects were only observed at extremely high doses and prolonged treatments . however , it is necessary to precisely pinpoint the possible harmful effects of the anthranoid laxatives , since recently and from results by siegers , it has been suggested that the chronic use of laxatives such as aloe ( aloe spp . ) , frangula ( rhamnus frangula ) , and cascara sagrada ( rhamnus purshiana dc ) could constitute a risk factor for the development of colorectal cancer . the objective of this article was to review scientific - medical publications found in different databases ( toxnet , ovid , ibids , sciencedirect , scirus , pubmed ) with keywords such as senna , sen , senna alexandrina , cassia angustifolia , sennosides , and laxative toxicity . web pages of products and companies that publicize or commercialize these types of laxatives were not included . the oral administration of sennosides ( 2030 mg / kg ) to fasting dogs induces a strong and prolonged inhibition of the myoelectric activity of the colon that is evident after a delay of 610 hours that corresponds to the orocecal transit and to the metabolism in the colon accompanied by an abundant diarrhea . when the sennosides are administered 1 hour prior to feeding , the habitual postprandial increase of colon motility does not appear . the modulation of colon motility by the sennosides has been broadly documented and the appearance of 3 to 10 giant contractions of high amplitude has been confirmed under its effect . these single contractions propagate in the second portion of the colon at a velocity of 0 , 52 cm / min . it has also been confirmed that these contractions are not only produced by sennosides but also by other compounds such as guanethidine , neostigmine , castor oil , and intraluminal hypertonic glucose . there is a direct influence on intestinal epithelial cells after the administration of the sennoside metabolite rhein - anthrone . at low doses , there is a change in cellular form and of the organelles clearly related to an increase in metabolism . it seems that the interaction between epithelial cells and the monocyte - type cells also induces the release of type e prostaglandins . when rhein - anthrone is added to a group of epithelial cells and mononuclear peripheral blood cells , there is a 140 % increase of the control value of pge2 . this finding indicates that rhein - anthrone is activating intestinal immune system components and may induce the secretion and motility . the oral administration of 50 mg / kg of sennosides modifies the net secretion of water , na and cl after 6 hours , a return to normal values occurs during the next 18 hours . after 24 hours , a significant increase in the secretion of k and ca is also observed . the sennosides do not modify the activity of the na k pump of the mucosa nor of the phophodiesterase enzyme ; the levels of camp do not vary either . at a reproductive toxicity level , by 1986 , u. mengs had established that the intragastric administration of sennosides did not induce embryolethal , theratogenic , or fetotoxic effects . in his assays , using rats and rabbits , he also determined that the sennosides did not have an effect on the postnatal development of young animals , on their mother 's behavior , nor on the masculine or feminine fertility . in 1987 , hietala et al . investigated the laxative and toxic activity using different fractions of senna on mice . their results showed that it was possible to identify the laxative components of those components that showed an acute toxic activity . these studies , however , only considered acute toxicity ( 24 hours ) and were carried out using very high doses . the sennosides were classified as not very toxic in rats and mice after administrating an oral dose . the ld50 values were 5000 mg / kg in both species . whatever the case , the cause of death was probably due to an intense water and electrolyte loss following an intense diarrhea . in subacute studies with rats and dogsto which a maximum dose of 20 mg / kg and 500 mg / kg was administered , respectively , the sennosides did not cause local nor systemic toxicity . a low weight increase was observed in the rat kidneys which was irrelevant . in a more prolonged study in ratsto which a dose of up to 100 mg / kg was administered , no toxic effects were observed after 6 months . the effects on food consumption , weight gain , and some biochemical parameters , in addition to slight renal lesions , were interpreted as secondary effects that arise as a consequence of a chronic diarrhea . in the same study , another toxicity study designed a treatment of rats with senna fruit extracts 1 , 25 , 100 , and 300 mg / kg / day for 104 weeks . based on clinical signs related to the laxative effect , such as the mucosity of the faeces , the 300 mg / kg / day dosethe animals reduced their body weight , increased their water consumption , and experienced notable changes of electrolytes with increases in k and cl in the plasma and decreases in cl , na , and k in the urine . after a gastric administration of 100 mg of sennosides / kg body weight , morphological changes are not observed in the rat colon . in the electronic microscopy examen , no damage in the intramural nervous tissue appeared . according to dufour and gendre , in 1988 , some animal and human studies revealed damages in the myenteric plexus and the colon epithelium , but they recognized that other studies had revealed the inexistence of such changes under similar treatments . these same authors carried out a histological and ultrastructural study to try and evidence the toxicity of sennosides in rats , acknowledging that they were unable to find intestinal mucosal damage after a long - term treatment . the comparison of the effect of the sennosides and an anthracenic derivative 1,8 - dihidroxyanthraquinone on the jejunum and colon of rats showed that only the synthetic compound caused anomalies in the myenteric plexus . this was interpreted as a good tolerance of the intestinal mucosa to sennosides , as opposed to nonglucosidic compounds . another study investigated the effect of the sennosides on the myenteric plexus of the colon . rats and mice were treated for 4 - 5 months with sennosides administered in drinking water . a decrease in the body weightwas observed while the colon weight increased in relation to the body weight of the animals tested . the determination of the number of neurons in the rat colon was not affected but an increase in relation to the controls was observed in mice . no evidence was obtained of destruction by toxicity or variation in the neuron population ; the appearance of isolated somas or axons was not observed by antibody staining , which would have detached from the myenteric plexus . it was concluded that senna did not destroy the myenteric neurons from the rat or mouse colon . it has been shown that the sennosides induce cytochemical changes in epithelium cells of the cecum , rectum , and colon of rats . after 12 weeks of treatment , an increase in the total acidic content of mucine with a decrease of sulfomucin and increase of sialomucin was observed . the results were interpreted as being of functional origin , and the association to early precancerous lesions was discarded . a light and electronic microscope study in intestine of guinea pigs treated for 14 consecutive days with senna , sennosides , danthron , and bisacodyl by gastric intubations showed a darkening of the mucous del cecum and the ascending colon except the group treated with bisacodyl . a degeneration of the cytoplasm and an increase of the apoptosis on the epithelial surface of the colon were observed with all the laxatives . the intestinal changes were more accentuated in the cecum and decreased toward the distal region of the colon . it was concluded that the morphological changes in the large intestine were similar in the treatments with anthranoid and nonanthranoid laxatives , however , the pigments found in the macrophage differed in color and were not always detected macroscopically . in 1968 and 1972 preliminary evidences appeared that led to a certain unease of the potential damaging effect of the stimulating laxatives . these initial investigations proposed that the laxatives containing anthraquinones induced degenerative changes in the nervous tissue of the colon ; however , when analyzed by various authors , these evidences received wide criticism due to the methodology used . recent results have undermined the importance of preliminary observations . in rats that were subjected during two years to a treatment with purified sennaextract in daily doses of 0 , 5 , 15 , and 25 mg / kg , administered with drinking water , it was discovered that no ultrastructural changes were produced in the myenteric plexus of the colon and jejunum . although the stimulating laxatives can cause structural damage to the surface of the intestinal epithelial cells , the damage results from an uncertain functional significance ; there is no convincing evidence that its chronic use brings as a consequence a structural and / or functional alteration of the enteric nerves or the smooth intestinal muscle . a clinical study was designed to determine the effects of sennosides on the histology of the colon mucosa and in the intestinal preparation for the diagnostic exam . a number of 84 patients received a maximum of 150 mg sennosides a and b , and an intestinal wash was carried out with 35 l ; the controls only received the intestinal wash solution . the samples from the patients treated with sennosides showed a marked increase in the infiltration of the lamina propria by mononuclear cells . with respect to the tolerance or quality of the intestinal preparation , there were no significant differences . however , because of the microscopic variations that appeared , the use of laxatives containing sennosides was not recommended in patients who were preparing for colonic biopsies . on the other hand , a recent study has concluded that an elevated dose of oral senna is a valid alternative to the conventional use of an intestinal wash solution with polyethylene glycol and electrolytes in the preparation of patients for a colonoscopy . the incidence of adverse effects was similar in both alternatives and patients who used senna commented on less nauseas and vomiting though more abdominal pain . in the necropsy of rats treated for 13 consecutive weeks with a senna preparation , the highest dose of which was 1500 mg / kg / day , a discoloration of the kidneys was observed together with histopathological changes . the latter was observed starting from the 300 mg / kg dose and consisted of a slight - to - moderate tubular basophilia and pigment deposit . this , however , did not correlate to functional changes in the kidney using the determination of set parameters in the laboratory . after an eight - week suspension of the use of the laxative , no histopathological anomalies were found , with the exception of the brown pigmentation of the kidneys . another toxicity study designed a rat treatment with senna fruit extracts 0 , 25 , 100 , and 300 mg / kg / day for 104 weeks . in the necropsy , a dark discoloration was observed on the kidneys of all the groups treated . in the histology , changes in the kidneys of all the animals of the groups treated were observed that included a slight - to - moderate tubular basophilia and pigment deposits . furthermore , slight - to - moderate hyperplasia was confirmed in the colon and the cecum . a similar condition to the human melanosis coli has been observed in the large intestine of the guinea pig after a daily administration of the anthraquinone danthron . each treatment provokes a transitory and dose - related wave of apoptosis on the surface of colon epithelial cells . the majority of the apoptotic bodies are phagocytosed by intraepithelial macrophages and transported through the fenestra of the basal epithelial membrane to the lamina propria . here , the apoptotic bodies transform into typical lipofucsin pigments in the lysosomes of the macrophages . the continuous administration of danthron provokes a progressive accumulation of pigmented macrophages on the intestinal wall while the migration of pigmented macrophages toward the lymphatic nodes region provokes , the sequential loss of the pigmented cells from the superficial and deep lamina propria , once the administration of danthrona ceases , suggesting a similar process in the formation of pigment in man . melanosis coli is experimentally induced using anthranoid laxatives and has been considered for a long time as a pigmentation that does not provoke damage in the colon and rectum and which is associated with the use of laxatives containing anthraquinones . in 1997 , a retrospective analysis of 2229 patients who used anthraquinone laxatives was carried out in search of a relation between melanosis coli and the use of laxative with the development of colorectal cancer . although the colorectal adenomas were found with a greater frequency in patients with melanosis than those without , the presence of colorectal cancer was not associated with melanosis coli or the use of laxatives . the adenomas related with melanosis coli were significantly smaller than those not associated with melanosis coli ( p .0001 ) and were located predominantly in the proximal colon . differences in the degree of dysplasia or adenomas between patients with or without melanosis coli were not found either . it seems there is no association between colorectal cancer and melanosis coli or the use of laxatives . although the colorectal adenomas are found more frequently in patients with melanosis coli , they do not contain the melanin pigment type . the association of adenomas with melanosis coli can be explained by the easy detection of polyps as white stains in a dark colored colonic mucosa . as has already been indicated , the chronic use of sennoside laxatives on some occasions causes pseudomelanosis coli and this has been associated to an increase in the risk of colorectal cancer . in patients subjected to enemas containing senna extracts , it was observed that the sennosides induce an acute massive loss of intestinal cells , possibly because of apoptosis , and alter the length of the colonic crypts causing the appearance of shorter crypts and an increase of the cellular proliferation and inhibition of the restoring apoptosis of the cellular function . these effects could be the basis of the mechanism that would explain a supposed cancer promoter effect of the chronic use of sennosides . it has been proven that the sennosides administered in an acute manner induce apoptosis of the epithelial cells of the colon , supposedly through the protein p53 genome guardian , mediated by p21 / waf , which results in shorter crypts . in conditions where severe melanosis coli was observed , apoptosis seems to be delayed , causing longer crypts without an increase of the proliferating activity or the expression of bcl - 2 , antiapoptotic gene . it has been suggested that the loss of a possible protective mechanism may increase the risk of carcinogenesis during the chronic use of sennosides . the focus of aberrant crypts is microscopic lesions of the colon mucosa which is suspected to be preneoplastic . the research was carried out to evaluate the cause - effect relation between putative risk factors and colorectal cancer . the anthraquinonic glycosides have been signaled as weak inducers of aberrant crypt foci in the rat colon mucosa , and , therefore , weak promoters of carcinogenesis of rat colon . the introduction in the rat diet of high dose of senna after 56 days did not provide evidence of the appearance of aberrant crypt foci and only enhanced the activity of dimethyl hydrazine , known inducer of aberrant crypt foci , when the highest doses of anthraquinonic glucosides were evaluated . in another study carried out in ratstreated daily for 1328 weeks with 10 mg / kg po of senna pods extract , a weak laxative effect was observed , which did not provoke an increase of the aberrant crypt foci or tumors in the rat colon ; while a diarrheogenic dose ( 100 mg / kg ) , capable of inducing chronic diarrhea for three months , increased the appearance of induced tumors by azoximethan known tumor inducer . it is worth mentioning that the usual daily dose in humans is of 0.4 mg / kg . in a study carried out in the universita di napoli , italy , and published in 2005 , the carcinogenic potential of the anthraquinones used was evaluated using an extract of senna pods . with this objective , healthy rats and rats treated with a tumor - indicating agent of azoximethanthe rats were administered 30 and 60 mg / kg of the senna extract for 110 weeks with no development of aberrant crypt foci or tumors in the healthy rats . surprisingly , the rats that had already been treated with azoximethan reduced the aberrant crypt foci and the tumors , suggesting that a chronic treatment with senna does not predispose to colon cancer and that in contrast , senna could have an antitumoral effect on the colon carcinogenesis . some years earlier in a review which tried to establishif the stimulating laxatives were harmful for the colon , it was assured that there was no reliable data that connected the chronic use of stimulating laxatives of colorectal cancer and other tumors . in the same article , it was indicated that the risks of stimulating laxatives had been overemphasized and that this had minimized its use by doctors . another study with patients with sigmoidal cancer and diverticular disease studied the possible association between sigmoidal cancer and constipation , use of anthranoid laxative and melanosis coli using the analysis of aberrant crypt foci as an additional research tool . in the study ,55 surgical patients with sigmoidal cancer were included , 41 surgery patients with diverticular disease , and 96 subjects without intestinal illness . constipation and use of anthranoid laxatives were similar between patients with sigmoidal cancer ( 30.9 % and 32.7 % , resp . ) and those with diverticular disease ( 39 % and 26.8 % ) but greater than in the controls ( 18.8 % and 8.3 % ) . melanosis coli was found in 38.2 % of the patients with sigmoidal cancer and in 39 % of those with diverticular disease . the median frequency of aberrant crypt foci was greater in patients with cancer sigmoidal ( 0.24 / cm ) than in those with diverticular disease ( 0.10 / cm ) and did not vary according to constipation , use of laxatives or melanosis coli in any of the groups . in this study , the hypothesis of a cause - effect relationship of the colorectal cancer with constipation , use of anthranoid laxatives , and melanosis coli was discarded . in the melbourne colorectal cancer study that included 685 cases of cancer colorectal and 723 controls , it was found that chronic constipation self - reported was more common between the cases of cancer than in the controls . constipation was discarded as a risk factor of intestinal cancer once previously determined dietary risk factors were included , indicating that the diet was associated with the risk of large intestine cancer and not constipation . this study concluded that it is unlikely that chronic constipation , diarrhea , and the frequency and consistency of intestinal movement , as well as the use of laxatives , are the etiological factors in the development of colorectal cancer . a retrospective study was carried out in 1993 with 2277 patients following a colonoscopy to determine if the use of laxatives and the existence of melanosis coli diagnosed by endoscopy were risk factors for colorectal neoplasm . results indicated that there was no increase in the rate of colorectal cancer neither in patients that used laxatives nor in those with melanosis coli . however , there was very significant association between the appearance of colorectal adenomas and use of laxatives ( between all patients : 1.72 ; patients that use laxatives without melanosis coli : 1.47 ) . since polyps can be diagnosed easily in the dark mucous of patients with melanosis coli , the authors of this study concluded that the risk of 2.19 seemed to be related to a generalized risk of laxative intake rather than a special group of laxatives that contain anthranoids . a prospective study carried out in the erlangen university , germany , investigated the risk of the use of anthranoid laxatives in the development of colorectal adenomas or carcinomas . a total of 202 patients with a recent diagnosis of carcinoma colorectal , 114 patients with adenomatous polyps , and 238 control patients without colorectal neoplasm were included . the use of anthranoid preparations was established in a standard interview , and the existence of melanosis coli visible endoscopically or by microscope was studied by a histopathological exam . there was no statistically significant risk for the use of anthranoids in the development of colorectal adenomas or carcinomas . the presence of macroscopic or microscopic melanosis coli was not a significant risk factor for the development of adenomas or carcinomas . the authors concluded that neither the use of long - term anthranoid laxatives nor melanosis coli were associated with a significant risk of developing colorectal adenoma or carcinoma . in experimental studies carried out in 1993 , the effects of the sennosides on cellular proliferation of the epithelium of the ileum and the large intestine were analyzed in rats in vivo . cell proliferation was examined by the brdurd labelling technique after 2 , 6 , and 12 weeks of continuous treatment . none of the laxatives used , bisacodyl , sennosides , sodium picosulphate , and lactulose , provoked an increase in the cellular proliferation as determined by the techniques used , and the pattern of proliferation remained constant along the crypts . the author concluded the study confirming that the contact laxatives do not have influence on the proliferation of the colon and should not be considered as tumor - promoting substances . subsequently , another article described that danthrone and sennoside a induced a significant cellular proliferation in the intestine of male f344 rats , after oral administration for 7 days . significantly , in the same study , it was indicated that the 1 - hidroxianthraquinone induced a slight proliferation of the epithelium in the cecum and colorectum with very little or no toxicity . one of the investigators of the melbourne colorectal cancer study carried out in australia in 1988 indicated in 1993 that the analysis of the patients that used laxatives grouped according to the type of laxative used , also allowed the establishment that the prior use of anthraquinone - like laxatives was not associated to colorectal cancer risk either ? . another study , carried out in rats treated for 2 years with a purified sen extract and which was administered through drinking water , centered on the possible carcinogenicity of this product , placing special emphasis on gastrointestinal alterations . the histopathological exam of the gastrointestinal tract , liver , adrenal kidneys , and other tissues with anomalies did not show differences in the incidence of neoplasic lesions , concluding that there was no relation between long - term administration of a senna extract and the appearance of gastrointestinal tumors or any other type in rat . another study on carcinogenicity and toxicity designed a treatment of rats with 0 , 25 , 100 , and 300 mg / kg / day of senna fruit extracts for 104 weeks . with the results obtained , it was possible to prove that there was minimal to no hyperplasia in the colon and cecum . neoplasic changes associated to the treatment with senna were not observed in any of the organs . based on their results , the authors concluded that senna is not carcinogenic in rats even after a daily administration for two years in doses of up to 300 mg / kg / day . the mutagenicity of crude senna preparations and of its glycoside was investigated by sandnes et al . in 1992 using different strains of salmonella typhimurium . the fruit and leaf senna extracts showed a weak activity in some strains ( ta97a , ta100 , and ta102 ) . the senna glycosides were inactive in all strains , except for a slight but significant increase in the mutation frequency of ta102 . nonidentified compounds in the crude senna preparations contributed to the low but biologically significant , dose - dependent mutagenicity ( greatest in strain ta98 ) . the weak or absent activity of the anthraquinone aglycones in the salmonella strains assayed indicates that the mutagenicity can not be attributed solely to the anthraquinone content of these plant materials . previously , in 1990 using a variety of structurally related hidroxyanthraquinones , it had been shown that the genotoxicity depends on certain structural requirements . in salmonella , the majority of compounds assayed were mutagenic on strain ta1537 , but only the hydroxyanthraquinones with a hydroxymethyl side chain such as lucidin and aloe - emodin were active on other strains . in v79 cells only those with 2 hydroxy groups in the 1 , 3 positions such as 1,3 - dihydroxyantraquinone , purpurin , and emodin or those with a hydroxymethyl side chain ( lucidin and aloe - emodin ) were mutagenic . other genotoxicity studies have been carried out by various laboratories with senna fructus , senna extract , sennosides , rhein , and aloe - emodin . the first three did not increase the mutation frequency in the following tests : bacterial systems ( reverse mutation test in salmonella and / or mutation test in escherichia coli ) , mammal cell cultures ( hypoxanthine guanine phosphorybosiltransferase test , lymphoma test in rat , chromosome aberration test with chinese hamster ovary cells ) , medulla osea ( micronucleus test , chromosomal aberration test ) , and melanoblast cells of rats ( stain test in rat ) . aloe - emodin showed mutagenic effects in vitro in the chromosome aberration test with chinese hamster ovarian cells and in the salmonella test . in in vivo studies , in the micronuclear test with nmri rat germ cells , chromosome aberration test with wistar rat germ cells , and others , there were no indices of mutagenic activity for aloe - emodin . the relevance of the absence of mutagenic potential in in vivo test systems was re - enforced by the fact that aloe - emodin could be found in the sanguine plasma after an oral administration of senna . senna extracts have been defined as nonmutagenic and as inhibitors of the mutagenicity induced by benzo [ a ] - pyrene , shamma , aflatoxin b1 , and methyl methanosulfonate in the ames histidine reversion assay using the salmonella typhimurium test strain ta98 . the determination of the genotoxicity profile of senna products , particularly emodin and aloe - emodin in light of other metabolism data in animals and humans or kinetic studies , clinical assays in humans and carcinogenic studies do not support the affirmation that senna - based laxatives mean a genotoxic risk in humans when ingested according to a prescription . anthraquinones glycosides of cassia angustifolia and c. fistula were investigated according to their capacity to induce a clastogenic effect in germ cells of swiss albino rats . the oral exposure to different doses of anthraquinone and the equivalent quantities in senna leaves and pods did not induce a significant number of chromosomal aberrations or aberrant cells . this reaffirms the concept that anthraquinone sennoside b and rhein are weakly genotoxic . in vivogenotoxic assays of senna extracts , analytically well characterized , have shown that after an oral dose administration of 2,000 mg of senna extract / kg to nmri , rats of both sexes , equivalent to 119 mg of potential rhein / kg , 5.74 mg of potential aloe - emodin / kg , and 0.28 mg of potential emodin / kg , did not provoke an increase in the levels of micronuclei assay in medulla ossea cells . the clastogenic activity of the senna extract observed in vitro could not be confirmed in the micronucleus assay . the authors of this study concluded that there is no conclusive indication that there is a risk of genotoxicity for patients who consume senna - based laxatives . as a summary , this analysis establishes that ( 1 ) there is no convincing evidence that the chronic use of senna brings as a consequence a structural and / or functional alteration of the enteric nerves or of the smooth intestinal muscle , ( 2 ) there is no relation between the long - term administration of a senna extract and the appearance of gastrointestinal tumors or of any other type in rat , ( 3 ) senna is not carcinogenic in rats even after a daily administration during 2 years in dose up to 300 mg / kg / day , and ( 4 ) the evidence currently available does not show that there is a risk of genotoxicity for patients who consume senna - based laxatives .\noutput:\n" }, { "from": "agent", "value": "due to their natural origin , apparent low oral toxicity , effectiveness , and accessibility without a medical prescription , the anthranoid laxatives are a popular remedy for constipation and are frequently used abusively . therefore , it is important to characterize its harmful and / or toxic effects . the sennosides , main active metabolites of senna , exhibit a very low toxicity in rats , and its genotoxic activity in bacterial strains as well as mammal cells was classified as weak in those cases where it was shown to be significant . the toxicological and mutagenic status of the crude extract of senna , however , is not as well characterized , and it is necessary to do so since it is frequently , and at the same time incorrectly , believed that the chronic use of anthranoid laxatives is a risk factor for the development of colorectal cancer . the objective of this article was to review the information that arises in various scientific medical databases using key words such as senna , sen , senna alexandrina , cassia angustifolia , sennosides , laxative toxicity , mainly isi and non - isi articles of journals with an editorial committee . web pages of products or companies that publicize or commercialize this type of laxative were not included . this analysis establishes that ( 1 ) there is no convincing evidence that the chronic use of senna has , as a consequence , a structural and / or functional alteration of the enteric nerves or the smooth intestinal muscle , ( 2 ) there is no relation between long - term administration of a senna extract and the appearance of gastrointestinal tumors or any other type in rats , ( 3 ) senna is not carcinogenic in rats even after a two - year daily dose of up to 300 mg / kg / day , and ( 4 ) the current evidence does not show that there is a genotoxic risk for patients who take laxatives containing senna extracts or sennosides ." } ]

[ { "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 world health organization defines dementia as a syndrome ; usually of a chronic or progressive nature , in which there is deterioration in cognitive function ( i.e. , the ability to process thought ) beyond what might be expected from normal aging . it affects memory , thinking , orientation , comprehension , calculation , learning capacity , language , and judgment . dementia is one of the major causes of disability and dependency among older people worldwide . worldwide , 47.5 million people have dementia , with just over half ( 58 % ) living in low - and middle - income countries . the estimated proportion of the general population aged 60 and over with dementia at a given time is 58 per 100 people . in 2010 , it is estimated that over 3.7 million people are affected by dementia in india . india 's demographic dividend is shifting to aging population and with this the numbers of persons with dementia will double every 5 years of age . hence , india will have one of the largest numbers of elders with this problem . evidence suggests that modifiable risk factors which can be targeted by prevention are vascular diseases , such as diabetes , midlife hypertension ( htn ) , mid - life obesity , midlife cholesterol , mid - and late - life depression as well as lifestyle factors such as smoking , physical inactivity , and poor diet . midlife htn is a highly predictive parameter of subsequent cognitive deterioration . in the framingham study , cognitive functioningwas negatively correlated with the initial systolic and diastolic blood pressure ( sbp and dbp , respectively ) values measured 1214 years before . diabetes mellitus ( dm ) causing micro and macrovascular complications is a well - known risk factor for stroke which if they accumulate or strike vital brain segments may cause dementia . a better understanding of the risk factors and identification of factors which would protect or may reduce the risk for dementia is essential for controlling this silent epidemic . this article reviews major modifiable risk factor such as htn and dm for dementia through a combination of observational studies . we comprehensively searched the national library of medicine 's pubmed database and google scholar from february to july 2016 . we used combinations of medical subject headings ( mesh ) and free text words that included search terms related to the exposure ( e.g. , prevalence , htn , raised bp , high bp , diabetes , high blood sugar , dm , india , state ) , which were combined with search terms related to the outcomes ( e.g. , prevalence , disease burden , estimate , dementia , india ) . the filters included were english for the language category and humans for the study category . we identified articles eligible for further review by performing an initial screen of identified titles or abstracts , followed by a full - text review . articles included in the review were cross - sectional or cohort ; studies conducted among adult populations ( 18 years old ) published after year 1995 . articles on the prevalence of dementia were searched first and were segregated region wise . the states or regions with reported dementia prevalencewere added in the mesh to search - related exposure ( dm and htn ) in that state . since chronic conditions such as cognitive decline start developing years after the incidence of htn , the studies on risk factors obtained were those published before or during the prevalence data of dementia . htn was defined as sbp more than or equal to 140 and or dbp more than or equal to 90 mmhg , and dm was defined as fasting blood sugar 126 mg / dl or postprandial blood sugar 200 mg / dl . articles were excluded if they were letters , abstracts , conference proceedings , case series , case control studies , reviews , and meta - analysis ; not conducted on humans ; not community - based studies , and not pertaining to regions with reported dementia prevalence . two independent reviewers ( desraj and mitasha singh ) screened the titles and abstracts of the initially identified studies to determine whether they would satisfy the selection criteria . any disagreements about selection were resolved through consensus or consultation with a third author ( manoj kumar gandhi ) . the retrieved studies were assessed again by two independent authors ( sunil kumar raina and vishav chander ) to ensure that they satisfied the inclusion criteria . this form was used by two independent reviewers to extract the relevant information from the selected studies ( des raj and mitasha singh ) . the data collection form included questions on year of publication , design , geographic origin and setting , and information on the reported exposure and outcomes ( e.g. , percentage of population with dementia , percentage of hypertensive patients , and percentage of diabetic patients ) . regression analysis was run for each of exposure variable ( dm and htn ) in linear regression analysis . we comprehensively searched the national library of medicine 's pubmed database and google scholar from february to july 2016 . we used combinations of medical subject headings ( mesh ) and free text words that included search terms related to the exposure ( e.g. , prevalence , htn , raised bp , high bp , diabetes , high blood sugar , dm , india , state ) , which were combined with search terms related to the outcomes ( e.g. , prevalence , disease burden , estimate , dementia , india ) . the filters included were english for the language category and humans for the study category . we identified articles eligible for further review by performing an initial screen of identified titles or abstracts , followed by a full - text review . articles included in the review were cross - sectional or cohort ; studies conducted among adult populations ( 18 years old ) published after year 1995 . the states or regions with reported dementia prevalence were added in the mesh to search - related exposure ( dm and htn ) in that state . since chronic conditions such as cognitive decline start developing years after the incidence of htn , the studies on risk factors obtained were those published before or during the prevalence data of dementia . htn was defined as sbp more than or equal to 140 and or dbp more than or equal to 90 mmhg , and dm was defined as fasting blood sugar 126 mg / dl or postprandial blood sugar 200 mg / dl . articles were excluded if they were letters , abstracts , conference proceedings , case series , case control studies , reviews , and meta - analysis ; not conducted on humans ; not community - based studies , and not pertaining to regions with reported dementia prevalence . two independent reviewers ( desraj and mitasha singh ) screened the titles and abstracts of the initially identified studies to determine whether they would satisfy the selection criteria . any disagreements about selection were resolved through consensus or consultation with a third author ( manoj kumar gandhi ) . the retrieved studies were assessed again by two independent authors ( sunil kumar raina and vishav chander ) to ensure that they satisfied the inclusion criteria . this form was used by two independent reviewers to extract the relevant information from the selected studies ( des raj and mitasha singh ) . the data collection form included questions on year of publication , design , geographic origin and setting , and information on the reported exposure and outcomes ( e.g. , percentage of population with dementia , percentage of hypertensive patients , and percentage of diabetic patients ) . regression analysis was run for each of exposure variable ( dm and htn ) in linear regression analysis . the pubmed search initially identified 269 references , and a total of 204 abstracts were screened by inclusion criteria . full - text assessment of 136 articles on the prevalence of dementia resulted in 20 relevant articles , from which the different regions of the country were identified . based on the search conducted according to the regions , 287abstracts of the prevalence of htn and 577 on the prevalence of dmthere were 43 full - text articles on prevalence of htn and diabetes from the regions where the prevalence of dementia was available . the prevalence of dementia has been studied using different criteria in different regions of the country . the highest prevalence in the above table 1 was observed from the southern state of tamil nadu from district vellore ( rural area ) reported prevalence of 10.6 % and from chennai ( urban ) reported a prevalence of 7.5 % using 10/66 dementia diagnosis criteria . the study ( 10/66 ) which reported dementia prevalence also reported prevalence of htn and diabetes in tamil nadu . the prevalence of htn ( 68.6 % ) and diabetes ( 12.1 % ) was higher in urban area as compared to rural ( 45.6 % and 6.6 % , respectively ) . list of observational studies included in north , punjab reported a high prevalence of dementia in district ludhiana , 8.5 % in urban , and 9.3 % in rural area using hindi version of mini - mental state examination ( hmse ) . another study in same region reported a prevalence of 35.9 % and 20.9 % of htn in the rural and urban area , respectively . the prevalence of dm was also reported to be higher in urban area as compared to rural area ( 14.2 % and 8.3 % , respectively ) . a higher prevalence of dementia was observed in the north , in the state of uttar pradesh in an urban area of lucknow city ; 6.2 % using mmse scale followed by cambridge examination for mental disorders of the elderly revised . another study also reported prevalence of dementia as 2.74 % using a series of tests from rural area of varanasi . the prevalence of htn was reported to be higher in rural area of varanasi ; 53.8 % as compared to urban area of lucknow ( 32.2 % ) . the state of maharashtra in west in a study from urban region of pune reported the prevalence of dementia to be 4.05 % , and the prevalence of htn and diabetes in this region as reported by india , ab study was 30.9 % and 10.9 % , respectively . reported a prevalence of dementia to be 3.77 % in an urban area of thiruvananthapuram using a cognitive screening battery followed by diagnostic evaluation , whereas another study from the same region reported 54.5 % prevalence of htn and 12.4 % prevalence of dm . a study from himachal pradesh in north reported the prevalence of dementia as 3.2 % from urban area , 1.4 % from rural area , and 1.25 % from tribal area using hmse scale . other studies from same region reported a higher prevalence of htn from rural area ( 37.4 % ) as compared to urban ( 28.1 % ) and tribal area ( 10.7 % ) . the prevalence of dm was reported to be 7.8 % from urban area and 3.9 % from tribal area . the prevalence of diabetes and htn with dementia from table 1 was subjected to linear regression analysis . table 2 depicts the pearson 's correlation coefficient of the relation between the prevalence of exposure and outcome . an imperfect positive association was observed for both htn ( r - 0.17 , p - 0.62 ) and diabetes ( r - 0.22 , p - 0.57 ) with dementia . the same has been shown in scatter plots of figures 1 and 2 . correlation between prevalence of hypertension and dementia correlation between the prevalence of diabetes mellitus and dementiahtn has been identified as one of the most important controllable risk factors for stroke , which in turn can result in vascular dementia . according to barnes and yaffe , given the available literature from epidemiological studies and randomized controlled trials only mid - life , not late - life htn is associated with an increased risk of ad and dementia . about 5 % ( 1.7 million ) of ad cases worldwide are potentially attributable to mid - life htn according to barnes and yaffe . , of 14 eligible longitudinal population - based studies , the risk of dementia is , in general , increased in patients with dm , and this increased risk seems to include both alzheimer 's disease and vascular dementia . on analysis by pasquier et al. of prospective and cross - sectional studies , found evidence of an elevated risk of both vascular dementia and ad in patients with strong interaction of other factors such as htn , dyslipidemia , and apoe genotype . pasqueler et al . also found that dm type 2 to be an independent predictor of poststroke dementia . the current study points to a positive association between diabetes , htn , and dementia even though the association is not perfect . the results from a study conductive by us previously also pointed to an association between raised bp and dementia although we were not able to establish a relation between diabetes and dementia . although there is uncertainty regarding the relationship between bp and risk of dementia , alzrisk does promote that the benefits of bp control on cardiovascular risk are sufficient to justify the role of preventing htn to prevention of dementia . however the same can not be said of diabetes and dementia . according to biessels et al . , there is still a need for studies on large population - based cohorts of elderly people with diabetes . despite the uncertainty in the role , the data analysis , therefore , points to a role in the prevention of htn and diabetes to prevent dementia .\noutput:\n" }, { "from": "agent", "value": "background : evidence suggests that modifiable risk factors which can be targeted by prevention are vascular diseases , such as diabetes , midlife hypertension ( htn ) , midlife obesity , midlife cholesterol , mid - and late - life depression as well as lifestyle factors such as smoking , physical inactivity , and poor diet.methods : a comprehensive search of the national library of medicine 's pubmed database and google scholar was conducted . a combinations of medical subject headings and free text words that included search terms related to the exposure ( e.g. , prevalence , htn , raised bp , high bp , diabetes , high blood sugar , dm , india , state ) , were combined with search terms related to the outcomes ( e.g. , prevalence , disease burden , estimate , dementia , india ) . the filters included were english for the language category and humans for the study category.results : the pubmed search initially identified 269 references , and a total of 204 abstracts were screened by inclusion criteria . full - text assessment of 136 articles on prevalence of dementia resulted in 20 relevant articles from which the different regions of the country were identified . based on the search conducted according to the regions ; 287abstracts of the prevalence of htn and 577 on the prevalence of diabetes mellitus were screened . there were 43 full - text articles on the prevalence of htn and diabetes from the regions where the prevalence of dementia was available . of these potentially relevant articles were 14 in number.conclusion : despite the uncertainty in the role , the data analysis , therefore , points to a role in the prevention of htn and diabetes to prevent dementia ." } ]

[ { "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: more than 10 years after the pandemic caused by the sars ( severe acute respiratory syndrome ) coronavirus ( cov ) , no anticoronaviral regimens have been developed for the treatment of sars - cov or any other human coronaviruses ( hcov ) infection . sars - cov was established as the causative agent of the fatal global outbreak of respiratory disease in humans during 20022003 that resulted in a case - fatality rate ( cfr ) of 11 % . in october 2012 , the centers for disease control and prevention ( cdc ) added sars - cov to the select agents list of the department of health and human services ( hhs ) . among many aspects that make sars - cov a potential threat to the human population , the lack of effective vaccines or anticoronaviral drugs had a significant impact in its classification as a select agent . however , even with the most extensive preventive measures , the reemergence of sars - cov or other virulent human coronaviruses poses a continuing threat . a powerful reminder of this , as well as of the fatal repercussions of the interspecies transmission potential of covs , was brought to the forefront in september 2012 by the emergence of a new sars - like respiratory virus ( previously termed hcov - emc , now designated middle east respiratory syndrome coronavirus , mers - cov ) . as in the case of sars - cov , the mers - cov is likely of zoonotic origin and closely related to bat coronaviruses from the betacoronavirus genus ( group 2 ) . reminiscent of the initial stages of sars - cov pandemic , global travel has contributed to the spread of mers coronavirus , with a total of 178 laboratory - confirmed cases and a cfr of 43 % . the infected individuals display sars - like symptoms , including a severe respiratory infection ( sri ) , and sometimes exhibit an acute renal failure which is a unique signature of mers infection . today , a total of 6 human coronaviruses are known , of which sars - cov and mers - cov are recognized as highly pathogenic with the potential for human - to - human transmission . without an efficacious antiviral agent or vaccine , the prevention of current and emerging coronaviruses continues to rely strongly on public health measures to contain outbreaks . therefore , research toward the development of anticoronaviral drugs continues to be of paramount importance . although a number of coronaviral proteins have been identified as potential drug targets , further development of drug candidates has been compromised by the general lack of antiviral data and biological evaluations , which can be done only in bsl - 3 facilities with select agent certification for laboratories in the u.s . two of the most promising drug targets are the sars - cov - encoded cysteine proteases , 3clpro ( chymotrypsin - like protease ) and plpro ( papain - like protease ) . plpro , in addition to playing an essential role during virus replication , is proposed to be a key enzyme in the pathogenesis of sars - cov . the well - established roles of plpro enzymatic activities include processing of the viral polyprotein , deubiquitination ( the removal of ubiquitin ) , and deisgylation ( the removal of isg15 ) from host - cell proteins . these last two enzymatic activities result in the antagonism of the host antiviral innate immune response . the sars - cov plpro inhibitors ( compounds 24 ( 14 ) and 15g , h ) , previously identified in our lab via high - throughput screening ( hts ) , have low micromolar inhibitory potency with minimal associated cytotoxicity in sars - cov - infected vero e6 cells and are therefore viable leads for the development of drug candidates ( figure 1 ) . detailed reports of the synthesis and biological evaluation of inhibitors 24 ( 14 ) and 15g ( 15 ) and their x - ray structures in complex with sars - cov plpro have been previously described . compounds 24 , 15h , and 15 g share a number of chemical and structural features ( figure 1 ) , including the presence of a naphthyl group adjacent to a stereogenic center containing a methyl group and a nitrogen - centered hydrogen bond ( h - bond ) donor ( at a physiological ph ) . in addition , these leads share carboxamide linkers of opposite orientation to differentially substituted benzenoid groups . activity relationships ( sars ) have shown that in both inhibitor subtypes the naphthyl ring is optimally substituted at c - 1 and the presence of the methyl group at the aforementioned stereogenic center is important for potency . interestingly , sars - cov plpro exhibited significant stereopreference for the ( r ) - enantiomer of 24 ( ic50 = 0.6 m , ec50 = 15 m ) , while minimal stereochemical selectivity was observed between enantiomers ( r ) - 15 g and ( s ) - 15h ( ic50 values of 0.67 and 0.56 m , respectively ; ec50 of 9.1 m for both ) . chemical structures of previously characterized sars - cov plpro inhibitors : ( a ) hit ( 1 ) from a primary hts from which lead 24 was developed ; ( b ) hit ( 2 ) from a primary hts from which 15 g and 15h were developed . the chiral center for the nearly equipotent isomers derived from hit 2 is indicated with an asterisk . the structural bases for the high binding affinity of inhibitors 24 and 15g , h are also quite similar . the x - ray crystal structures of plpro24 and plpro15 g complexes revealed several hydrophobic interactions resultant of the highly hydrophobic naphthyl ring and few hydrogen bonds . in addition , significant conformational changes within the active site are prominent between the apo and inhibitor - bound structures . specifically , there is a highly mobile - turn / loop ( gly267 - gly272 ) adjacent to the active site that closes upon inhibitor binding , thereby changing the orientation of the enzyme s backbone to allow for h - bonding with the inhibitor s core . however , relative to the conformation adopted with the smaller inhibitor 24 , compound 15 g requires a different and slightly more opened conformation to accommodate the longer piperidine -4-carboxamide scaffold and the bulkier 1,3 - benzodioxole ring . because the antiviral potencies of these sars - cov plpro inhibitors are likely not yet sufficient to make them therapeutically viable , further optimization of their inhibitory potencies , as well as physicochemical properties , is necessary . toward this goal , we utilized our previous sar analysis and the x - ray structure of compound 15 g in complex with sars - cov plpro to develop a second generation of plpro inhibitors . here , we disclose sar of a new series of potent sars - cov plpro inhibitors , their selectivity , antiviral efficacy , biological evaluation , and a detailed report of the molecular interactions between sars - cov plpro and inhibitors 3k and 3j aided by x - ray crystallographic studies . compound 3k was established to be the most potent sars - cov plpro inhibitor identified thus far in vitro . furthermore , this compound displayed effective perturbation of sars - cov replication in vero e6 cells while displaying low cytotoxicity and high selectivity for sars - cov plpro over human homologue enzymes . the improved resolution of the sars - cov plpro3k and plpro3j x - ray structures revealed novel factors accounting for the observed high binding affinities of the piperidine - containing compounds and the previously elusive molecular contributions of the benzyl substituent of the carboxamide . therefore , our data highlight 3k , as well as two slightly less potent but more metabolically stable analogues 3e and 5c , as good candidates for advancing to preclinical evaluations . in addition , we demonstrate the effective inhibition of plp2 from hcov - nl63 , a potentially fatal pathogen in children and elderly , by compound 3k and related analogues . importantly , these compounds may also present an opportunity for the development of broader - spectrum antiviral drugs against infections caused by both sars - cov and hcov - nl63 . the preparation of analogues 1a d bearing substitution off the - methyl group is summarized in schemes 13 . reagents and conditions : ( a ) 1 - naphthyl - mgbr , ether , rt ; ( b ) aq hcl ; ( c ) lah , thf , rt ; ( d ) ms2o , diea , dcm , 0 c ; ( e ) ethyl isonipecotate , rt ; ( f ) aq naoh , etoh , thf ; ( g ) piperonylamine , edci , hobt , diea , rt . the appropriate nitriles 8a , c were treated with 1 - naphthyl grignard reagent , and the intermediary imines were hydrolyzed to the ketones 9a , c under acidic conditions ( scheme 1 ) . the ketones were then reduced by the action of lah to the alcohols 10a , c , which were mesylated and displaced by treatment with ethyl isonipecotate to provide the amino esters 11a , c . saponification to the carboxylic acids was followed by coupling with piperonylamine to give final racemic analogues 1a , c . a similar displacement strategy was employed to obtain hydroxyl analogue 1b ( scheme 2 ) .12 ( 18 ) was reduced with lah to the diol 13 , and the primary alcohol was selectively protected as the tert - butyldimethylsilyl ( tbs ) ether to give 14 . the free secondary alcohol was mesylated and displaced by ethyl isonipecotate , and the resulting amino ester 16 was hydrolyzed to the corresponding acid and coupled with piperonylamine to provide the tbs - protected compound 17 . the silyl ether was removed with csf to afford the desired hydroxy analogue 1b . reagents and conditions : ( a ) lah , thf , rt ; ( b ) tbscl , imidazole , ether , rt ; ( c ) ms2o , diea , dcm , rt ; ( d ) ethyl isonipecotate , rt ; ( e ) aq naoh , etoh , 40 c ; ( f ) piperonylamine , edci , hobt , diea , rt ; ( g ) csf , aq acn , rt . the displacement route used in schemes 1 and 2 was not successful with the more hindered phenyl analogue 1d , so we had to employ the lengthier approach previously reported by ghosh et al .1 - naphthonitrile 18 was treated with benzylmagnesium chloride , and the resulting imine was hydrolyzed under acidic conditions to the ketone 19 . this amine was then condensed with the bis - aldehyde derived from dimethyl 2,2 - bis ( ( 1,3 - dioxolan -2-yl ) methyl ) malonate to give the dihydropyridine dimethyl ester 21 , which was readily reduced to the piperidine 22 by heterogeneous hydrogenation . the diester was converted into the monoester 23 by the krapcho method and was subsequently hydrolyzed to the acid and coupled with piperonylamine to give the desired analogue 1d . reagents and conditions : ( a ) bnmgcl , ether , rt ; ( b ) 1 m hcl , ether , 90 c ; ( c ) ch3onh2 , pyridine , rt ; then bh3thf , 80 c ; ( d ) dimethyl 2,2 - bis ( ( 1,3 - dioxolan -2-yl ) methyl ) malonate , hcl / thf ; ( e ) 20 , rt , 20 h ; ( f ) h2 , pd / c , 40 psi , rt ; ( g ) nacn , dmf , 145 c ; ( h ) 1 m aq naoh , etoh , 60 c ; ( i ) piperonylamine , edci , hobt , diea , rt . reagents and conditions : ( a ) rnh2 , edci or hatu , diea . the starting ( r ) - 1 - ( 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylic acid 25 was prepared according to the method of ghosh et al . coupling of the acid to various arylmethylamines and arylethylamines was effected either by edci in the presence of diea or by the uronium - based coupling reagent hatu . reagents and conditions : ( a ) memgcl , thf , 78 c ; ( b ) ms2o , diea , dcm ; ( c ) ethyl isonipecotate , dcm , rt ; ( d ) 1 m naoh , meoh ; ( e ) edci , hobt , diea , 3 - fluorobenzylamine , thf . the racemic quinolinyl and isoquinolinyl analogues ( 4a c ) were generated from the corresponding aldehydes 26a c by treatment with methylmagnesium chloride to give the methylcarbinols 27a c ( scheme 5 ) . alternatively , carbinol 27d was prepared from 1 - cyanoisoquinoline by addition of methylmagnesium chloride followed by sodium borohydride reduction of the resulting ketone , as described in the experimental section . displacement of the corresponding mesylates with ethyl isonipecotate afforded esters 28a d ( scheme 5 ) . saponification followed by edci - mediated coupling with 4 - fluorobenzylamine provided the final amides 4a d . reagents and conditions : ( a ) nabh3cn , nh4oac , proh , reflux , 44 h ; ( b ) dimethyl 2,2 - bis ( ( 1,3 - dioxolan -2-yl ) methyl ) malonate , hcl / thf ; ( c ) 30 , nahco3 , rt , 72 h ; ( d ) h2 , pto2 , ea , 40 psi , 5 h ; ( e ) nacn , dmf , reflux , 16 h ; ( f ) aq lioh , thf / meoh , rt ; ( g ) 3 - fluorobenzylamine , edci , hobt , diea , rt , 16 h. conformationally restricted analogue 7 was prepared as outlined in scheme 6 . reductive amination of ketone 29 with ammonium acetate and sodium cyanoborohydride provided amine 30 in quantitative yield . conversion to piperidine ester 33 was effected with a three - step sequence analogous to that employed in scheme 3 . saponifiction with lioh in a mixture ( 3:1:1 ) of thf / meoh / h2o furnished the free acid . finally amide coupling with 3 - fluorobenzylamine , edci , hobt , and diea led to the production of the target analogue 7 . it is worth noting that the shorter ethyl isonipecotate displacement route used in schemes 1 , 2 , and 5 was not successful with the mesylate derived from reduction / mesylation of 29 , presumably because of excessive steric hindrance . compound 15 g is a competitive inhibitor of sars - cov plpro that displays potent enzymatic inhibition ( ic50 = 0.67 m ) and low micromolar antiviral activity against sars - cov . it evolved from a small sar study on the hts hit 2 ( figure 1 ) and is therefore an attractive lead for the development of anti - sars drug candidates . compound 15 g is composed of the central piperidine -4-carboxamide core decorated with 1 - naphthalenylethyl and 1,3 - benzodioxolylmethyl substituents at the piperidinyl and carboxamide nitrogens , respectively . previous sar has established the preference for the 1 - naphthyl over the 2 - naphthyl substitution pattern and the requirement of a single methyl substituent at the methylene linker for effective inhibition ( when compared to both unsubstituted and gem - dimethyl derivatives ) , with minimal stereochemical preference . x - ray crystallographic studies of the sars - cov plpro15 g complex show that the methyl group of the ( r ) - enantiomer extends into a small pocket that has both hydrophobic and polar features and is filled with water molecules . to explore the dimensions and availability of this pocket to substituents as well as h - bond opportunities , the first set of analogues explores the incorporation of larger or polar substituents ( 1a , - me ; 1b , - oh ; 1c , - ome ; 1d , - ph ) at the methyl group ( position r1 in table 1 ) . addition of substituents to r1 resulted in higher ic50 values for all substitutions , and loss of inhibitory potency was proportional to substituent size . these trends indicate that the corresponding pocket might be less accessible than predicted by the crystal structure , with no clear opportunities for extra h - bonding or lipophilic interactions . it also appears that the potential entropic gain by displacing the water molecules with larger r1 groups is not achieved likely because of a larger enthalpic penalty of breaking the h - bonds formed between these water molecules and asp165 , arg167 , tyr274 , thr302 , and asp303 . as a result , unlike the previously reported predictions by fragment mapping program ( ftmap ) in which all water molecules were removed before computational analyses , here we demonstrate experimentally that this pocket is unlikely to provide any extra ligand - binding sites or room for larger substituents . we next examined the effect of incorporating substituents at the benzylic position r2 to form a second stereogenic carbon , using unsubstituted compound 2a ( ic50 = 2.20.1 m ) as the comparator . diastereoisomeric epimers 2b and 2c , with a methyl group at r2 , decreased the inhibitory activity by a comparable extent ( ic50 of 13.51.2 and 12.70.3 m , respectively ) , indicative of a steric clash with sars - cov plpro . interestingly , a 10-fold stereopreference was observed for ( s ) - methoxymethyl 2e ( ic50 = 1.90.1 m ) , compared to epimeric 2d ( ic50 = 18.01.9 m ) , which could be indicative of a h - bond in that region or simply the ability of the more active enantiomer 2e to retain the methoxy in a solvent - exposed environment , thereby avoiding a desolvation penalty . however , because the most active analogue in this series , 2e , did not surpass the effectiveness of the initial unsubstituted compound , 2a , we surmise that substitutions at position r2 do not engage the active site of the enzyme in favorable interaction and are therefore unlikely to lead to activity improvement . values are reported as mean standard deviation based on a minimum of triplicate measurements . previous sar studies on the aromatic substitution pattern of the benzyl group were limited to m - and p - methoxy analogues , which were as potent as the lead benzodioxolane analogue , 15 g . in the x - ray structure of the sars - cov plpro15 g complex , one of the 1,3 - dioxolane oxygens is within 3 of the gln270 side chain amide nitrogen , suggesting the potential for forming an h - bond . however , because of the poor electron density for the gln270 side chain , the oxygen s contribution to inhibitory potency was uncertain . therefore , we mutated gln270 to an alanine , glutamate , or aspartate residue and purified the mutant enzymes and determined the ic50 values with 15 g . we found that the ic50 values for the mutant enzymes are the same as for wild type sars - cov plpro , indicating that gln270 does not contribute to the binding of 15 g via interaction with the dioxolane ring ( data not shown ) . as observed with compound 2a , removal of the dioxolane ring from 15 g results in a 3-fold decrease in potency , suggesting that the dioxolane group provides a significant contribution to inhibitory potency but not through interaction with gln270 . therefore , to elucidate the nature of interactions provided by the 1,3 - benzodioxole group , benzene ring derivatives with diverse substituents at position r3 were explored . the incorporation of a p - ethyl group at r3 ( 3a ) had a more than 4-fold improvement in potency over unsubstituted prototype 2a , surpassing that of the dioxolane lead ( 15 g ) . a comparable effect was achieved with both p - and m - methylcarboxamide derivatives 3b ( ic50 = 0.600.02 m ) and 3c ( ic50 = 0.630.01 m ) respectively displaying both h - bonding donors and acceptors . reversal of the amide direction to the acetamido group resulted in significantly differing activity levels for para and meta positional isomers 3d ( ic50 = 5.70.5 m ) and 3e ( ic50 = 0.390.01 m ) , respectively . further extension of the acetamido group from the meta position , favored in the previous pair , dramatically decreases activity of the corresponding derivative ( 3f , ic50 = 20.41.2 m ) . a reversal in the meta vs para trend is seen with the corresponding pair of chloro derivatives 3 g ( ic50 = 27.24.1 m ) and 3h ( ic50 = 0.580.01 m ) , with the halogen tolerated only at the para position . finally , derivatives 3j and 3k , featuring the monofluoro substitution at para and meta positions , respectively , displayed a significant improvement over the parental 2a structure , with the 3 - fluorobenzyl variant possessing a more than 10-fold higher activity level ( ic50 = 0.150.01 m ) . surprisingly , 3,4 - difluoro substitution in 3i ( ic50 = 29.22.1 m ) had a significantly detrimental effect , decreasing the inhibitory potency by 200-fold when compared to 3k . in general , neither steric nor electronic factors can be invoked to rationalize systematically the effects of the substitution pattern at r3 and r4 on the inhibitory activity , with groups as diverse as 1,3 - dioxolane , 4 - ethyl , 3 - and 4 - carboxamido , 3 - acetamido , 3 - and 4 - fluoro , and 4 - chloro achieving a similar level of activity , despite presenting a wide range in polarity , size , and h - bonding capacity . significantly , the monosubstitution at the meta position with the smallest and yet the most electron - withdrawing fluoro group , capable of inducing dramatic polarization effects in the - system of the associated benzene ring , resulted in the most potent sars - cov plpro inhibitor identified thus far . in an attempt to improve the solubility of our most potent compound , 3k , the bioisosteres of naphthalene and benzene ( quinoline and pyridine , respectively ) were exploited by synthesizing corresponding derivatives ( table 2 ) . a detrimental effect on activity is observed upon replacement of the naphthyl ring system by quinolines ( 4a , ic50 = 7.00.7 m and 4b , ic50 = 4.50.2 m ) and isoquinolines , ( 4c , ic50 = 6.80.3 m and 4d , ic50 = 30.82.6 m ) , all tested as racemates . the replacement of the phenyl ring in the 2a prototype by the isosteric 3 - and 4 - pyridinyls ( 5a , ic50 = 26.32.3 m and 5b , ic50 = 18.30.9 m ) decreased potency by over an order of magnitude . interestingly , the activity was rescued by the addition of a 3 - methoxy group to the 4 - pyridinyl ring of the 5b analogue ( 5c , ic50 = 0.350.02 m ) , confirming the benefit of having a h - bonding group at c - 3 of the aromatic ring . we tested whether gln270 was involved in an interaction with compound 5c by determining its ic50 value with each of the sars plpro mutant enzymes ( gln270ala , gln270asp , and gln270glu ) . we observed no differences in the ic50 values within experimental error , indicating that no significant interaction is involved ( data not shown ) . analysis of the active site for other potential hydrogen - bonding residues produced no obvious candidates . extending the separation of the two aromatic centers in compounds 3h and 3k by one carbon atom resulted in weakening of inhibition activity in corresponding variants 6a ( ic50 = 1.60.3 m ) and 6b ( ic50 = 1.90.1 m ) . the effect is surprisingly minor , considering the nature of this perturbation , and is perhaps indicative of a significant amount of flexibility in the active site of sars - cov plpro in the region bound by the benzene moiety . values are reported as mean standard deviation based on a minimum of triplicate measurements . finally , tricyclic analogue 7 was prepared as a conformationally restricted analogue of our most potent inhibitor 3k ( figure 2 ) . it was designed to lock the conformation of the bond joining c - 1 of the naphthyl ring to the piperidinylethyl group to that observed in the x - ray structure of the sars - cov plpro15 g complex . this modification , however , led to a significant loss of activity ( ic50 = 5.10.5 m ) . these results suggest an inhibitor - induced - fit mechanism of association , in which the size and conformational freedom of compound 3k allow the optimal fit to be achieved . the conformationally restricted analogue 7 was designed to lock the conformation of compound 3k to the conformation observed in the x - ray crystal structure of sars - cov plpro bound to 15 g . to gain structural insight into the enhanced potency of compound 3k , sars - cov plpro was cocrystallized as a complex with 3k ( pdb code 4ow0 ) and 3j ( pdb code 4ovz ) using an approach similar to that for 15 g . crystals for each sars - plpro complex resulted after screening over 3000 crystallization conditions for diffraction quality crystals . complete x - ray data sets were collected for the sars - cov plpro3k and plpro3j complexes to resolutions of 2.1 and 2.5 , respectively ( table 3 ) . both sars - cov plproinhibitor complexes crystallized in space group c2 and contained two monomers per asymmetric unit . after identification of a molecular replacement solution and performance of initial rounds of refinement of the sars - cov plpro structural model in the absence of any ligand or water , strong ( 3 ) residual electron density was observed in fofc maps for both 3k and 3j in the active sites of each monomer within the asymmetric unit . the strong and continuous electron density for the inhibitors allowed for their unequivocal positioning and modeling within the ligand - binding site ( figure 3a and figure 3b ) . both 3k and 3j bind to the sars - cov plpro active site in the same orientation ( figure 3c and figure 3d ) . x - ray crystal structures of sars - cov plpro in complex with 3k and 3j . stereoviews of sars - cov plpro ( blue ribbon representation and gray surfaces ) in complex with 3k ( orange ball and sticks ) are shown in ( a ) and ( c ) , and sars - cov plpro ( cyan ribbon representation and gray surface ) in complex with 3j ( pink ball and sticks ) are shown in ( b ) and ( d ) . fc electron density omit maps ( inhibitor atoms omitted ) contoured at 3 are shown as gray mesh . important amino acids for inhibitor binding are shown , and the h - bonds between inhibitor atoms and amino acid residues are depicted as dotted lines . a superimposition of sars - cov plpro3k and plpro3j complexes is shown in ( e ) with conserved water molecules displayed as blue and cyan spheres for the 3k and 3j complexes , respectively . a superimposition of sars - cov plpro15 g complex ( sars - cov plpro displayed as a gray ribbon and 15 g displayed as gray balls and sticks , pdb : 3mj5 ) with sars - cov plpro3k and plpro3j complex is shown in ( f ) . as described previously for compounds 24 and 15 g , compounds 3k and 3j bind adjacent to the active site at the enzyme s3s4 subsites ( figure 3c and figure 3d ) , exclusive of any interactions with the catalytic triad ( cys112 - his273 - asp287 ) . upon inhibitor binding , the - turn / loop ( gly267 - gly272 ) containing tyr269 adopts a closed conformation via an induced - fit mechanism to interact with the inhibitors . this enables the formation of a 3 h - bond between the backbone carbonyl of tyr269 and the carboxyamide nitrogen of the inhibitors . an additional and important interaction is observed between the piperidine ring nitrogen and the side chain carboxylate of asp165 . the puckering of the piperidine ring positions the cationic nitrogen within a distance of 2.8 from an oxygen of the carboxylate of asp165 , thereby forming a charge - to - charge mediated h - bond . a structural superimposition of the two sars - cov plpro3k and plpro3j complexes ( figure 3e ) shows that the 1 - naphthyl rings align identically and that they pack against the two tandem prolines , pro248 and pro249 , in a hydrophobic pocket formed by the side chains of the prolines , tyr265 , tyr269 , and thr302 ( figure 3c and figure 3d ) . this pocket orients the ( r ) - methyl group into a small cavity lined by hydrophobic and hydrophilic side chains wherein some h - bond opportunities exist with the side chains of asp303 , thr302 , and tyr274 . the enhanced resolution of plpro3k and plpro3j complex compared to plpro15 g complex allowed for the better placement of three conserved water molecules that are present within this cavity ( figure 3e ) . the presence of these water molecules increases the polarity and decreases the effective size of the otherwise larger and mostly hydrophobic cavity . this smaller cavity explains our observed sar with hydrophobic or polar extensions at the ( r ) - methyl ( position r1 in table 1 ) whereby the larger groups were all detrimental to binding affinity . these observations suggest that the potential entropic gain in binding energy by displacement of the water molecules can not be achieved by incorporation of larger or polar substituents , as the enthalpy necessary to break the h - bonds between water molecules and the side chains must be too large to overcome . a superimposition of plpro in complex with 15 g , 3k , and 3j is shown in figure 3f . as discussed above , previous structural and computational analyses of the 15g - bound structure showed that the 1,3 - benzodioxole moiety can move within 3 of the amide nitrogen of gln270 side chain . however , mutation of gln270 to ala , glu , or asp showed no significant change in inhibitory potency when tested against 15 g , 3k , and 3j , indicative of no h - bond interactions with the side chain of gln270 . interestingly , while the superimposition between plpro15 g , plpro3k , and plpro3j complexes shows a near perfect overlap of the 1 - naphthyl rings , there is a 1 difference in the position of the carboxamide nitrogen of 15 g when compared to 3k and 3j . this causes a slight tilt on the orientations of the benzene rings to allow for the accommodation of the different benzene substituents . as a result , we conclude that the slightly enhanced inhibitory activity of compound 3k compared to 3j and 15 g is due to its ability to form collectively stronger van der waals interactions between the m - fluorobenzene and the side chain of tyr269 , and slightly stronger interactions with the backbone oxygen atoms of tyr269 and gln270 ( figure 3f ) . the development of an enzyme inhibitor with broad - spectrum specificity is an attractive approach for the treatment of infections caused by current and future - emerging human coronaviruses . however , to avoid drug - induced toxicity and potential side effects , it is crucial to maintain high inhibitory potency without cross - reactivity of critical homologues , the cellular deubiquitinating enzymes ( dubs ) . first , to assess compound selectivity , a set of the most potent analogues were tested against a panel of human dubs , including representative ubiquitin specific proteases ( usps ) with structural similarity to plpro , along with the human cysteine proteases caspase 3 and cathepsin k ( table 4 ) . compounds were tested at 31 m . if the inhibitory activity was less than 10 % , no inhibition is reported . if the inhibitory activity was between 10 % and 15 % or between 15 % and 20 % , then ic50 values of 100 or 31 m are reported . importantly , we can detect no significant inhibition of the human dubs or cysteine protease enzymes tested above 20 % at 31 m , indicating that these plpro inhibitors are selective and are unlikely to have significant off - target activity . next , we evaluated the potential of this set of analogues for the development of broader - spectrum coronaviral inhibitors . all of the analogues in tables 1 and 2 were counterscreened against the viral orthologue plp2 enzyme from the human coronavirus nl63 ( hcov - nl63 ) , a member of the - coronaviruses . hcov - nl63 is one of the causative agents of croup in children , and infection can result in hospitalization . currently there are no specific treatments for individuals infected with hcov - nl63 . for those analogues that showed 30 % inhibition at a single dose concentration of 100 m , full dose response curves of hcov - nl63 plp2 inhibition versus increasing compound concentration up to 100 m were determined . six compounds , including compound 3k , produced typical dose response curves , and the inhibition data were fit to determine the ic50 and maximum percent inhibition values ( table 5 ) . the results show that inhibition of hcov - nl63 plp2 is achieved by this series of compounds , albeit significantly weaker inhibition than for sars - cov plpro ( micromolar versus nanomolar range ) , and suggest that sars - cov plpro and hcov - nl63 plp2 may display sufficient structural similarities at the active site for the potential development of a dual - target inhibitor . compound 3k exhibits lower topological polar surface area ( tpsa = 32.2 ) relative to the initial inhibitor 15 g ( tpsa = 50.8 ) and therefore is proposed to enhance cell permeability and thus antiviral activity relative to 15 g . on the basis of these possible improvements , compound 3k along with seven of the most potent analogues and two quinolone derivatives were subjected to antiviral assays using our well - established method and bsl - 3 protocols . in this assay , compounds are titrated in both mock - and sars - cov - infected vero e6 cells , and the resulting dose response curves are fitted to the four - parameter logistic equation . curves were then compared to the mock - infected cells to assess drug - induced cytotoxicity in vero e6 and hek293 cell lines . the resultant ec50 values and cytotoxic concentrations ( cc50 ) are shown in table 6 . because of their greater potency , all tested compounds displayed low cytotoxicity levels ( cc5068 m ) with improved therapeutic index ( ti ) values in vero e6 cell when compared to 15 g . compounds with ic50 values of 2 m ( 2a , 4a , and 4c ) had no antiviral activity displaying ec50 values of 50 m ( data not shown ) . compounds 3e , 5c , 3j , and 2e displayed similar to slightly improved antiviral activity when compared to the initial compound 15 g . however , in the case of our best compound , 3k , which has a 4-fold improved ic50 value , an additional 2-fold improvement in antiviral activity was observed ( ec50 = 5.40.6 m ) when compared to 15 g . values are reported in m as mean standard deviation based on a minimum of triplicate measurements . ec50 , the half maximal effective concentration in sars - cov infected vero e6 cells ; cc50 , 50 % cytotoxic concentration ; ti , the therapeutic index defined as the ratio of cc50 / ec50 . with the ultimate goal of achieving protection from coronaviral infection in vivo , we evaluated the stability of our best new analogues to phase i metabolism by mouse liver microsomes ( table 7 ) . the lead compound 15 g proved to be exceedingly unstable , being completely consumed within 15 min . this was not entirely unexpected because of the presence of the 3,4 - methylenedioxy moiety , which renders the benzyl aromatic ring electron - rich and is itself a known target of cytochrome p450s . somewhat surprisingly , the much more electron - poor 3 - fluorobenzylamide 3k was still metabolized rapidly , suggesting that most of the metabolism is occurring distal to the benzylamide . consistent with this hypothesis , the less lipophilic bis ( amide ) 3e and methoxypyridine 5c were significantly more stable , with 20 % and 30 % parent drug remaining after 15 min , respectively , and half - lives 4 - to 5-fold longer than that of 15 g . the initial concentration of the parent compound was 1 m . half - life ( minutes ) of parent compound . because the binding of an antiviral drug to human serum proteins may result in reduced antiviral activity , we evaluated the plasma binding ability of the compounds in table 6 by measuring the shifts in their ic50 values in various concentrations of human plasma protein ( serum shift assays ) . we observed no significant changes in the ic50 values for the compounds in the serum shift assays , which were performed in the presence of 5 % , 10 % , and 20 % human serum albumin ( hsa ) ( data not shown ) , the most abundant protein in human plasma ( 40 mg / ml ) . this observation suggests that no specific interactions between the compounds and hsa take place . a second - generation series of highly potent sars - cov plpro inhibitors was designed and evaluated biologically to further advance anticoronavirus drug development . four compounds ( 3k , 3e , 3j , and 5c ) were found to have more potent sars - cov plpro inhibition and sars - cov antiviral activity than the most potent first generation inhibitor , 15 g . none of these five compounds exhibit cytotoxicity or off - target inhibitory activity of a series of human dub and cysteine protease enzymes , nor do any of these five inhibitors bind to human serum albumin ( hsa ) . the second - generation compounds 3k , 3e , and 5c exhibit significantly improved metabolic stability compared to 15 g . although compound 3k is the most potent sars - cov plpro inhibitor ( ic50 = 0.15 m ) and the most effective antiviral compound in cell culture ( ec50 = 5.4 m ) , it is significantly less metabolically stable compared to compounds 3e and 5c , which are similarly effective in inhibiting sars - cov plpro ( ic50 = 0.39 m and ic50 = 0.35 m ) and inhibiting sars - cov infected vero cells ( ec50 = 8.3 m and ec50 = 9.5 m ) . thus , compounds 3e and 5c are likely to be the better candidates to advance to animal efficacy models . finally , the high resolution of the inhibitor - bound crystal structures of plpro with 3k and 3j revealed novel aspects for the inhibitor binding mode , providing guidance for the further optimization of plpro inhibitors . h and c spectra were obtained in dmso - d6 or cdcl3 at room temperature , unless otherwise noted , on varian inova 400 mhz , varian inova 500 mhz , bruker avance drx 500 , or bruker avance dpx 300 instrument . chemical shifts for the h nmr and c nmr spectra were recorded in parts per million ( ppm ) on the scale from an internal standard of residual tetramethylsilane ( 0 ppm ) . rotamers are described as a ratio of rotamer a to rotamer b if possible . otherwise , if the rotamers can not be distinguished , the nmr peaks are described as multiplets . purity of all tested compounds was assessed by hplc using an agilent 1100 series with an agilent zorbax eclipse plus c18 column ( 254 nm detection ) with the following gradient : 10 % acn / water ( 1 min ) , 1090 % acn / water ( 6 min ) , and 90 % acn / water ( 2 min ) . values for each compound are included at the end of each experimental procedure , and all are over 95 % pure . solvent abbreviations used are the following : meoh ( methanol ) , dcm ( dichloromethane ) , etoac ( ethyl acetate ) , hex ( hexanes ) , dmso ( dimethylsulfoxide ) , dmf ( dimethylformamide ) , h2o ( water ) , thf ( tetrahydrofuran ) , acn ( acetonitrile ) . reagent abbreviations used are the following : hatu ( o - ( 7 - azabenzotriazol -1-yl ) - n , n , n,n - tetramethyluronium hexafluorophosphate ) , hoat ( 1 - hydroxy -7-azabenzotriazole ) , hobt ( 1 - hydroxy -1,2,3-benzotriazole ) , edci ( n - ( 3 - dimethylaminopropyl ) - n - ethylcarbodiimide hydrochloride ) , diea ( diisopropylethylamine ) , tfa ( trifluoroacetic acid ) , mgso4 ( magnesium sulfate ) , na2so4 ( sodium sulfate ) , nahco3 ( sodium bicarbonate ) , na2co3 ( sodium carbonate ) , cs2co3 ( cesium carbonate ) , nh4cl ( ammonium chloride ) , k2co3 ( potassium carbonate ) , koh ( potassium hydroxide ) , hcl ( hydrogen chloride ) , naoh ( sodium hydroxide ) , lioh ( lithium hydroxide ) , lah ( lithium aluminum hydride ) , etoh ( ethanol ) , nacn ( sodium cyanide ) , et2o ( diethyl ether ) , csf ( cesium fluoride ) , nacl ( sodium chloride ) , tbscl ( tert - butyldimethylsilyl chloride ) , ms2o ( methanesulfonic anhydride ) , mscl ( methanesulfonyl chloride ) , acoh ( acetic acid ) , nabh4 ( sodium borohydride ) , nabh3cn ( sodium cyanoborohydride ) , h2 ( hydrogen ) , n2 ( nitrogen ) , ms ( molecular sieves ) . assay abbreviations are the following : luc ( luciferase ) , mtt ( ( 3 - ( 4,5 - dimethylthiazol -2-yl ) -2,5-diphenyltetrazolium bromide . additional abbreviations are the following : aq ( aqueous ) , saturated ( saturated ) , rt ( room temperature ) . ethyl 1 - ( 1 - ( naphthalen -1-yl ) propyl ) piperidine -4-carboxylate 11a ( 480 mg , 1.48 mmol ) was dissolved in a 1:1:2 mixture of thf / etoh / 1 m aqueous naoh , total volume of 8 ml . this was stirred at 60 c for 5 h. the mixture was allowed to cool , and the organic solvents in the mixture were mostly removed by rotary evaporation . the ph was then reduced by addition of concentrated hcl to ph 4 , and the resulting white precipitate was collected over a filter to give the desired carboxylic acid ( 364 mg , 83 % ) without further purification . then the following was added sequentially to anhydrous dmf ( 1 ml ) : 3 molecular sieves , 1 - ( 1 - ( naphthalen -1-yl ) propyl ) piperidine -4-carboxylic acid ( 50 mg , 0.17 mmol ) , diea ( 0.088 ml , 0.504 mmol ) , edci ( 36 mg , 0.19 mmol ) , hobt ( 28 mg , 0.19 mmol ) , and finally piperonylamine ( 0.031 ml , 0.252 mmol ) . this was stirred at room temperature for 16 h , at which time the material was partitioned between 10 % na2co3 solution and etoac , and the organic layer was washed with 10 % na2co3 solution ( 320 ml ) and brine ( 120 ml ) . the organic layer was dried with anhydrous mgso4 , filtered , and concentrated in vacuo . purification was accomplished via flash chromatography ( 4 g silica redisep gold column on a combiflash , eluted with 70 % etoac / hex ) to give the desired product ( 34 mg , 47 % ) . h nmr ( 500 mhz , chloroform - d ) 8.44 ( bs , 1h ) , 7.917.84 ( m , 1h ) , 7.77 ( d , j = 8.1 hz , 1h ) , 7.537.40 ( m , 4h ) , 6.786.66 ( m , 3h ) , 5.94 ( s , 2h ) , 5.875.81 ( m , 1h ) , 4.32 ( d , j = 5.6 hz , 2h ) , 3.93 ( bs , 1h ) , 3.393.26 ( m , 1h ) , 2.942.80 ( m , 1h ) , 2.25 ( bs , 1h ) , 2.061.66 ( m , 8h ) , 0.68 ( t , j = 7.1 hz , 3h ) . silyl ether 17 ( 46 mg , 0.08 mmol ) was dissolved in acn ( 4 ml ) and h2o ( 2 ml ) . to thiswas added csf ( 51 mg , 0.34 mmol ) , and the mixture was stirred at room temperature for 24 h. the mixture was then partitioned between 10 % aqueous na2co3 ( 30 ml ) and etoac ( 50 ml ) and extracted . the extract was dried with anhydrous mgso4 , filtered , and concentrated in vacuo . the residue was then purified by flash chromatography ( 4.7 g amine - activated silica redisep column , 50 % etoac / hex ) to give the final product ( 28 mg , 77 % ) . chloroform - d ) 8.29 ( d , j = 8.2 hz , 1h ) , 7.90 ( d , j = 8.0 hz , 1h ) , 7.877.81 ( m , 1h ) , 7.587.45 ( m , 4h ) , 6.816.64 ( m , 3h ) , 5.95 ( s , 2h ) , 5.69 ( t , j = 4.7 hz , 1h ) , 4.644.49 ( m , 1h ) , 4.32 ( d , j = 5.6 hz , 2h ) , 4.09 ( dd , j = 11.0 , 7.8 hz , 1h ) , 3.81 ( dd , j = 10.9 , 5.2 hz , 1h ) , 3.27 ( d , j = 11.2 hz , 1h ) , 3.00 ( d , j = 11.5 hz , 1h ) , 2.321.75 ( m , 7h ) . tof es + ms : ( m + h ) 433.1 , ( m + na ) 455.1 . ethyl 1 - ( 2 - methoxy - 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylate 11c ( 80 mg , 0.23 mmol ) was dissolved in etoh ( 2 ml ) and 6 m naoh ( 5 ml ) . this was stirred at 50 c for 3 h. the ph was dropped to 2 by dropwise addition of concentrated hcl , and material was extracted with 1:1 etoac / et2o ( 310 ml ) . the solvent was then dried with anhydrous mgso4 , filtered , and removed in vacuo to give 1 - ( 2 - methoxy - 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylic acid ( 30 mg , 41 % ) without further purification . then the following was added sequentially to anhydrous dmf ( 1 ml ) : 3 molecular sieves , 1 - ( 2 - methoxy - 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylic acid ( 20 mg , 0.06 mmol ) , diea ( 0.033 ml , 0.191 mmol ) , edci ( 14 mg , 0.07 mmol ) , hobt ( 11 mg , 0.07 mmol ) , and finally piperonylamine ( 0.012 ml , 0.096 mmol ) . this was stirred at room temperature for 24 h , at which time the material was partitioned between 10 % aqueous na2co3 solution and etoac , and the organic layer was washed with 10 % aqueous na2co3 solution ( 310 ml ) and brine ( 110 ml ) . the organic layer was dried with anhydrous mgso4 , filtered , and concentrated in vacuo . the material was purified via alumina flash chromatography ( 8 g basic alumina redisep cartridge , 30 % etoac / hex ) to give the final desired compound ( 13 mg , 46 % ) . chloroform - d ) 8.37 ( d , j = 7.8 hz , 1h ) , 7.88 ( d , j = 7.2 hz , 1h ) , 7.78 ( d , j = 8.1 hz , 1h ) , 7.60 ( d , j = 7.0 hz , 1h ) , 7.547.47 ( m , 2h ) , 7.45 ( t , j = 7.6 hz , 1h ) , 6.796.71 ( m , 3h ) , 5.96 ( s , 2h ) , 5.73 ( s , 1h ) , 4.34 ( d , j = 5.6 hz , 2h ) , 4.21 ( s , 1h ) , 3.93 ( dd , j = 10.1 , 6.3 hz , 1h ) , 3.67 ( dd , j = 10.3 , 3.5 hz , 1h ) , 3.36 ( d , j = 11.1 hz , 1h ) , 3.31 ( s , 3h ) , 2.85 ( d , j = 11.4 hz , 1h ) , 2.24 ( t , j = 10.8 hz , 1h ) , 2.162.09 ( m , 1h ) , 2.071.69 ( m , 5h ) . tof es + ms : ( m + h ) 447.1 , ( m + na ) 469.1 . methyl 1 - ( 1 - ( naphthalen -1-yl ) -2-phenylethyl ) piperidine -4-carboxylate 23 ( 38 mg , 0.10 mmol ) was dissolved in a 1:1:2 mixture of thf / etoh / 1 m aqueous naoh , total volume of 4 ml . this was stirred at 60 c for 4 h. the mixture was allowed to cool , and the ph was reduced by addition of concentrated hcl to ph 4 , and the resulting white precipitate was collected over a filter to give 1 - ( 1 - ( naphthalen -1-yl ) -2-phenylethyl ) piperidine -4-carboxylic acid ( 30 mg , 82 % ) as a white powder . then the following was added sequentially to anhydrous dmf ( 1 ml ) : 3 molecular sieves , 1 - ( 1 - ( naphthalen -1-yl ) -2-phenylethyl ) piperidine -4-carboxylic acid ( 30 mg , 0.08 mmol ) , diea ( 44 l , 0.25 mmol ) , edci ( 18 mg , 0.09 mmol ) , hobt ( 14 mg , 0.09 mmol ) , and piperonylamine ( 16 l , 0.13 mmol ) . this was stirred at room temperature for 17 h , at which time the material was partitioned between 10 % aqueous na2co3 solution and etoac , and the organic layer was washed with 10 % aqueous na2co3 solution ( 320 ml ) and brine ( 120 ml ) . the organic layer was dried with anhydrous mgso4 , filtered , and concentrated in vacuo . the residue was then purified by flash chromatography ( 10 g silica , 50 % etoac / hex ) to give the final product ( 20 mg , 44 % ) . h nmr ( 500 mhz , chloroform - d ) 8.47 ( bs , 1h ) , 7.867.80 ( m , 1h ) , 7.72 ( d , j = 8.8 hz , 1h ) , 7.46 ( dt , j = 6.3 , 3.3 hz , 2h ) , 7.31 ( bs , 2h ) , 7.127.00 ( m , 3h ) , 6.89 ( bs , 2h ) , 6.776.70 ( m , 3h ) , 5.95 ( s , 2h ) , 5.835.74 ( m , 1h ) , 4.33 ( d , j = 5.7 hz , 2h ) , 3.46 ( dd , j = 13.6 , 4.8 hz , 1h ) , 3.41 ( s , 1h ) , 3.20 ( dd , j = 13.6 , 9.1 hz , 1h ) , 2.95 ( d , j = 9.8 hz , 1h ) , 2.152.04 ( m , 3h ) , 1.911.70 ( m , 4h ) . tof es + ms : ( m + h ) 493.1 , ( m + na ) 515.1 . to a solution of hoat ( 0.07 g , 0.35 mmol ) in dry dmf ( 5 ml ) were added hatu ( 0.19 g , 0.49 mmol ) , ( r ) - 1 - ( 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylic acid 25 ( 0.1 g , 0.35 mmol ) , and amine ( 0.42 mmol ) followed by diea ( 0.05 g , 0.35 mmol ) . the mixture was stirred overnight at room temperature , then diluted with saturated aqueous nahco3 and extracted with etoac ( 3 ) . the combined organic extracts were washed with saturated nacl ( 3 ) , dried ( mgso4 ) , and concentrated . the residue was purified by silica gel flash chromatography ( 14 % meoh / dcm ) . to a solution of ( r ) - 1 - ( 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylic acid 25 ( 0.06 g , 0.21 mmol ) in dry dmf ( 5 ml ) were added edci ( 0.05 g , 0.28 mmol ) , hobt ( 0.04 g , 0.25 mmol ) , and diea ( 0.07 ml , 0.53 mmol ) , followed by amine ( 0.21 mmol ) and stirred overnight at room temperature . after this time , the reaction mixture was diluted with saturated nahco3 and extracted with etoac ( 3 ) . the combined organic extracts were washed with saturated nacl ( 3 ) , dried ( mgso4 ) , and concentrated . the residue was purified by silica gel flash chromatography ( 15 % meoh / dcm ) . h nmr ( 400 mhz , dmso - d6 ) 8.44 ( br s , 1h ) , 7.807.90 ( m , 1h ) , 7.757.79 ( m , 1h ) , 7.237.61 ( m , 10h ) , 5.88 ( s , 1h ) , 5.45 ( br s , 1h ) , 4.32 ( m , 2h ) , 4.20 ( br s , 1h ) , 3.233.34 ( m , 1h ) , 2.882.91 ( m , 2h ) , 1.842.03 ( m , 4h ) , 1.43 ( m , 3h ) . h nmr ( 400 mhz , dmso - d6 ) 8.44 ( d , j = 4.7 hz , 1h ) , 7.867.88 ( m , 1h ) , 7.76 ( d , j = 6.48 , 1h ) , 7.56 ( br s , 1h ) , 7.427.48 ( m , 3h ) , 7.327.34 ( m , 5h ) , 5.68 ( br s , 1h ) , 5.135.16 ( m ,1 h ) , 4.13 ( br s , 1h ) , 3.25 ( d , j = 8.5 hz , 1h ) , 2.29 ( d , j = 6.4 hz , 1h ) , 2.022.10 ( m , 2h ) , 1.891.91 ( m , 1h ) , 1.671.79 ( m , 4h ) , 1.461.48 ( m 3h ) . h nmr ( 400 mhz , dmso - d6 and cdcl3 ) 8.22 ( m , 1h ) , 7.868.1 ( m , 2h ) , 7.727.81 ( m , 2h ) , 7.327.48 ( m , 4h ) , 7.327.38 ( m , 3h ) , 6.96 ( br s , 1h ) , 5.11 ( br s , 1h ) , 4.894.91 ( m , 1h ) , 5.135.16 ( m ,1 h ) , 4.654.4.69 ( m , 1h ) , 3.723.79 ( m , 2h ) , 3.683.72 ( m , 1h ) , 3.683.65 ( m , 1h ) , 2.29 ( m , 1h ) , 2.022.12 ( m , 1h ) , 1.891.91 ( m , 1h ) ,1.621.74 ( m , 3h ) , 1.461.48 ( m 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.43 ( d , j = 8.0 hz , 1h ) , 7.827.85 ( m , 1h ) , 7.73 ( m , 1h ) , 7.56 ( d , j = 7.2 hz , 1h ) , 7.437.46 ( m , 2h ) , 7.247.46 ( m , 5h ) , 6.17 ( d , j = 7.6 hz , 1h ) , 5.15 ( d , j = 7.2 hz , 1h ) , 4.094.11 ( m ,1 h ) , 3.63 ( d , j = 4.7 hz , 2h ) , 3.31 ( s , 3h ) , 3.23 ( d , j = 11.3 hz , 1h ) , 2.89 ( d , j = 11.4 hz , 1h ) , 1.992.27 ( m , 3h ) , 1.571.95 ( m , 4h ) , 1.47 ( d , j = 6.7 hz , 2h ) . h nmr ( 400 mhz , chloroform - d ) 8.43 ( d , j = 8.0 hz , 1h ) , 7.827.84 ( m , 1h ) , 7.72 ( d , j = 8.2 hz , 1h ) , 7.56 ( d , j = 7.2 hz , 1h ) , 7.357.52 ( m , 2h ) , 6.997.35 ( m , 5h ) , 6.12 ( d , j = 7.7 hz , 1h ) , 5.14 ( d , j = 7.1 hz , 1h ) , 4.10 ( m ,1 h ) , 3.63 ( d , j = 4.7 hz , 2h ) , 3.32 ( s , 3h ) , 3.22 ( d , j = 11.3 hz , 1h ) , 2.88 ( d , j = 11.6 hz , 1h ) , 1.992.28 ( m , 3h ) , 1.951.50 ( m , 4h ) , 1.46 ( d , j = 6.7 hz , 2h ) . h nmr ( 400 mhz , chloroform - d ) 8.41 ( d , j = 7.9 hz , 1h ) , 7.827.83 ( m , 1h ) , 7.717.73 ( m , 1h ) , 7.397.45 ( m , 4h ) , 7.127.16 ( m , 4h ) , 5.68 ( m , 1h ) , 4.37 ( d , j = 5.5 hz , 2h ) , 3.994.20 ( m , 1h ) , 3.22 ( d , j = 11.2 hz , 1h ) , 2.87 ( d , j = 11.2 hz , 1h ) , 2.61 ( q , j = 7.6 hz , 2h ) , 1.912.24 ( m , 4h ) , 1.571.81 ( m , 3h ) , 1.45 ( d , j = 6.7 hz , 3h ) , 1.20 ( td , j = 7.6 , 0.6 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.38 ( s , 1h ) , 7.767.99 ( m , 1h ) , 7.73 ( d , j = 8.2 hz , 1h ) , 7.597.70 ( m , 2h ) , 7.537.32 ( m , 4h ) , 7.207.32 ( m , 2h ) , 6.20 ( s , 2h ) , 4.42 ( d , j = 6.0 hz , 2h ) , 4.16 ( d , j = 16.5 hz , 1h ) , 3.22 ( d , j = 10.8 hz , 1h ) , 2.933.09 ( m , 2h ) , 2.91 ( d , j = 7.4 hz , 1h ) , 1.322.28 ( m , 9h ) . to a solution of tert - butyl 3 - ( methylcarbamoyl ) benzoic acid ( 0.3 g , 1.1 mmol ) in dry dmf ( 15 ml ) were added edci ( 0.26 g , 1.36 mmol ) , hobt ( 0.21 g , 1.36 mmol ) , and diea ( 0.39 ml , 2.27 mmol ) , followed by methanamine ( 0.03 g , 1.10 mmol ) . after dilution with saturated aqueous nahco3 , the aqueous layer was extracted with etoac ( 2 ) . the combined organic layers were washed with saturated nacl ( 3 ) and dried ( mgso4 ) , concentrated in vacuo , and purified by flash chromatography ( 14 % meoh / dcm ) to provide the intermediate ( 0.1 g , 54 % ) . h nmr ( 400 mhz , chloroform - d ) 8.01 ( s , 1h ) , 7.617.69 ( m , 2h ) , 7.287.41 ( m , 3h ) , 4.32 ( br s , 2h ) , 2.99 ( d , j = 4.3 hz , 3h ) , 1.49 ( s , 9h ) . this material was treated with 4 m hcl in dioxane and stirred overnight at room temperature . after being concentrated in vacuo , the crude 3 - ( aminomethyl ) - n - methylbenzamide was coupled with 25 using method b to afford the desired compound ( 0.02 g , 11 % ) . h nmr ( 400 mhz , chloroform - d ) 8.40 ( s , 1h ) , 7.84 ( d , j = 7.5 hz , 1h ) , 7.73 ( d , j = 8.1 hz , 1h ) , 7.63 ( d , j = 13.5 hz , 2h ) , 7.377.54 ( m , 2h ) , 7.35 ( d , j = 4.6 hz , 1h ) , 6.20 ( m , 1h ) , 5.87 ( m , 1h ) , 4.44 ( d , j = 5.8 hz , 2h ) , 4.11 ( d , j = 7.2 hz , 1h ) , 3.23 ( s , 1h ) , 2.99 ( d , j = 4.8 hz , 2h ) , 2.91 ( s , 1h ) , 0.752.24 ( m , 13h ) . h nmr ( 400 mhz , chloroform - d ) 8.42 ( d , j = 8.0 hz , 1h ) , 7.767.89 ( m , 3h ) , 7.72 ( d , j = 8.1 hz , 1h ) , 7.55 ( d , j = 7.2 hz , 1h ) , 7.337.49 ( m , 5h ) , 6.22 ( m , 1h ) , 5.83 ( m , 1h ) , 4.08 ( q , j = 6.5 hz , 1h ) , 3.64 ( s , 3h ) , 3.12 ( d , j = 11.4 hz , 1h ) , 2.81 ( d , j = 11.3 hz , 1h ) , 2.132.40 ( m , 1h ) , 1.952.15 ( m , 2h ) , 1.841.97 ( m , 1h ) , 1.641.84 ( m , 3h ) , 1.45 ( d , j = 6.7 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.41 ( d , j = 7.8 hz , 1h ) , 7.787.93 ( m , 1h ) , 7.72 ( d , j = 8.2 hz , 1h ) , 7.307.64 ( m , 5h ) , 7.23 ( d , j = 6.6 hz , 2h ) , 6.95 ( d , j = 7.6 hz , 1h ) , 5.80 ( s , 1h ) , 4.36 ( d , j = 5.7 hz , 2h ) , 3.904.25 ( m , 2h ) , 3.21 ( d , j = 11.1 hz , 1h ) , 2.87 ( d , j = 11.1 hz , 1h ) , 1.942.24 ( m , 5h ) , 1.531.94 ( m , 2h ) , 1.45 ( d , j = 6.6 hz , 3h ) , 1.24 ( td , j = 7.1 , 0.6 hz , 2h ) . hplc tr = 5.0 min , 95 % purity . to a solution of 1,3 - phenylenedimethanamine ( 0.2 g , 1.4 mmol ) in thf ( 20 ml ) was added acetic anhydride ( 0.07 ml , 0.73 mmol ) in thf ( 10 ml ) dropwise . the resulting mixture was stirred overnight at room temperature , then concentrated , and the residue was purified by silica gel flash chromatography ( 15 % meoh / dcm ) , providing n - ( 3 - ( aminomethyl ) benzyl ) acetamide ( 0.06 g , 23 % yield , tofes + ms , ( m + h ) 178.1 ) which was subsequently coupled with 25 using method b to afford the final compound ( 0.02 g , 12 % ) . h nmr ( 400 mhz , chloroform - d ) 8.42 ( d , j = 7.4 hz , 1h ) , 7.767.94 ( m , 1h ) , 7.73 ( m , 1h ) , 7.497.62 ( m , 5h ) , 7.327.48 ( m , 3h ) , 4.08 ( m , 2h ) , 3.64 ( s , 3h ) , 3.12 ( d , j = 12.2 hz , 1h ) , 2.80 ( d , j = 12.2 hz , 1h ) , 2.232.27 ( m , 1h ) , 1.912.06 ( m , 2h ) , 1.641.81 ( m , 6h ) , 1.44 ( dd , j = 6.7 , 3.7 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 7.797.81 ( m , 2h ) , 7.70 ( s , 1h ) , 7.237.26 ( m , 5h ) , 7.327.54 ( m , 2h ) , 7.117.13 ( m , 1h ) , 5.81 ( br s , 1h ) , 4.40 ( d , j = 5.8 hz , 2h ) , 3.86 ( s , 1h ) , 3.573.61 ( m , 1h ) , 2.902.95 ( m , 1h ) , 2.281.93 ( m , 6h ) , 1.45 ( d , j = 6.7 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.39 ( s , 1h ) , 7.797.96 ( m , 1h ) , 7.73 ( d , j = 8.2 hz , 1h ) , 7.327.66 ( m , 5h ) , 7.197.32 ( m , 2h ) , 7.017.19 ( m , 2h ) , 5.73 ( br s , 1h ) , 4.36 ( d , j = 5.9 hz , 2h ) , 4.11 ( br s , 1h ) , 3.22 ( d , j = 10.9 , 1h ) , 2.89 ( br s , 1h ) , 1.732.09 ( m , 6h ) , 1.47 ( s , 3h ) . h nmr ( 400 mhz , chloroform - d ) 7.797.81 ( m , 3h ) , 7.70 ( s , 1h ) , 7.43 - 7.51 ( m , 3h ) , 7.037.12 ( m , 2h ) , 6.96 ( br s , 1h ) , 5.83 ( br s , 1h ) , 4.37 ( d , j = 8.0 hz , 2h ) , 3.593.64 ( m , 1h ) , 3.323.39 ( m , 1h ) , 2.912.94 ( m , 1h ) , 1.932.28 ( m , 3h ) , 1.751.89 ( m , 4h ) , 1.43 ( d , j = 6.7 hz , 3h ) .8.428.44 ( m , 1h ) , 7.857.87 ( m , 1h ) , 7.737.74 ( d , j = 8.2 hz , 1h ) , 7.557.56 ( m , 1h ) , 7.467.54 ( m , 3h ) , 7.207.22 ( m , 3h ) , 7.017.11 ( m , 2h ) , 5.73 ( s , 1h ) , 4.384.39 ( d , j = 4.8 hz 2h ) , 4.094.11 ( m , 1h ) , 3.22 ( d , j = 8.8 hz , 1h ) , 2.89 ( d , j = 9.2 hz , 1h ) , 1.912.06 ( m , 3h ) , 1.711.84 ( m , 3h ) , 1.47 ( d , j = 5.3 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.43 ( s , 1h ) , 7.847.85 ( m , 1h ) , 7.73 ( d , j = 6.5 hz , 1h ) , 7.567.57 ( m , 1h ) , 7.417.48 ( m , 2h ) , 7.217.27 ( m , 1h ) , 7.027.06 ( m , 1h ) , 6.936.95 ( m , 1h ) , 5.75 ( s , 1h ) , 4.42 ( d , j = 4.6 hz , 2h ) , 4.12 ( br s , 1h ) , 3.24 ( d , j = 7.8 , 1h ) , 2.90 ( d , j = 9.7 , 1h ) , 1.992.14 ( m , 2h ) , 1.901.93 ( m , 1h ) , 1.571.80 ( m , 5h ) , 1.46 ( s , 3h ) . ethyl 1 - ( 1 - ( quinolin -8-yl ) ethyl ) piperidine -4-carboxylate 28a ( 0.38 g , 1.30 mmol ) was dissolved in methanol ( 20 ml ) , followed by the addition of 1 n sodium hydroxide ( 2.6 ml , 2.6 mmol ) in one portion . the resulting mixture was stirred for 18 h at room temperature , then concentrated in vacuo and partitioned between ether and a minimum amount of water . the layers were separated , and the aqueous layer was treated with acoh dropwise until the solution was acidic by ph paper . the solution was then concentrated in vacuo and dried under high vacuum overnight at room temperature , and the resulting acid was used without further purification . to a solution of ( r , s ) - 1 - ( 1 - ( quinolin -8-yl ) ethyl ) piperidine -4-carboxylic acid ( 0.1 g , 0.35 mmol ) in dry dmf ( 5 ml ) was added edci ( 0.07 g , 0.35 mmol ) , hobt ( 0.07 g , 0.42 mmol ) , and diea ( 0.06 ml , 0.35 mmol ) followed by ( 3 - fluorophenyl ) methanamine ( 0.04 g , 0.35 mmol ) . this reaction mixture was stirred overnight at room temperature , after which it was diluted with saturated nahco3 and extracted with etoac ( 1 ) . the combined organic layers were washed with saturated nacl ( 3 ) and dried ( mgso4 ) , then concentrated and purified by silica flash chromatography ( 15 % meoh / dcm ) to obtain 4a ( 0.05 g , 33 % yield ) . h nmr ( 400 mhz , dmso - d6 ) 8.758.98 ( m , 2h ) , 8.35 ( m , 1h ) , 8.27 ( t , j = 6.0 hz , 1h ) , 7.87 ( d , j = 8.4 hz , 1h ) , 7.607.72 ( m , 1h ) , 7.427.59 ( m , 2h ) , 7.217.42 ( m , 2h ) , 7.00 ( ddd , j = 23.3 , 16.7 , 9.5 hz , 2h ) , 3.844.40 ( m , 4h ) , 2.94 ( d , j = 10.8 hz , 1h ) , 2.76 ( d , j = 10.8 hz , 1h ) , 1.882.30 ( m , 2h ) , 1.391.76 ( m , 2h ) , 1.37 ( d , j = 6.6 hz , 3h ) . ethyl 1 - ( 1 - ( quinolin -5-yl ) ethyl ) piperidine -4-carboxylate 28b ( 0.67 g , 2.15 mmol ) was dissolved in methanol ( 20 ml ) , followed by 1 n sodium hydroxide ( 4.29 ml , 4.29 mmol ) in one portion . the resulting mixture was stirred 18 h at room temperature , concentrated in vacuo , and partitioned between ether and a minimum amount of water . the layers were separated , and the aqueous layer was treated with acoh dropwise until the solution measured acidic by ph paper . the solution was concentrated in vacuo , dried under high vacuum , and the resulting carboxylic acid was used without further purification in the next step . to a solution of ( r , s ) - 1 - ( 1 - ( quinolin -5-yl ) ethyl ) piperidine -4-carboxylic acid ( 0.100 g , 0.352 mmol ) in dry dmf ( 5 ml ) were added edci ( 0.067 g , 0.350 mmol ) , hobt ( 0.060 g , 0.420 mmol ) , and diea ( 0.060 ml , 0.35 mmol ) followed by ( 3 - fluorophenyl ) methanamine ( 0.040 g , 0.350 mmol ) . the mixture was stirred overnight at room temperature , diluted with saturated nahco3 , and extracted with etoac . the combined organic layers were washed with saturated nacl ( 3 ) and dried ( mgso4 ) , then concentrated and purified by silica gel flash chromatography ( 15 % meoh / dcm ) to provide the target compound ( 0.05 g , 33 % ) as a colorless oil . h nmr ( 400 mhz , chloroform - d ) 8.848.89 ( m , 1h ) , 7.96 ( d , j = 8.4 hz , 1h ) , 7.427.76 ( m , 2h ) , 7.35 ( dd , j = 8.6 , 4.2 hz , 1h ) , 7.137.32 ( m , 2h ) , 6.747.07 ( m , 3h ) , 6.025.97 ( s ,1 h ) , 4.154.39 ( q , j = 6.1 hz , 2h ) , 4.02 ( q , j = 6.7 hz , 1h ) , 2.963.23 ( m , 1h ) , 2.652.96 ( m , 1h ) , 1.942.17 ( m , 6h ) , 1.541.88 ( m , 4h ) , 1.44 ( d , j = 6.7 hz , 3h ) . ethyl 1 - ( 1 - ( isoquinolin -5-yl ) ethyl ) piperidine -4-carboxylate 28c ( 0.50 g , 1.61 mmol ) was dissolved in methanol ( 20 ml ) , followed by 1 n sodium hydroxide ( 3.2 ml , 3.2 mmol ) in one portion . the resulting mixture was stirred for 18 h at room temperature , concentrated in vacuo , and partitioned between ether and a minimum amount of water . the layers were separated , and the aqueous layer was treated with acoh dropwise until the solution measured acidic by ph paper . the solution was concentrated in vacuo , dried under high vacuum , and the resulting carboxylic acid was used without further purification in the next step . to a solution of ( r , s ) - 1 - ( 1 - ( isoquinolin -5-yl ) ethyl ) piperidine -4-carboxylic acid ( 0.100 g , 0.350 mmol ) in dry dmf ( 5 ml ) were added edci ( 0.067 g , 0.350 mmol ) , hobt ( 0.070 g , 0.420 mmol ) , and diea ( 0.061 ml , 0.352 mmol ) followed by ( 3 - fluorophenyl ) methanamine ( 0.044 g , 0.352 mmol ) . the mixture was stirred overnight at room temperature , diluted with saturated nahco3 , and extracted with etoac ( 2 ) . the combined organic extracts were washed with saturated nacl ( 3 ) , dried ( mgso4 ) , then purified by silica gel flash chromatography ( 15 % meoh / dcm ) to afford the final compound ( 0.02 g , 16 % ) . h nmr ( 400 mhz , chloroform - d ) 9.19 ( s , 1h ) , 8.47 ( d , j = 6.1 hz , 1h ) , 8.18 ( d , j = 6.1 hz , 1h ) , 7.627.93 ( m , 2h ) , 7.427.62 ( m , 1h ) , 7.107.42 ( m , 1h ) , 6.647.10 ( m , 3h ) , 5.98 ( t , j = 5.8 hz , 1h ) , 4.39 ( d , j = 5.9 hz , 2h ) , 4.02 ( q , j = 6.7 hz , 1h ) , 3.14 ( m , 1h ) , 2.563.04 ( m , 1h ) , 1.892.37 ( m , 3h ) , 1.531.89 ( m , 3h ) , 1.42 ( d , j = 6.6 hz , 3h ) . hplc tr = 4.0 min , 95 % purity . to a solution of 27d ( 50 mg , 0.16 mmol ) in meoh ( 10 ml ) was added naoh ( 11 mg , 0.48 mmol ) , and the mixture was allowed to stir at 50 c for 6 h. the solution was concentrated in vacuo and acidified with 4 m hcl in dioxane ( 5 ml ) . the crude carboxylic acid was dissolved in dmf ( 10 ml ) , and edci ( 49 mg , 0.38 mmol ) , hobt ( 43 mg , 0.32 mmol ) , diea ( 103 mg , 0.80 mmol ) , and 3 - fluorobenzylamine ( 24 mg , 0.20 mmol ) were added and allowed to stir at 23 c for 16 h. the reaction was quenched with saturated nahco3 ( 25 ml ) , washed with h2o ( 220 ml ) , brine ( 120 ml ) , dried ( mgso4 ) , and concentrated in vacuo . the residue was purified by flash chromatography ( 14 % meoh / dcm ) to furnish the desired material ( 23 mg , 37.1 % ) as a dark brown oil . h nmr ( 400 mhz , chloroform - d ) 8.66 ( d , j = 8.5 hz , 1h ) , 8.44 ( d , j = 5.7 hz , 1h ) , 7.79 ( d , j = 8.1 hz , 1h ) , 7.65 ( t , j = 7.9 hz , 1h ) , 7.597.49 ( m , 2h ) , 7.096.96 ( m , 2h ) , 6.92 ( t , j = 8.3 hz , 2h ) , 5.81 ( dd , j = 7.5 , 1.9 hz , 1h ) , 4.40 ( d , j = 5.8 hz , 2h ) , 3.09 ( d , j = 10.1 hz , 1h ) , 2.91 ( d , j = 11.5 hz , 1h ) , 2.362.26 ( m , 1h ) , 2.182.07 ( m , 2h ) , 1.77 ( dd , j = 8.5 , 3.5 hz , 3h ) , 1.53 ( d , j = 6.7 hz , 3h ) . tof es + ms : ( m + h ) 392.2 . h nmr ( 400 mhz , chloroform - d ) 8.488.51 ( m , 2h ) , 7.83 ( d , j = 7.8 hz , 3h ) , 7.76 ( s , 1h ) , 7.477.53 ( m , 4h ) , 7.237.25 ( m , 1h ) , 6.08 ( s , 1h ) , 4.444.45 ( m , 2h ) , 3.26 ( d , j = 11.5 hz , 1h ) , 3.04 ( d , j = 11.5 hz , 1h ) , 2.112.48 ( m , 2h ) , 1.632.11 ( m , 7h ) , 1.48 ( s , 3 m ) . h nmr ( 400 mhz , chloroform - d ) 8.51 ( d , j = 5.1 hz , 2h ) , 7.797.83 ( 3h ) , 7.71 ( s , 1h ) , 7.437.54 ( m , 3h ) , 7.13 ( d , j = 5.1 hz , 2h ) , 6.06 ( t , j = 6.2 hz , 1h ) , 4.43 ( d , j = 6.1 hz , 2h ) , 3.63 ( q , j = 6.7 hz , 1h ) , 3.173.20 ( m , 1h ) , 2.92 - 2.95 ( m , 1h ) , 1.96 - 2.16 ( m , 4h ) , 1.651.91 ( m , 3h ) , 1.47 ( d , j = 6.6 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.38 ( br s , 1h ) , 8.06 ( d , j = 5.3 hz , 1h ) , 7.697.91 ( m , 3h ) , 7.58 ( br s , 1h ) , 7.45 ( m , 3h ) , 6.72 ( m , 1h ) , 6.56 ( s , 2h ) , 5.85 ( br s , 1h ) , 4.36 ( d , j = 6.0 hz , 2h ) , 4.10 ( m , 1h ) , 3.89 ( s , 3h ) , 3.25 ( m , 1h ) , 2.94 ( m , 1h ) , 1.582.15 ( m , 5h ) , 1.41 ( m , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.41 ( d , j = 7.5 hz , 1h ) , 7.83 ( dd , j = 7.1 , 2.1 hz , 1h ) , 7.72 ( d , j = 8.2 hz , 1h ) , 7.54 ( m , 1h ) , 7.297.50 ( m , 3h ) , 7.137.33 ( m , 3h ) , 6.867.18 ( m , 2h ) , 5.41 ( s , 1h ) , 4.08 ( s , 1h ) , 3.45 ( q , j = 6.8 hz , 1h ) , 3.18 ( d , j = 11.2 hz , 1h ) , 2.762.98 ( m , 1h ) , 2.382.76 ( m , j = 6.8 hz , 2h ) , 1.522.16 ( m , 7h ) , 1.45 ( d , j = 6.8 hz , 3h ) . h nmr ( 400 mhz , chloroform - d ) 8.42 ( d , j = 7.8 hz , 1h ) , 7.778.04 ( m , 1h ) , 7.73 ( d , j = 8.2 hz , 1h ) , 7.487.65 ( m , 1h ) , 7.327.48 ( m , 3h ) , 7.187.32 ( m , 1h ) , 6.656.99 ( m , 3h ) , 5.42 ( s , 1h ) , 4.08 ( d , j = 5.9 hz , 1h ) , 3.373.56 ( m , 1h ) , 3.19 ( d , j = 11.2 hz , 1h ) , 2.782.90 ( m , 1h ) , 2.77 ( s , 1h ) , 1.872.09 ( m , 5h ) , 1.541.86 ( m , 4h ) , 1.45 ( d , j = 6.6 hz , 3h ) . to a solution of 33 ( 97 mg , 0.23 mmol ) in thf / meoh / h2o ( 3:1:1 ) ( 7 ml ) at 0 c was added lioh ( 19 mg , 0.45 mmol ) , and the mixture was allowed to stir at room temperature for 16 h. the reaction mixture was concentrated in vacuo , acidified using hcl dioxane , and crystallized with the addition of etoac ( 5 ml ) . the product was filtered to furnish the carboxylic acid ( 65 mg , 70 % ) as a white solid . this acid was carried forward without purification and was dissolved ( 63 mg , 0.2 mmol ) in dry dmf ( 5 ml ) , followed by edci ( 41 mg , 0.27 mmol ) , hobt ( 37 mg , 0.27 mmol ) , diea ( 133 mg , 1.03 mmol ) , and 3 - fluorobenzylamine ( 28 mg , 0.23 mmol ) , and the reaction mixture was allowed to stir at room temperature for 16 h. the reaction mixture was then diluted with etoac , quenched with saturated nahco3 , washed with h2o ( 210 ml ) , saturated nacl ( 110 ml ) , dried ( mgso4 ) , and concentrated in vacuo . the residue was purified by silica gel flash chromatography ( 4060 % etoac / hex ) to furnish 7 ( 26 mg , 30 % ) as a dark oil . h nmr ( 400 mhz , chloroform - d ) : 8.37 ( d , j = 8.4 hz , 1h ) , 7.74 ( d , j = 8.0 hz , 1h ) , 7.63 ( d , j = 8.4 hz , 1h ) , 7.40 ( dt , j = 21.1 , 7.2 hz , 2h ) , 7.24 ( d , j = 4.5 hz , 2h ) , 7.16 ( d , j = 8.4 hz , 1h ) , 6.95 ( dd , j = 28.2 , 8.1 hz , 3h ) , 5.68 ( s , 1h ) , 4.46 ( t , j = 4.4 hz , 1h ) , 4.39 ( d , j = 5.8 hz , 2h ) , 3.022.87 ( m , 2h ) , 2.842.74 ( m , 1h ) , 2.58 ( ddd , j = 14.2 , 9.9 , 4.3 hz , 2h ) , 2.33 ( t , j = 10.7 hz , 1h ) , 2.272.14 ( m , 1h ) , 2.08 ( ddt , j = 11.7 , 8.0 , 3.9 hz , 1h ) , 2.011.91 ( m , 1h ) , 1.85 ( d , j = 10.5 hz , 1h ) , 1.74 ( dd , j = 10.8 , 5.5 hz , 2h ) , 1.61 ( d , j = 12.1 hz , 1h ) , 1.421.30 ( m , 1h ) .2 - methoxyacetonitrile 8c ( 0.25 ml , 3.33 mmol ) was dissolved in a 250 mm solution of naphthalen -1-ylmagnesium bromide ( 20 ml , 5.0 mmol ) in thf and stirred for 14 h at room temperature .2 m hcl ( 10 ml ) was added , and this was stirred at room temperature for 8 h. at this time , material was extracted with a 1:1 solution etoac / et2o , dried with anhydrous mgso4 , filtered , and the filtrate was concentrated in vacuo . the residue was purified by flash chromatography ( 20 g silica , 520 % etoac / hex ) to give the desired product ( 118 mg , 18 % ) . h nmr ( 500 mhz , chloroform - d ) 8.66 ( d , j = 8.6 hz , 1h ) , 8.05 ( d , j = 8.2 hz , 1h ) , 7.91 ( d , j = 8.1 hz , 1h ) , 7.86 ( d , j = 7.2 hz , 1h ) , 7.64 ( t , j = 7.7 hz , 1h ) , 7.617.55 ( m , 1h ) , 7.53 ( t , j = 7.7 hz , 1h ) , 4.74 ( s , 2h ) , 3.57 ( s , 3h ) .1 - ( naphthalen -1-yl ) propan -1-one 9a ( 100 mg , 0.54 mmol ) , prepared from nitrile 8a by the literature method , was dissolved in anhydrous thf ( 1 ml ) in dry glassware and cooled to 78 c . lah ( 1 m in thf , 0.27 ml , 0.27 mmol ) was added dropwise to the solution . the mixture was allowed to warm to room temperature and stirred for 4 h or until complete by tlc . the reaction was then worked up according to the fieser method , and the resulting precipitate was filtered off . the filtrate was collected and concentrated in vacuo . the residue was then purified by flash chromatography ( 15 g silica , 20 % etoac / hex ) to provide the desired product ( 85 mg , 85 % ) . h nmr ( 500 mhz , chloroform - d ) 8.13 ( d , j = 7.8 hz , 1h ) , 7.947.89 ( m , 1h ) , 7.81 ( d , j = 8.2 hz , 1h ) , 7.65 ( d , j = 7.1 hz , 1h ) , 7.577.47 ( m , 3h ) , 5.445.34 ( m , 1h ) , 2.32 ( s , 1h ) , 2.092.00 ( m , 1h ) , 1.991.89 ( m , 1h ) , 1.06 ( t , j = 7.4 hz , 3h ) .2 - methoxy - 1 - ( naphthalen -1-yl ) ethanone 9c ( 118 mg , 0.59 mmol ) was dissolved in anhydrous et2o ( 6 ml ) in an ice bath , and a 1 m ( in thf ) solution of lah ( 0.59 ml , 0.59 mmol ) was added under n2 . this was stirred at room temperature for 3 h , at which time the fieser workup was employed . precipitate was filtered off and the filtrate concentrated in vacuo to give the desired product as an oil ( 104 mg , 87 % ) used without further purification . h nmr ( 500 mhz , chloroform - d ) 8.09 ( d , j = 8.3 hz , 1h ) , 7.937.89 ( m , 1h ) , 7.83 ( d , j = 8.2 hz , 1h ) , 7.79 ( d , j = 7.1 hz , 1h ) , 7.587.50 ( m , 3h ) , 5.75 ( dd , j = 8.9 , 2.5 hz , 1h ) , 3.80 ( dd , j = 10.1 , 2.8 hz , 1h ) , 3.57 ( dd , j = 9.9 , 9.0 hz , 1h ) , 3.50 ( s , 3h ) , 3.30 ( bs , 1h ) . 1 - ( naphthalen -1-yl ) propan -1-ol 10a ( 326 mg , 1.75 mmol ) was dissolved in dcm ( 4 ml ) at 0 c with 3 molecular sieves . diea ( 0.92 ml , 5.25 mmol ) was added , and with continuous stirring at 0 c , ms2o ( 396 mg , 2.27 mmol ) was added dropwise . the solution was stirred for 40 min at 0 c , at which point ethyl piperidine -4-carboxylate ( 1.62 ml , 10.5 mmol ) was added . the mixture was then stirred for 48 h at room temperature . at that time , etoac was added and washed with 10 % aqueous na2co3 ( 325 ml ) . the organic layer was then dried ( mgso4 ) , filtered , and removed in vacuo . purification was accomplished via flash chromatography ( 20 g silica , gradient 040 % etoac / hex ) to give the desired product ( 480 mg , 84 % ) as a slightly yellow oil . h nmr ( 500 mhz , chloroform - d ) 8.48 ( bs , 1h ) , 7.907.86 ( m , 1h ) , 7.78 ( d , j = 8.1 hz , 1h ) , 7.547.43 ( m , 4h ) , 4.14 ( q , j = 7.1 hz , 2h ) , 3.94 ( bs , 1h ) , 3.293.16 ( m , 1h ) , 2.872.75 ( m , 1h ) , 2.27 ( tt , j = 11.3 , 4.1 hz , 1h ) , 2.121.93 ( m , 5h ) , 1.851.66 ( m , 3h ) , 1.26 ( t , j = 7.1 hz , 3h ) , 0.70 ( t , j = 7.3 hz , 3h ) .2 - methoxy - 1 - ( naphthalen -1-yl ) ethanol 10c ( 104 mg , 0.51 mmol ) was dissolved in dcm ( 4 ml ) at 0 c , and the following was added sequentially : 3 molecular sieves , diea ( 0.27 ml , 1.54 mmol ) , and ms2o ( 116 mg , 0.67 mmol ) . this was stirred for 40 min at 0 c , at which time ethyl piperidine -4-carboxylate ( 0.48 ml , 3.09 mmol ) was added . the material was extracted with etoac , and this was washed with 10 % na2co3 ( 325 ml ) . the organic layer was dried over mgso4 , filtered , and the filtrate was concentrated in vacuo . the residue was purified by flash chromatography ( 20 g silica , 010 % etoac / hex gradient ) to give the desired product ( 91 mg , 52 % ) . h nmr ( 500 mhz , chloroform - d ) 8.41 ( d , j = 8.2 hz , 1h ) , 7.927.86 ( m , 1h ) , 7.80 ( d , j = 8.2 hz , 1h ) , 7.63 ( d , j = 7.0 hz , 1h ) , 7.577.44 ( m , 3h ) , 4.334.19 ( m , 1h ) , 4.15 ( q , j = 7.1 hz , 2h ) , 3.95 ( dd , j = 10.3 , 6.2 hz , 1h ) , 3.69 ( dd , j = 10.3 , 3.7 hz , 1h ) , 3.33 ( s , 3h ) , 3.323.25 ( m , 1h ) , 2.862.77 ( m , 1h ) , 2.382.23 ( m , 2h ) , 2.14 ( t , j = 10.2 hz , 1h ) , 2.031.93 ( m , 1h ) , 1.911.69 ( m , 3h ) , 1.27 ( t , j = 7.1 hz , 3h ) .2 - hydroxy - 1 - ( naphthalen -1-yl ) ethanone 12 ( 200 mg , 1.07 mmol ) , prepared previously by the literature method , was dissolved in anhydrous thf ( 2 ml ) and was cooled in an ice bath . 1 m lah in thf ( 1.07 ml , 1.07 mmol ) was slowly added dropwise to the solution . the mixture was then allowed to warm to room temperature and was stirred for 2 h. after this time , the reaction was worked up by the fieser method , the aluminum was filtered off , and the filtrate solvent was removed in vacuo to give a white solid . this was purified by flash chromatography ( 10 g silica , 50 % etoac / hex ) to give the desired product ( 168 mg , 83 % ) as a white solid . h nmr ( 500 mhz , dmso - d6 ) 8.16 ( d , j = 8.3 hz , 1h ) , 7.93 ( d , j = 8.0 hz , 1h ) , 7.82 ( d , j = 8.1 hz , 1h ) , 7.66 ( d , j = 7.1 hz , 1h ) , 7.577.48 ( m , 3h ) , 5.44 ( d , j = 4.2 hz , 1h ) , 5.33 ( dt , j = 7.7 , 4.0 hz , 1h ) , 4.87 ( t , j = 5.8 hz , 1h ) , 3.66 ( ddd , j = 10.1 , 6.0 , 4.0 hz , 1h ) , 3.50 ( ddd , j = 11.3 , 7.4 , 5.9 hz , 1h ) .1 - ( naphthalen -1-yl ) ethane -1,2-diol 13 ( 280 mg , 1.49 mmol ) was dissolved in anhydrous dmf ( 8 ml ) , followed by imidazole ( 253 mg , 3.72 mmol ) and tbscl ( 247 mg , 1.64 mmol ) . this was stirred at room temperature for 4 h , after which time the mixture was partitioned between h2o ( 25 ml ) and etoac ( 25 ml ) and extracted . the extract was washed with h2o ( 120 ml ) and brine ( 120 ml ) and dried over mgso4 and concentrated in vacuo . the crude residue was then purified by flash chromatography ( 10 % etoac / hex ) to give the silyl ether ( 445 mg , 99 % ) as a nearly colorless oil . h nmr ( 500 mhz , methanol - d4 ) 8.12 ( d , j = 8.3 hz , 1h ) , 7.82 ( d , j = 8.1 hz , 1h ) , 7.767.69 ( m , 2h ) , 7.497.39 ( m , 3h ) , 5.55 ( dd , j = 6.6 , 4.5 hz , 1h ) , 4.94 ( d , j = 4.2 hz , 1h ) , 3.963.83 ( m , 2h ) , 0.84 ( s , 9h ) , 0.04 ( s , 3h ) , 0.09 ( s , 3h ) .2 - ( ( tert - butyldimethylsilyl ) oxy ) - 1 - ( naphthalen -1-yl ) ethanol 14 ( 320 mg , 1.06 mmol ) was dissolved in dcm ( 6 ml ) with 3 molecular sieves , followed by diea ( 0.28 ml , 1.59 mmol ) . mscl ( 0.10 ml , 1.27 mmol ) was added dropwise , and the mixture was allowed to stir at room temperature for 3 h. ethyl piperidine -4-carboxylate ( 0.82 ml , 5.29 mmol ) was then added dropwise and the mixture stirred for 23 h at room temperature . the solution was washed with aqueous 10 % aqueous na2co3 ( 320 ml ) and brine ( 115 ml ) , dried with anhydrous mgso4 , filtered , and the filtrate was concentrated in vacuo . the crude residue was then purified by flash chromatography ( 20 g silica , 10 % etoac / hex ) to give the desired product ( 276 mg , 59 % ) as an oil . h nmr ( 500 mhz , chloroform - d ) 8.41 ( d , j = 7.8 hz , 1h ) , 7.87 ( d , j = 7.2 hz , 1h ) , 7.77 ( d , j = 8.1 hz , 1h ) , 7.61 ( d , j = 7.0 hz , 1h ) , 7.517.41 ( m , 3h ) , 4.174.11 ( m , 3h ) , 4.114.07 ( m , 1h ) , 3.913.86 ( m , 1h ) , 3.423.33 ( m , 1h ) , 2.852.76 ( m , 1h ) , 2.352.24 ( m , 2h ) , 2.12 ( t , j = 11.3 hz , 1h ) , 2.011.92 ( m , 1h ) , 1.881.64 ( m , 3h ) , 1.26 ( t , j = 7.1 hz , 3h ) , 0.81 ( s , 9h ) , 0.12 ( s , 3h ) , 0.15 ( s , 3h ) . ethyl 1 - ( 2 - ( ( tert - butyldimethylsilyl ) oxy ) - 1 - ( naphthalen -1-yl ) ethyl ) piperidine -4-carboxylate 16 ( 100 mg , 0.23 mmol ) was dissolved in ethanol ( 6 ml ) and 7 m aqueous naoh ( 3 ml ) and stirred at 40 c for 3 h. the mixture was then cooled to 0 c and acidified ( ph 2 ) with concentrated hcl . the resulting white precipitate was collected over filter and dried under high vacuum overnight to give the desired carboxylic acid ( 70 mg , 75 % ) as a white powder . the crude solid was added to a solution of diea ( 0.059 ml , 0.338 mmol ) , edci ( 42.2 mg , 0.220 mmol ) , and hobt ( 33.7 mg , 0.220 mmol ) in anhydrous dmf ( 1 ml ) over 3 molecular sieves . piperonylamine ( 0.032 ml , 0.254 mmol ) was added , and the mixture was allowed to stir for 32 h at room temperature . after this time , a 1:1 solution of et2o / etoac ( 25 ml ) was added and washed with 10 % aqueous na2co3 ( 320 ml ) and brine ( 110 ml ) , dried with anhydrous mgso4 , and concentrated in vacuo . the crude oil was purified by flash chromatography ( 25 g silica , 10 % etoac / hex ) to give the desired product ( 46 mg , 50 % ) as an oil . h nmr ( 500 mhz , chloroform - d ) 8.39 ( d , j = 7.4 hz , 1h ) , 7.87 ( d , j = 9.1 hz , 1h ) , 7.77 ( d , j = 8.2 hz , 1h ) , 7.61 ( d , j = 6.9 hz , 1h ) , 7.537.39 ( m , 3h ) , 6.806.69 ( m , 3h ) , 5.96 ( s , 2h ) , 5.73 ( bs , 1h ) , 4.35 ( d , j = 5.6 hz , 2h ) , 4.174.05 ( m , 2h ) , 3.88 ( dd , j = 10.5 , 4.0 hz , 1h ) , 3.46 ( d , j = 11.1 hz , 1h ) , 2.85 ( d , j = 11.3 hz , 1h ) , 2.28 ( t , j = 10.7 hz , 1h ) , 2.192.09 ( m , 1h ) , 2.092.01 ( m , 1h ) , 1.951.72 ( m , 4h ) , 0.81 ( s , 9h ) , 0.12 ( s , 3h ) , 0.15 ( s , 3h ) . 1 - naphthonitrile 18 ( 1.00 g , 6.53 mmol ) was dissolved in anhydrous et2o ( 20 ml ) in dry glassware , followed by the addition of benzylmagnesium chloride ( 7.83 ml , 7.83 mmol ) under n2 . this was stirred at room temperature for 18 h. at this time , 1 m hcl was added ( 5 ml ) and the mixture was stirred at 90 c for 35 min ( during which time it was necessary to add more et2o ) , then allowed to cool to room temperature , at which point material was extracted by etoac / et2o , dried with anhydrous mgso4 and the filtrate was concentrated in vacuo . the resulting residue was purified by flash chromatography ( 20 g silica , 10 % etoac / hex ) to give the desired ketone ( 1.35 g , 84 % ) . h nmr ( 500 mhz , chloroform - d ) 8.60 ( d , j = 8.8 hz , 1h ) , 8.00 ( ddd , j = 9.8 , 7.1 , 1.1 hz , 2h ) , 7.90 ( d , j = 7.3 hz , 1h ) , 7.627.50 ( m , 3h ) , 7.387.28 ( m , 5h ) , 4.41 ( s , 2h ) . dimethyl 2,2 - bis ( ( 1,3 - dioxolan -2-yl ) methyl ) malonate ( 578 mg , 1.90 mmol ) was dissolved in a 1:1 mixture of thf ( 10 ml ) to 10 % aqueous hcl ( 10 ml ) and stirred at room temperature for 18 h. at this time , the reaction was neutralized with solid nahco3 and a solution of 1 - ( naphthalen -1-yl ) -2-phenylethanamine 20 ( 446 mg , 1.80 mmol ) , prepared previously by the literature method from 19 , in thf ( 6 ml ) was added . the mixture was stirred at room temperature for 20 h. at this time , the solution was extracted with etoac ( 250 ml ) and the combined extracts were dried over anhydrous mgso4 and the filtrate was concentrated in vacuo . the residue was then purified via flash chromatography ( 15 g silica , 15 % etoac / hex ) to give the desired condensed product ( 470 mg , 58 % ) as a yellow oil . h nmr ( 300 mhz , chloroform - d ) 7.927.85 ( m , 3h ) , 7.66 ( d , j = 0.9 hz , 1h ) , 7.577.48 ( m , 3h ) , 7.357.26 ( m , 5 h ) , 6.08 ( d , j = 8.5 hz , 2h ) , 5.21 ( dd , j = 4.8 , 9.7 hz , 1h ) , 4.69 ( d , j = 8.5 hz , 2 h ) , 3.72 ( s , 6h ) , 3.563.35 ( m , 2 h ) . dimethyl 1 - ( 1 - ( naphthalen -1-yl ) -2-phenylethyl ) pyridine - 4,4 ( 1h ) - dicarboxylate 21 ( 80 mg , 0.187 mmol ) was dissolved in n2 - sparged meoh ( 5 ml ) , and 10 % pd / c was added . this was mixed under 40 psi of h2 for 8 h at room temperature . this was then filtered through celite and the filtrate concentrated in vacuo to give the desired product ( 57 mg , 71 % ) without further purification . h nmr ( 500 mhz , chloroform - d ) 8.51 ( bs , 1h ) , 7.877.79 ( m , 1h ) , 7.71 ( d , j = 8.2 hz , 1h ) , 7.507.43 ( m , 2h ) , 7.29 ( bs , 2h ) , 7.107.01 ( m , 3h ) , 6.82 ( bs , 2h ) , 4.13 ( s , 1h ) , 3.74 ( s , 6h ) , 3.44 ( dd , j = 13.5 , 4.6 hz , 1h ) , 3.17 ( dd , j = 13.5 , 9.3 hz , 1h ) , 2.72 ( bs , 2h ) , 2.51 ( bs , 2h ) , 2.292.08 ( m , 4h ) . dimethyl 1 - ( 1 - ( naphthalen -1-yl ) -2-phenylethyl ) piperidine -4,4-dicarboxylate 22 ( 103 mg , 0.24 mmol ) was dissolved in anhydrous dmf ( 3 ml ) , and nacn ( 17.6 mg , 0.36 mmol ) was added to the solution . this was stirred at 145 c for 16 h. the mixture was allowed to cool . h2o was added , and material was extracted with etoac ( 350 ml ) . the resulting residue was purified via flash chromatography ( 10 g silica , 20 % etoac / hex ) to give the desired monoester ( 38 mg , 43 % ) . h nmr ( 500 mhz , chloroform - d ) 8.49 ( s , 1h ) , 7.83 ( dt , j = 6.9 , 3.5 hz , 1h ) , 7.72 ( d , j = 8.5 hz , 1h ) , 7.47 ( dt , j = 6.4 , 3.3 hz , 2h ) , 7.377.22 ( m , 2h ) , 7.116.99 ( m , 3h ) , 6.89 ( s , 2h ) , 4.27 ( s , 1h ) , 3.68 ( s , 3h ) , 3.46 ( dd , j = 13.6 , 4.9 hz , 1h ) , 3.31 ( s , 1h ) , 3.20 ( dd , j = 13.5 , 9.1 hz , 1h ) , 2.90 ( d , j = 11.5 hz , 1h ) , 2.28 ( tt , j = 11.2 , 4.0 hz , 1h ) , 2.222.04 ( m , 2h ) , 1.93 ( d , j = 13.1 hz , 1h ) , 1.841.66 ( m , 3h ) . to a 78 c solution of quinoline -8-carbaldehyde 26a ( 0.5 g , 3.18 mmol ) in dry thf under n2 was added methylmagnesium chloride ( 3.82 ml , 3.82 mmol ) dropwise . nh4cl was added , and the mixture was stirred for 10 min before diluting with etoac / et2o and washing with saturated nacl and drying over mgso4 . the residue was purified by flash chromatography ( 1040 % etoac / hex ) to afford the desired compound ( 0.435 g , 79 % ) . h nmr ( 400 mhz , chloroform - d ) 8.84 ( dd , j = 4.3 , 1.9 hz , 1h ) , 8.18 ( dd , j = 8.3 , 1.9 hz , 1h ) , 7.72 ( dd , j = 8.1 , 1.6 hz , 1h ) , 7.327.62 ( m , 3h ) , 6.09 ( s , 1h ) , 5.44 ( q , j = 6.7 hz , 1h ) , 1.73 ( dd , j = 6.6 , 0.4 hz , 3h ) . to a 78 c solution of quinoline -5-carbaldehyde 26b ( 0.82 g , 5.2 mmol ) in dry thf under n2 was added methylmagnesium chloride ( 6.3 ml , 6.3 mmol ) dropwise . saturated aqueous nh4cl was added , and the mixture was stirred for 10 min before being diluted with etoac / et2o , washed with saturated nacl , and dried over mgso4 . the residue was purified by silica flash chromatography ( 1040 % etoac / hex ) to afford the target compound ( 0.77 g , 86 % ) as a yellow oil . h nmr ( 400 mhz , chloroform - d ) 8.87 ( d , j = 1.7 hz , 1h ) , 8.53 ( d , j = 8.6 hz , 1h ) , 7.908.13 ( m , 1h ) , 7.607.68 ( m , 2h ) , 7.40 ( dd , j = 8.6 , 4.2 hz , 1h ) , 5.59 ( q , j = 6.5 hz , 1h ) , 2.32 ( br s , 1h ) , 1.65 ( d , j = 6.5 hz , 3h ) . to a 78 c solution of isoquinoline -5-carbaldehyde 26c ( 1.13 g , 7.19 mmol ) in dry thf under n2 was added methylmagnesium chloride ( 8.63 ml , 8.63 mmol ) dropwise . saturated aqueous nh4cl was added , and the mixture was stirred 10 min before diluting with etoac / et2o . concentration provided a white solid which was triturated in ether , filtered , and dried under high vacuum to give 1 - ( isoquinolin -5-yl ) ethanol 26c ( 1.1 g , 88 % yield ) . h nmr ( 400 mhz , chloroform - d ) 8.88 ( d , j = 1.4 hz , 1h ) , 8.48 ( d , j = 7.8 hz , 1h ) , 7.65 ( m , 2h ) , 7.58 ( m , 1h ) , 7.287.41 ( m , 2h ) , 4.69 ( q , j = 6.3 hz , 1h ) , 1.49 ( d , j = 6.3 hz , 3h ) . to a solution of 1 - cyanoisoquinoline ( 301 mg , 1.96 mmol ) in dry et2o ( 10 ml ) at 0 c , 3.92 ml of 1 m memgbr ( 3.92 mmol ) was added and allowed to stir for 3 h to produce a bright orange solution . the reaction was quenched with h2o ( 15 ml ) and 6 m hcl ( 5 ml ) and stirred for 1 h at 80 c . the solution was basified with saturated nahco3 , extracted with et2o ( 225 ml ) , dried over mgso4 , and concentrated in vacuo . the residue was purified by silca flash chromatography ( 30 % etoac / hex ) to furnish 1 - ( isoquinolin -1-yl ) ethanone ( 304 mg , 91 % ) as a yellow oil . h nmr ( 400 mhz , chloroform - d ) 8.95 ( d , j = 8.4 hz , 1h ) , 8.57 ( d , j = 5.5 hz , 1h ) , 7.887.82 ( m , 1h ) , 7.80 ( d , j = 5.5 hz , 1h ) , 7.69 ( pd , j = 6.9 , 1.3 hz , 2h ) , 2.86 ( s , 3h ) . this compound ( 304 mg , 1.78 mmol ) was then dissolved in meoh ( 6 ml ) , and nabh4 was added and the mixture was allowed to stir at 0 c for 18 h. the mixture was concentrated in vacuo and treated with saturated aqueous nh4cl . the solution was extracted with dcm ( 310 ml ) , dried under mgso4 , and concentrated in vacuo . the residue was purified by silica flash chromatography ( 30 % etoac / hex ) to furnish the desired compound ( 226.5 mg , 73.6 % ) as a clear oil . h nmr ( 400 mhz , chloroform - d ) 8.43 ( d , j = 5.7 hz , 1h ) , 8.03 ( d , j = 8.5 hz , 1h ) , 7.86 ( d , j = 8.2 hz , 1h ) , 7.70 ( ddd , j = 8.2 , 7.0 , 1.1 hz , 1h ) , 7.667.54 ( m , 2h ) , 5.58 ( p , j = 5.7 hz , 1h ) , 5.375.23 ( m , 1h ) , 1.59 ( d , j = 6.5 hz , 3h ) . to a 0 c solution of 1 - ( quinolin -8-yl ) ethanol 27a ( 0.47 g , 2.71 mmol ) in dry dcm was added diea ( 1.05 g , 8.14 mmol ) followed by ms2o ( 0.71 g , 4.10 mmol ) . then ethyl piperidine -4-carboxylate ( 0.39 g , 1.27 mmol , 47 % yield ) was added in one portion . the resulting mixture was stirred overnight at room temperature , after which time the mixture was diluted with aqueous nahco3 and extracted with dcm . the extracts were dried over mgso4 , concentrated , and purified by flash chromatography ( 1050 % etoac / hex ) to provide 28a as a clear oil ( 0.39 g , 47 % ) . h nmr ( 400 mhz , chloroform - d ) 8.87 ( d , j = 4.2 , 1h ) , 8.53 ( d , j = 8.6 hz , 1h ) , 7.908.13 ( m , 1h ) , 7.607.81 ( m , 2h ) , 7.40 ( dd , j = 8.6 , 4.2 hz , 1h ) , 5.59 ( q , j = 6.5 hz , 1h ) , 3.283.30 ( m. 1h ) , 2.772.81 ( m , 1h ) , 2.222.30 ( m , 1h ) , 1.921.30 ( m , 8h ) , 1.40 ( d , j = 6.5 hz , 3h ) , 1.23 ( dd , j = 6.6 , 0.4 hz , 3h ) . to a 0 c solution of 1 - ( quinolin -5-yl ) ethanol 27b ( 0.47 g , 2.70 mmol ) in dry dcm was added diea ( 1.0 g , 8.14 mmol ) followed by ms2o ( 0.71 g , 4.07 mmol ) . the resulting mixture was stirred for 40 min at 0 c , and then ethyl piperidine -4-carboxylate ( 0.70 g , 83 % yield ) was added in one portion . the resulting mixture was stirred overnight at room temperature , after which time the mixture was diluted with nahco3 and extracted with dcm . the extracts were dried over mgso4 , concentrated , and purified by flash chromatography ( 1050 % etoac / hex ) to give the desired compound ( 0.70 g , 83 % ) as a clear oil . h nmr ( 400 mhz , chloroform - d ) 8.878.91 ( m , 1h ) , 7.98 ( d , j = 8.5 hz , 1h ) , 7.477.67 ( m , 2h ) , 7.36 ( m , 2h ) , 3.874.33 ( m , 2h ) , 3.02 ( d , j = 11.2 hz , 1h ) , 2.76 ( d , j = 11.2 hz , 1h ) , 2.24 ( m , 1h ) , 1.922.19 ( m , 2h ) , 1.521.92 ( m , 5h ) , 1.45 ( dd , j = 6.7 , 0.7 hz , 3h ) , 1.21 ( td , j = 7.1 , 0.7 hz , 3h ) . to a 0 c solution of 1 - ( isoquinolin -5-yl ) ethanol 27c ( 0.47 g , 2.71 mmol ) in dry dcm was added diea ( 1.05 g , 8.14 mmol ) followed by ms2o ( 0.71 g , 4.07 mmol ) . the resulting mixture was stirred for 40 min at 0 c , and then ethyl piperidine -4-carboxylate ( 0.52 g , 1.67 mmol , 61.3 % yield ) was added in one portion . the resulting mixture was stirred overnight at room temperature , diluted with saturated nahco3 , and extracted with dcm . the extracts were dried over mgso4 , concentrated , and purified by flash chromatography ( 1050 % etoac / hex ) to provide 27c as a clear oil ( 0.52 g , 61 % yield ) . h nmr ( 400 mhz , chloroform - d ) 9.22 ( d , j = 0.9 hz , 1h ) , 8.49 ( dd , j = 6.1 , 0.7 hz , 1h ) , 8.20 ( dd , j = 6.1 , 1.0 hz , 1h ) , 7.677.95 ( m , 2h ) , 7.467.67 ( m , 1h ) , 3.874.21 ( m , 3h ) , 3.05 ( d , j = 11.2 hz , 1h ) , 2.74 ( d , j = 11.2 hz , 1h ) , 2.25 ( tt , j = 11.2 , 4.2 hz , 1h ) , 1.952.17 ( m , 2h ) , 1.571.95 ( m , 4h ) , 1.43 ( dd , j = 6.7 , 0.7 hz , 3h ) , 1.21 ( t , j = 7.1 hz , 3h ) . to a solution of 27d ( 215 mg , 1.24 mmol ) in dry dcm were added diea ( 482 mg , 3.73 mmol ) and ms2o ( 326 mg , 1.87 mmol ) , and the mixture was allowed to stir for 40 min at 0 c . to the solution , ethyl isonipecotate ( 586 mg , 3.73 mmol ) was added dropwise , and the mixture was allowed to stir at 23 c for 18 h. the mixture was acidified using 6 m hcl ( 6 ml ) and extracted with dcm ( 215 ml ) . the aqueous layer was then basified using saturated nahco3 ( 15 ml ) and extracted with dcm ( 315 ml ) . the residue was purified by flash chromatography ( 1050 % etoac / hex ) to furnish the desired compound ( 62 mg , 16 % ) as a yellow oil . h nmr ( 400 mhz , chloroform - d ) 8.69 ( d , j = 8.5 hz , 1h ) , 8.45 ( d , j = 5.7 hz , 1h ) , 7.79 ( d , j = 8.1 hz , 1h ) , 7.677.61 ( m , 1h ) , 7.577.47 ( m , 2h ) , 4.36 ( q , j = 6.7 hz , 1h ) , 4.08 ( q , j = 7.1 hz , 2h ) , 2.25 ( dtt , j = 22.2 , 8.2 , 3.5 hz , 2h ) , 2.11 ( td , j = 11.3 , 2.7 hz , 1h ) , 1.881.75 ( m , 2h ) , 1.751.67 ( m , 2h ) , 1.651.61 ( m , 1h ) , 1.52 ( d , j = 6.7 hz , 3h ) , 1.20 ( t , j = 7.1 hz , 3h ) . to a solution of 2,3 - dihydrophenanthren - 4 ( 1h ) - one 29 ( 305 mg , 1.55 mmol ) in isopropanol ( 50 ml ) were added nacnbh3 ( 677 mg , 10.8 mmol ) and nh4 ( oac ) ( 4.831 g , 62.68 mmol ) , and the mixture was allowed to stir at reflux for 72 h under n2 atmosphere . approximately 50 % of the solvent was evaporated , and the reaction mixture was extracted with dcm ( 340 ml ) , dried under mgso4 , and concentrated in vacuo to afford the desired compound ( 301 mg , 98 % ) as a dark oil , which was sufficiently pure to use in the next step . h nmr ( 400 mhz , chloroform - d ) 8.18 ( d , j = 8.5 hz , 1h ) , 7.79 ( d , j = 8.1 hz , 1h ) , 7.64 ( d , j = 8.5 hz , 1h ) , 7.53 ( t , j = 7.3 hz , 1h ) , 7.42 ( t , j = 7.4 hz , 1h ) , 7.19 ( d , j = 8.4 hz , 1h ) , 4.72 ( s , 1h ) , 2.92 ( dd , j = 10.4 , 5.7 hz , 2h ) , 2.151.84 ( m , 4h ) . to a solution of dimethyl 2,2 - bis ( ( 1,3 - dioxolan -2-yl ) methyl ) malonate ( 464 mg , 1.53 mmol ) in thf ( 10 ml ) was added a 10 % hcl solution ( 9.3 ml ) dropwise . the reaction mixture was allowed to stir at room temperature for 16 h. the reaction mixture was neutralized with aqueous na2co3 . amine 30 ( 301 mg , 1.53 mmol ) was dissolved in thf ( 3 ml ) and added dropwise to the reaction mixture . the ph was adjusted to 5 using acoh , and the reaction mixture was allowed to stir at room temperature for 72 h. the reaction mixture was quenched with saturated aqueous nahco3 , extracted with etoac ( 215 ml ) , dried over mgso4 , and concentrated in vacuo . the residue was purified by silica flash chromatography ( 20 % etoac / hex ) to furnish 31 ( 221 mg , 38 % ) as an oil . h nmr ( 400 mhz , chloroform - d ) 7.77 ( d , j = 7.9 hz , 2h ) , 7.71 ( d , j = 8.5 hz , 1h ) , 7.48 ( t , j = 7.5 hz , 1h ) , 7.41 ( t , j = 7.3 hz , 1h ) , 7.21 ( d , j = 8.4 hz , 1h ) , 6.05 ( d , j = 7.7 hz , 2h ) , 4.97 ( s , 1h ) , 4.66 ( d , j = 7.8 hz , 2h ) , 3.68 ( s , 5h ) , 3.132.74 ( m , 4h ) , 2.282.08 ( m , 2h ) . to a solution of 31 ( 221 mg , 0.59 mmol ) in etoac ( 25 ml ) was added pto2 ( 20 mg ) , and n2 was bubbled through for 15 min . the mixture was placed under h2 ( 40 psi ) at room temperature for 5 h , and reaction progress was monitored by hplc . the residue was then purified by silica flash chromatography ( 510 % etoac / hex ) to furnish the desired compound ( 150 mg , 67 % ) as a yellow oil . h nmr ( 400 mhz , chloroform - d ) 8.37 ( d , j = 8.5 hz , 1h ) , 7.74 ( d , j = 7.7 hz , 1h ) , 7.63 ( d , j = 8.3 hz , 1h ) , 7.457.35 ( m , 2h ) , 7.15 ( d , j = 8.4 hz , 1h ) , 4.43 ( t , j = 5.4 hz , 1h ) , 3.69 ( s , 6h ) , 2.88 ( t , j = 5.4 hz , 1h ) , 2.822.76 ( m , 1h ) , 2.54 ( dd , j = 7.3 , 3.6 hz , 2h ) , 2.192.11 ( m , 1h ) , 2.02 ( dd , j = 7.0 , 3.4 hz , 1h ) , 1.94 ( dd , j = 7.3 , 3.0 hz , 2h ) , 1.71 ( dq , j = 9.8 , 5.3 , 4.7 hz , 2h ) , 1.301.20 ( m , 2h ) , 0.920.77 ( m , 2h ) . to a solution of 32 ( 150 mg , 0.39 mmol ) in dmf ( 10 ml ) was added nacn ( 29 mg , 0.59 mmol ) , and the mixture was allowed to stir at reflux for 16 h under n2 atmosphere . the reaction mixture was cooled and diluted with etoac ( 10 ml ) , quenched with aqueous nahco3 , and washed with saturated nacl ( 210 ml ) . the extract was dried over mgso4 , concentrated in vacuo , and the residue was purified by silica flash chromatography ( 010 % etoac / hex ) to furnish the desired compound ( 97 mg , 76 % ) as a yellow oil . h nmr ( 400 mhz , chloroform - d ) 8.40 ( d , j = 8.2 hz , 1h ) , 7.74 ( d , j = 7.8 hz , 1h ) , 7.63 ( d , j = 8.3 hz , 1h ) , 7.457.32 ( m , 2h ) , 7.16 ( d , j = 8.4 hz , 1h ) , 4.44 ( t , j = 4.9 hz , 1h ) , 3.62 ( s , 3h ) , 2.962.86 ( m , 2h ) , 2.832.75 ( m , 1h ) , 2.602.49 ( m , 2h ) , 2.382.27 ( m , 1h ) , 2.242.15 ( m , 2h ) , 2.051.90 ( m , 1h ) , 1.84 ( d , j = 14.0 hz , 1h ) , 1.74 ( td , j = 12.0 , 10.7 , 4.7 hz , 3h ) , 1.65 ( d , j = 14.5 hz , 1h ) , 1.34 ( qd , j = 12.1 , 4.1 hz , 1h ) . sars - cov pet - 15b - plpro ( 15411855 ) ( cloned between the restriction sites bamh i and bpu1102 i ) and the hcov - nl63 pet - 15b - plp2 ( 15651894 ) ( cloned between the restriction sites bamh i and bpu1102 i ) were obtained from dr . susan baker s lab at loyola university chicago , stritch school of medicine . for crystallization , sars - cov plpro ( 15411855 ) fused at the n - terminus to tev protease cleavage sites and a 6 histidine tag was synthetized and codon optimized and cloned into pet11a using the restriction sites nde i and bpu1102 i by biobasic inc . synthetic peptide substrate , z - rlrgg - amc , used for ic50 determination was purchased from bachem . the 5 ml hitrap chelating hp column and the superdex 200 were obtained from ge healthcare , life sciences . bradford reagent and bsa standard solution used for quantification of protein concentration were purchased from bio - rad . a9511 , purity 9799 % ) for serum shift assays was obtained from sigma - aldrich . the expression plasmids containing sars - cov pet - 15b - plpro ( 15411855 ) , sars - cov pet - 11a - plpro ( 15411855 ) , and hcov - nl63 pet - 15b - plp2 ( 15651894 ) were transformed into e. coli bl21 ( de3 ) for protein expression . all purifications were performed at 4 c with slight variations in the purification procedures . one liter of cells containing sars - cov pet - 15b - plpro ( 15411855 ) wild type and mutants , sars - cov pet - 11a - plpro ( 15411855 ) , or hcov - nl63 pet - 15b - plp2 ( 15651894 ) were grown for 24 h at 25 c in medium containing 3 g of kh2po4 , 6 g of na2hpo4 , 20 g of tryptone , 5 g of yeast extract , 5 g of nacl , ph 7.2 , supplemented with 0.2 % lactose , 0.6 % glycerol , 0.05 % glucose , and 50 g / ml carbenicilin . after growth , the cells were pelleted by centrifugation ( 18500 g , 30 min at 4 c ) and an amount of 12 g of cell pellet was resuspended in 50 ml of buffer a ( 20 mm tris , ph 7.5 , 500 mm nacl , 10 mm imidazole ) containing lysozyme and dnase i. the resuspended cells were lysed on ice via sonication using a 600 w model vcx ultrasonicator ( 78 min at 70 % amplitude ; 5.5 pulse on , 9.9 pulse off ) or a 400 w 450 model digital sonifier cell disruptor ( 10 min at 60 % amplitude ; 5.5 pulse on , 9.9 pulse off ) . cells debris were pelleted by centrifugation ( 30000 g , 25 min , 4 c ) . for sars - cov plpro wt and mutants ( pet - 15b - plpro ( 15411855 ) and pet - 11a - plpro ( 15411855 ) ) , the clarified lysate was loaded at 2 ml / min onto a 5 ml hitrap chelating hp column ( ge healthcare ) charged with co and equilibrated with buffer a. unbound proteins were washed with five column volumes ( cv ) of buffer a. bound proteins were eluted with a linear gradient of 0100 % buffer b ( 20 mm tris , ph 7.5 , 500 mm nacl , 500 mm imidazole ) , at 2 ml / min , followed by a 5 cv 100 % buffer b wash . fractions containing sars - cov plpro were exchanged and concentrated into buffer c ( 20 mm tris , ph 7.5 , 20 % glycerol , 10 mm dtt ) to 510 mg / ml . aliquots of 500 l of the concentrated protein were flash frozen in liquid nitrogen for 10 min , then stored at 80 c . hcov - nl63 plp2 ( 15651894 ) was purified by the same protocol as sars - cov plpro except that a 5 ml histrap ff column ( ge healthcare ) precharged with ni was used and 10 mm - mercaptoethanol was included in the purification buffers . for crystallization , the eluted fractions of the pet - 11a - plpro ( 15411855 ) from the co columnwere concentrated and supplemented with 1 mg of tev protease per 30 mg of plpro and dialyzed for 18 h at 4 c against 1 l ( 1000 dilution ) of dialysis buffer ( 20 mm tris , ph 7.5 , 10 % glycerol , 10 mm - mercaptoethanol ) . following dialysisthe - mercaptoethanol was removed by buffer exchange and the his - tagged tev protease was removed by loading the sample onto a 5 ml hitrap chelating hp column . cleaved untagged sars - cov plpro was obtained in the flow - through and concentrated to 25 mg / ml prior to loading onto a superdex 20026 / 60 gel filtration column equilibrated with buffer d ( 20 mm tris , ph 7.5 , 100 mm nacl , and 10 mm dtt ) . the protein was eluted at a flow rate of 0.5 ml / min with equilibrium buffer , and the fractions containing sars - cov plpro were concentrated to 6 and 12 mg / ml . for all proteins , the protein concentration was determined by cuvette - based bradford assay and purity was monitored by sds page analysis and by calculating the specific activity at every step of the purification . the 100 l inhibition assays were performed in triplicate in a 96 - well plate format as previously described . the final enzymes concentrations were 0.14 and 0.4 m for sars - cov plpro and hcov - nl63 plp2 , respectively . the assays were performed at 25 c , and the enzyme activity was monitored by measuring the plp - mediated release of amc from the rlrgg - amc peptide substrate ( 50 m ) , using the envision multimode plate reader from perkinelmer . human serum albumin ( hsa ) was dissolved to a final concentration of 50 mg / ml in buffer containing 50 mm hepes , ph 7.5 , 2.5 mm dtt . serum shift assays were performed by determining the ic50 values for selected compounds as described above except that the assays contained 5 % , 10 % , or 20 % hsa , where 40 mg / ml is 100 % . the nl63 - hcov plp2 counterscreening assay was performed in a 100 l reaction volume including 400 nm enzyme , 100 m compound , and 50 m rlrgg - amc substrate in assay buffer ( 50 mm hepes , ph 7.5 , 0.1 mg / ml bsa , 2 mm dtt ) . the assay was performed at 25 c in triplicate for each inhibitor , and the enzyme activity was monitored as described above . the counterscreens with human usp and cysteine proteases were determined using purified enzymes available from progenra , inc . as part of their dub screening service . the assays were performed in triplicate using 31.6 m compounds and ub - rhodamine 110 as a substrate for usps , nedd8 - ekl for den1 , and commercially available fluorogenic peptide substrates for caspase 3 and cathepsin k. sars - cov antiviral activity in infected vero e6 cells was performed as previously described in a bsl - 3 laboratory . briefly , vero e6 cells were seeded into 96 - well culture plates at 110 cells per well 24 h prior to infection with sars - cov . cells were mock or sars - cov infected for 48 h in the presence of increasing concentrations of compounds . upon incubation , cell viability was determined using cell titer - glo luminescent cell viability assay ( promega ) . both the half maximal effective concentration ( ec50 ) and the 50 % cytostatic concentration ( cc50 ) values were calculated using a four - parameter logistic equation by means of sigma plot 10 or graphpad prism software . culturing and cell viability measurements of hek 293 cells were performed as described above , in triplicate , 48 h after compound addition . compounds ( 1 m ) were incubated with mouse liver microsomes ( 0.5 mg / ml ) and nadph in 0.1 m phosphate buffer at 37 c as previously described . the mutagenesis of gln270 to ala , glu , or asp was performed by quickchange site - directed mutagenesis as described by zhen et al . mutant enzymes were purified as described above for the wild - type sars - plpro enzyme . prior to crystallization , untagged sars - cov plpro in 25 mm tris , ph 7.5 , 100 mm nacl , 10 mm dtt at concentrations of 6 or 12 mg / ml was incubated with 2 mm inhibitor ( dissolved in dmso or ethanol ) added to a 100 dilution and incubated overnight at 4 c . crystallization was performed at 20 c using the sitting - drop vapor - diffusion method by mixing equal amounts of protein / inhibitor with reservoir solution containing 100 mm sodium citrate , ph 5.5 , 40 % ( v / v ) peg 600 . crystals were soaked in cryosolution consisting of reservoir solution , 2 mm inhibitor , and 20 % glycerol . crystals were flash - frozen in liquid nitrogen and stored until synchrotron time was available . crystals were transferred from liquid nitrogen into a stream of dry nitrogen gas at 100 k for x - ray data collection . x - ray data were collected at the life sciences - collaborative access team ( ls - cat ) on beamline 21 - id - f at the advanced photon source , argonne national laboratory . the sars - cov plpro3k and plpro3j complex crystallized as two monomers in the asymmetric unit . crystals belong to space group c2 with unit cell dimensions of a = 119 , b = 74 , c = 98 , = 104 . the inhibitor - bound structures diffracted to resolutions of 2.1 and 2.5 for 3k and 3j , respectively . the initial phases were determined from molecular replacement solutions using the sars - cov plpro15 g inhibitor complex structure ( pdb : 3mj5 ) as a search model and the molrep program of the ccp4 suite . model building and refinement was performed using the programs refmac , phenix , and coot . the final x - ray data processing and refinement statistics are summarized in table 3 . the final coordinates have been deposited in the protein data bank under pdb code 4ow0 for plpro3k complex and pdb code 4ovz for plpro3j complex .\noutput:\n" }, { "from": "agent", "value": "structure - guided design was used to generate a series of noncovalent inhibitors with nanomolar potency against the papain - like protease ( plpro ) from the sars coronavirus ( cov ) . a number of inhibitors exhibit antiviral activity against sars - cov infected vero e6 cells and broadened specificity toward the homologous plp2 enzyme from the human coronavirus nl63 . selectivity and cytotoxicity studies established a more than 100-fold preference for the coronaviral enzyme over homologous human deubiquitinating enzymes ( dubs ) , and no significant cytotoxicity in vero e6 and hek293 cell lines is observed . x - ray structural analyses of inhibitor - bound crystal structures revealed subtle differences between binding modes of the initial benzodioxolane lead ( 15 g ) and the most potent analogues 3k and 3j , featuring a monofluoro substitution at para and meta positions of the benzyl ring , respectively . finally , the less lipophilic bis ( amide ) 3e and methoxypyridine 5c exhibit significantly improved metabolic stability and are viable candidates for advancing to in vivo studies ." } ]

[ { "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 exact role of surveillance imaging following treatment for oropharynx cancer remains undefined . until recently , the national comprehensive care network ( nccn ) and the american head and neck society ( ahns ) limited imaging recommendations after treatment of head and neck cancers to yearly chest radiographs . despite these guidelines , a survey of head and neck surgeons conducted by paniello et al . found heterogeneity regarding the use of post treatment locoregional imaging of head and neck cancers , including advanced imaging for surveillance of disease recurrence . multiple authors have argued in favor of post - treatment imaging in head and neck cancers . studies have demonstrated that a baseline post - treatment study carries prognostic information regarding locoregional control and allows for comparison to subsequent studies , making it possible to detect tumor recurrences or treatment complications with more confidence . nonetheless , the evidence for periodic routine surveillance imaging is not established . some authors argue that it may lead to earlier detection of recurrence allowing for more prompt salvage therapies and improved long - term outcomes . others believe that the longer survival rates reported with surveillance imaging protocols may be due to lead - time bias . the nccn recently amended their recommendations to call for cross - sectional imaging of the primary site and neck within six months of treatment completion and reimaging based on clinical signs and symptoms . commonly available choices of imaging modality include computed tomography ( ct ) , magnetic resonance imaging ( mri ) , diffusion - weighted mri , positron emission tomography ( pet ) , and pet - ct . , mri has been the preferred modality for locoregional surveillance after treatment of head and neck cancers . we previously reported our institutional experience of patients who underwent intensity - modulated radiation therapy combined with concurrent platinum - based chemotherapy for stage iii or iv oropharyngeal carcinoma between april 2000 and september 2004 . this dataset represents a relatively uniform population of similarly staged and treated head and neck cancer patients . the purpose of the current investigation was to determine the utility of routine surveillance mri to detect locoregional treatment failure for advanced - stage oropharyngeal carcinoma treated with chemoradiation . a waiver of informed consent was granted by our institution 's committee on human research to conduct this retrospective review . we identified patients with stage iii - iv oropharyngeal carcinoma who underwent chemoradiation therapy between april 2000 and september 2004 and underwent longitudinal follow - up care at the university of california , san francisco ( ucsf ) comprehensive cancer center . patients who received clinical and radiographic follow - up at outside institutions were excluded . prior to treatment , all patients underwent complete history and physical examination , panendoscopy and biopsy , ct or mri of the head and neck region , laboratory studies and chest radiography , dental evaluation , and nutritional , speech and swallowing evaluation . recommended post treatment surveillance included clinical history and physical examination at a frequency of every 1 - 2 months for the first year , 2 - 3 months for the second year , 3 - 4 months for the third and fourth years , and 6 months for the fifth year . all patients underwent a post treatment baseline mri approximately two months after completion of chemoradiation therapy . surveillance mris were performed approximately every 3 - 4 months in the first year post treatment and approximately every 6 months in subsequent years . mri sequences included axial , coronal , and sagittal pregadolinium t1 ; fat - saturated axial fast spin echo t2 ; and fat - saturated axial and coronal postgadolinium t1 . adjunctive studies , such as pet / ct scans , were performed as clinical evaluation dictated , but were not specifically analyzed in this study . patient charts were retrospectively reviewed for disease staging , treatment and surveillance information , and recurrence . for patients who experienced locoregional failure , charts were reviewed for description of recurrence , imaging and physical exam findings , and patient symptomatology at time of diagnosis . time until treatment failure was defined as the difference from chemoradiation completion until radiographic or definitive clinical evidence of recurrence , whichever came first . radiographic failure was defined by language within the finalized mri report specifically implicating the presence of tumor or suggesting tumor presence by interval growth or concerning radiographic features such as signal characteristics . additionally , for patients with clinical symptoms or questionable findings on mri scans , review at tumor board by the multidisciplinary head and neck team routinely occurred , including the presence of an experienced head and neck radiologist . these definitions were then used to calculate mri diagnostic accuracy measurements , including sensitivity , specificity , positive predictive value , and negative predictive value . disease persistence versus recurrence was defined as disease identified within or after a 3 - month - time frame post treatment , respectively . invasive procedures performed within 4 months of chemoradiation completion , such as neck dissection , were considered to be an extension of primary treatment rather than investigations into disease recurrence . we based our estimates from current charge data for an mri neck with gadolinium , which was $ 4,942 as of april , 2010 . seventy - one patients with advanced ( stage iii or iv ) oropharynx carcinoma were treated with concurrent chemoradiation at ucsf between april 2000 and september 2004 . forty - three patients met our inclusion criteria of clinical and radiologic mri imaging surveillance follow - up performed at our institution . three of these 43 patients had malignant disease identified within three months of completion of their treatment and were considered to have persistent disease . the remaining 40 patients were considered to have been rendered disease free by their initial treatment and were the focus of the remainder of our analysis . our study group consisted of 35 men and 5 women with a median age of 58 years ( range , 4181 years ) . the primary site of disease included base of tongue ( 27 ) , tonsil ( 11 ) , and oropharyngeal wall ( 2 ) . table 1 provides the t - stage and n - stage distributions of the patients according to the 2002 ajcc staging classification system . the disease was stage iii in 11 patients ( 28 % ) and stage iv in 29 patients ( 72 % ) . four patients experienced locoregional failure after an initial complete clinical and radiographic response to treatment . three additional patients experienced distant metastatic disease without locoregional failure , identified at a mean of 11 months post treatment ( range , 420 months ) . table 2 displays patient characteristics for these patients . among the four patients with locoregional recurrence following an initial complete treatment response , two experienced local failure and two experienced regional failure . two of the four patients experienced recurrence within 12 months of completing chemoradiation . as shown in table 3 , the mean time until detection of recurrence was 20.3 months ( range , 540 months ) . the physical exam findings and patient symptomatology of the 4 patients with locoregional recurrence are summarized in table 4 . surveillance mri imaging identified recurrent disease in two completely asymptomatic patients ( patients 1 , 4 ) . routine mri scans revealed a new , enhancing mass in the tongue base ( patient 1 ) and a cluster of enlarged level ii nodes with focal necrosis ( patient 4 ) . the first patient ( patient 1 ) was found by mri to have cancer recurrence five months post chemoradiation and underwent salvage resection with glossectomy and modified radical neck dissection , but died of disease within three months of surgery . the second patient ( patient 4 ) experienced isolated cervical nodal recurrence 26 months after completion of treatment and underwent a salvage neck dissection ; this patient remains free of disease at two - year follow - up . both patients were undergoing regular clinical follow - up ; patients 1 and 4 had negative head & neck examinations five and 16 weeks prior to mri detection of tumor recurrence , respectively . two patients ( patients 2 , 3 ) exhibited signs and / or symptoms prior to mri evidence of disease . symptoms included pharyngeal discomfort with foreign body sensation ( patient 2 ) and worsening unilateral otalgia ( patient 3 ) . the first patient ( patient 2 ) had concerning physical exam findings in the form of tongue base mucosal irregularity ; a subsequent mri scan was suspicious for locally recurrent disease . this patient underwent brachytherapy at the site of recurrence and remained free of disease at over two - year follow - up . the other patient ( patient 3 ) informed his physician of otalgia at a regularly scheduled clinic follow - up ; a new , enlarging neck mass was noted which was subsequently confirmed on fine - needle aspiration biopsy . this patient ( patient 3 ) was treated with additional chemotherapy , but ultimately died of progressive cervical nodal disease . a total of 229 mri surveillance imaging studies were performed ( a mean of 5.6 studies per patient ; an average of 2.0 studies per patient - year ) . the four patients with locoregional recurrence underwent a total of 23 studies , an average of 5.8 per patient ( range , 39 studies ) . the overall sensitivity and specificity of the mri surveillance program for advanced oropharynx carcinoma were 50 and 83 percent , respectively ( table 5 ) . the positive predictive value was 25 % and the negative predictive value was 94 % . to perform a simple cost analysis of our mri surveillance program , we used the standard charge at our institution for an mri of the neck with gadolinium , which was $ 4,942 in april 2010 . the total expense for the mri surveillance program approximated $ 1.13 million and averaged $ 28,293 per patient . six patients experienced false - positive imaging results , all of whom underwent interventions to validate the suspicious imaging scans . all patients had normal physical exams and no clinical concerns at the time of positive mri findings . four patients underwent panendoscopy with biopsies , and two patients underwent fine - needle aspiration biopsies . for the 4 patients with concerning findings at the primary site , mri demonstrated concerning asymmetry with enhancement , t2 prolongation , or both ; all 4 mri reports raised the possibility of tumor recurrence and suggested direct visualization , biopsy , further radiographic imaging , or a combination thereof . mri studies for the two patients that underwent fine needle aspiration biopsies revealed enlarging or persistently large lymph nodes . mri reports for these 2 patients both suggested the possibility of malignancy in lymph nodes . none of these six patients complained of new or worsening symptomatology at the time of radiographic study , nor did any display concerning physical exam findings . no patient suffered complications from the testing procedures , and none has subsequently shown any evidence of recurrence with a minimum of 6 - month follow - up . among our cohort of patients with advanced - stage oropharynx carcinoma treated with chemoradiation therapy , a surveillance imaging program with mri was equal to patient symptomatology and physical examination in detecting cancer recurrence . a total of 229 mri scans were performed to identify two asymptomatic patients with cancer recurrence . despite early detection and salvage therapy in both patients , this outcome mirrored the identification of cancer recurrence via clinical history and physical examination , in which two patients were identified , one of whom achieved a disease - free state following salvage therapy . the overall sensitivity of detecting recurrence based on patient symptomatology and physical examination was also 50 percent . the anatomic location of the oropharynx is not easily accessible for physical examination , thus increasing the potential for radiologic imaging to detect subclinical recurrence . on the other hand , current chemoradiation treatment protocols for oropharynx cancers , particularly hpv - related tumors in nonsmokers , can achieve low recurrence and second primary rates . as previously reported , among our study population of advanced oropharynx carcinoma patients who were rendered disease free by initial concurrent chemoradiation treatment , less than 10 % suffered locoregional recurrence . this low recurrence rate likely reduces the benefit of any surveillance program as compared to a similar program for a cancer site with a worse prognosis . the recent literature on imaging for head and neck squamous cell carcinoma ( hnscc ) reveals a preponderance of studies on pet and pet / ct rather than other modalities such as mri , ct , and ultrasound . pet has been reported to be a highly sensitive technique for detection of hnscc in the postchemoradiation setting . a recent report of mri for the detection of clinically suspected persistent or recurrent hnscc showed similar high sensitivity . while mri provides the superior soft - tissue delineation and anatomic detail , the application of pet for cancer detection is unique in relying on differential metabolism of malignant versus benign tissue . there have been few studies comparing the efficacy of pet versus mri for the detection of recurrent hnscc , and the best imaging modality for the detection of recurrent hnscc remains undetermined . when the patients in our study were undergoing treatment and follow - up , pet / ct had only been recently introduced to our institution . pet / ct was only used as an adjunctive tool to mri in our cohort and did not influence the frequency or timing of detection of recurrences by mri . we are currently comparing the utility of pet / ct versus mri scans for oropharyngeal cancer surveillance . however , given the high locoregional control rates for oropharynx cancer that we continue to achieve with our concurrent chemoradiation protocols , we believe it is doubtful that we will see substantially different results with pet / ct compared to what we observed with mri in the current investigation . our study is limited by its overall small cohort , single institution status , and retrospective nature . regardless , our results suggest that , for advanced - stage oropharyngeal carcinoma treated with chemoradiation , a routine imaging surveillance program with mri offers limited benefit in detecting cancer recurrence and improving long - term outcome when compared to standard clinical follow - up . this assessment is further bolstered when considering the overall expense of a routine advanced radiographic imaging program , which averaged nearly $ 10,000 per patient annually , and the potential patient morbidity resultant from interventions initiated by findings identified by the imaging program . six patients in our cohort experienced a false - positive imaging study , which led to invasive procedures to evaluate the imaging findings . although there were no complications associated with these interventions , there can be significant emotional stress associated with a positive radiologic imaging report . we acknowledge that routine surveillance imaging may be of benefit in detecting recurrence in a specific subset of patients at high risk for recurrence , but within the limitations of our study , such a cohort could not be identified . analysis of larger , multi - institutional patient populations directed at this question could help further define the benefits and limitations of a routine imaging surveillance program following chemoradiation for advanced head and neck cancer . in patients with advanced - stage oropharyngeal carcinoma treated with chemoradiation , this study suggests limited benefit from routine surveillance mri scans for detecting cancer recurrence as compared to close clinical follow - up . further analysis is needed to identify patients at highest risk of recurrence who would most benefit from routine surveillance imaging .\noutput:\n" }, { "from": "agent", "value": "objectives . to determine the utility of routine surveillance mri in detecting locoregional recurrence following definitive chemoradiation in advanced - stage oropharynx carcinoma . methods . we identified patients with stage iii - iv oropharynx carcinoma who were treated with chemoradiation between april 2000 and september 2004 and underwent longitudinal followup care at our institution . patient charts were retrospectively reviewed for findings on mri surveillance imaging , clinical signs and symptoms , and recurrence . results . forty patients received a total of 229 surveillance mri scans with a minimum follow - up of three years ( mean of 5.6 scans per patient ) . six patients experienced false - positive surveillance studies that resulted in intervention . four patients experienced recurrent disease , two of whom had new symptoms or exam findings that preceded radiographic identification of disease . surveillance mri scans identified recurrent disease in two asymptomatic patients who were salvaged , one of whom remains free of disease at follow - up . the overall sensitivity and specificity of the mri surveillance program were 50 and 83 percent , respectively . the mean charge to each patient for the surveillance program was approximately $ 10,000 annually . conclusion . in oropharyngeal cancer patients who have been treated with chemoradiation , an imaging surveillance program utilizing mri produces limited opportunity for successful salvage ." } ]

[ { "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: contraceptive - pills and immobilisation such as during long air flight are known risk factors for the development of pulmonary emboli . a previously healthy 28 - year - old colombian female taking contraceptive pills with a recent longer flight was admitted to the emergency department because respiratory failure . her medical history involved six days of progressive tachypnea , diffuse chest and back pain , escalating into severe respiratory failure . there was no history of trauma . at the arrival by ambulance in the emergency room she had a saturation of 80 % breathing room air , a breathing rate of 50 breaths per minute and pulse hard to palpable . an electrocardiogram ( ecg ) that was sent in to the emergency department ( ed ) from the ambulance showed sinus tachycardia at a rate of 147 per minute , and t - wave inversion in anterior precordial leads and incomplete right bundle - branch block . a focus assessed transthoracic echo ( fate ) and ultrasound abdomen showed liver venous stasis but no other sign of right ventricular failure and no signs of fluid in the right upper quadrant . the patient suddenly went into cardiopulmonary arrest with pulse - less electrical activity ( pea ) shortly after arrival in the emergency room . cardiopulmonary resuscitation ( cpr ) manual chest compression and artificial ventilation were performed but to relieve the emergency department staff from manual compressions the lucas chest compression system was applied and initiated . the lucas device was placed and strapped in accordance to the instructions for use , but the neck strap was loosened in order to gain a central venous access , an internal jugular vein puncture . the cpr was ineffective and in order to gain further information around the cause for the cardiac arrest and pea and a second fate and ultrasound abdomen was performed that could n't reveal sign of right ventricular strain but were positive for fluid in the tight and left upper quadrant and also in the lower quadrant assessed as abdominal bleed . a decision to perform an exploratory laparotomy was made and the patient was brought to the operating theatre under cpr white lucas . a massive bleeding due to a liver laceration was found . a 4 - quadrant packing and manual sub diaphragmatic aortic compression were performed . the ecmo - team arrived at the time for the explorative laparotomy and her right femoral vein and artery were surgically cannulated and connected to the ecmo - circuit . the ecmo had adequate flow and the patients was transported to the ecmo - centre . time from cardiac arrest to adequate ecmo flow was 1 h and 35 min . the blood tests at arrival and during the first 4 h are presented in table 1 . postoperative ct - scan of thorax showed a massive central pe that had almost totally occluded both pulmonary arteries . ct - scan of the brain 9 h after the cardiac arrest showed significant sign general brain swelling and life - threatening cerebral herniation . ecmo - and icu - treatment were withdrawn 12 h after the cardiac arrest and the patient died shortly thereafter . our patient had right after arrival in the emergency department cardiac arrest most certainly caused by massive pe . our patient had extensive resuscitation efforts including , cpr , laparotomy to stop the liver bleeding , massive transfusion and extra - corporeal circulatory assist she still developed signs of severe brain ischemia and therapy was withdrawn 12 h later . the suspicion of pe was raised early but initial emergent bedside ultra - sound was nt fully confirmatory . according to european guidelines key - factors for suspecting pe are predisposing factors , symptoms and objective sign . our patient had predisposing factors for pe including contraceptive - pills and immobility due to sitting during longer flight . her symptoms with dyspnoea and pleuritic chest pain are symptoms correlated with pe , syncope is infrequent seen and does not correlate with pe and none of these symptoms are specific for the pe diagnosis . our patient developed arterial hypotension and shock which is seen in the most severe cases and indicates central pe and / or a severely reduced hemodynamic reserve and a high pe - related early mortality risk . our patient showed signs of massive pe with an increase in pulmonary artery pressure and subsequent acute right ventricular failure ( rvf ) . rvf also contributes to backward failure transmitted directly to the hepatic veins and sinusoids and leads to a passive congestion of the liver . in long termthere are no explicit studies , evidence that patient with liver enlargement , e.g. caused by backward failure of the right heart have a higher risk for liver laceration during cpr but the connection is theoretically appealing . cpr per see may in a low incidence cause abdominal bleed caused by laceration injury to the liver . liver injury associated to cpr , sternal compression is rare , occurring at a rate of 0.6 % 2 % , , . in a multicentre studydid not see any difference in incidence of liver injuries between lucas compared to manual compression but they conclude that mechanical chest compressions adds 1415 % more patients with rib fractures . our patient had normal liver enzymes at admission and there was no obvious finding suggesting liver stasis , however the ultra - sound did show slightly except distended liver veins possibly related to right ventricular strain . we can not explicitly state towhat extent the backward failure and increased venous pressure and liver stasis could have contributed to the liver laceration and the massive bleeding . the imported factors for developing intra - abdominal complication during cpr seem to be the placement of the hands or the piston rather the aetiology to the cardiac arrest . it should also be acknowledged that our patient did receive a loading dose of heparin right before going into cardiac arrest . we can not state whether the lacerations occurred during the manual or the mechanical compressions and we are unable to provide any firm suggestion how to avoid the risk for liver laceration during cpr in patients having a cardiac arrest cause by massive pulmonary emboli . optimising the positioning of hands andpulmonary emboli compromising cardiac function with subsequent forward as well as backward failure creates parenchymal organ stasis increases the risk for laceration and internal bleeding caused by external forces . the risk for bleeding must not be forgotten taking care of massive pulmonary emboli . cpr during cardiac arrest caused by pe should be performed with vigilant positioning of the hand or the mechanical compression device . this manuscript has been supported by the department of anaesthesia & intensive care , no extern funding has been received for the preparation of the case report . the event had a fatal outcome and we have discussed the ethics in publishing with the head of the institution for clinical science , head of institution supports it publication without further consent . the event has been reported to the swedish medicinal product agency as a potential device incident .\noutput:\n" }, { "from": "agent", "value": "highlightslarge pulmonary emboli may cause forward as well as backward cardiac failure.large pulmonary emboli and subsequent backwards stasis may increase the risk for parenchymal organ swelling.cpr should be readily initiated in cause of cardiac arrest.external forces e.g. cpr may cause hepatic rupture and profound bleeding.positioning of the manual as well as mechanical compression during cpr should be frequently be controlled ." } ]

[ { "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 term spontaneous abortion or miscarriage refers to pregnancy loss at 20 weeks of gestation in the absence of elective medical or surgical measures to terminate the pregnancy . as many as 80 % of miscarriages occur before 12 weeks of gestation , with miscarriage rates decreasing sharply after the first trimester . there are many causes of miscarriage including chromosomal abnormalities , uterine abnormalities , infection , endocrinological abnormalities , and autoimmune diseases . thyroid hormones have been found to be crucial in brain development , maturation , and normal function . optimal maternal thyroid hormone concentrations can play a critical role in maintaining a balanced inflammatory response in early pregnancy to prevent fetal immune rejection and promote normal placental development through the regulation of the secretion of critical cytokines and angiogenic growth factors by human decidual cells . thyroid dysfunction , in particular hypothyroidism , can affect the health of both mother and fetus during pregnancy . hypothyroidism has a higher prevalence than hyperthyroidism ( 2.5 % vs. 0.2 % ) during the gestational period and has a statistically significant relationship with recurrent pregnancy loss in the first trimester . free radicals or reactive oxygen species ( ros ) are reactive molecules with an unpaired electron , and they are continuously produced in cells deliberately or as accidental by - products of metabolic routes . a series of oxidation - reduction reactions in the metabolic transformation of dietary proteins , carbohydrates and fats take place in the mitochondria of animal cells . a sophisticated defense mechanism against these ros exerts its effect on balancing the harmful consequences of oxidative stress . superoxide dismutase ( sod ) is found in the cytoplasm of aerobic cells and converts superoxide anion to hydrogen peroxide ( h2 o2 ) . on the other hand , glutathione peroxidase has an important function in the detoxification of h2 o2 into water and nonreactive oxygen molecule . malondialdehyde ( mda ) is a major breakdown product split off from lipid peroxides and can be used to assess the degree of lipid peroxidation . oxidative attack on essential cell components by ros as a result of a disturbed oxidant - antioxidant system balance is recognized in the pathogenesis of placental deficiency syndromes such as preeclampsia and fetal growth restriction . elevated ros levels can influence the oocytes and embryos in their environments , i.e. , follicular or peritoneal fluid . oxidative stress affects both implantation and early embryo development by modifying the key of transcription and hence modifying the gene expression . recently , it has been found that oxidative stress plays a key role in uterine contractions by stimulating free radicals induced prostaglandins which subsequently results in pregnancy loss . although the relationship between spontaneous abortions and some circulating biomarkers of oxidative stress has been evaluated in some animal and human studies , sadly the levels are estimated only in women after two or more episodes of miscarriage while the data regarding their imbalance in one pregnancy loss is inadequate . moreover , there are very few researches which demonstrate the association of thyroid hormones and oxidative stress in the process of spontaneous abortion . the aim of this study was to assess the status of serum mda , sod , thyroid stimulating hormone ( tsh ) , t3 , t4 and their association with each other in women with spontaneous abortion of one episode before 24 weeks of gestation . the subjects were enrolled from the department of obstetrics and gynecology , of a tertiary care hospital attached to a medical college , between september 2014 and june 2015 . furthermore , information about socioeconomic status , personal history like hypertension / diabetes mellitus / smoking / alcohol / drug abuse was taken . patients with a history of diabetes mellitus , thyroid dysfunction , heart disease , hypertension , uterine fibroid , infectious disease , smokers , and alcoholics were excluded from the study . five milliliters of blood samples were obtained before administration of any medication and before any medical or surgical intervention by venipuncture under all aseptic conditions . the separated serum samples were immediately processed for mda and sod analysis and remaining serum samples were stored at 20c for hormonal analysis . tsh , t3 , and t4 levels in serum were estimated using st aia - pack on aia - 360 fully automatic analyzer , tosoh , japan . sod activity in serum was estimated by method of marklund and marklund . all statistical analysis , study , the results of laboratory tests in the study and control groups were summarized as mean standard deviation . comparison between subjects ( both participating groups ) was done using student 's unpaired t - test .95 % confidence interval was taken into consideration and p 0.05 was regarded as statistically significant . correlation ( pearson ) analysis was used to test the linear relationship between parameters . the mean maternal age , paternal age , gestational age , body mass index , blood pressure , hb , and sugar did not differ significantly in both the participating groups . on the other hand , gravida ( 2.231.14 ) and parity ( 1.671.18 ) were found to be significantly ( p = 0.0146 , 0.0320 ) higher in women with miscarriage on comparison with controls ( 1.60.77 , 0.60.77 ) , respectively . comparison of demographic characteristics and biochemical parameters in study and control group table 2 shows a comparison of the measured thyroid profile and oxidative stress results between both the participating groups . these results showed that mean serum tsh levels were higher , while mean serum t3 levels were found to be lower in the study group than the control group and difference was found to be statistically significant ( p = 0.0115 , 0.0003 ) . serum t4 levels were found to be lower than control group , but the difference was not significant . serum mda levels were found to be higher ( 6.8461.5 ) than controls ( 4.5881.17 ) while sod levels were found to be lower in women with miscarriage ( 2.260.66 ) than that of control group ( 3.161.13 ) and difference were found to be highly significant ( p = 0.0005 , 0.0001 ) , respectively . comparison of serum thyroid hormone and serum malondialdehyde and superoxide dismutase status in study and control group impact of tsh , t3 , and t4 on the mda and sod levels in patients with miscarriage and women with normal pregnancy was verified using linear ( pearson ) correlation analysis . table 3 shows significant positive correlation of tsh ( r = 0.6205 , p = 0.0003 ) with mda levels and negative correlation of tsh ( r = 0.3474 , p = 0.060 ) with sod levels in women with spontaneous loss of pregnancy . on the other hand , both t3 and t4 levels had negative correlation with mda ( r = 0.1094 , 0.1507 ) and positive correlation with sod levels ( r = 0.2655 , 0.1404 ) , respectively . correlation of thyroid profile with malondialdehyde and superoxide dismutase in study group a partial positive correlation of tsh with mda ( r = 0.03497 , p = 0.8544 ) and negative correlation with sod ( r = 0.1354 , p = 0.4756 ) has been found in the group of women with normal ongoing pregnancy as shown in table 4 . the results also depicted that t3 has a positive correlation with both mda ( r = 0.08055 , p = 0.6722 ) and sod levels ( r = 0.1905 , p = 0.3133 ) , t4 has negative correlation with mda ( r = 0.06225 , p = 0.7838 ) and positive correlation with sod ( r = 0.2957 , p = 0.1126 ) . correlation of thyroid profile with malondialdehyde and superoxide dismutase in control group table 5 shows that there is significant negative correlation of mda with sod levels in study ( r = 0.4512 , p = 0.0123 ) and control ( r = 0.4567 , p = 0.0112 ) group . the purpose of the present study was to evaluate the status of serum thyroid hormones , mda and sod in women with spontaneous abortion and also to examine the association between serum thyroid hormones and levels of serum mda and sod . thyroid hormones are essential for the sustenance of the developing fetus and fetus thyroid gland is not fully functional until after 12 weeks of pregnancy . therefore , if the mother does not have sufficient thyroid hormones , she may be at increased risk of miscarriage . in the present study , the results showed the significant elevation in serum tsh ( 3.83.5 , p = 0.0115 ) levels and significant decrease in serum t3 ( 1.330.68 , p = 0.0003 ) . although serum t4 were also found to be lower in women with loss of pregnancy , we found no significant difference on comparison with controls . these findings are in consistence with the study of barapatre and vaidya that elevated serum tsh levels without alteration in t3 and t4 during pregnancy increases the risk for miscarriage in both first and second trimester . allan et al . also reported that women with tsh levels above 6 miu / ml has a significant increased risk for still birth and further risk of miscarriage increases by 15 % for each 1 miu / ml elevation of tsh level . both overt hypothyroidism and subclinical thyroid dysfunction can have adverse effects on fetal and maternal outcome , but in women with subclinical hypothyroidism , gestational age is low at the time of abortion . thyroid hormones play an important role in maintaining a viable pregnancy and contributing to healthy offspring . during pregnancy , increased thyroid hormone demand leads to increased iodine uptake and hence increased synthesis of thyroid hormones . estrogen induces a rise in serum thyroid binding globulin , and the placenta releases several thyroid stimulatory factors in excess , for example , human chorionic gonadotropin , alpha subunit of which is identical to tsh and with a weak thyrotropic activity . maternal thyroxin is particularly critical early in pregnancy , because of reliance of fetus on transplacental passage of maternal thyroxine until about 12 weeks of gestation . from this timeonward , maternal as well as fetal thyroid hormones seem to be necessary for normal neurodevelopment . thyroid disease interferes with human reproductive physiology , reduces the likelihood of pregnancy and adversely affects pregnancy outcome , thus becoming relevant in algorithm of reproductive dysfunction . subclinical hypothyroidism too appears to have an adverse impact on the pregnancy with increased incidence of miscarriage , gestational diabetes mellitus , gestational hypertension , and preeclampsia . hence , it is evident that increased tsh levels and inadequate thyroid hormone supply might be one of the causative factors for spontaneous abortion . therefore , it is suggested that the universal screening for detection of thyroid dysfunction among pregnant women attending antenatal clinic should be done compulsorily and the treatment of thyroid dysfunction should be started as early as possible after the diagnosis of thyroid dysfunction to reduce thyroid manifestations in maternal complications . oxidative stress of placenta plays an important role in pathogenesis of many pregnancy complications including miscarriages , preeclampsia , and preterm labor . the current study showed that serum mda levels were found to be significantly higher ( 6.8461.5 , p 0.0001 ) in women with loss of pregnancy than control group ( 4.5881.17 ) consistent with earlier studies . study of sane et al . also reported elevations of serum mda levels in women with either induced or spontaneous abortions compared with controls . since mda is a byproduct of lipid peroxidation , therefore , an elevation in mda levels may reflect an overproduction of lipid peroxides and / or impaired antioxidant defense mechanism . these lipid peroxides are produced mainly in the placenta due to membrane disruption and concentration of lipid peroxide increases in the deciduas of women undergoing early pregnancy loss . herealso a significant positive correlation ( r = 0.6205 , p = 0.0003 ) was found between serum tsh and serum mda levels indicating that raised oxidative stress with consequent enhanced lipid peroxidation as the tsh levels increased further increase the risk of miscarriage . increased levels of antioxidants have been documented in normal pregnancy , whereas loss of antioxidant defense has been observed in patients with recurrent spontaneous abortion as a result of their increased consumption . in the present study , there was a significant reduction in serum sod levels ( 2.260.66 , p = 0.0005 ) in women with spontaneous loss of pregnancy on comparison to the healthy pregnant controls ( 3.161.13 ) consistent with earlier studies . this oxidative stress in terms of decreased sod activity might be involved in the termination of spontaneous abortions through stimulating prostaglandins synthesis . saad et al . also reported that elevation in plasma levels of mda along with decreased levels of sod and other antioxidant enzymes was associated with enhanced lipid peroxidation , which may end in spontaneous abortion . serum sod activity is reported to be important for corpus luteum activity , embryonic development , and maintenance of early pregnancy . in the gestational corpus luteum , thecahence , sod activity might be an important factor for the maintenance of fertility and early pregnancy and reduced sod levels may results in loss of otherwise wanted pregnancy . this depletion of sod could also be as a result of increased free radical production in terms of raised levels of mda as pregnancies that went successfully to term were reported to be associated with increased plasma levels of sod early in the first trimester . the present investigation also pointed out the negative correlation of tsh with levels of sod indicating that increased tsh levels might be involved in the decrease of sod levels resulting in enhanced oxidative stress , imbalance in antioxidant / oxidant ratio and hence loss of pregnancy . increased serum tsh and serum mda levels and decreased serum t3 and sod levels in women with spontaneous abortion up to 24 weeks of gestational age indicate that alteration in thyroid profile results in enhanced oxidative stress and loss of antioxidant defense , which may subsequently result in the termination of pregnancy and expulsion of products of conception out of the uterine cavity . thus , there is need of hour to look at this arena of research to decrease the oxidative stress , increase the levels of antioxidants in pregnant women with disturbed thyroid profile .\noutput:\n" }, { "from": "agent", "value": "background : spontaneous abortion or miscarriage is defined as the loss of a clinically recognized pregnancy that occurs before 20 weeks of gestational age . changes in thyroid function can impact greatly on reproductive function before , during , and after conception . oxidative stress affects both implantation and early embryo development by modifying the key of transcription . malondialdehyde ( mda ) is a major breakdown product of split off from lipid peroxidation . superoxide dismutase ( sod ) is responsible for detoxification of superoxide anion and required for normal health and reproduction.aim : the aim of this study was to define the involvement of thyroid hormones , mda and sod levels and to establish mda levels as an index of lipid peroxidation in women with spontaneous abortion by comparing the results with healthy pregnant females as controls.materials and methods : a cross - sectional case - control study was designed with two groups of women with 30 each in healthy pregnancy and with spontaneous abortion.results : demographic characteristics such as maternal age , paternal age , gestational age , body mass index , waist - hip ratio as well as biochemical parameters such as blood pressure , hemoglobin ( hb ) , sugar levels were found to be similar in both the participating groups . characteristics like gravida and parity were found to be higher in the study group and differ significantly from control group . spontaneous abortion before 24 weeks of gestational age was found to be associated with significant increase in mean serum thyroid stimulating hormone ( tsh ) ( p = 0.0115 ) and mda ( p = 0.0001 ) levels and a significant decrease in mean serum t3 ( p = 0.0003 ) and sod ( p = 0.0005 ) levels . the linear ( pearson ) correlation analysis demonstrated a significant positive correlation of tsh with mda and negative correlation with sod in women with spontaneous abortion.conclusion : the study demonstrates that altered thyroid profile , increased lipid peroxidation in terms of increased mda levels and decreased sod levels might be involved in the termination of otherwise wanted pregnancy ." } ]

[ { "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: triple therapy ( tt ) with vitamin k - antagonists ( vka ) , aspirin and clopidogrel is the recommended antithrombotic treatment following percutaneous coronary intervention with stent implantation ( pci - s ) in patients with an indication for oral anticoagulation , such as those with atrial fibrillation at moderate to high thromboembolic risk , mechanical heart valves , previous cardiogenic thromboembolism and recent deep vein thrombosis or pulmonary embolism . owing to the superior efficacy of vka compared to dual antiplatelet therapy ( dapt ) with aspirin and clopidogrel in preventing thromboembolic and thrombotic complications in patients with atrial fibrillation and mechanical aortic valve , , and owing to the superior efficacy of dapt compared to vka , with or without aspirin , in preventing adverse cardiac events following pci - s , tt with vka , aspirin and clopidogrel is regarded as the optimal antithrombotic regimen in patients with an indication for vka undergoing pci - s . previous studies , and recent meta - analyses , have indeed shown that tt is associated with the lowest incidence of stroke compared to dapt or the combination of vka and a single antiplatelet agent ( either aspirin or clopidogrel ) . such result , however , appears to come at the price of an increased incidence of bleeding complications during follow - up . , , , these bleedings are mostly major , and appear to increase in rate as tt prolongs over time . , because of that , tt is often not prescribed to patients in whom it is indicated , and even when prescribed , it is maintained for duration shorter than optimal . in addition , drug - eluting stents are generally not implanted , owing to the need for prolonged clopidogrel , and hence tt , administration . as a consequence of the reported increase in major bleeding complications with prolonged tt , treatments of proven efficacy , such as a 12 - month course of clopidogrel after pci - s for an acute coronary syndrome , regardless of whether a bare - metal or a drug - eluting stent has been implanted , or the implantation of a drug - eluting stent in a diabetic patient , especially in the presence of a long lesion in a small vessel , may be denied to patients in whom the highest benefit is anticipated . as previously pointed out , , however , uncertainty still exists over whether the safety profile of tt is really suboptimal . the evidence on which this assumption is based , in fact , is in general of poor quality : most of the studies are retrospective , and the few prospective studies are generally small and by single - center . , furthermore , outcome comparisons were carried out within the same study cohort only in a minority of studies , while in most of them either no comparison or comparison against contem porary populations of patients with no indication for oral anticoagulation undergoing pci - s and receiving dapt was performed . , finally , only seldom the occurrence of in - hospital bleedings , which are related more to procedural variables ( i.e. , vascular access site , use of glycoprotein iib / iiia inhibitors , use of heparin bridging strategies after temporary vka interruption , etc . ) than to tt itself , have been reported separately from those occurring after discharge . , the international normalized ratio ( inr ) at the bleeding event has also been rarely reported , as well as the antithrombotic treatment actually ongoing at the time of bleeding , when that initially assigned might have already been changed ( i.e. , withdrawal of clopidogrel after a due course of several weeks or months ) . , while waiting for a definitive clarification of the efficacy in preventing thromboembolic and thrombotic complications of tt compared to other regimens , such as the combination of vka and clopidogrel , it is now of paramount importance to determine the true safety profile of tt . in this paper , the available studies where data on the bleeding rate in patients treated with tt after pci - s are separately reported , will be critically reviewed . various combinations of key words such as percu - taneous coronary intervention , stent , oral anticoagulation , warfarin , antiplatelet agents were used for medline search . all english language , full - text articles from january 2004 to december 2010 reporting safety outcomes in patients with indication for vka treatment who underwent pci - s were selected for this review . one study was excluded owing to subsequent duplicate publication after inclusion of more patients , leaving therefore 27 studies available for the analysis.of the 27 studies included in this review , the vast majority had a retrospective , single - center design ( 52 % ) , while the remaining were either prospective , single - center ( 15 % ) , prospective , multi - center ( 15 % ) , prospective , multi - center with the data on tt patients analyzed post - hoc ( 11 % ) , or retrospective , multi - center ( 7 % ) ( table 1 ) . the overall number of patients receiving tt in the published studies is 3,791 ( table 1 ) . the indications for vka are reported in 93 % of the studies ( table 1 ) . in five studies ( 19 % ) , only patients with atrial fibrillation were included ( table 1 ) . in the remaining studies , atrial fibrillation was the most frequent indication for vka ( mean 57 % ; range : 24 % 84 % ) , followed by prosthetic heart valves ( mean 9 % ; range : 0 % 25 % ) and previous stroke ( mean : 3 % ; range : 0 % 13 % ) ( table 1 ) . the indications for pci - s are reported in 78 % of the studies ( table 1 ) . while in one study ( 4 % ) , st - elevation myocardial infarction ( stemi ) was the only indication for pci - s , in the remaining the mean prevalence of stemi , non st - elevation acute coronary syndromes and stable ischemic heart disease was 24 % ( range : 3 % 57 % ) , 40 % ( range : 0 % 80 % ) , and 36 % ( range : 0 % 85 % ) , respectively ( table 1 ) . among the procedural variables which may influence the occurrence of in - hospital bleeding , the use of radial approach , glycoprotein iib / iiia inhibitors , and bridging strategies with heparin after temporary vka withdrawal was reported in 44 % , 63 % and 22 % of studies , respectively ( table 2 ) . apart from one study ( 4 % ) where the radial approach was used in all patients , in the remaining it was used on average in 28 % ( range : 0 % 66 % ) of cases ( table 2 ) . the mean use of glycoprotein iib / iiia inhibitors was 29 % ( range : 2.5 % 61 % ) , while that of heparin bridging strategies in the 96 % of the studies where it was not used as the standard approach for all cases , was on average 36 % ( range : 0 % 88 % ) , ( table 2 ) . the time points at which data on the incidence of major bleeding during follow - up are available include : hospital lization ( 26 % of studies ) , 1 month ( 15 % ) , 6 months ( 19 % ) , 12 months ( 41 % ) , and 12 months ( 19 % ) ( table 3 ) . similarly , minor bleedings were evaluated at 1 month ( 19 % of studies ) , 6 months ( 7 % ) , 12 months ( 7 % ) , and 12 months ( 15 % ) ( table 3 ) , respectivy . vka : vitamin k - antagonists ; pci - s : percutaneous coronary intervention with stent implantation . tt : triple therapy ; af : atrial fibrillation ; stemi : st - elevation myocardial infarction ; nste - acs : non st - elevation acute coronary syndromes ; pts : patients . the incidence of major and minor bleedings reported at the various time points of follow - up is reported in table 4 . as derived from the above data , definitive conclusions regarding the true safety of tt appear currently precluded . apart from acknowledging that the overall population on tt which has been examined so far accounts for only about 4,000 patients , it must be noted that the analyses of the data were carried out retrospectively in 70 % of the studies . while being subject to biases of various nature , the analyses did not correlate the bleeding event with the antithrombotic treatment actually ongoing at the time of complication . it is obvious that hemorrhagic complications occurring weeks or months after tt has been completed , can not plausibly be attributed to this regimen , even though the analysis is carried out according to the initially assigned treatment . indeed , in one study where such evaluation was carried out , in half of patients who had been initially treated with tt clopidogrel had already been withdrawn at the time of bleeding , when only the combination of vka and aspirin was ongoing . the international normalized ratio ( inr ) value at the time of bleeding was reported in 5 studies ( 19 % ) for major bleeding and in 3 ( 11 % ) for minor bleedings . as regards major bleedings , the inr value was above the therapeutic range in 35 % of patients ( range 0 % 100 % ) . also , no valuable information about the inr value at the time of bleeding , which has been shown to increase the risk of bleeding in patients on tt when above a cut - off value of 2.6 , can be obtained from the available studies . while in one study all patients experiencing a major bleeding had the inr above the therapeutic range , in two studies major bleeding occurred regardless of the fact that the inr was within the therapeutic range ( table 3 ) . when focusing on the absolute incidence of major bleeding , an increase is apparent as follow - up prolongs ( table 4 ) . while acknowledging that a more prolonged exposure to tt may intuitively be associated with and increased risk of bleeding , it should be noted once again that clear information about the ongoing treatment throughout the entire duration of follow - up is lacking . it is of note , however , that the in - hospital major bleeding rate was limited to about 3 % ( table 3 ) . such figure is not substantially different from that reported in the overall population of patients undergoing pci - s , therefore supporting the concept that tt in itself does not substantially impact on the incidence of early major bleeding . further reduction of the in - hospital major bleeding rate may probably be obtained by more extensively using the radial approach , which has been shown to virtually eliminate the occurrence of bleeding at the vascular access site , and by further limiting the use of glycoprotein iib / iiia inhibitors , as well as of heparin bridging strategies following the ( likely unnecessary ) peri - procedural withdrawal of vka , which both have been found associated with early hemorrhagic complications . , when examining the absolute incidence of major bleeding after discharge , it should be noted that the figures are not substantially different from those reported with dapt , for example in the credo trial . in this study , the 1 - and 12 - month incidence of major bleeding was 4.7 % and 8.8 % , respectively , as compared to the average 5.1 % and 9.0 % , respectively , reported in patients receiving tt ( table 3 ) . subtracting the about 3 % rate of in - hospital bleeding , which as previously mentioned has more to do with procedural variables than with tt itself , the true incidence of major bleeding during medium - term follow - up should be more likely in the reassuring order of 2 % to 6 % . indeed , these figures have been reported in better quality studies , such those prospective and with a tight control of the inr which was also targeted to the lower end of the therapeutic range . , , , , the lower incidence of major bleeding at a follow - up longer than 12 months may be explained by the limited number of studies reporting on that and by the variable duration of follow - up following the first year . also not surprisingly is the non - linear course , as well as the variable absolute incidence , of minor bleedings because they often go undetected not inducing patients to seek medical attention . tt with vka , aspirin and clopidogrel is the recom mended antithrombotic regimen following pci - s in patients with an indication for vka . although being not clear - cut , current available evidence suggests that tt is associated with an increased risk of bleeding , apparently increasing as treatment prolongs . the absolute incidence of major bleeding at short - to medium - term follow - up appears not substantially different from that of dapt , which however can not be used alone in these patients because of the high risk of thromboembolic and thrombotic complications . since major bleedingsmay be life threatening or may determine the withdrawal of one or more of the antithrombotic agents ( therefore exposing patients to the risks of thrombeombolism and / or stent thrombosis ) , and minor bleedings may induce physicians or patients to withdraw clopidogrel ( again exposing patients to the potentially catastrophic stent thrombosis ) , it is prudent to limit the duration of tt for as short as possible , therefore using drug - eluting stents restrictively . however , when drug - eluting stent implantation is clinically necessary , the use of newer generation drug - eluting stents ( especially polymer - free ) that exhibit accelerated reendo thelization is preferred . this does not imply that patients receiving a newer generation drug - eluting stent should receive clopidogrel for 12 months ( current guidelines recommend at least 12 months of clopidogrel therapy following drug - eluting stent implantation ) , but rather the use of newer generation drug - eluting stent allows for the safer early interruption of clopidogrel if the need should arise . finally , throughout tt , which should be limited to three to six months in vka patients undergoing pci - s in the context of an acute coronary syndrome ( where current guidelines recommend 12 months of clopidogrel treatment ) , the inr should be frequently and carefully monitored , along with being targeted at the lower end of the therapeutic range ( i.e. , 2.0 to 2.5 in patients with atrial fibrillation ) . , while waiting for the ongoing , large - scale , registries and clinical trials to clarify the few facts and to answer the many questions regarding the risk of bleeding of tt , this treatment should not be denied to patients with an indication for vka undergoing pci - s provided that the above mentioned measures and cautions are implemented . tt with vka , aspirin and clopidogrel is the recom mended antithrombotic regimen following pci - s in patients with an indication for vka . although being not clear - cut , current available evidence suggests that tt is associated with an increased risk of bleeding , apparently increasing as treatment prolongs . the absolute incidence of major bleeding at short - to medium - term follow - up appears not substantially different from that of dapt , which however can not be used alone in these patients because of the high risk of thromboembolic and thrombotic complications . since major bleedings may be life threatening ormay determine the withdrawal of one or more of the antithrombotic agents ( therefore exposing patients to the risks of thrombeombolism and / or stent thrombosis ) , and minor bleedings may induce physicians or patients to withdraw clopidogrel ( again exposing patients to the potentially catastrophic stent thrombosis ) , it is prudent to limit the duration of tt for as short as possible , therefore using drug - eluting stents restrictively . however , when drug - eluting stent implantation is clinically necessary , the use of newer generation drug - eluting stents ( especially polymer - free ) that exhibit accelerated reendo thelization is preferred . this does not imply that patients receiving a newer generation drug - eluting stent should receive clopidogrel for 12 months ( current guidelines recommend at least 12 months of clopidogrel therapy following drug - eluting stent implantation ) , but rather the use of newer generation drug - eluting stent allows for the safer early interruption of clopidogrel if the need should arise . finally , throughout tt , which should be limited to three to six months in vka patients undergoing pci - s in the context of an acute coronary syndrome ( where current guidelines recommend 12 months of clopidogrel treatment ) , the inr should be frequently and carefully monitored , along with being targeted at the lower end of the therapeutic range ( i.e. , 2.0 to 2.5 in patients with atrial fibrillation ) . , while waiting for the ongoing , large - scale , registries and clinical trials to clarify the few facts and to answer the many questions regarding the risk of bleeding of tt , this treatment should not be denied to patients with an indication for vka undergoing pci - s provided that the above mentioned measures and cautions are implemented .\noutput:\n" }, { "from": "agent", "value": "backgroundtriple therapy ( tt ) with vitamin k - antagonists ( vka ) , aspirin and clopidogrel is the recommended antithrombotic treatment following percutaneous coronary intervention with stent implantation ( pci - s ) in patients with an indication for oral anticoagulation . tt is associated with an increased risk of bleeding , but available evidence is flawed by important limitations , including the limited size and the retrospective design of most of the studies , as well as the rare reporting of the incidence of in - hospital bleeding and the treatment which was actually ongoing at the time of bleeding . since the perceived high bleeding risk of tt may deny patients effective strategies , the determination of the true safety profile of tt is of paramount importance.methodsall the 27 published studies where the incidence of bleeding at various time points during follow - up has been reported separately for patients on tt were reviewed , and the weakness of the data was analyzed.resultsthe absolute incidence of major bleeding upon discharge at in - hospital , 1 month , 6 months , 12 months and 12 months was : 3.3 % 1.9 % , 5.1 % 6.7 % , 8.0 % 5.2 % , 9.0 % 8.0 , and 6.2 % 7.8 % , respectively , and not substantially different from that observed in previous studies with prolonged dual antiplatelet treatment with aspirin and clopidogrel.conclusionswhile waiting for the ongoing , large - scale , registries and clinical trials to clarify the few facts and to answer the many questions regarding the risk of bleeding of tt , this treatment should not be denied to patients with an indication for vka undergoing pci - s provided that the proper measures and cautions are implemented ." } ]

[ { "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 global prevalence of diabetes is rapidly increasing .1,2 in norway , the prevalence of the population treated with blood glucose - lowering drugs increased from 2.4 % in 2004 to 3.1 % in 2010.3,4 both type 1 and type 2 diabetes ( t2d ) may occur at any age , but t2d is mainly diagnosed after the age of 40 years , while type 1 diabetes is more common in children and young adults .2,5 t2d is a metabolic disorder , with high blood glucose levels caused by insulin resistance and a relative deficiency of insulin . according to the american diabetes association , t2d accounts forat least 90 % of all cases of diabetes .6 hypertension and dyslipidemia , such as low high - density lipoprotein ( hdl ) levels and hypertriglyceridemia are risk factors for t2d ,79 and also increase the risk of cardiovascular complications in patients with diabetes .10 overweight and obesity are also strongly associated with t2d .11,12 early identification of the population at risk is important in preventing t2d .13 an icelandic study showed that high levels of body mass index ( bmi ) , triglycerides , and blood pressure were present long before the onset of t2d .14 obesity is an important risk factor for t2d , but a question for further research is why every individual with obesity does not develop t2d .15 the aim of our study was to quantify the risk of t2d associated with various combinations of levels of bmi , triglycerides , and blood pressure , in a norwegian cohort of men and women aged 4045 years . we also wanted to quantify the relative importance of these three risk factors , plus others , such as nonfasting glucose , as predictors for t2d . measurements of weight , height , blood pressure , triglycerides , total cholesterol , hdl cholesterol , and glucose in the period 19951999 were obtained from norwegian health studies . questionnaires completed by participants in the studies included information about cardiovascular disease , diabetes , and use of antihypertensives . the health study program began in 1985 , but measurements of glucose and hdl cholesterol were not included before 1994 and 1995 , respectively . all norwegian men and women aged 4042 years and some aged 4345 years were invited to participate in the studies . fifteen of the 19 norwegian counties participated in the program in 19951999 and are represented in our study population . a description of the health study in the county of nordland has been published .16 the response rate declined from about 80 % in 1985 to 60 % in 1999 . weight , height , and blood pressure were measured at the screening site according to standardized procedures . after a 2 - minute rest , three recordings of systolic and diastolic blood pressure were performed at one - minute intervals using an automated device . weight was measured to the nearest 0.5 kg , and height to the nearest cm . bmi was calculated as weight ( kg ) divided by height ( m ) squared . individuals who reported cardiovascular disease , diabetes , and antihypertensive use at screening were excluded . individuals with missing data and those who died or emigrated before january 1 , 2004 were also excluded . overall , 6834 individuals were excluded , leaving 109,796 for analysis ( 50,711 men and 59,085 women ) . information from the health studies and the norwegian prescription database ( norpd ; see below ) were linked using the unique 11 - digit personal identification number assigned to every person living in norway at birth or immigration . all participants included from the health studies gave consent for use of their data in research . permission for linkage was given by the norwegian data inspectorate and the regional committee for medical research ethics . since january 2004 , all pharmacies in norway have been obliged to send information about every dispensed prescription to the norpd electronically .3 blood glucose - lowering drugs are classified in anatomical therapeutic chemical classification group a10 . insulins are classified in subgroup a10a and noninsulins in a10b .17 individuals who had at least one prescription for a blood glucose - lowering drug ( a10 ) dispensed in the period january 1 , 2004 to december 31 , 2009 were defined in our study as having t2d . the variables described above were ranked according to the strength of their association with incident t2d by using the deviance from univariate logistic regression models . deviance is a measure of how well the statistical model describes the observed data , with a lower deviance implying a better fit ( see appendix for details ) . the effects of each additional risk factor when the more important risk factors were accounted for were assessed as follows : starting with a model including only the variable yielding the smallest deviance , all the other variables were added , one by one . the variable that led to the largest decrease in deviance was added at each step . first , each individual was allocated to one of three bmi groups ( b1 , b2 , or b3 ) , one of three triglyceride groups ( t1 , t2 , or t3 ) , and one of three diastolic blood pressure groups ( d1 , d2 , or d3 ) , based on the 50 % and 90 % quantiles of the respective variables for each gender . they were further allocated to one of the 27 combined bitjdk groups , where i , j , and k = 1 , 2 , or 3 . for example , a person with a bmi below the 50 % quantile ( b1 ) , triglycerides above the 90 % quantile ( t3 ) , and diastolic blood pressure between the 50 % and 90 % quantile ( d2 ) was allocated to group b1t3d2 . the incidence of t2d was calculated for each bitjdk group . the relative risks associated with belonging to group bitjdk were calculated with b1t1d1 and bit1d1 as reference groups , adjusted for year of birth , hdl cholesterol , total cholesterol , and glucose . the motivation for the asymmetric choice of quantiles was to have sufficiently large reference groups ( bit1d1 , i = 1 , 2 , 3 ) to contain a reasonable number of individuals who later developed t2d . relative risks were chosen rather than odds ratios because relative risks are easier to interpret , but because the poisson regression did not describe the relationship between glucose as a continuous variable and t2d well , we entered glucose as a 12 - level categorical variable defined by the 10 , 20 , 30 , 40 , 50 , 60 , 70 , 80 , 90 , 95 , and 99 % quantiles by gender . the analyses were done in r , using the generalized linear model function to compute relative risks and deviances , and the vcovhc function of the sandwich package was used to compute robust standard error estimates for the relative risk estimates .1820 measurements of weight , height , blood pressure , triglycerides , total cholesterol , hdl cholesterol , and glucose in the period 19951999 were obtained from norwegian health studies . questionnaires completed by participants in the studies included information about cardiovascular disease , diabetes , and use of antihypertensives . the health study program began in 1985 , but measurements of glucose and hdl cholesterol were not included before 1994 and 1995 , respectively . all norwegian men and women aged 4042 years and some aged 4345 years were invited to participate in the studies . fifteen of the 19 norwegian counties participated in the program in 19951999 and are represented in our study population . a description of the health study in the county of nordland has been published .16 the response rate declined from about 80 % in 1985 to 60 % in 1999 . weight , height , and blood pressure were measured at the screening site according to standardized procedures . after a 2 - minute rest , three recordings of systolic and diastolic blood pressure were performed at one - minute intervals using an automated device . weight was measured to the nearest 0.5 kg , and height to the nearest cm . bmi was calculated as weight ( kg ) divided by height ( m ) squared . individuals who reported cardiovascular disease , diabetes , and antihypertensive use at screening were excluded . individuals with missing data and those who died or emigrated before january 1 , 2004 were also excluded . overall , 6834 individuals were excluded , leaving 109,796 for analysis ( 50,711 men and 59,085 women ) . information from the health studies and the norwegian prescription database ( norpd ; see below ) were linked using the unique 11 - digit personal identification number assigned to every person living in norway at birth or immigration . all participants included from the health studies gave consent for use of their data in research . permission for linkage was given by the norwegian data inspectorate and the regional committee for medical research ethics . since january 2004 , all pharmacies in norway have been obliged to send information about every dispensed prescription to the norpd electronically .3 blood glucose - lowering drugs are classified in anatomical therapeutic chemical classification group a10 . insulins are classified in subgroup a10a and noninsulins in a10b .17 individuals who had at least one prescription for a blood glucose - lowering drug ( a10 ) dispensed in the period january 1 , 2004 to december 31 , 2009 were defined in our study as having t2d . the variables described above were ranked according to the strength of their association with incident t2d by using the deviance from univariate logistic regression models . deviance is a measure of how well the statistical model describes the observed data , with a lower deviance implying a better fit ( see appendix for details ) . the effects of each additional risk factor when the more important risk factors were accounted for were assessed as follows : starting with a model including only the variable yielding the smallest deviance , all the other variables were added , one by one . the variable that led to the largest decrease in deviance was added at each step . first , each individual was allocated to one of three bmi groups ( b1 , b2 , or b3 ) , one of three triglyceride groups ( t1 , t2 , or t3 ) , and one of three diastolic blood pressure groups ( d1 , d2 , or d3 ) , based on the 50 % and 90 % quantiles of the respective variables for each gender . they were further allocated to one of the 27 combined bitjdk groups , where i , j , and k = 1 , 2 , or 3 . for example , a person with a bmi below the 50 % quantile ( b1 ) , triglycerides above the 90 % quantile ( t3 ) , and diastolic blood pressure between the 50 % and 90 % quantile ( d2 ) was allocated to group b1t3d2 . the relative risks associated with belonging to group bitjdk were calculated with b1t1d1 and bit1d1 as reference groups , adjusted for year of birth , hdl cholesterol , total cholesterol , and glucose . the motivation for the asymmetric choice of quantiles was to have sufficiently large reference groups ( bit1d1 , i = 1 , 2 , 3 ) to contain a reasonable number of individuals who later developed t2d . relative risks were chosen rather than odds ratios because relative risks are easier to interpret , but because the poisson regression did not describe the relationship between glucose as a continuous variable and t2d well , we entered glucose as a 12 - level categorical variable defined by the 10 , 20 , 30 , 40 , 50 , 60 , 70 , 80 , 90 , 95 , and 99 % quantiles by gender . the analyses were done in r , using the generalized linear model function to compute relative risks and deviances , and the vcovhc function of the sandwich package was used to compute robust standard error estimates for the relative risk estimates .1820 the variables described above were ranked according to the strength of their association with incident t2d by using the deviance from univariate logistic regression models . deviance is a measure of how well the statistical model describes the observed data , with a lower deviance implying a better fit ( see appendix for details ) . the effects of each additional risk factor when the more important risk factors were accounted for were assessed as follows : starting with a model including only the variable yielding the smallest deviance , all the other variables were added , one by one . the variable that led to the largest decrease in deviance was added at each step . first , each individual was allocated to one of three bmi groups ( b1 , b2 , or b3 ) , one of three triglyceride groups ( t1 , t2 , or t3 ) , and one of three diastolic blood pressure groups ( d1 , d2 , or d3 ) , based on the 50 % and 90 % quantiles of the respective variables for each gender . they were further allocated to one of the 27 combined bitjdk groups , where i , j , and k = 1 , 2 , or 3 . for example , a person with a bmi below the 50 % quantile ( b1 ) , triglycerides above the 90 % quantile ( t3 ) , and diastolic blood pressure between the 50 % and 90 % quantile ( d2 ) was allocated to group b1t3d2 . the relative risks associated with belonging to group bitjdk were calculated with b1t1d1 and bit1d1 as reference groups , adjusted for year of birth , hdl cholesterol , total cholesterol , and glucose . the motivation for the asymmetric choice of quantiles was to have sufficiently large reference groups ( bit1d1 , i = 1 , 2 , 3 ) to contain a reasonable number of individuals who later developed t2d . relative risks were chosen rather than odds ratios because relative risks are easier to interpret , but because the poisson regression did not describe the relationship between glucose as a continuous variable and t2d well , we entered glucose as a 12 - level categorical variable defined by the 10 , 20 , 30 , 40 , 50 , 60 , 70 , 80 , 90 , 95 , and 99 % quantiles by gender . the analyses were done in r , using the generalized linear model function to compute relative risks and deviances , and the vcovhc function of the sandwich package was used to compute robust standard error estimates for the relative risk estimates .1820 bmi was the single variable that best predicted t2d in both genders , followed by triglycerides in women and glucose in men ( figure 1 ) . in women , glucose was the second most important variable for both men and women ( figure 1 ) . for women , this indicates that knowing only their triglyceride or hdl cholesterol level was more informative than knowing only the glucose level with respect to predicting t2d . however , if the bmi was already known , additional information about glucose was more important for prediction purposes than additional information about triglycerides . little was gained by adding variables other than bmi , glucose , triglycerides , and blood pressure ( figure 1 ) . the bmi , triglyceride , and diastolic blood pressure groups , used to define the bitjdk groups , are given in table 1 , and baseline characteristics for selected groups are given in table 2 . a total of 2523 subjects ( 2.3 % of the study population ) had at least one prescription of blood glucose - lowering drugs dispensed between january 1 , 2004 and december 31 , 2009 , indicating that they had developed t2d . the prevalence varied from 0.15 % in the female b1t1d1 group to 21.8 % in the female b3t3d3 group ( table 3 , figure 2 ) . for both men and women , a bmi around 3233 kg / m at baseline , combined with the lowest levels of blood pressure and triglycerides , was associated with approximately the same incidence of t2d as a bmi of 2023 kg / m combined with the highest level of blood pressure and triglycerides ( figure 2 ) . the incidence of t2d in the b3t3d3 group compared with the b1t1d1 group was 39 times higher in men and 142 times higher in women , decreasing to relative risks of 18 and 43 , respectively , after adjustment . within the three bmi groups , the incidence of t2d varied substantially with blood pressure and triglyceride levels ( table 3 ) . at defined levels of bmi and triglycerides , the t2d incidence increased with increasing blood pressure , and at defined levels of bmi and blood pressure , the t2d incidence increased with increasing levels of triglycerides ( table 3 , figure 2 ) . a similar analysis with diastolic blood pressure replaced by nonfasting glucose as the third grouping variable was performed . as expected , the variation in t2d incidence with triglycerides and glucose within the bmi groups was larger than the variation when diastolic blood pressure was used ( efigure 2 ) . bmi was the single variable that best predicted t2d in both genders , followed by triglycerides in women and glucose in men ( figure 1 ) . in women , glucose was the second most important variable for both men and women ( figure 1 ) . for women , this indicates that knowing only their triglyceride or hdl cholesterol level was more informative than knowing only the glucose level with respect to predicting t2d . however , if the bmi was already known , additional information about glucose was more important for prediction purposes than additional information about triglycerides . little was gained by adding variables other than bmi , glucose , triglycerides , and blood pressure ( figure 1 ) . the bmi , triglyceride , and diastolic blood pressure groups , used to define the bitjdk groups , are given in table 1 , and baseline characteristics for selected groups are given in table 2 . a total of 2523 subjects ( 2.3 % of the study population ) had at least one prescription of blood glucose - lowering drugs dispensed between january 1 , 2004 and december 31 , 2009 , indicating that they had developed t2d . the prevalence varied from 0.15 % in the female b1t1d1 group to 21.8 % in the female b3t3d3 group ( table 3 , figure 2 ) . for both men and women , a bmi around 3233 kg / m at baseline , combined with the lowest levels of blood pressure and triglycerides , was associated with approximately the same incidence of t2d as a bmi of 2023 kg / m combined with the highest level of blood pressure and triglycerides ( figure 2 ) . the incidence of t2d in the b3t3d3 group compared with the b1t1d1 group was 39 times higher in men and 142 times higher in women , decreasing to relative risks of 18 and 43 , respectively , after adjustment . within the three bmi groups , the incidence of t2d varied substantially with blood pressure and triglyceride levels ( table 3 ) . at defined levels of bmi and triglycerides , the t2d incidence increased with increasing blood pressure , and at defined levels of bmi and blood pressure , the t2d incidence increased with increasing levels of triglycerides ( table 3 , figure 2 ) . a similar analysis with diastolic blood pressure replaced by nonfasting glucose as the third grouping variable was performed . as expected , the variation in t2d incidence with triglycerides and glucose within the bmi groups was larger than the variation when diastolic blood pressure was used ( efigure 2 ) . obesity is positively associated with hypertriglyceridemia and hypertension , and all three are known risk factors for t2d .12 in our study of norwegians aged 4045 years , bmi was the single variable that best predicted t2d 515 years later . however , at defined levels of bmi , the t2d incidence varied substantially with triglyceride levels and diastolic blood pressure , also after adjustment for nonfasting glucose , hdl cholesterol , total cholesterol , and year of birth . in deviance analyses including glucose , the strongest predictors for development of t2d were bmi , glucose , triglycerides , and blood pressure . additional information about hdl cholesterol and total cholesterol had little impact on the prediction . in the framingham study , clinical models including bmi ( trichotomized ) , fasting glucose , triglycerides , hdl cholesterol , blood - pressure ( all dichotomized ) , age ( categorized ) , gender , and parental history predicted t2d equally as well as other models including more detailed clinical information .5 when risk factors are modeled as continuous rather than categorical , even less information could be needed . bmi is a measure of general obesity . from a clinical aspect , abdominal and visceral obesitywaist circumference and waist - hip ratio are used as measures of abdominal fat . in a meta - analysis of 32 studies , the three measurements were almost identical with regard to their ability to predict incident t2d .21 in our study population , information about waist and hip circumference was available for a subsample of 76,560 individuals . in this sample , bmi and waist circumference were equally good predictors for t2d ( efigure 3 ) , which is logical because the two were strongly correlated ( correlation 0.82 for men and 0.85 for women ) . the waist - hip ratio was less correlated with bmi ( correlation about 0.5 ) and less related to t2d . other variables , such as smoking , physical activity , alcohol consumption , education , and heart rate , were included as variables in early analyses , but because they only marginally decreased the deviance in the multivariate analyses they were excluded in the final analysis . however , these variables increased the predictability in groups with low metabolic scores in another norwegian study .22 the relationships between the variables examined and t2d incidence were fairly well described by logistic regression models ( efigure 4 ) . in many risk prediction models , continuous variables are categorized ,23 which implies loss of information . a multivariate model , such as the one used for calculating deviances in our study , can also be used for risk prediction . the main strength of this study was the large study population in a narrow age range where medicine use and mortality could be traced . the size of the study population made it possible to create combined groups with various levels of bmi , triglycerides , and blood pressure to study their combined effect on incidence of t2d . self - reported diabetes at baseline was used as an exclusion criterion , but erroneous self - reports may have led to inclusion of individuals who had already been diagnosed with diabetes . in okuraet al , 99 ( 66 % ) of 150 american patients who had a diabetes diagnosis in their medical records answered yes when asked whether a medical practitioner had informed them that they had diabetes .24 the percentage was 77 % in the age group of 4565 years . margolis et al reported roughly the same response in a population of 161,808 american women aged 5079 years .25 however , it should be noted that 37 of the 51 false - negative responders in the study by okura et al answered yes when asked whether they had a diagnosis of borderline diabetes . for example , of 58 people in our study population with a nonfasting blood glucose of 15mmol / l between the time of screening and follow - up26 may imply that some individuals who were not diagnosed with t2d at screening would have been diagnosed during follow - up , even though their fasting plasma glucose levels were unchanged . all biomarkers in our study were measured in nonfasting blood samples and this will probably give higher levels compared with fasting samples . another limitation of the study was that the subjects were not monitored during follow - up . their bmi , blood pressure , triglycerides , and other biomarkers may have changed because of lifestyle modification and use of antihypertensives and lipid - modifying agents ( statins ) , which may have blurred the associations .27,28 finally , we had no information about genetic disposition in our study population , but this is unlikely to have influenced the results significantly . a case - control study with 2598 controls and 2309 cases showed that inclusion of genetic information in a model with bmi , age , and genderonly marginally increased td2 predictability .29 the use of dispensed blood glucose - lowering drugs as a proxy for t2d eliminates the problem of recall bias in self - reporting , but can also lead to false negatives ( untreated or undiagnosed t2d ) and false positives ( people without t2d being treated with diabetes medicine ) . t2d patients who are controlled only with lifestyle measures ( eg , physical activity and dietary modification ) will not be identified and neither will individuals with unknown t2d . according to the norwegian diabetes association , very few , if any , individuals in our study population would be prescribed blood glucose - lowering drugs for diabetes without having the disease . however , individuals who were dispensed insulin only could be either patients with type 1 diabetes or t2d . in total , 137 individuals were only treated with insulin in our population ( 5 % of total cases ) , and given that our study population was middle - aged , most of them probably had t2d . the main strength of this study was the large study population in a narrow age range where medicine use and mortality could be traced . the size of the study population made it possible to create combined groups with various levels of bmi , triglycerides , and blood pressure to study their combined effect on incidence of t2d . self - reported diabetes at baseline was used as an exclusion criterion , but erroneous self - reports may have led to inclusion of individuals who had already been diagnosed with diabetes . in okuraet al , 99 ( 66 % ) of 150 american patients who had a diabetes diagnosis in their medical records answered yes when asked whether a medical practitioner had informed them that they had diabetes .24 the percentage was 77 % in the age group of 4565 years . margolis et al reported roughly the same response in a population of 161,808 american women aged 5079 years .25 however , it should be noted that 37 of the 51 false - negative responders in the study by okura et al answered yes when asked whether they had a diagnosis of borderline diabetes . for example , of 58 people in our study population with a nonfasting blood glucose of 15mmol / l to 7.0 mmol / l between the time of screening and follow - up26 may imply that some individuals who were not diagnosed with t2d at screening would have been diagnosed during follow - up , even though their fasting plasma glucose levels were unchanged . all biomarkers in our study were measured in nonfasting blood samples and this will probably give higher levels compared with fasting samples . another limitation of the study was that the subjects were not monitored during follow - up . their bmi , blood pressure , triglycerides , and other biomarkers may have changed because of lifestyle modification and use of antihypertensives and lipid - modifying agents ( statins ) , which may have blurred the associations .27,28 finally , we had no information about genetic disposition in our study population , but this is unlikely to have influenced the results significantly . a case - control study with 2598 controls and 2309 cases showed that inclusion of genetic information in a model with bmi , age , and gender only marginally increased td2 predictability .29 the use of dispensed blood glucose - lowering drugs as a proxy for t2d eliminates the problem of recall bias in self - reporting , but can also lead to false negatives ( untreated or undiagnosed t2d ) and false positives ( people without t2d being treated with diabetes medicine ) . t2d patients who are controlled only with lifestyle measures ( eg , physical activity and dietary modification ) will not be identified and neither will individuals with unknown t2d . according to the norwegian diabetes association , very few , if any , individuals in our study population would be prescribed blood glucose - lowering drugs for diabetes without having the disease . however , individuals who were dispensed insulin only could be either patients with type 1 diabetes or t2d . in total ,137 individuals were only treated with insulin in our population ( 5 % of total cases ) , and given that our study population was middle - aged , most of them probably had t2d . our study confirms that bmi is the strongest predictor of t2d . however , at defined levels of bmi , the incidence of t2d varied substantially with triglyceride levels and blood pressure . the addition of other variables to bmi , triglycerides , glucose , and blood pressure in multivariate models had little impact on the prediction of t2d . thus , triglyceride and blood pressure control in middle - aged individuals should also be targeted to prevent later onset of t2d . deviance is a goodness - of - fit measure defined as -2 times the difference in log - likelihood between the current model and a saturated model ( ie , a model that fits the data perfectly ) . in the logistic regression case , log ( i ) + ( 1yi ) log ( 1i ) ] where yi are the observed data ( 1 if individual i has t2d , 0 if not ) and i are the fitted values from the maximum likelihood model . if adding a new covariate to a given multivariate model does not lead to a reduction in deviance , its inclusion has little benefit because it does not decrease the discrepancy between the model and the data . the null - deviance is the deviance from the model with no covariates , where i = nyi ( the predicted t2d risk for each individual equals the average incidence of t2d in the population , independent of the characteristics of the individual ) . notes : colored points : incidence in 27 groups defined by the 50 % and 90 % quantiles of bmi , triglycerides , and glucose , by gender . bmi groups are distinguished by vertical dashed lines , triglyceride groups by color ( blue , orange , and red indicate increasing levels ) , and glucose groups by point size ( increasing size for increasing levels ) . the x coordinate of each point indicates the mean bmi in the corresponding bitjgk group . white lines : smoothing spline estimate of incidence of type 2 diabetes by glucose only , with 95 % bootstrapped confidence band . the 50 % and 90 % quantiles for glucose were 5.1 and 6.4 for men and 5.0 and 6.1 for women , the quantiles for bmi and triglycerides are given in table 1 . deviance from univariate and multivariate logistic regression models , with incident t2d as the outcome variable and the explanatory variables given on the x axis . notes : for the multivariate models , the variables to the left for , and including , the actual variable were included in the model . population : 35,281 men and 41,279 women screened between 1996 and 1999 with measurements of waist and hip circumference . abbreviations : bmi , body mass index ; bp , blood pressure ; chol , cholesterol ; t2d , type 2 diabetes ; hdl , high - density lipoprotein ; circumf , circumference ; triglyc , triglycerides . incidence of t2d for women in groups defined by the 1 , 5 , 15 , 25 , 35 , 45 , 55 , 65 , 75 , 85 , 95 , 96 , 97 , 98 , 99.5 , 99.8 , and 99.95 % quantiles of the actual variables , with 95 % binomial confidence intervals . notes : the x values for the points equal the means of the groups . a vertical dashed line is drawn at the 99 % quantile for each variable . the curves show the fits of poisson ( black ) and logistic ( red ) regressions . abbreviations : bmi , body mass index ; bp , blood pressure ; chol , cholesterol ; t2d , type 2 diabetes ; hdl , high - density lipoprotein . predicted probability ( white curves / numbers ) for developing t2d before age 60 years for a 42 - year - old man ( top ) and woman ( bottom ) with bmi equal to 20 , 25 , 30 or 35 kg / m at given levels of triglycerides and blood pressure . notes : the color of each cell indicates the number of individuals in the study population with the given level of triglycerides and blood pressure according to the color scale on the right y axes . blue cells ( value 0 ) have zero individuals , and at each level of bmi the red cell ( value 1 ) is the most common combination of triglycerides and blood pressure . an orange cell ( value 0.8 ) the probabilities were predicted from the fit of a multivariate logistic regression model to 175,079 men and 194,897 women participating in the health studies between 1985 and 1999 . the variables included were bmi , triglycerides , and diastolic blood pressure ( with interaction terms ) and year of birth and year of screening ( without interaction terms ) .\noutput:\n" }, { "from": "agent", "value": "backgroundobesity , hypertension , and hypertriglyceridemia are important risk factors for type 2 diabetes ( t2d ) . we wanted to assess the risk associated with these three factors alone and in combination , and the relative importance of these and several other risk factors ( eg , nonfasting glucose ) as predictors of t2d.methodsrisk factors in a norwegian population ( n = 109,796 ) aged 4045 years were measured in health studies in 19951999 . blood glucose - lowering drugs dispensed in 20042009 were used to estimate the incidence of t2d . groups based on combinations of body mass index ( bmi ) , diastolic blood pressure , and triglycerides were defined by using the 50 % and 90 % quantiles for each variable for men and women . the relative importance of bmi , triglycerides , total cholesterol , high - density lipoprotein cholesterol , glucose , blood pressure , and year of birth for predicting t2d was assessed using deviance from univariate and multivariate logistic regression models . height , weight , and blood pressure were measured . all biomarkers were measured in nonfasting blood samples.resultsin the various groups of bmi , triglycerides , and diastolic blood pressure , the incidence of t2d ranged from 0.5 % to 19.7 % in men and from 0.15 % to 21.8 % in women . bmi was the strongest predictor of incident t2d , followed by triglyceride levels in women and glucose levels in men . the inclusion of risk factors other than bmi , glucose , triglycerides , and blood pressure in multivariate models only marginally improved the prediction.conclusionbmi was the strongest predictor of type 2 diabetes . at defined levels of bmi , the incidence of t2d varied substantially with triglyceride levels and blood pressure . thus , controlling triglycerides and blood pressure in middle - aged individuals should be targeted to prevent later onset of t2d ." } ]

[ { "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: dna methylation is a core epigenetic process that influences a wide variety of biological mechanisms , including gene expression , chromosomal stability , imprinting , and cellular differentiation ( bernstein et al . , 2007 ) . methylation can mediate environmental influences on gene expression and can modulate disease risk associated with genetic variation ( foley et al . , 2009 ) . abnormal dna methylation patterns ( including genome - wide hypomethylation and gene - specific hypo - and hypermethylation ) have been shown to be associated with a range of health outcomes ( ozanne and constancia , 2007 ) . in cancer and certain other diseases , most of these changes have been observed at the tissue level ( esteller et al . , 2001 ; rodenhister and mann , 2006 ) . data relating to whether dna methylation changes in peripheral blood cells can serve as useful , informative biomarkers for different health outcomes is much more limited , but new information is rapidly emerging ( heyn and esteller , 2012 ) . a number of methods are available for the analysis of global dna methylation levels [ total content of 5 - methylcytosine ( 5 - mc ) ] ( terry et al . , 2011 ) . there are over 500,000 long - interspersed nuclear elements ( lines ) and 1,500,000 short - interspersed nuclear elements ( sines ) across the human genome . alu elements are the most common sine ; comprising 11 % the human genome and containing a third of all methylation sites ( deininger and batzer , 1999 ) . the substantial representation of these repetitive elements throughout the genome makes their effectiveness as proxies for global dna methylation highly evident . indeed , methylation levels in alu and line - 1 repeats have been shown in previous studies to be associated with total genomic methylation content ( weisenberger et al . , 2005 ; yang et al . , 2004 ) . estimates of these are increasingly being used in epidemiological investigations owing to their relatively low - cost , high - throughput , and the fact that they can offer quantitative results ( weisenberger et al . , 2005 ) . interestingly , global methylation measures in blood dna have been shown to vary in relation to demographic and lifestyle characteristics , including age , sex , smoking status , alcohol consumption , physical activity , and diet ( heyn and esteller , 2012 ; zhu et al . , 2012 ) . however , there are still few studies of the relationship between dna methylation and weight status . obesity is simply defined as a condition of abnormal or excessive fat accumulation in adipose tissue , to the extent that health may be impaired . obesity is the result of the interplay between external ( environmental ) and internal ( genetic ) factors . it has been cited as the epidemic of our time , with obesity rates sharply and steadily rising in many parts of the world , leading to increased morbidity and mortality due to type 2 diabetes and cardiovascular disease ( danaei et al . , 2009 ) . obesity - related mortality by far exceeds mortality caused by other common diseases ( anderson and caswell , 2009 ) . moreover , about 20 % of all cancers are caused by overweight , and obesity has been shown to be associated with increased risk and worse outcomes following diagnosis ( wolin et al . , 2010 ) . furthermore , the incidence of some types of cancer have been shown to be strongly associated with body mass index ( bmi ) , which has historically been used to define obesity ( renehan et al . , 2008 ) . our understanding of how and why obesity develops is incomplete . to date , several studies concerning dna methylation and obesity have focused primarily on gene - specific methylation and had relatively small sample sizes ( carless et al . , 2013 ; feinberg et al . , 2010 ; fujiki et al . , 2009 ; currently , studies of global methylation levels in blood dna and bmi have yielded inconsistent results ( kim et al . , 2009 ; , 2011 ; wang et al . , 2010 ; zhang et al . , 2011a ; 2011b ; zhu et al . , 2012 ) bmi is now considered to be an important determinant of methylation biomarkers in the blood of women of reproductive age ( van driel et al . , 2009 ) . interestingly , recent evidence has shown that alterations in global dna methylation may be an important contributor to incidence risk of cancer and cardiovascular disease ( baccarelli et al . , 2010 ; terry et al . ,2011 ) . in this study , in order to investigate the specific effects of bmi on global dna methylation and develop blood - based biomarker as initial screening test for obesity - related disease , we quantified the methylation of alu elements in the peripheral blood dna of 244 women with a range of bmis using pyrosequencing technology . study subjects were 244 apparently healthy women aged between 20 and 51 years ( mean 327.9 years ) . this study was approved by the institutional review board of kyungpook national university hospital . additionally , informed written consentwas obtained from all subjects before they participated in the study . demographic information and lifestyle factorswere determined for all participants by trained interviewers using a standardized questionnaire via face - to - face interviews . bmi is easy to obtain [ calculated by weight divided by height squared ( kg / m ) ] and is considered to be an acceptable proxy for under and overweight . bmi has also been shown to be directly related to health risks and mortality in many populations . according to the current international standard ( who 1998 ) , a bmi of over 25 kg / m is considered to indicate overweight and a bmi of over and 30 kg / m is considered to indicate obesity . however , the bmi cutoff values for overweight and obesity vary in asian populations from 22 to 25 kg / m and the increased risk of co - morbidities conferred by obesity have been shown to occur at a lower bmi in several asian populations ( low et al . , 2009 ) . we therefore divided the participants into 3 categories based on bmi normal weight ( bmi 23 kg / m ) , overweight ( 23 kg / m bmi 30 kg / m ) , and obese ( bmi 30 kg / m ) . blood samples were obtained via venipuncture after overnight fasting , and serum samples were separated by centrifugation and transferred to uncontaminated bottles with teflon - coated caps . genomic dna was extracted from whole - blood samples using a qiaamp dna blood kit ( qiagen , usa ) . one microgram dna was bisulfite - modified using an ez dna methylation - gold kit ( zymo research , usa ) according to the manufacturer s instructions . final elution was performed with 30 l m - elution buffer ( zymo research ) and was stored at 70c until analyzed . built - in analysis of non - cpg cytosine residues provided an internal control for the completeness of bisulfate treatment . following treatment with bisulfiteit is possible to insert a c / t single - nucleotide polymorphism into the sequence to be analyzed , and this will result in 100 % ts if conversion is efficient . alu methylation analysis was quantitatively performed on the bisulfite - treated dna using pyrosequencing with the polymerase chain reaction ( pcr ) primers and conditions previously described ( bollati et al . , 2007 ) . in brief , the bisulfite - treated samples ( 50 ng ) were amplified with a biotin - labeled primer via pcr , which enables the conversion of the pcr product to a single - stranded dna template suitable for pyrosequencing . confirmation of the quality of the pcr products and their freedom from contamination was established on 2 % agarose gels with ethidium bromide staining . after purification of pcr products using sepharose beads on pyromark vacuum prep workstation ( qiagen ) , pyrosequencing was carried out using the pyromark q96md system ( qiagen ) according to manufacturer s instructions , including a single - strand binding protein . the percentage of methylatation was expressed for each dna locus as % 5 - mc divided by the sum of methylated and unmethylated cytosines . we tested each marker 3 times and used the average percentage in the statistical analysis . one well was filled with water to ensure no contamination , and 2 wells were filled with cpgenome universal methylated and unmethylated dna ( chemicon , usa ) to evaluate the repeatability of the assay . statistical analysis and plottingcontinuous variables were compared using one - way analysis of variance or analysis of covariance and pairwise post hoc comparison identified statistical differences following bonferroni adjustment . study subjects were 244 apparently healthy women aged between 20 and 51 years ( mean 327.9 years ) . this study was approved by the institutional review board of kyungpook national university hospital . additionally , informed written consentwas obtained from all subjects before they participated in the study . demographic information and lifestyle factorswere determined for all participants by trained interviewers using a standardized questionnaire via face - to - face interviews . bmi is easy to obtain [ calculated by weight divided by height squared ( kg / m ) ] and is considered to be an acceptable proxy for under and overweight . bmi has also been shown to be directly related to health risks and mortality in many populations . according to the current international standard ( who 1998 ) , a bmi of over 25 kg / m is considered to indicate overweight and a bmi of over and 30 kg / m is considered to indicate obesity . however , the bmi cutoff values for overweight and obesity vary in asian populations from 22 to 25 kg / m and the increased risk of co - morbidities conferred by obesity have been shown to occur at a lower bmi in several asian populations ( low et al . , 2009 ) . we therefore divided the participants into 3 categories based on bmi normal weight ( bmi 23 kg / m ) , overweight ( 23 kg / m bmi 30 kg / m ) , and obese ( bmi 30 kg / m ) . blood samples were obtained via venipuncture after overnight fasting , and serum samples were separated by centrifugation and transferred to uncontaminated bottles with teflon - coated caps . genomic dna was extracted from whole - blood samples using a qiaamp dna blood kit ( qiagen , usa ) . one microgram dna was bisulfite - modified using an ez dna methylation - gold kit ( zymo research , usa ) according to the manufacturer s instructions . final elution was performed with 30 l m - elution buffer ( zymo research ) and was stored at 70c until analyzed . built - in analysis of non - cpg cytosine residues provided an internal control for the completeness of bisulfate treatment . following treatment with bisulfiteit is possible to insert a c / t single - nucleotide polymorphism into the sequence to be analyzed , and this will result in 100 % ts if conversion is efficient . alu methylation analysis was quantitatively performed on the bisulfite - treated dna using pyrosequencing with the polymerase chain reaction ( pcr ) primers and conditions previously described ( bollati et al . , 2007 ) . in brief , the bisulfite - treated samples ( 50 ng ) were amplified with a biotin - labeled primer via pcr , which enables the conversion of the pcr product to a single - stranded dna template suitable for pyrosequencing . confirmation of the quality of the pcr products and their freedom from contamination was established on 2 % agarose gels with ethidium bromide staining . after purification of pcr products using sepharose beads on pyromark vacuum prep workstation ( qiagen ) , pyrosequencing was carried out using the pyromark q96md system ( qiagen ) according to manufacturer s instructions , including a single - strand binding protein . the percentage of methylatation was expressed for each dna locus as % 5 - mc divided by the sum of methylated and unmethylated cytosines . we tested each marker 3 times and used the average percentage in the statistical analysis . one well was filled with water to ensure no contamination , and 2 wells were filled with cpgenome universal methylated and unmethylated dna ( chemicon , usa ) to evaluate the repeatability of the assay . continuous variables were compared using one - way analysis of variance or analysis of covariance and pairwise post hoc comparison identified statistical differences following bonferroni adjustment . growing evidence indicates that there are sex differences in global dna methylation in the blood ( terry et al . , 2011 ; zhu et al . , 2012 ) . obesity is a common disorder affecting approximately 1 in 3 women and the prevalence of extreme obesity is about 50 % higher among women than men ( ryan and braverman - panza , 2014 ) . moreover , prevalence of metabolic syndrome is associated with obesity and its escalation has been steeper in women , particularly in young women ( regitz - zagrosek et al . , 2007 ) . second , recent result has shown that bmi is a strong determinant of methylation biomarkers in women of child - bearing age ( van driel et al . ,2009 ) , indicating a greater likelihood of bmi effects on global dna methylation in women . finally , previous studies investigating the effect of bmi on global dna methylation include mainly male populations ( zhu et al . , 2012 ) . in addition , we have found that alu assays may be a more sensitive method for detecting global dna hypomethylation in peripheral blood leukocytes in the general population than line - 1 assays ( kim et al . , 2009 ) . most studies have focused primarily on line - 1 methylation as a surrogate for global dna methylation ( perng et al . , 2013 ; piyathilake et al . , 2011 ; zhang et al . , 2011a ; 2011b ) . in this study , we determined alu methylation levels in a population of korean women . obese participants had higher baseline hemoglobin , serum glutamic - oxaloacetic transaminase ( got ) , serum glutamicpyruvic transaminase ( gpt ) , total cholesterol ( tc ) , and triglyceride ( tg ) levels than normal weight and overweight participants . scatter plot and linear regression analyses showed that these biochemical parameters were positively correlated with bmi ( fig .1 ) , which is consistent with recent observations that got and gpt levels are strongly associated with bmi , tc , and tg in asian populations ( lin et al . , 2010 ; sull et al . , taken together , our data support the hypothesis that bodyweight may be the major factor in determining serum liver enzyme levels . moreover , a significantly lower level of alu methylation was found in overweight participants compared with normal weight or obese participants ( p 0.0001 ) , but no significant difference was observed between the latter 2 groups , indicating a u - shaped association between alu methylation and bmi ( table 2 and fig . however , age , smoking status , and alcohol consumption were not significantly associated with alu methylation levels in blood cells ( data not shown ) . similarly , previous studies have reported no association between smoking , alcohol consumption , and leukocyte dna methylation ( hsiung et al . , 2007 ; kim et al . , 2009 ; terry et al . , 2011 ; zhu et al . , 2012 ) to date , studies of global methylation levels of blood dna and bmi have yielded inconsistent results ( kim et al . , 2009 ; perng et al . , 2013 ; piyathilake et al . , 2011 ; wang et al . , 2010 ; zhang et al . most previous studies reported no significant association between bmi and global dna methylation ( kim et al . in contrast , higher bmi has been reported to be associated with lower line - 1 methylation ( perng et al . , 2013 ; piyathilake et al . , 2011 ) . notably , we observed that participants with a bmi of 25 to 30 kg / m had the lowest methylation levels compared with the other groups , and that alu methylation was elevated among those with a bmi higher or lower than that range . to the best of our knowledge , this is the first study to report a novel u - shaped association between bmi and alu methylation . interestingly , the association between bmi and all - cause mortality has previously been shown to be u - shaped , with the concave region corresponding to bmis of between 22 and 26 kg / m ( berrington de gonzalez et al . , 2010 ; whitlock et al . , 2009 ; zheng et al . , 2011recently , we have observed that persistent organic pollutants , polychlorinated biphenyls are related to mgmt hypermethylation with an inverted u - shaped curve ( p for quadratic term 0.01 ) . the prevalence of hypermethylation was highest in the subjects in the 2 quintile ( 28.4 % ) ; however the subjects in the 5 quintile had a low prevalence of hypermethylation ( 8.2 % ) ( unpublished data ) . taken together , these data suggest the biphasic ( hermetic ) dose response model in which adaptive responses to low doses otherwise harmful conditions improve the functional ability of the cells and organism , resulting in a u or inverted u - shaped dose response ( calabrese , 2010 ) . accordingly , several lines of evidence are presented that dna methylation may be an attractive candidate molecular mechanism for hormesis - like response ( vaiserman , 2011 ) . although the exact mechanism underlying the elevated alu methylation observed in the blood cells of obese people is not known , several possible explanations have been suggested . first , it is reasonable to speculate that sleeping disturbance might contribute to increases in alu methylation in obese people . obstructive sleep apnea ( osa ) is highly prevalent among obese patients ( young et al . ,1993 ) and methylation of the endothelial nitric oxide synthase and forkhead box p3 genes in blood dna has been shown to be linearly associated with the severity of osa ( kheirandish - gozal et al . , 2013 ; kim et al . , 2012 ) . this suggests that global methylation can be influenced by osa and other sleep disorders . in support of this theory , we found that scored sleep management was higher in normal and overweight subjects compared with obese ones ( data not known ) , indicating that obese individuals may have poorer sleep quality than non - obese people . second , although bmi does not differentiate between muscle mass and adipose tissue , people with high bmi can be inferred to have high levels of body fat , causing higher levels of inflammatory markers such as interleukin ( il ) - 6 ( ramkumar et al . , 2004 ) . moreover , persistent inflammation may cause global dna hypermethylation in peripheral blood cells via il - 6 signaling ( stenvinkel et al . , 2007 ) . thus , it is likely that elevated alu methylation in people with high bmi is a consequence of a low but continuous inflammatory drive of obesity .2010 ) demonstrated that the expression of dna methyltransferase 3a is markedly up - regulated in the adipose tissue of obese mice . similarly , a significantly higher frequency of rassf1a , p16 and hmlh1 methylation is observed in nonmalignant tissues of obese patients ( peters et al . , 2007 ; ye et al . , 2006 ) . in light of evidence that tissue - specific methylation profiles are reflected in circulating cell epigenomics ( yang et al . , 2010 ) , it is tempting to speculate that obesity can increase global methylation levels in peripheral blood dna . fourth , there is compelling evidence that heterogeneity in the number of specific leukocytes has the potential to confound methylation measurements using whole blood dna and that increased total leukocytes are associated with obesity ( talens et al . thus , a plausible hypothesis is that a progressively uprising trend at high bmi might be due to differential lymphocyte counts associated with adiposity development . in this respect , it is noteworthy that dna methylation is closely related to lymphocyte count ( zhu et al . , 2012 ) . finally , these divergent results may be due to the specific racial / ethnic characteristics of the study population or the small sample size . further studies to confirm the u - shaped association between alu methylation and bmi by measuring line - 1 methylation and to understand the biological mechanisms underlying observed relationship are also required . collectively , the present study showed a novel u - shaped association between alu methylation and bmi , suggesting that bmi - global dna methylation relationship might play a convoluted role in etiology and pathogenesis of obesity as a hermetic dose response . in addition , the correlation could be a potential biomarker for the initial screening of other obesity - related disease . furthermore , our results showed magnitude of obesity in general healthy population as korean reproductive aged women .\noutput:\n" }, { "from": "agent", "value": "obesity is known to be strongly associated with cardiovascular disease and cancer , the leading causes of mortality worldwide , and develops owing to interactions between genes and the environment . dna methylation can act as a downstream effector of environmental signals , and analysis of this process therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk . global dna methylation of peripheral blood cells has recently been proposed as a potential biomarker for disease risk . repetitive element dna methylation has been shown to be associated with prominent obesity - related chronic diseases , but little is known about its relationship with weight status . in this study , we quantified the methylation of alu elements in the peripheral blood dna of 244 healthy women with a range of body mass indexes ( bmis ) using pyrosequencing technology . among the study participants , certain clinical laboratory parameters , including hemoglobin , serum glutamic oxaloacetic transaminase , serum glutamic - pyruvic transaminase , total cholesterol , and triglyceride levels were found to be strongly associated with bmi . moreover , a u - shaped association between bmi and alu methylation was observed , with the lowest methylation levels occurring at bmis of between 23 and 30 kg / m2 . however , there was no significant association between alu methylation and age , smoking status , or alcohol consumption . overall , we identified a differential influence of bmi on global dna methylation in healthy korean women , indicating that bmi - related changes in alu methylation might play a complex role in the etiology and pathogenesis of obesity . further studies are required to elucidate the mechanisms underlying this relationship ." } ]

[ { "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: obsessive - compulsive disorder ( ocd ) includes a range of clinical characteristics with two major components . there is firstly the intrusion of thoughts , ideas , or compulsions ; and secondly , the resulting triggering of abnormal behaviors or rituals . these actions may serve to resolve the mental imperative of the intrusive thoughts by inducing the person to perform repeated actions or movements that often appear ritualistic . the ritual is composed of sets or sequences of these behaviors , often in order , and may consume much of the patient 's waking attention . ocd is not rare , and occurs with a lifetime prevalence of up to 3 % . even with medication as well as behavioral modification , more than one in ten patients are significantly impaired in their activities of daily living . obsessive - compulsive symptoms ( ocs ) may be seen in ocd itself , or may appear in other psychiatric conditions , . however , despite a number of case reports , no unifying theory of causation has been clearly established . an increased prevalence of ocs , however , has been noted in refractory epilepsy , particularly with temporal lobe epilepsy ( tle ) . epilepsy can affect up to 1 % of the population , and is one of the commoner groups of neurological disorders in adults . this group of disorders is defined as the clinical expression of repeated epileptic seizures occurring spontaneously ( unprovoked ) . these include genetic conditions with onset at various ages and stages of development , and a large spectrum of acquired insults such as conferred by trauma , strokes , neoplasia , inflammation , or infections . most patients with frequent seizures are offered medical treatments , but even with a wide choice of antiepileptic drugs ( aeds ) , over one quarter of patients are refractory to medical treatment . patients with epilepsy may also express a number of patterns of behavioral abnormality and personality characteristics , and experience memory , emotional , behavioral , and social disabilities . up to 40 % of epilepsy patients may be so disabled , particularly in the patients with pharmacoresistant seizures . ertekin and colleagues ' review notes that in refractory epilepsy , some 70 % had psychiatric disorders ; prevalence of axis i psychiatric disorders ranged up to 80 % ; and that using the symptom checklist - 90 - revised ( scl90 - r ) , adults with partial epilepsy had a prevalence of 88 % mental health complaints when scoring for symptoms in the index . in epilepsy , mood disorders , including depression and anxiety , are frequent . in over 200 patients , this review will examine the links between ocd and epilepsy , and review the evolution of the literature on case reports , case series , and larger retrospective controlled studies . included will be the components of ocd seen in epilepsy , effects of medical and surgical treatments , and an overview of the theoretical neurobiological underpinnings that might link the two disorders . teasing out the elements , types , and causes of behavioral disturbance in epilepsy presents a challenge . it is not clear whether the behavioral changes that occur following seizures or with epilepsy may , for example : ( i ) arise from the epilepsy itself ; ( ii ) may appear as a form of forced change induced by the seizure ; ( iii ) might arise from reactive or released behaviors after the seizure ( as a postictal phenomenon ) ; or ( iv ) may be a comorbid psychiatric condition ( which often occur in epilepsy ) . quite aside from the acute effects of acute seizures , is the possibility that it is the chronic progression of the epileptic disorder that might predispose to the appearance of ocs among the many possible psychiatric consequences of epilepsy . these mechanisms might also apply to the many different types of seizures that exist in the family of epilepsy syndromes , along with the various underlying and differing cerebral insults ( both etiological and anatomical ) that can cause epilepsy . in looking at possible seizure types that are associated with ocd , it seems that exclusively generalized tonic - clonic seizures are rarely associated with ocs . psychiatric problems in general were greater in tle ( 80 % ) than in juvenile myoclonic epilepsy ( jme ) , a genetic nonfocal epilepsy others have failed to be able to link epilepsy type with psychopathology . there has been a long association between tle and ocd , as will be explored below . there has been a long - standing observation that patients with various types of epilepsy had a higher incidence of many psychiatric conditions . many years ago tizard suggested that epilepsy generated , or was associated with , a number of personality traits that had obsessional characteristics , suggesting that particular types of epilepsy cause certain types of psychopathology waxman and geschwind described an interictal behavior syndrome characterizing the religious , hypergraphic , and circumstantiality features in epilepsy patients , and others have noted that such qualities in an epilepsy population leads to a low quality of life . there were suggestions that this tle syndrome characterized by religiosity , hyposexuality , hypergraphia , and obsessional features might correspond to a lateralized temporal lobe focus , but patients with ocd were found in some reports or studies to have left - or right - sided epileptic foci this was further underscored by the study by bear and fedio who isolated some of these psychological features , particularly elements of ocd . patients with the appearance or resolution of ocd features with the onset or regression of neurological disease strengthened these possible associations . bear and fedio suggested that the 2.5 % prevalence of ocd in the general population would be exceeded in patients with tle ( for example ) if there were associative or causative factors to link the two disorders . individual case reports or small series have led to the suggestion that a right hemisphere proclivity exists for manifestation of ocd in patients with tle . furthermore , it had been found that some patients with ocd features had right hemisphere structural abnormalities . there have also been other reports of lateralized abnormalities when tle patients with ocd had magnetic resonance imaging ( mri ) studies which revealed structural abnormalities , or had electroencephalographic ( eeg ) asymmetries . schmitz and colleagues , however , failed to find that tle laterality correlated with varying degrees of personality characteristics , or obsessionality . although a number of studies with a small number of subjects indicated a link between tle and ocd , there were few group studies . it awaited the development of better retrospective and prospective studies to explore the similarity noted between the forced thinking seen in some patients with tle and ocd , and to determine whether there was merely a chance comorbidity , or a clear association . hence , there was a need to build upon the casual clinical impression and the several case reports of tle and ocd , and design more systematic investigations in the form of case series or controlled studies . these studies would have to use structured neuropsychological instruments , trained personnel , and a control population to help eliminate biases inherent in many case series . in order to systematize and lend validity tothe association of ocd and epilepsy , isaacs and colleagues looked at the profile of symptoms in tle to see if tle and ocd shared common neural mechanisms , and to facilitate diagnosis and symptom treatment in tle . to do this , they measured the prevalence of oc features using an obsessive - compulsive inventory and compared their results with those of normative controls . they found that patients with ocd manifested abnormalities on neuropsychological tests that involved nonverbal memory and visuospatial tasks . this has been endorsed by some imaging studies in patients with ocd without epilepsy , but other reports indicate a more bilateral involvement . hence , from their findings , it is unclear to what degree a right hemisphere predominance of abnormalities prevails in tle with ocd . the symptoms in the tle group included doubting , ordering , hoarding , checking , neutralizing and washing , emphasizing the more compulsive components rather than the obsessive moiety of this duality . this study thus indicated the possibility that the neurobiological pathways subserving compulsive thought processes may differ from those underlying obsessive traits . isaacs and colleagues suggest that doubting , checking , and hoarding in particular might represent the effects of behavioral impairments in patients with tle , for example related to a problem in memory ; while hoarding might reflect deficits in organization stemming from frontal lobe problems . there has been a distinction made between the concept of traits ( features ) of a particular individual , or a state , arising from the role that a disease might play in a patient 's life . as monaco andcolleagues have pointed out , this analytical approach has been used with quantitative evaluation techniques that use personality psychometrics , but have been less used with neurological disorders . these comprise possible selection bias , the absence of systematic data , and a reliance on self - rating scales without confirmation of validity , and finally an underuse of more prevalent psychometric tools . in their review of consecutive patients with tle versus patients with nonfocal idiopathic generalized ( genetic ) epilepsy ( ige ) , monaco and colleagues studied subjects employing investigators who were fully trained in clinical psychology and who used a structured clinical interview for sdm - iv patient version for ocd diagnosis and the yale - brown obsessive compulsive scale ( y - bocs ) . they evaluated obsessionality as a trait using a minnesota multiphasic personality inventory 2 ( mmpi - 2 ) version addressing the pt clinical scale and obs content scales that contain evaluations of characteristics of compulsions , excessive doubts , obsessions , perfectionist personality traits , and fear . the particular oc features investigated included neutralizing , checking , doubting , ordering , hoarding , and washing . the obs content scale identifies ocs and behaviors , maladaptive ruminations , and obsessive thoughts . these scales were supplemented by the beck depression inventory and state - trait anxiety inventory y1 and y2 . of the 164 enrolled subjects matched with 82 controls , aeds , seizure control , age , gender , duration , eeg , and mri among many items , were evaluated . tle patients scored higher on the pt and obs scales than ige and normal controls , unrelated to seizure control , severity of epilepsy , medication , or etiology . this indicated that obsessionality is a tle trait in patients with a biological predisposition , with a prior psychiatric history . in turn , this would suggest that there is a link between mesolimbic regions and particular personality characteristics , a link previously believed to exist in tle patients . the study further supports the concept that involvement of particular brain areas , by the various epilepsy syndromes will be relevant to the appearance of specific psychopathological expression and psychiatric conditions . of note was the fact that the results in the normal controls resembled those of ige patients , differentiating these two groups from tle . such findings contrasted with the isaacs study which found that 22 % of tle patients had features of ocd , but which had examined a refractory tle population . an unsettling finding in the monaco study is that only one of the nine patients had been previously diagnosed with ocd , indicating that ocd is poorly recognized in an outpatient epilepsy patient population . one reason may well be the relative lack of investigators trained in psychiatry in an outpatient epilepsy clinic setting . regarding mechanisms , the authors note that the amygdala is involved in ocd , and has major connections with the striatum . such affective and motivational components facilitate the conduction of automated often ritualistic behavior in response to danger . the reciprocal links to the amygdala , ventral striatum , and stria terminalis may serve the anxiety - modulating effects of rituals and repetitive behaviors . ertekin and colleagues built on the prior investigations and constructed a study to evaluate the associations of tle arising from unilateral mesial temporal sclerosis ( mts ) , and ige with psychiatric comorbidities including ocd they compared 29 tle patients with 27 ige patients from an epilepsy clinic population , and with 30 control subjects , they employed investigators experienced in epilepsy and psychiatry . this team evaluated the three groups , and supplemented their evaluations with mri imaging and eeg . using a structured clinical interview ( scid - i ) and y - bocs symptom checklist that includes some 50 types of obsessive and compulsive characteristics , they were able to rate severity and type of symptom , including patients with subsyndromal characteristics of ocd . the authors found that about 10 % of tle patients had ocd , 24 % had subsyndromal ocd , which was higher than in the matched ige group ( 3.7 % and 7.4 % - not statistically significant ) . the commonest comorbidity with ocd was depression , and there was a left - sided predominance in this association with tle . lending support to the effect of the chronicity of an enduring condition , is the study by swinkels and colleagues who noted that both predisposition and brain dysfunction played a part . they speculated that anatomical factors , however , were more important than the chronicity of the disease . confirming observations by monaco and colleagues , ertekin and colleagues found that depressionwas highly associated with ocd in tle , also supporting conclusions by isaacs and colleagues who used an obsessive compulsive inventory ( oci ) , but not a scid - ip or y - bocs to delineate an ocd diagnosis . they found that patients with tle have greater obsessions with contamination and a compulsion to wash than do patients with ige ; similarly with symmetry / exactness obsessions and ordering compulsion ; while isaacs and colleagues found greater washing , ordering , checking , hoarding , doubting , and neutralizing . frontal lobe epilepsy ( fle ) is another likely candidate as a fellow traveler with ocd , possibly because of the executive and behavioral functions subserved by this part of the brain . from a neurobiological perspective , dysfunction in this regionaffects part of the frontal - cingulate - thalamic - limbic circuit , and hence might favor the functional dysregulation of this circuit , thus inducing elements of ocd . another candidate is limbic epilepsy , with its unusual automatisms which may simulate the ritualistic behavior of ocs . other rarer conditions may possess both epilepsy and rituals or at least repetitive behaviors as clinical expressions of a particular disease . examples include the handwringing seen with rett syndrome , and other behavioral features noted with angelman syndrome and autism spectrum disorder . various theories have been advanced , and have been supported by the findings of ocd triggered by a number of neurological conditions . modell and colleagues suggest that there are two principal loops or circuits underlying control of the behaviors involved in ocd . they are comprised of a thalamo - orbitofrontal connection mediated by glutamate , and a collateral loop that includes striatal - orbitofrontal - thalamic interconnections mediated additionally by serotonin , dopamine , and gammaaminobutyric acid ( gab a ) . normally , orbitofrontal cortex activates the caudate and then the pallidum so as to inhibit the medial thalamic nucleus that then feeds into the frontal cortex . in this mannerdysfunction of these circuits might produce ocd , with increased activity inducing obsessive characteristics and compulsive traits . however , complicating this paradigm is the paradoxical clinical resolution in some cases of established ocd by the new appearance of one of strokes , tumors , or by deep brain stimulation . nonetheless , such serendipitous associations have spawned a neurobiological underpinning for ocd that includes the malfunctioning of various brain circuits . abnormally functioning circuits include the thalamus , basal ganglia , anterior cingulate gyrus , and the orbito - frontal cortex . it has been postulated that there is an abnormality in the circuit linking frontal regions to the basal ganglia . these circuits pass through the frontal - thalamic - pallidal - striatal areas and back to the frontal regions , transiting via the anterior cingulate gyrus and the internal capsule . to support the concept of this specific circuitryunderlying ocd is the finding that disruption of this pathway by surgical anterior internal capsulotomy and anterior cingulotomy enables improvements in ocd . a new model for ocd has been proposed by huey and colleagues based on studies using functional mri , mri , and positron emission tomography . they examined patients with ocd who had other neurological disorders , and compared them to patients with idiopathic ocd . ocd had undergone surgery or deep brain stimulation believed to decrease hyperactivity in regions thought to provoke ocd . the group postulated that three regions are implicated in both types of ocd : orbitofrontal cortex which directs appropriate behavior , the basal ganglia that acts as a gate in connecting behaviors to subsequent reward , and the anterior cingulate region that modulates perception of which behavioral choice will result in reward . patients with ocd from neurological disease had less anxiety with the compulsion than did those with the idiopathic form . huey and colleagues postulated that the anxiety and impulse towards particular behaviors are requited only when the behavior is completed . theories underlying the particular association between ocd and epilepsy include not only a possible shared mechanism , but an incidental ocd problem in patients with epilepsy . however , a compelling explanation for the ocs - epilepsy association is the interruption of a pathological shared organization when certain types of focal brain neurosurgery are performed , with the effect of causing regression of seizures , but also allowing latent ocd traits to appear . a sudden cessation of seizures after surgery might be seen as a form of forced normalization . hence the surgical removal of excitation , and preponderance of inhibition , would enable the occurrence of psychiatric disorders , and have been termed the forced normalizationof note however , many postoperative tle seizure patients never develop psychiatric problems . one of the components of ocd involving the perception of forced thoughts may occur from seizures themselves . in the classification of seizures , those seizures that involve part of the brain and which do not impair vigilance or memory , are termed simple partial seizures . it has long been noted that obsessive thoughts can occur in the preictal period , be caused by simple partial seizures as an ictal phenomenon , or occur in the postictal period . kroll and drummond have suggested that the comorbidity of ocd and tle might be due to kindling . the theory of kindling is that focal chemical or electrical brain stimulation can later result in a more persistent condition ( eg , epilepsy ) . some speculate that this might occur in the limbic circuit , and induce ocd problems . however , there is little evidence for this theory . problems with this theory are the absence of a single focus of neuronal deficit in ocd . in contrast , several regions have been implicated in ocd , including the basal ganglia , cingulate , and frontal areas , with limbic areas involved in ocd and tle . the results of studies revealing a right - hemisphere tle focus predilection , suggested an increased vulnerability to oc in this tle population . there may be a role of aeds in ocd , as they might convey a neuropharmacological susceptibility to ocd . ertekin and colleagues found in their tle patients that most were on carbamazepine , while patients with ige ( with less ocd ) were on valproate . this suggests that epilepsy syndrome aside , one drug might favor , or the other drug might hinder , the development of ocd . because of the finding of depressive comorbidity with ocd in epilepsy , limbic dysfunction might represent an underlying neurobiological underpinning . in contrast to the appearance or the worsening of ocd with temporal lobe surgery as mentioned above , a subgroup of patients with particularly temporal - lobe foci may significantly benefit from resective surgery . surgery is also sometimes effective in extratemporal foci , or with more widespread epileptic conditions with multiple seizure types ( eg , lennox - gastaut syndrome ) , in which partial interruption of the corpus callosum may decrease certain types of seizures , particularly atonic seizures . many types of underlying premorbid psychopathology may get worse following epilepsy surgery , even when epilepsy improves . there are reports of depression and psychosis , and in some cases suicide and death after temporal lobe surgery . leinonen and colleagues commented on new - onset schizophrenia in a group of 57 subjects after surgery . such tendencies can be evaluated before surgery and may well factor in the decision whether to advocate this treatment in affected patients . although kulaksizoglu and colleagues found no particular risk factors for de novo postoperative psychiatric problems , most problems appeared to manifest within the first 2 months after surgery six of 74 patients undergoing temporal lobectomy had new - onset psychosis with 6 suicide attempts in the first month . in another series , by 6 weeks post - temporal lobectomy , of the previously nonsymptomatic patients for psychiatric disorders , half developed anxiety and depression , and almost half had emotional lability other studies suggest that nondominant hemisphere surgery favors the appearance of more severe psychiatric problems , even if lesions on either side may induce ocd in nonepileptic patients . other neurosurgical studies support the involvement of neural loops in ocd in patients with epilepsy , and the subsequent improvement that can occur following surgery to reinforce the involvement of frontal pathways , kulaksizoglu and colleagues review the reports on the dysfunction of frontal subcortical circuits , and the abnormalities in visual - spatial and nonverbal tasks that particularly implicate right subcortical frontal circuits in the process . there is much work to be done in establishing the causation of ocd , and possible links to epilepsy . future studies should extend investigation to nonepilepsy neurological groups as well as a psychiatry group with ocd . multicenter studies would be valuable in looking at the entire severity spectrum of ocd in tle . in addition , with the findings of greater religiosity and writing compulsions in patients with epilepsy , research into ocd in epilepsy would be enhanced by developing specific tools or scales that measure these parameters . greater attention might be directed at the comorbidity of depression and anxiety in ocd in patients with epilepsy , with examination of the neurobiological and structural relationships to clinical expression . as with any implied association , prospective larger studies with optimally trained personnel with experience in psychiatric testing instruments , the development of tailored characterization of ocd subtypes and feature categorization , and the application of these tools and trained personnel to carefully categorized populations of different types of epilepsy , are warranted . multicenter trials would have a good chance of lending support to the neurobiology , causes , and optimal management in patients with the several types of epilepsies and varieties of ocd .\noutput:\n" }, { "from": "agent", "value": "obsessive - compulsive disorder ( ocd ) has long been associated with epilepsy . the link with temporal lobe ( usually refractory ) epilepsy ( tle ) is particularly prominent . of tle patients , 10 % to 22 % of patients may have ocd , often underdiagnosed in the outpatient clinic . data on the links include case reports , case series , and controlled studies . three larger , controlled studies in tle patients , using comprehensive epilepsy and ocd classifications , in aggregate , have noted the obsessive qualities of washing , symmetry / exactness , and ordering , with a greater preoccupation with certain aspects of religion , compared with controls or patients with idiopathic generalized epilepsy . tle foci may be either left - or right - sided . social and neurobiological factors are involved in ocd in tle . the neurobiology implicates a pathophysiological or structural impairment of the orbitofrontal - thalamic , and frontothalamic - pallidal - striatal - anterior cingulate - frontal circuits . discrete anatomic lesions in these pathways , or their surgical removal , may induce ( or conversely ) improve ocd in tle 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: intestinal obstruction is a common complication in patients with advanced abdominal or pelvic cancer and has a significant impact on their quality of life . in patients with inoperable malignant bowel obstruction , the synthetic somatostatin analogue octreotide relieves nausea , vomiting and pain , and decreases drainage from a nasogastric tube . here , we report the use of the long - acting somatostatin analogue lanreotide autogel ( somatuline ; ipsen nv ) in the treatment of bowel obstruction in a patient with adenocarcinoma and peritoneal carcinomatosis . in january 2012 , a 60 - year - old woman presented with a 3 - month history of increasing abdominal pain and a change in the stool pattern with a single episode of anal red blood loss in the past week . an ultrasound of the abdomen showed several masses dispersed over the peritoneum , compatible with significant peritoneal metastasis . colonoscopy revealed a large ulcerating lesion at the level of the sigmoid colon , which was diagnosed as a moderately differentiated adenocarcinoma after biopsy . chemotherapy with 18 biweekly cycles ( 1 cycle every 2 weeks ) of folfiri and bevacizumab ( avastin , roche ) was started . folfiri was administered according to the following schedule : day 1 , irinotecan 180 mg / m ; days 1 and 2 , leucovorin 100 mg / m , 5 - fluorouracil bolus 400 mg / m and 5 - fluorouracil infusion 600 mg / m . avastin was given at a dose of 5 mg / kg every 2 weeks . if the patient had responded to this treatment , the possibility of performing debulking surgery and hyperthermic intraperitoneal chemotherapy would have been considered . the abdominal pain disappeared after the first month of chemotherapy , while the ascites disappeared after 6 weeks . there was also a slight regression of the peritoneal masses . during the 5th , 6th and 7th cycle of chemotherapy , the patient was hospitalized because of clinical signs of intestinal subocclusion ( vomiting , absence of stools and flatus ) that evolved into complete obstruction . a ct scan of the abdomen did not reveal the cause of the obstruction or deterioration of the oncological lesions . based on this observation , a folfiri - induced mucositis , motility disturbances due to peritoneal metastasis or a combination of these two factors were suspected . during hospitalization , fluids , alizapride ( litican , 300 mg / day ; sanofi - aventis ) and methylprednisolone sodium succinate ( solu - medrol , 40 mg / day ; pfizer inc . ) were administered intravenously , paracetamol ( 1 g / dose ) was administered intravenously 4 times a day and octreotide ( sandostatin , 0.5 mg / dose ; novartis ) was administered subcutaneously 3 times a day until the obstruction resolved . oral consumption of food and fluids was withheld , and a nasogastric tube was placed . at each of the 3 hospitalization episodes , after the first episode of obstruction , the dose of folfiri was decreased to 75 % , while the dose of avastin was not decreased . all episodes of obstruction resolved after 3 days , and the chemotherapy was reintroduced after 12 weeks following resolution of the obstruction . after the third episode of obstruction , we initiated treatment with lanreotide autogel 120 mg , injected deep subcutaneously once every 4 weeks . the 120 - mg dose was chosen based on our experience that the 90 - mg dose has a lower efficacy . the treatment with lanreotide autogel continued during the remaining 11 cycles of chemotherapy , and no further episodes of intestinal subocclusion or obstruction occurred . because tumor response following the 18 cycles of chemotherapy was not sufficient , debulking surgery or hyperthermic intraperitoneal chemotherapy treatment were not recommended . after a 3 - month break in the chemotherapy treatment requested by the patientthe patient is currently undergoing second - line chemotherapy with folfox4 at 75 % of the usual dose , administered once every 2 weeks in 12 cycles according to the following schedule : day 1 , oxaliplatin 85 mg / m at 75 % ; days 1 and 2 , 75 % of leucovorin 100 mg / m , 5 - fluorouracil bolus 400 mg / m and 5 - fluorouracil infusion 600 mg / m . the 4 - weekly lanreotide autogel injections have been continued without interruption to support the quality of life of the patient . no new episodes of obstruction occurred until november 2013 , and the patient reported no side effects due to lanreotide autogel . intestinal obstruction is reported in up to 51 % of the patients with ovarian cancer and up to 28 % of those with gastrointestinal cancer and has an important impact on their quality of life . due to contraindications such as intra - abdominal carcinomatosis , poor nutritional status or a large volume of ascites , surgery is not an option in a substantial portion of these patients . a nasogastric tube can be placed to drain secretions ; however , this often causes a great amount of distress in the patient as well as nasal or pharyngeal irritation , nasal cartilage erosion , occlusion of the tube or spontaneous expulsion . short - acting somatostatin analogues such as octreotide ( sandostatin ) are antisecretory drugs used in the treatment of patients with inoperable bowel obstruction . somatostatin was initially discovered as an inhibitor of growth hormone release , but was later found to play an inhibitory role in the regulation of several organ systems such as the central nervous system , the immune system , vessel walls , the pancreas and the gastrointestinal tract . somatostatin analogues are valuable in the treatment of patients with malignant bowel obstruction because of their inhibitory effect on gastrointestinal motility and secretions and their ability to increase the absorption of water and electrolytes from the intestinal lumen . the efficacy of short - acting somatostatin analogues in the management of symptoms due to malignant bowel obstruction has been reported in numerous patients , with control of vomiting obtained in more than 60 % of the patients ( reviewed in ) . reversal of malignant bowel obstruction after treatment with short - acting somatostatin analogues has also been reported . the synthetic somatostatin analogue lanreotide has shown efficacy in the symptomatic treatment of inoperable bowel obstruction in patients with peritoneal carcinomatosis when administered in the form of microparticles . here , we report a case of intestinal obstruction in a patient with adenocarcinoma , which resolved after treatment with octreotide . however , new episodes of obstruction occurred , which each time led to a delay in the administration of chemotherapy . after the third episodeuntil november 2013 , the patient received eighteen 4 - weekly injections of lanreotide autogel and did not experience any further episodes of obstruction , suggesting that lanreotide prevents recurrence of intestinal obstruction in patients with intestinal cancer . another advantage is that while short - acting octreotide has to be administered 3 times a day , lanreotide autogel is administered only once a month , improving a patient 's quality of life . treatment with lanreotide autogel prevented recurring episodes of obstruction , allowing the patient to continue the chemotherapy course without further delays and to start the second course . to our knowledge , this is the first report of a successful use of lanreotide autogel in the management of malignant bowel obstruction . our results indicate that lanreotide autogel could be used as an alternative to a long - acting formulation of octreotide , which has recently shown efficacy in the symptomatic treatment of inoperable malignant bowel obstruction due to peritoneal carcinomatosis . a long - term treatment with lanreotide , as reported herein , is further supported by the results of a study in which 3 patients with malignant bowel obstruction due to ovarian cancer received a monthly - administered long - acting depot form of octreotide ( sandostatin lar depot ) for a period of over 9 months , with no significant toxicities reported . the efficacy and safety of lanreotide in the palliative treatment of inoperable malignant intestinal obstructionare currently being investigated in a phase ii clinical trial ( www.clinicaltrials.gov : nct01076803 ) .\noutput:\n" }, { "from": "agent", "value": "intestinal obstruction is a common complication in patients with advanced abdominal or pelvic cancer . the synthetic somatostatin analogue octreotide can help relieve nausea , vomiting and pain in patients with inoperable obstruction . here , we report a case of recurrent intestinal obstruction in a patient with adenocarcinoma . although the obstruction was resolved after 3 days of treatment with octreotide , new episodes of obstruction occurred , resulting in a delay of the chemotherapy treatment . after 3 episodes of obstruction , we initiated treatment with a longer - acting somatostatin analogue , lanreotide autogel 120 mg , administered once every 4 weeks . the treatment with lanreotide autogel is being continued , allowing for continuation of the chemotherapy without further episodes of intestinal subocclusion or obstruction . until november 2013 , the patient received eighteen 4 - weekly injections of lanreotide autogel and did not report side effects . this case report demonstrates the successful treatment of intestinal obstruction with lanreotide autogel in a patient with adenocarcinoma ." } ]

[ { "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: autism , asperger s syndrome , and atypical autism / pdd - nos are behaviourally defined by compositions of impairments in three domains : reciprocal social interaction , mutual verbal and nonverbal communication alongside with inflexible behaviour patterns , interests and activities ( dsm - iv - tr / icd - 10 ) . the diagnoses are clinically increasingly summarized under the label of autism spectrum disorders ( asd ) . indeed , a multitude of research shows that the diagnoses are hard to differentiate and probably form one clinical spectrum of behaviour problems , not circumscribed entities ( macintosh and dissanayake 2004 ; witwer and lecavalier 2008 ) . dsm - v will probably dissolve the single disorders in favour of the autism spectrum concept , indicating differing grades of severity of one diagnosis ( lord 2009 ) . studies on the phenotype in first degree relatives of people with autism have shown that a substantial part of parents and siblings tend to show normative ( subclinical ) variants of full - blown asd , called the broader or extended autism phenotype , perhaps reflecting a vulnerability for the clinical picture of asd ( dawson et al . recent epidemiological research indicates that asd rather present the extreme of a trait ( spiker et al . traits reflect habitual patterns of behavior , thought , and emotion , which are stable over time and exist in all individuals to a varying degree ; often normal distribution of these features is postulated . as opposed to disorders , traits are viewed to be quantitatively ( dimensional ) , not qualitatively distributed in the general population . some disorders , particularly learning disabilities and mental retardation are already dimensionally defined to a large degree in dsm - iv - tr / icd - 10 . grounding a disorder on either categorical or dimensional viewsmay appear insignificant in the first place , as a line is drawn somewhat arbitrarily between normality and abnormality in both cases and there is always an additional clinical ( categorical ) decision to be made , whether a persons needs care or not . nevertheless , a paradigm shift from categorical to dimensional in asd would have major scientific and clinical impact on the exploration of its genetic and neurobiological roots , on intervention studies , statistical power and the clarification of the phenomenon to patients and their parents ( constantino 2009 ) . there would also be a certain move of autism from psychiatry and clinical psychology to differential and personal psychology , because asd assessment would preferably be done by using psychometric tools designed for and standardized in the general population . it is therefore of pivotal importance for research and clinical purposes to carefully evaluate the clinical validity of diagnostic instruments claiming to be appropriate in assessing autism as a trait . aside from the autism - spectrum quotient ( baron - cohen et al .2006 ; auyeung et al . 2008 ) and the childhood autism spectrum test ( williams et al .2008 ) , the social responsiveness scale ( srs ; constantino and gruber 2005 ) and the social and communication disorders checklist ( scdc ; skuse et al . they have both demonstrated good psychometric properties , continuously distributed scores in large general population samples , single factor solutions and high heritability of the features assessed ( constantino and todd 2003 ; constantino et al . the srs has also demonstrated cross - cultural validity ( blte et al . 2008b ) . the srs is a 65 item ( likert scale 0 to 3 ) parent / teacher report form , and generates a singular scale with a maximum score of 195 for behaviour shown in last six months . in the original us american standardization , the mean raw score for parent reported autistic traits in 1,081 typically developed school children aged 418 years from missouri and california was 33.7 ( sd = 20.9 ) in boys and 27.6 ( sd = 18.1 ) in girls . the expected score in asd lies between 101.5 ( sd = 23.6 ) for pdd - nos and 117.1 ( sd = 22.2 ) for core autism . other mental disorders have shown to yield intermediate scores , e.g. attention - deficit hyperactivity disorder ( adhd ) ( 51.1 , sd = 32.9 ) ( constantino and gruber 2005 ) . correlations with gold standard clinical asd instruments are consistent with expectations , e.g. r = .52 to .74 with subscales of the autism diagnostic interview - revised ( adi - r ) . receiver operating characteristics ( roc ) analyses in 133 cases of asd vs. 126 non - asd cases ( adhd , unspecific developmental disorder , other child psychiatric diagnoses ) showed that a srs - total score of 75 had a sensitivity of .85 and a specificity of .75 for any asd , while a total score of .85 had a sensitivity of .70 and a specificity of .90 . the scdc is a time and cost effective parent questionnaire including 12 items ( likert scale 0 to 2 ) with a maximum score of 24 for current behaviour . the mean value in 118 typically developed children and adolescents from mainstream schools in the uk was found to be 3.25 ( sd = 4.15 ) for boys and 2.39 ( sd = 3.14 ) for girls . in asd , reported values were 16.6 ( sd = 5.7 ) in 208 clinically diagnosed autism and atypical autism and 13.0 ( sd = 6.1 ) in 76 clinically diagnosed conduct disorder , adhd , pragmatic language disorder , tourette s , and obsessive compulsive disorder ( skuse et al . 2005 ) . the scdc has shown correlations with adi - r algorithm output equivalents ( generated by the 3di interview ; skuse et al . roc analyses in the initial standardization study showed that a scdc - total score of 9 reached a sensitivity of .90 and a specificity of .69 for asd . ( 2009 ) in a cohort of 8,094 eight year olds including 31 register - based educational service diagnoses of asd , 70 specific learning disability , 92 moderate learning disability , 15 severe learning disability , 2 profound and multiple learning , 57 emotional and behavioural maladjustment , 25 speech , language and communication needs , and 22 physical and sensory disabilities reported a sensitivity of .88 and a specificity of .91 for a scdc - total score of 8 . the latter is in the area of the discriminative power identified for the revised algorithms of the autism diagnostic observation schedule ( ados ) ( gotham et al . overall , these results convincingly endorse the clinical validity of the srs and scdc for usage in research and clinical practice of asd . in addition , the clinical samples used to establish their diagnostic validity for asd were somewhat limited in terms of phenotypic characterization , clinical heterogeneity and syndrome severity . the objective of the current study was therefore to compare the convergent and diagnostic validity of the srs and scdc for asd using exactly the same methods in a single well characterized child and adolescent psychiatric sample ( clin ) , and typically developing control mainstream school children ( typ ) . the total sample consisted of n = 480 participants : n = 148 with idiopathic asd , n = 255 clin and n = 77 typ . asd and clin had been collected in the years 2005 to 2008 within the clinical routine at the department of child and adolescent psychiatry , frankfurt / m . university hospital , and within a long - term research project on the genetic fundamentals of autism ( well.ox.ac.uk/monaco/autism/imgsac.html ) . the asd sample included 98 individuals with autism , 34 with atypical autism / pdd - nos and 16 with asperger s syndrome . for inference statistics , autism , asperger syndrome and atypical autism / pdd - nos participants were pooled , as , owing to a rich body of evidence , the spectrum concept will replace the aforementioned single diagnosis in the upcoming dsm - v ( see www.dsm5.org , for details ) . there were 121 males and 27 females aged 4 to 18 years ( m = 11.2 , sd = 4.1 ) with an average iq of 88.95 ( sd = 25.5 ) . in clinthere were 98 cases of adhd , 41 with anxiety disorders , 37 with combined adhd and cd , 28 cd , and 41 had other diagnoses ( mental retardation without asd , affective disorder , tics , learning disability , eating disorder , psychosis , mutism , attachment disorder , enuresis , pica ) . there were 185 males and 70 females in clin aged 4 to 18 years ( m = 9.9 , sd = 3.7 ) , with an average iq of 98.5 ( sd = 15.9 ) . they were consensus diagnoses of the author s department s experienced clinicians , corroborated by findings from standardized diagnostic scales , such as the adi - r and ados for asd or the kiddie - schedule for affective disorders and schizophrenia ( kaufman et al . 1997 ) for other clinical diagnoses . a diagnosis of asperger syndrome was given , if the adi - r autism algorithm cut - off was met , but no history of language delay was apparent on the items first words / first phrases , and ados autism spectrum cut - off was met . a diagnosis of atypical autism / pdd - nos was assigned , if two domain cut - offs were met in the adi - r ( one of which was the social interaction domain ) and ados autism spectrum cut - off was met . the typ were recruited from regular local preschools , primary and secondary schools as well as from authors private personal contacts , and had no history or current indication of psychiatric or school problems according to parent information . typ consisted of 41 males and 36 females with a mean age of 9.3 years ( sd = 3.2 ) . sample characteristics are summarized in table 1 . table 1sample characteristicsautism spectrum disorders ( asd ) clinical controls ( clin ) typical controls ( typ ) n14825577age , years : m ( sd ) 11.2 ( 4.1 ) 9.9 ( 3.7 ) 9.3 ( 3.2 ) sex : male / female121 / 27185 / 7041 / 36iq : m ( sd ) 88.95 ( 25.5 ) 98.5 ( 15.9 ) srs score : m ( sd ) 101.1 ( 31.8 ) 62.7 ( 30.9 ) 26.0 ( 13.6 ) ( boys ) 106.7 ( 33.9 ) 62.9 ( 27.3 ) 20.9 ( 9.6 ) ( girls ) scdc score : m ( sd ) 15.6 ( 5.8 ) 12.6 ( 6.7 ) 5.9 ( 4.6 ) ( boys ) 15.3 ( 4.1 ) 11.4 ( 6.7 ) 5.1 ( 3.0 ) ( girls ) asd clin typ ( p .0001 ) , girls = boys ( p .26 ) sample characteristics asd clin typ ( p .0001 ) , girls = boys ( p .26 ) the german adaptations of the srs and scdc were compared in this study . consistent with the english original , the german version of the srs ( blte and poustka 2008 ) has demonstrated a single factor structure and good to excellent psychometric properties ( blte et al . however , mean srs total scores for typically developed girls and boys as well as values for asd were lower in the german sample , while scores for conduct disorder ( cd ) and adhd / cd combined were higher . the scdc was translated into german , independently retranslated into english , adjusted by a native english speaking clinician and tested in practice for understandability before using it in this study . in order to establish the convergent validity of the srs and scdc , the german adaptations of gold standard asd instruments , namely the adi - r and the ados , as well as the social communication questionnaire ( scq ) were also assessed in the asd sample . comparable to the originals , all have demonstrated good to excellent psychometric properties ( poustka et al .1996 ; blte and poustka 2004 ; blte et al . 2006 , 2008a ) . the srs , scdc and scq were either send out for completion by parents as a part of pre - appointment assessment or completed during a clinical visit of their child . in most cases , completion of the srs , scdc and scq preceded the adi - r and ados or other in depths clinical examinations . in clin the srs and scdcsrs and scdc data in typ were obtained at personal contacts of the authors with the parents or by teachers handing - out and re - collecting the questionnaires . iq was assessed in the asd and clin participants using either wechsler intelligence batteries or the raven s matrices , which mostly result in qualitatively comparable scores in higher functioning asd ( iq 85 ) and clin ( blte et al .16.0 was used for data analysis . partial correlation ( controlled for iq and age ) was computed in asd to determine convergent validity ( correlation with measures aiming to assess similar constructs ) of the srs and the scdc with the algorithm domain scores of the adi - r ( deficits in social interaction , deficits in communication , stereotypic behaviors ; reflecting behavior at age 4 to 5 years or lifetime ) and ados ( deficits in social interaction , deficits in communication ; reflecting current behavior ) as well as the total score of the scq ( reflecting behavior at age 4 to 5 years and lifetime ) . here , to avoid underestimation of true associations , correlations were corrected for direct range restrictions applying the case ii formula by thorndike ( 1949 ) , because adi - r , ados and scq are categorical scales , not intended to generate variability . the formula uses ( a ) the correlation of the restricted sample , ( b ) the standard deviation of the independent variable in the restricted sample and ( c ) in the unrestricted sample to provide an estimate of the correlation in the population . diagnostic validity ( value for diagnostic classification ) , was analyzed by roc - analyses for asd vs. typ and asd vs. clin , as well as for asd vs. each of the largest clin subgroups , adhd , and anxiety disorders . area under the curve ( auc ) with p - values , sensitivities and specificities for recommended srs and scdc cut - offs were calculated . group and sex differences on the srs and scdc were examined using ancovas and post - hoc tukey tests . internal consistencies ( cronbach s alpha ) for the srs and scdc are were computed within asd , clin , and typ . the total sample consisted of n = 480 participants : n = 148 with idiopathic asd , n = 255 clin and n = 77 typ . asd and clin had been collected in the years 2005 to 2008 within the clinical routine at the department of child and adolescent psychiatry , frankfurt / m . university hospital , and within a long - term research project on the genetic fundamentals of autism ( well.ox.ac.uk/monaco/autism/imgsac.html ) . the asd sample included 98 individuals with autism , 34 with atypical autism / pdd - nos and 16 with asperger s syndrome . for inference statistics , autism , asperger syndrome and atypical autism / pdd - nos participants were pooled , as , owing to a rich body of evidence , the spectrum concept will replace the aforementioned single diagnosis in the upcoming dsm - v ( see www.dsm5.org , for details ) . there were 121 males and 27 females aged 4 to 18 years ( m = 11.2 , sd = 4.1 ) with an average iq of 88.95 ( sd = 25.5 ) . in clinthere were 98 cases of adhd , 41 with anxiety disorders , 37 with combined adhd and cd , 28 cd , and 41 had other diagnoses ( mental retardation without asd , affective disorder , tics , learning disability , eating disorder , psychosis , mutism , attachment disorder , enuresis , pica ) . there were 185 males and 70 females in clin aged 4 to 18 years ( m = 9.9 , sd = 3.7 ) , with an average iq of 98.5 ( sd = 15.9 ) . they were consensus diagnoses of the author s department s experienced clinicians , corroborated by findings from standardized diagnostic scales , such as the adi - r and ados for asd or the kiddie - schedule for affective disorders and schizophrenia ( kaufman et al . 1997 ) for other clinical diagnoses . a diagnosis of asperger syndrome was given , if the adi - r autism algorithm cut - off was met , but no history of language delay was apparent on the items first words / first phrases , and ados autism spectrum cut - off was met . a diagnosis of atypical autism / pdd - nos was assigned , if two domain cut - offs were met in the adi - r ( one of which was the social interaction domain ) and ados autism spectrum cut - off was met . the typ were recruited from regular local preschools , primary and secondary schools as well as from authors private personal contacts , and had no history or current indication of psychiatric or school problems according to parent information . typ consisted of 41 males and 36 females with a mean age of 9.3 years ( sd = 3.2 ) . sample characteristics are summarized in table 1 . table 1sample characteristicsautism spectrum disorders ( asd ) clinical controls ( clin ) typical controls ( typ ) n14825577age , years : m ( sd ) 11.2 ( 4.1 ) 9.9 ( 3.7 ) 9.3 ( 3.2 ) sex : male / female121 / 27185 / 7041 / 36iq : m ( sd ) 88.95 ( 25.5 ) 98.5 ( 15.9 ) srs score : m ( sd ) 101.1 ( 31.8 ) 62.7 ( 30.9 ) 26.0 ( 13.6 ) ( boys ) 106.7 ( 33.9 ) 62.9 ( 27.3 ) 20.9 ( 9.6 ) ( girls ) scdc score : m ( sd ) 15.6 ( 5.8 ) 12.6 ( 6.7 ) 5.9 ( 4.6 ) ( boys ) 15.3 ( 4.1 ) 11.4 ( 6.7 ) 5.1 ( 3.0 ) ( girls ) asd clin typ ( p .0001 ) , girls = boys ( p .26 ) sample characteristics asd clin typ ( p consistent with the english original , the german version of the srs ( blte and poustka 2008 ) has demonstrated a single factor structure and good to excellent psychometric properties ( blte et al . however , mean srs total scores for typically developed girls and boys as well as values for asd were lower in the german sample , while scores for conduct disorder ( cd ) and adhd / cd combined were higher . the scdc was translated into german , independently retranslated into english , adjusted by a native english speaking clinician and tested in practice for understandability before using it in this study . in order to establish the convergent validity of the srs and scdc , the german adaptations of gold standard asd instruments , namely the adi - r and the ados , as well as the social communication questionnaire ( scq ) were also assessed in the asd sample . comparable to the originals , all have demonstrated good to excellent psychometric properties ( poustka et al .1996 ; blte and poustka 2004 ; blte et al . 2006 , 2008a ) . the srs , scdc and scq were either send out for completion by parents as a part of pre - appointment assessment or completed during a clinical visit of their child . in most cases , completion of the srs , scdc and scq preceded the adi - r and ados or other in depths clinical examinations . in clin the srs and scdcsrs and scdc data in typ were obtained at personal contacts of the authors with the parents or by teachers handing - out and re - collecting the questionnaires . iq was assessed in the asd and clin participants using either wechsler intelligence batteries or the raven s matrices , which mostly result in qualitatively comparable scores in higher functioning asd ( iq 85 ) and clin ( blte et al . 2009 ) .16.0 was used for data analysis . partial correlation ( controlled for iq and age ) was computed in asd to determine convergent validity ( correlation with measures aiming to assess similar constructs ) of the srs and the scdc with the algorithm domain scores of the adi - r ( deficits in social interaction , deficits in communication , stereotypic behaviors ; reflecting behavior at age 4 to 5 years or lifetime ) and ados ( deficits in social interaction , deficits in communication ; reflecting current behavior ) as well as the total score of the scq ( reflecting behavior at age 4 to 5 years and lifetime ) . here , to avoid underestimation of true associations , correlations were corrected for direct range restrictions applying the case ii formula by thorndike ( 1949 ) , because adi - r , ados and scq are categorical scales , not intended to generate variability . the formula uses ( a ) the correlation of the restricted sample , ( b ) the standard deviation of the independent variable in the restricted sample and ( c ) in the unrestricted sample to provide an estimate of the correlation in the population . diagnostic validity ( value for diagnostic classification ) , was analyzed by roc - analyses for asd vs. typ and asd vs. clin , as well as for asd vs. each of the largest clin subgroups , adhd , and anxiety disorders . area under the curve ( auc ) with p - values , sensitivities and specificities for recommended srs and scdc cut - offs were calculated . group and sex differences on the srs and scdc were examined using ancovas and post - hoc tukey tests . internal consistencies ( cronbach s alpha ) for the srs and scdc are were computed within asd , clin , and typ . the correlation between srs and scdc scores was r = .49 ( p .01 ) . correlations of the srs and the scdc with age in asd , clin and typ ( r = .01 to .08 ) and iq in asd and clin ( r = .10 to -.21 ) were low ( n.s ) . alpha for the srs was .96 in asd , .94 in clin and .91 in typ . for the scdc alphas were .78 in asd , .91 in clin and .80 in typ . in asd , mean srs score was 102.2 ( sd = 32.1 ) [ girls : 106.7 ( sd = 33.9 ) ; boys : 101.1 ( sd = 31.8 ) ] and mean scdc score was 15.6 ( sd = 5.6 ) [ girls : 15.3 ( sd = 4.1 ) ; boys : 15.6 ( sd = 5.8 ) ] . mean srs scores were 105.4 ( sd = 30.1 ) in autism , 100.1 ( sd = 32.0 ) in asperger s syndrome and 88.5 ( sd = 35.1 ) in atypical autism / pdd - nos . mean scdc scores were 15.9 ( sd = 4.9 ) in autism , 15.5 ( sd = 5.2 ) in asperger s syndrome and 14.9 ( sd = 6.0 ) in atypical autism / pdd - nos . in clin , mean srs score was 62.8 ( sd = 29.9 ) [ girls : 62.9 ( sd = 27.3 ) ; boys : 62.7 ( sd = 30.9 ) ] and mean scdc score was 12.2 ( sd = 6.7 ) [ girls : 11.4 ( sd = 6.7 ) ; boys : 12.6 ( sd = 6.7 ) ] . within clin , mean score for adhd was 54.7 ( sd = 27.8 ) on the srs and 12.1 ( sd = 6.6 ) on the scdc . mean score for anxiety disorders was 61.5 ( sd = 26.4 ) on the srs and 10.5 ( sd = 7.3 ) on the scdc . mean score for typ on the srs was 26.0 ( sd = 13.6 ) for boys and 20.9 ( sd = 9.6 ) for girls . for the scdc , figures in typ were 5.9 ( sd = 4.6 ) for boys and 5.1 ( sd = 3.0 ) for girls . the roc analysis for the srs yielded an auc of .98 ( p .0001 ) for asd vs. typ ( fig . 1 ) . a total srs score of 75 had a sensitivity of .80 and a specificity of 1.0 for asd , a score of 85 had a sensitivity of .74 and a specificity of 1.0 for asdroc analysis for asd vs. clin yielded an auc of .81 ( p .0001 ) ( fig . 2 ) . a total srs score of 75 had a sensitivity of .80 and a specificity of .69 for asd , a score of 85 had a sensitivity of .74 and a specificity of .79 for asd . roc analysis for asd vs. adhd showed an auc of .86 ( p .0001 ) , with sensitivities of .80 / .74 and specificities of .78 / .83 for asd using srs cut - offs . roc analysis for asd vs. anxiety disorders showed an auc of .82 ( p .0001 ) , with sensitivities of .81 / .65 and specificities of .74 / .80 asd using the recommended srs cut - offs.fig .1 receiver operating characteristics ( roc ) curve of the social responsiveness scale ( srs ) for the condition autism spectrum disorder ( n = 148 ) versus typical development ( n = 77 ) ; area under the curve = .98 ( p .0001 ) fig .2 receiver operating characteristics ( roc ) curve of the social responsiveness scale ( srs ) for the condition autism spectrum disorder ( n = 148 ) versus clinical controls ( n = 255 ) ; area under the curve = .81 ( p .0001 ) receiver operating characteristics ( roc ) curve of the social responsiveness scale ( srs ) for the condition autism spectrum disorder ( n = 148 ) versus typical development ( n = 77 ) ; area under the curve = .98 ( p .0001 ) receiver operating characteristics ( roc ) curve of the social responsiveness scale ( srs ) for the condition autism spectrum disorder ( n = 148 ) versus clinical controls ( n = 255 ) ; area under the curve = .81 ( p .0001 ) the roc analysis for the scdc yielded an auc of .93 ( p .0001 ) for asd vs. typ ( fig . 3 ) . a total scdc score of 8 had a sensitivity of .90 and a specificity of .75 for asd , a score of 9 had a sensitivity of .87 and a specificity of .82 for asd . roc analysis for asd vs. clin yielded an auc of .64 ( p .0001 ) ( fig . 4 ) . a total scdc score of 8 had a sensitivity of .89 and a specificity of .28 for asd , a score of 9roc analysis for asd vs. adhd showed an auc of .65 ( p .0001 ) , with sensitivities of .90 / .85 and specificities of .29 / .43 for asd using scdc cut - offs . roc analysis for asd vs. anxiety disorders showed an auc of .68 ( p .0001 ) , with sensitivities of .90 / .87 and specificities of .34 / .44 for asd using the recommended scdc cut - offs.fig .3 receiver operating characteristics ( roc ) curve of the social and communication disorders checklist ( scdc ) for the condition autism spectrum disorder ( n = 148 ) versus typical development ( n = 77 ) ; area under the curve = .93 ( p .0001 ) fig .4 receiver operating characteristics ( roc ) curve of the social and communication disorders checklist ( scdc ) for the condition autism spectrum disorder ( n = 148 ) versus clinical controls ( n = 255 ) ; area under the curve = .64 ( p .0001 ) receiver operating characteristics ( roc ) curve of the social and communication disorders checklist ( scdc ) for the condition autism spectrum disorder ( n = 148 ) versus typical development ( n = 77 ) ; area under the curve = .93 ( p .0001 ) receiver operating characteristics ( roc ) curve of the social and communication disorders checklist ( scdc ) for the condition autism spectrum disorder ( n = 148 ) versus clinical controls ( n = 255 ) ; area under the curve = .64 ( p .0001 ) srs and scdc total scores differed highly significant between groups ( f2 / 46954.9 , p .0001 , eta .19 ) , with asd scoring higher than clin , and clin scoring higher than typ ( p .0001 ) in both scales . there were no effects of sex ( f1 / 4691.2 , p .26 , eta .0001 ) or an interaction of sex by group ( f2 / 469 .79 , p .45 , eta .003 ) . convergent validity findings for asd are shown in table 2 . the srs total score correlated r = .45 with the adi - r social domain , r = .39 with the adi - r communication domain and r = .31 with the adi - r domain for stereotypies ( p .01 ) . the same correlations for the scdc were r = .35 , r = .23 and r = .24 ( p .05 ) . correlations of the srs with the ados social domain were r = .35 and for the communication domain r = .32 ( p .01 ) . the same correlations for the scdc were r = .18 and r = .17 ( n.s . ) . convergent validity with the scq was r = .50 for the srs and r = .36 for the scdc ( p .01 ) . table 2convergent validities of the social responsiveness scale ( srs ) and the social and communication disorders checklist ( scdc ) in the autism spectrum disorders samplesrsscdcadi - r social domain .45.35 communication domain .39.23 stereotypies domain .31.24 ados social domain .35.18 communication domain .32.17 scq total score .50.36 p .01 , p .05 , n.s . convergent validities of the social responsiveness scale ( srs ) and the social and communication disorders checklist ( scdc ) in the autism spectrum disordersthis study compared the diagnostic validity for asd of two questionnaires aiming at assessing autistic traits : the srs and scdc . in the same sample , both scales yielded moderate to good sensitivities to screen for asd , with sensitivity values being higher for the scdc than for the srs for both typical and clinical controls . srs specificities for asd were higher than its sensitivities and considerably higher than scdc specificities . therefore , it appears that the scdc generates somewhat less asd false negatives than the srs , while the srs generates far less asd false positives . the scdc might therefore be viewed superior to the srs to generate suspicion of asd . thus , the scdc seems indeed sensitive to clinically relevant social and communication problems , but less specific to social and communication problems being characteristic of asd . the srs appears more balanced regarding its sensitivity and specificity for social and communication deficits typical for asd . the latter is endorsed by higher convergent validities of the srs than the scdc with gold standard clinical asd instruments , namely the adi - r , ados and scq , although correlations of the srs with the adi - r were lower than reported previously ( constantino et al .2004 ) . while sensitivities and specificities found here for the srs , as well as sensitivities for the scdc , are consistent with previous reports ( constantino and todd 2003 ; constantino et al . 20042009 ) , the specificities identified in this study for scdc are substantially lower than reported before . the reason might be that compared to earlier research the current study included a more heterogeneous and possibly more severely affected child and adolescent psychiatric clinical control sample . this might have resulted in higher scdc scores even in non - asd clinical controls , and in lower discriminative power of the scdc to differentiate these subjects from autistic individuals . the scdc authors themselves found markedly lower scdc specificity in a clinical study ( .69 ) ( skuse et al .2005 ) compared to a population - based study ( .91 ) ( skuse et al . clinical controls had been identified on the basis of being provided with special education , whereas in the clinical study diagnoses where explicit expert classifications . in their clinical study , the current study examined n = 255 psychiatric controls , in the majority exhibiting childhood psychopathologies known to be associated with high scores on social problem scales ( adhd , conduct disorder ) . score 195 ) , while the scdc only contains 12 items scored 0 to 2 ( max . therefore , the srs s a priori likelihood being able to adequately reflect an empirical relative in a numerical relative and hence detect individual differences is considerably higher than for the scdc . it is also technically immanent that there is a higher probability for better indices of reliability and validity , due to the higher number of items ( scale lengths ) . the scdc s brevity is a definite quality in terms of time and cost economy as well as expected compliance in parents and teachers to fill - out the questionnaire . however , there is not much space to clarify the psychological construct and test s intention . thus , there is a certain risk that the core sensitivity of the scdc is for more general social - communicative psychopathology .2009 ) reported a robust correlation of the scdc with the total score of the strengths and difficulties questionnaire ( sdq ) , a scale to screen for general psychopathology . additionally , the correlations of the scdc with the sdq scales for peer problems and prosocial behavior were lower than for hyperactivity . such problems arise from the fact that items for population - based scales often have to be worded as concise , simple and understandable as possible to fit all children and adolescents , but particularly typical developed children . the consequence is that they can be perceived in different ways and clinically might seem to fit very different disorders . clinical asd scales , such as the scq , allow a more specific and complex questioning , but they are of limited value to tap autism outside a clinical setting . similar to the scdc , the srs has shown high correlations to general psychopathology as measured by the child behavior checklist ( cbcl ) . however , it has been demonstrated that the srs also covers deficits in reciprocal social behavior and communication , which are substantially independent from other domains of child psychopathology , and highest srs correlations with a cbcl - subscale have consistently emerged for social problems ( constantino et al . a limitation of the present study is that the typ group is likely not to be representative of the general population , owing to the methods used to recruit this group . the current study would also have benefited from general psychopathology assessment and iq testing in typ . future studies should also carefully collect data on functional behavior level , which is a pivotal parameter for the designation of any mental disorder . in summary , owing to its brevity and good sensitivity the scdc might be suited better than the srs to screen for unspecific social and communicative deficits including autistic problems in the general population . the srs shows better specificity and construct validity for asd and seems therefore more valuable than the scdc for specific asd screening and in clinical settings . the latter is supported by the fact that the srs also offers population - based norms and standard errors of measurement for individual diagnostic assessments and follow - ups . as research on the phenomenology , epidemiology , neurobiology and genetics of autism as a disorder and a traitcontinue , both the srs and scdc should be viewed as scales in progress , prone to revisions .\noutput:\n" }, { "from": "agent", "value": "research indicates that autism is the extreme end of a continuously distributed trait . the social responsiveness scale ( srs ) and the social and communication disorders checklist ( scdc ) aim to assess autistic traits . the objective of this study was to compare their clinical validity . the srs showed sensitivities of .74 to .80 and specificities of .69 to 1.00 for autism . sensitivities were .85 to .90 and specificities .28 to .82 for the scdc . correlations with the adi - r , ados and scq were higher for the srs than for the scdc . the scdc seems superior to the srs to screen for unspecific social and communicative deficits including autism . the srs appears more suitable than the scdc in clinical settings and for specific autism screening ." } ]

[ { "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: papillary thyroid carcinoma ( ptc ) is the most common form of thyroid gland carcinoma which accounts for 1 % of all human malignant tumors . it was reported that the prognosis of ptc is excellent with a 10 - year survival exceeding 90 % . however , approximately 2050 % of ptc patients were found to have central lymph node metastases ( clnms ) . there is still a recurrence rate of 825 % after primary surgical treatment , and many scholars hold the opinions that routine central lymph node dissection ( clnd ) may decrease the rate of recurrence . this retrospective study was approved by department of breast - thyroid - vascular surgery at shanghai general hospital of nanjing medical university . from january 2013 to february 2015 , a total of 543 ptc patients who underwent radical operation of thyroid were enrolled in this study . total thyroidectomy and ipsilateral clnd might be performed for unilateral ptc patients who met one or more of the following conditions according to the nccn guidelines : radiation history , known distance metastases , extrathyroidal extension , and tumor size 4 cm in diameter . other unilateral ptc patients underwent unilateral and contralateral partial resection of thyroid gland or hemithyroidectomy with ipsilateral clnd . its upper bound was to the thyroid cartilage , and its lower bound was to thymus , and both sides were to the inner side of the central bilateral carotid sheath , including lymph nodes prior to cricothyroid membrane , lymph nodes surrounding thyroid , and paratracheal and prelaryngeal lymph node . intraoperative frozen section ( fs ) is a popular method for doctors to determine surgical extent in surgery . it was reported that the accuracy rates for fs in thyroid surgery was 97.8 % . andpreoperative ultrasonography , preoperative thyroid function tests , and postoperative pathologic examination were performed in all patients . based on the nccn guidelines for ptc , all of the 543 patients with clinically lymph node that was negative according to the preoperative physical examination and ultrasound underwent the surgical treatment .79 patients underwent unilateral and contralateral partial resection of thyroid gland with bilateral / unilateral clnd . six patients performed secondary surgical intervention because they were diagnosed as having benign lesions according to intraoperative fs , but the postoperative pathological diagnosis of the first surgery was ptc . in this study , the preoperative fine needle aspiration was carried out on 337 patients , and 322 cases were diagnosed with ptc . from a total of 543 patients ,537 cases were diagnosed with ptc by the intraoperative fs , and 6 cases were diagnosed postoperatively after the histopathological examination of thyroid gland . lt4 was given to all the patients as an alternative treatment besides the inhibition of tsh therapy . chi - square test or fisher 's exact test was used to analyze the significance of differences of the categorical variables and logistic regression was performed to analyze the multiplicity . all the data were processed using statistic package for social science ( spss 22.0 ) and p 0.05 was considered as a statistically significant difference .410 ( 75.5 % ) females and 133 ( 24.5 % ) males were included in this study . the average age of all the patients was 47 years , ranging from 16 to 78 years . the mean size of the tumors was 0.950.73 cm ( ranging from 0.1 cm to 5 cm ) .132 ( 24.3 % ) patients had bilateral lesions , 180 ( 33.1 % ) cases had multifocal lesions , 517 ( 95.2 % ) cases had tumor 0.25 cm in size , and 36 ( 6.6 % ) cases had ptc with extrathyroidal extension . 190 ( 35.0 % ) cases had ptc with hashimoto 's thyroiditis ( ht ) and 78 ( 14.4 % ) cases had abnormal thyroid function . we analyzed these factors including the gender , age , bilaterality , multifocality , tumor size , extrathyroidal extension , ht , and abnormal thyroid function to find the risk factors for ptc patients with clnms . in the univariate analysis , male gender ( p = 0.012 ) , age 45 years ( p 0.001 ) , bilateral lesions ( p = 0.042 ) , tumor size 0.25 cm ( p = 0.003 ) , and external invasion ( p = 0.003 ) were significantly associated with clnms . multifocal lesions , ht , and abnormal thyroid function were not significant for clnms ( table 1 ) . the multivariate analysis ( table 2 ) showed that the male gender ( p 0.001 , or : 1.984 ) , age 45 years ( p 0.001 , or : 1.934 ) , bilateral lesions ( p = 0.006 , or : 1.585 ) , tumor size 0.25 cm ( p = 0.001 , or : 7.579 ) , and external invasion ( p = 0.002 , or : 2.370 ) were independent risk factors for clnms in ptc patients . we grouped all the ptc patients into five groups based on the size of tumors : 0.25 cm , 0.25 and 0.5 cm , 0.5 and 0.75 cm , 0.75 and 1 cm , 1 cm . and the rate of clnms increased as the tumor size increased . there were significant differences for these groups ( p 0.001 ) ( table 3 ) . among the 543 cn0table 4 showed that no clnms were found in all 7 males and 21 patients with unilateral lesion in cn0 ptc patients with tumor size 0.25 cm . the percentages of patients with clnms whose conditions met only zero , one , two , three , four , or all of the five risk factors were 0 ( 0/6 ) , 22.5 % ( 39/173 ) , 43.7 % ( 104/238 ) , 46.3 % ( 50/108 ) , 77.8 % ( 14/18 ) , and 0 . among the 6 patients without these five risk factors , 0 % ( 0/6 ) papillary thyroid carcinoma which is considered to have relatively good prognosis still has at least 10 % risk of recurrence in long - term follow - up . a large study found that the mortality of ptc patients with clnms was much higher than that of patients without clnms . pellegriti et al . kept the option that the development of distant metastases was associated with the presence of lymph node metastases at presentation . more and more scholars recommend that clnd is necessary for ptc patients because of the greater rate of clnms . wang et al . reported that 44.1 % cn0 ptc patients were found to have clnms . considered that clnms were associated with local recurrence and distant metastasis but did not impair survival . therefore , it is essential to investigate the indications for cn0 ptc patients . obviously , male gender , age 45 years old , bilaterality , tumor size 0.25 cm , and external invasion were independent risk factors for cn0 ptc patients . several studies demonstrated that male ptc patients have higher significant risk of clnms . however , jiang et al . found that the gender had no association with clnms . in our study , the proportion of the male gender with clnms was significantly higher than that of female gender ( 47.4 % versus 35.1 % , p 0.001 , or : 1.984 ) . age is often used to judge the stage of the differentiated thyroid carcinoma . we found that younger ptc patients ( 45 years old ) were at higher risk of occurring clnms ( 46.6 % versus 23.9 % , p 0.001 , or : 1.934 ) . analyzed 916 cn0 ptc patients and had similar finding that the rate of clnms was considerably higher in the cases of younger patients ( p 0.001 ; or : 2.357 ) . jiang et al . believed that age 35 years was a good prognostic factor for ptc patients with clnms . in agreement with pellegriti et al . and vasileiadis et al . , we found that bilateral lesions made a meaningful difference with a higher percentage to develop clnms from the unilaterality ( 45.5 % versus 35.7 % , p = 0.006 , or : 1.585 ) . chang et al . and zhang et al . have demonstrated that larger tumor size ( 0.5 cm , 0.6 cm ) was associated with clnms . in our study , ptc patients with tumor size 0.25 cm were more prone to develop clnms ( 39.7 % versus 7.7 % , p = 0.001 , or : 7.579 ) . many studies have demonstrated that external invasion is a risk factor of clnms for ptc patients . our study showed that nearly 61.1 % percent of ptc patients with external invasion was found to have clnms and the multivariate analysis indicated that external invasion was an independent risk factor for clnms ( 61.1 % versus 36.5 % , p = 0.002 , or : 2.370 ) . with the development of ultrasound , palpation , fine needle aspiration ( fna ) , and intraoperative frozen section , increasing small malignant thyroid noduleswere checked out . before the dispute regarding the operation for ptc patients with tumor size 1 cm , studies shall need to advance . in this study , the rate of tumor size with clnms increased , obviously , with the increase of tumor size in a certain range ( 0.25 cm : 7.6 % , 0.25 and 0.5 cm : 22.7 % , 0.5 and 0.75 cm : 30.1 % , 0.75 and 1 cm : 45.5 % , 1 cm : 53.4 % ) .7.6 % of ptc patients with tumor size 0.25 cm were confirmed to have metastases in central lymph node , while about 39.7 % of ptc patients whose tumor size was 0.25 cm were confirmed to have clnms . the incidence of clnms in ptc patients with tumor size 0.25 and 0.5 cm was 22.7 % . andthe incidence of clnms in ptc patients with tumor size 0.5 cm was reported to be 20.626.2 % . therefore , we think that clnd should be performed in ptc patients with tumor size 0.25 cm . in this study , similar studies in cn0 ptc patients reported that the incidence of clnms was 35.043.6 % . the clinic risk factors for ptc patients with clnms were analyzed above , and we also evaluated the incidence of clnms with every conceivable combination to further analyze the indication of clnd . eliminating tumor size 0.25 cm , no clnms were found in male patients and patients with unilateral lesion . in the present studies , clnd is necessary to be performed in the ptc patients because clnms are associated with a higher risk of recurrence . hence , clnd should be performed in the patients with risk factors , and we recommend that , in cn0 ptc patients with tumor size 0.25 cm , male patients and patients with unilateral lesion should be considered safe . in this study , some limitations should be considered . secondly , all patients are required to have long - term follow - up to analyze the significance of clnd for cn0 ptc patients . in summary , the incidence of ptc patients with clnms is 38.1 % in our study . male gender , age 45 years , bilaterality , tumor size 0.25 cm , and external extension were considered as independent risk factors for ptc patients . on this account , we think precautionary clnd should be considered for cn0 ptc patients with risk factors . and we believe that , in cn0 ptc patients with tumor size 0.25 cm , male patients and patients with unilateral lesion could avoid clnd .\noutput:\n" }, { "from": "agent", "value": "background . papillary thyroid carcinoma ( ptc ) with central lymph node metastases ( clnms ) is common . the objective of this study was to investigate the incidence and risk factors of lymph node metastasis patients with ptc . patients and methods . between january 2013 and february 2015 , a retrospective study of 543 patients with ptc undergoing hemithyroidectomy or total thyroidectomy with routine central lymph node dissection ( clnd ) was analyzed . clinicopathologic risk factors for clnm were studied using univariate and multivariate analysis by spss 22.0 software . results . the incidence of clnms in ptc patients was 38.1 % ( 207/543 ) . in the multivariate analysis , male gender ( p < 0.001 , or : 1.984 ) , age < 45 years ( p < 0.001 , or : 1.934 ) , bilaterality ( p = 0.006 , or : 1.585 ) , tumor size 0.25 cm ( p = 0.001 , or : 7.655 ) , and external extension ( p = 0.001 , or : 7.579 ) were independent risk factors of clnms . furthermore , in ptc patients with tumor size < 0.25 cm , all 7 males and 21 patients with unilaterality were not found to have clnms . conclusions . clnms are prevalent in the ptc patients with the following risk factors : male gender , age < 45 years , bilaterality , tumor size 0.25 cm , and external extension . ptc patients with tumor size < 0.25 cm , male patients , and patients with unilateral lesion could be considered safe from clnms ." } ]

[ { "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: diffusion - weighted imaging ( dwi ) is a recent , noninvasive magnetic resonance imaging ( mri ) technique that allows the user to measure the diffusion of water molecules in a given direction . diffusion tensor imaging ( dti ) describes the diffusion measured with dwi as a second - order tensor . dwi works on the knowledge that the diffusion of water molecules within biological tissue is influenced by the microscopic structure of the tissue . the theory of brownian motion dictates that molecules within a uniform volume of water will diffuse randomly in all directions , that is , the diffusion is isotropic . however , in the presence of objects that hinder the diffusion of water in some specific directions , the diffusion will become anisotropic . in fibrous tissue , the diffusion of water will be large in the direction parallel to the fibers and small in perpendicular directions . therefore , dwi data is used to deduce and analyze the structure of fibrous tissue , such as the white matter of the brain , and muscular tissue in the heart . dwi data has been used during the planning stages of neurosurgery , and in the diagnosis and treatment of certain diseases , such as alzheimer 's disease , multiple sclerosis , and strokes . since the tissue of the white matter is macroscopically homogeneous , other imaging techniques , such as t2 - weighted mri , are unable to detect the structure of the underlying fibers , making dwi uniquely suitable for in vivo inspection of white matter . the process of using the measured diffusion to reconstruct the underlying fiber structure is called fiber tracking . this paper focuses on an approach in which fibers are constructed by finding geodesics on a riemannian manifold defined by the dti data . this technique , called geodesic ray - tracing , has several advantages over other ones , such as its relatively low sensitivity to measurement noise , and its ability to identify multiple solutions between two points , which makes it suitable for analysis of complex structures . our goal is to overcome this problem by mapping the geodesic ray - tracing algorithm onto the highly parallel architecture of a graphical processing unit ( gpu ) , using the cuda programming language . since fibers can be computed independently of each other , the geodesic ray - tracing algorithm can be meaningfully parallelized . as a result , the running time can be reduced by a factor of up to 40 , compared to a multithreaded cpu implementation . the paper describes the structure of the cuda implementation , as well as the relevant design considerations . in the next section , we discuss the background theory related to our method , including dti and the geodesic ray - tracing algorithm . next , we give an overview of past research related to the gpu - based acceleration of fiber tracking algorithms . in section 4 , the implementation of the geodesic ray - tracing algorithm on a gpu using cuda is discussed . next , we show benchmarking results and optimization strategies for the cuda implementation in section 5 , followed by a discussion of the results in section 6 , and a conclusion in section 7 . dti allows us to reconstruct the connectivity of the white matter , thus giving us greater insight into the structure of the brain . after performing dwi for multiple different directions , we can model the diffusion process using a second - order tensor d . d is a 33 positive - definite tensor , which can be visualized as an ellipsoid defined by its eigenvectors and eigenvalues , as shown in figure 1 . using the eigenvalues of a tensor , we can quantify its level of anisotropy using anisotropy measures . in areas with nearly isotropic diffusion , tensor ellipsoids will be nearly spherical , and anisotropy measure values will be low , while in areas with highly anisotropic diffusion ( due to the presence of fibers ) , ellipsoids will be sharp and elongated , and anisotropy values will be high . in anisotropic areas , the eigenvector corresponding to the largest eigenvalue ( the main eigenvector ) will indicate the direction of the fibrous structure . dti fiber tracking is the process of digitally reconstructing the pathways of fibers in fibrous tissue using the dti tensor data , with the aim of deducing the structure of the tissue . a common approach to fiber tracking is to track lines from one or more seed points , using a set of differential equations . the most straightforward fiber tracking algorithm ( generally called the streamline method ) uses the direction of the main eigenvector as the local orientation of the fibers . thus , a fiber in biological tissue may be reconstructed by integration of the main eigenvector , using an ordinary differential equation ( ode ) solver such as euler 's method . fiber tracking algorithms based on this approach have been shown to achieve acceptable results , but are limited in their accuracy by a high sensitivity to noise and to the partial volume effect . one possible solution to the limitations of classic streamline methods is to use a global minimization solution , for example , a front - propagation method . in such a method , a front is propagated from a seed point throughout the entire volume . the local propagation speed of the front depends on the characteristics of the dti image , and fibers are constructed by back - tracing through the characteristics of the front . a subset of these front - propagation methods use the theory of geodesics to find potential fiber connections . these algorithms generally compute the geodesics ( defined as the shortest path through a tensor - warped space ) by solving the stationary hamilton - jacobi ( hj ) equation . geodesic algorithms have been shown to produce good results and are generally more robust to noise than simple streamline methods . one disadvantage , however , is that they generally only find a single possible connection between target regions , which is often not the correct solution in very complex areas . furthermore , research has shown it is possible to have multiple fiber connections between regions of the white matter . the focus of this paper is a relatively new fiber tracking algorithm based on geodesics , as proposed by sepasian et al . the main advantages of this algorithm , compared to those discussed in the previous section , are the fact that it provides a multivalued solution ( i.e. , it allows us to find multiple geodesics between regions in the brain ) , and the fact that it is able to detect fibers in regions with low anisotropy ( e.g. , regions of the white matter with crossing fiber bundles ) . in figure 3 , we show that this algorithm is capable of detecting complex structural features , such as the divergence of the corpus callosum , which can not be captured using streamline - based methods . detailed validation of this algorithm is considered beyond the scope of this paper ; for an in - depth discussion on the validity and applicability of the algorithm , we refer the reader to the works by sepasian et al . this is a real , differentiable manifold , on which each tangent space is equipped with a so - called riemannian metric , which is a positive - definite tensor . roughly speaking , the elements of the metric tensor are an indication of the cost of ( or energy required for ) moving in a specific direction . for dti data , large values in the dti tensor correspond to small values in its inverse , indicating low diffusion costs , and vice versa . locally , a geodesic will tend to follow the direction with the lowest metric value , which is analogous to the direction with the highest diffusion . we define the riemannian metric as g = d , where d is the diffusion tensor . in the algorithm discussed in this paper , the trajectory of a fiberthe odes used to compute the trajectory of the fiber are derived from the theory of geodesics in a riemannian manifold , as shown below . let x ( ) be a smooth , differentiable curve through a volume described by parameter = [ 0 , t ] , with derivative vector x ( ) . we define the riemannian length of x ( ) as follows : ( 1 ) l ( x ) = 0txtgxd . the geodesic is the line that minimizes the geodesic length of ( 1 ) . we can use the euler - lagrange equations to translate this function to a set of odes , as described in detail by jost . let x and x be the first and second derivatives with regard to , respectively , of the geodesic for dimension = ( 1 , 2 , 3 ) . the odes that allow us to compute the geodesics are given by the following equation : ( 2 ) x + = 13 = 13xx = 0 , where are the so - called christoffel symbols , defined as follows : ( 3 ) == 1312 [ g ( xg + xgxg ) ] . here , gij represents element ( i , j ) of the inverse diffusion tensor , while g represents an element of the original diffusion tensor . we note that , in order to compute all christoffel symbols , we need to compute the derivatives of the inverse dti tensor in all three dimensions . given an initial position and an initial direction , we can construct a path through the 3d dti image , using the second - order runge - kutta ode solver . the initial position is usually specified by the user , who is interested in a particular area of the tissue ( in our case , the white matter ) . for the initial direction , we can use a large number of directions per seed points ( distributed either uniformly on a sphere , or around the main eigenvector ) , and see which of the resulting fibers intersect some user - specified target region . doing so increases our chances of finding all valid connections between the seed point ( s ) and the target region ( s ) . this approach , which is referred to as the region - to - region connectivity approach , requires a suitable connectivity measure , which quantifies the strength of the connection between seed point and target region . in other words , this measure symbolizes the probability that a computed geodesic corresponds to an actual fibrous connection in the white matter . while this paper does not discuss the implementation of the region - to - region connectivity approach , we do note that in order to reliably find all geodesics between the seed point ( s ) and the target region , we need to compute a large amount of trajectories in all directions . this need for a large amount of fibers , in combination with the high computational complexity of the algorithm itself , motivates our decision to parallelize the geodesic ray - tracing algorithm . the possibility of using the gpu to accelerate fiber tracking algorithms ( using cuda or other languages ) has recently been explored in other literature . these implementations use either geometric shaders or fragment shaders to accelerate the streamline tracking algorithm . with the exception of mittmann et al . , who introduce a stochastic element , these papers all use the simple streamline method for fiber tracking , in which the main eigenvector of the dti tensor is used as the direction vector for the integration step . in addition to using algorithms with a lower computational complexity than the geodesic ray - tracing algorithm discussed in section 2.3 , these implementations differ from ours in the sense that they use gpu shaders to compute the fibers , while we use cuda , which offers higher flexibility and a more gentle learning curve than programmable gpu shaders . more recently , mittmann et al . introduced a gpu implementation of a simple streamline algorithm using cuda . compared to a multithreaded cpu implementation , this gpu implementation allows for a significantly higher frame rate , enabling real - time , interactive exploration of large groups of fibers . the speedup factor , based on the number of frames per second , is between 10 and 20 times . the paper 's main focus , however , is interactivity , and a technical discussion of the advantages and limitations of cuda in the context of fiber tracking algorithms is omitted . jeong et al . have developed a cuda implementation of a fiber tracking algorithm based on the hamilton - jacobi equation , which computes the fiber pathways by propagating a front throughout the entire volume . their solution parallelizes the propagation of the front by dividing the dti image into blocks of 43 voxels , after which the front is propagated through a number of such blocks in parallel . this approach has been shown to be 50 to 100 times faster than sequential implementations of similar algorithms on a cpu . however , as stated in section 2.3 , the hj algorithm on which they base their implementation is not able to find multiple connections between target regions . furthermore , the front - propagation algorithm used by jeong et al . requires a fundamentally different parallelization approach from our ray - tracing method . we therefore conclude that our solution is the first cuda - aided acceleration of a fiber tracking algorithm of this complexity . as will be shown in the next sections , the complex nature of the algorithm introduces a number of challenges to the parallelization process . furthermore , the advantages of the geodesic ray - tracing algorithm , as discussed in section 2.3 , suggest that its implementation will also have practical applications . in section 2.3 , we introduced a system of odes which can be used to compute the trajectory of a fiber , given an initial position and direction . the basis of our algorithm is an ode solver which numerically solves ( 2 ) using a fixed integration step length . specifically , let xi be the coordinate of point i along the fiber for dimension , and let xi be the local direction of the fiber in this point . using euler as the ode solver , we can compute xi +1 and xi +1 ( i.e. , the position and direction at the next time step ) as follows : ( 4 ) xi +1 = xi + hxi , xi +1 = xih = 13 = 13xx . here , h is a fixed step size , and is the christoffel symbol as defined in ( 3 ) . in the implementation described below , we use a second - order runge - kutta ode solver instead of the euler solver , but the basic method of numerically solving the system of odes remains the same . when computing the christoffel symbols , the four required tensors ( inverse dti tensors and its three derivates ) are interpolated using trilinear interpolation . to summarize , a single integration step of the ode solver consists of the following actions . compute the inverse diffusion tensor and its derivative in all three dimensions for the eight voxels surrounding the current fiber point ( xi ) . compute all christoffel symbols . according to ( 2 ) and ( 3 ) , we require nine symbols per dimension , for a total of 27 symbols . however , using the symmetric qualities of the diffusion tensor ( and therefore , of its inverse and the derivates of its inverse ) , we can reduce this to 18 unique symbols . using the christoffel symbols , , the only stopping condition is the fiber leaving the volume of the dti image . while this increases the amount of memory required by the algorithm , it also significantly decreases the number of required computations per integration step . this pre - processing step has been implemented in cuda , but due to its trivial implementation and relatively low running time ( compared the that of steps 2 through 5 ) , we do not discuss it in detail , instead focusing on the actual tracking process . figure 4 summarizes the tracking process of steps 2 through 5 , assuming the four input tensor fields have been computed in a pre - processing step . the region - to - region connectivity approach outlined in section 2.3 presents us with one significant problem : it requires the computation of a large number of geodesics . in combination with the relatively complex odes presented in ( 2 ) ( compared to the odes used for simpler fiber tracking methods ) , this makes this approach computationally expensive . our aim is to overcome this hurdle by implementing the algorithm in cuda , of which we give a quick overview in this section . nvidia 's compute unified device architecture ( cuda ) is a way to facilitate general - purpose computing on graphics processing units ( gpgpu ) . modern gpus contain large number of generic processors in parallel , and cuda allows a programmer to utilize this large computational power for nongraphical purposes . in cuda , a kernel ( usually a small , simple function ) is executed in parallel by a large number of threads , each working on one part of the input data . in a typical execution pattern , the host pc first uploads the input data to the gpu , then launches a number of threads that execute the kernel . the resulting data is then either downloaded back to the host pc or drawn on the screen . a cuda - enabled gpu generally consists of the device memory , which is between 512 mb and 2 gb on most modern gpus , and a number of multiprocessors . each multiprocessor contains eight scalar processors ( in most current - generation gpus ; newer generations will have more scalar processors per multiprocessor ) ; a register file ; a shared memory block , which enables communication between the scalar processors ; and an instruction unit , which dispatches instructions to the processors . the type of parallelism in these multiprocessors is called single instruction , multiple threads ( simt ) , which differs from single instruction , multiple data ( simd ) in the sense that the threads have some level of independence . ideally , all active threads in a multiprocessor will execute the same instruction at the same time ; however , unlike simd , simt also allows for branching threads using if - statements . while this does allow the programmer to create more complex kernels , it also adds an overhead in terms of execution time , since the different branches must be executed sequentially . the two memory blocks local to each multiprocessor the register file and the shared memory both have low memory access latencies . however , the available space in these two memory blocks is limited , with typical values of 16 kb for the shared memory , and 16 or 32 kb for the register file . the device memory has far more storage space , but accessing this memory adds a latency of between 400 and 900 clock cycles . the device memory contains four different memory spaces : constant memory , a small , read - only block best used for constant values ; texture memory , a read - only space optimized for texture reads ; global memory , the main random - access memory space ; local memory , a per - thread extension of the register file . local memory is used when the register file of a multiprocessor can not contain all variables of a kernel . since access latencies to the device memory are very high , the use of large kernels is generally best avoided . as a general rule , communication between the device memory and the multiprocessors should be kept as low as possible . a second important guidelineis that the size of the kernels , in terms of the number of registers per thread and the amount of shared memory used per thread block , should be kept small . doing so will allow the gpu to run more threads in parallel , thus increasing the occupancy of the scalar processors ( i.e. , the percentage of time that each scalar processor is active ) . keeping in mind the advantages and limitations of cuda as discussed in section 4.2 , we can design a cuda implementation for the algorithm introduced in section 2.3 . as mentioned in step 3 of the algorithm as outlined in section 4.1 , we require the derivatives of the inverse of the dti tensor in all three dimensions . we intuitively see that computing these derivatives for each point along the fiber would be far too costly in terms of the number of instructions , as computing these derivates for all eight surrounding voxels ( using two - sided numerical derivation ) would require the inversion of 32 diffusion tensors . this gives us four input tensors per voxel : the diffusion tensor and the three derivatives of its inverse . with six unique elements per tensor andfour bytes per value , this gives us a memory requirement of 464 = 96 bytes per voxel . the algorithm also has the seed points as input , which contain the initial position and direction for each fiber . these seed points are determined by the user , for example , by specifying a region of interest in the image . the output of the algorithm consists of a number of fibers , each consisting of a list of 3d coordinates . in postprocessing steps , these fibers can be filtered through the target region ( s ) and sorted according to their connectivity measure value , but these steps are not part of the cuda implementation discussed herein . since cuda does not support dynamic memory allocation , we hard - coded a limit in the number of iteration steps for each fiber , and statically allocated an output array per fiber of corresponding size . we note here that the choice of this limit may impact performance : for high limits , more fibers will terminate prematurely ( due to leaving the volume ) , leading to lower occupancy in later stages of the algorithm , while for lower limits , the start - up overhead of the cuda algorithm may become relevant . we intuitively recognize two different approaches for parallelization of the geodesic ray - tracing algorithm : per - region parallelization and per - fiber parallelization . the per - region approach would entail loading a small region of the image into the shared memory of a multiprocessor , tracking a number of fibers through this region ( using one thread per fiber ) , and then loading the next region . while this approach would guarantee low memory bandwidth requirements between the multiprocessors and the device memory , it is impractical due to two reasons . first , it is impossible to guarantee that a region will contain a sufficient number of fibers to enable meaningful parallelization . second , due to the limited size of the shared memory , these regions would be very small ( no more than approximately 160 voxels per region ) , which would defeat the purpose of this approach . in other words , this approach requires some degree of spatial coherence between the fibers , and since we do not know their trajectories beforehand , ensuring this spatial coherence is highly impractical . we therefore use the per - fiber parallelization approach , in which each thread computes a single fiber . the main advantage of this approach is that it does not require any spatial coherence between the fibers to efficiently utilize the parallelism offered by the gpu . as long as we have a high number of seed points and initial directions , all scalar processors of the gpu will be able to run their own threads individual of the other threads , thus minimizing the need for elaborate synchronization between threads , and guaranteeing a stable computational throughput for all active processors . the main disadvantage of this approach is that it requires a higher memory throughput than the per - region approach , as it does not allow us to avoid redundant memory reads . the kernel that executes the fiber tracking process executes the following steps , as summarized in figure 4 : fetch the initial position and direction of the fiber . for the current fiber position , fetch the diffusion tensor and the derivatives of its inverse , using trilinear interpolation . using these four tensors , using the symbols and the current direction , compute the next position and direction of the fiber , using the odes of ( 2 ) with a second - order runge - kutta step . stop if the fiber has left the volume or the maximum number of steps has been reached . as noted in the previous section , the main disadvantage of the per - fiber parallelization approach is that it does not allow us to avoid redundant reads . we can partially solve this problem by storing the input images in texture memory , rather than in global memory . unlike global memory reads , texture memory reads are cached through a number of small caches . these caches can contain about 8 kb per multiprocessor , although the actual amount varies per gpu . while we argue that cached memory reads could reduce the required memory throughput , we note that the lack of spatial coherence between the fibers , coupled with the small cache sizes , will largely negate the positive effects of cached memory reads . a second , more important advantage of the texture memory is the built - in texture filtering functionality . when reading texture data from a position located between grid points , cuda will apply either nearest - neighbor or linear interpolation using dedicated texture filtering hardware . when storing the input data in the global memory , all interpolation must be done in - kernel , which increases both the number of instructions per integration step , and the amount of memory required by the kernels . by delegating the interpolation process to this dedicated hardware , we are able to reduce both the size and the computational complexity of the kernels . the size is especially important in this case , as smaller kernels allow for a higher degree of parallelism . while we expect the use of texture - filtering interpolation to be beneficial for the running time of our algorithm ( which we will demonstrate in the next section ) , we do identify one possible trade - off . one property of in - kernel interpolation is that the values of the eight surrounding voxels can be stored in either the local memory of the thread , or in the shared memory of the multiprocessor . doing so increases the size of the threads , but also allows them to reuse some of this data , thus reducing the memory throughput requirements . using texture - filtering interpolation , we can not store the surrounding voxel values , so we need to read them again in every integration step . thus , in - kernel interpolation may require a significantly lower memory throughput than texture - filtering interpolation , especially for small step sizes ( in which case it takes multiple steps for a fiber to cross a cell ) . for the experiments presented in this section , we used a synthetic data set of 10246464 voxels with 2048 predefined seed points . the seed points were distributed randomly to mimic the low spatial coherence of the fibers , and their initial directions were chosen in such a way that no thread would terminate prematurely due to its fiber leaving the volume ( i.e. , all fibers stay within the volume for the predefined maximum number of integration steps , running parallel to the long edge of the volume ) . while neither the shape and content of the volume nor the fact that no fibers leave the volume prematurely can be considered realisticall experiments were conducted on an nvidia gtx 260 , a mid - range model with 24 multiprocessors ( for a total of 192 scalar processors ) and 1 gigabyte of device memory . it should be noted that we only consider the actual fiber tracking process for our benchmarks . the data preparation stage ( which includes preprocessing and inverting the tensors , and computing the derivatives of the inverse tensors ) has also been implemented in cuda , but is considered outside of the scope of this paper due to its low complexity , trivial parallelization , and low running times compared to the tracking stage . on the gtx 260 , the data preparation stage requires roughly 50 milliseconds per million voxels , and only needs to be executed once per image . the overhead resulting from the communication between the cpu and gpu lies in the order of a few milliseconds . in section 4.4 , we stated that using the dedicated texture filtering hardware for the trilinear interpolation step of our algorithm would significantly reduce the size and complexity of our kernel , allowing for an increase in performance . we also identified a possible trade - off : for small step sizes , in - kernel interpolation might be faster than texture - filtering interpolation , as the former allows for data reuse , while the latter does not . we test this hypothesis by varying the step size between 0.05 ( i.e. , twenty steps per cell on average ) and 0.5 ( two steps ) . the measured running times for the two proposed interpolation methods are shown in figure 6 . from this , we can conclude that , while small step sizes do indeed reduce the running times for in - kernel interpolation , texture - filtering interpolation is still the faster option for typical step size values ( between 0.1 and 0.2 ) . the performance of cuda programs is usually limited either by the maximum memory throughput between the device memory and the multiprocessors , or by the maximum computational throughput of the scalar processors . to find out which of these two is the limiting factor for our algorithm , we first compute its performance in terms of memory throughput and computational throughput . when computing 2048 fibers , each executing 4096 integration steps , the algorithm takes approximately 165 milliseconds to complete . for each integration step , a single thread needs to read 8 voxels 4 tensors 6 unique tensor elements 4 bytes = 768 bytes , and it writes 12 bytes ( 3d coordinates of the new point ) . this gives us a total memory transfer of 780204840966.54 gb . dividing this by the running time , we get an effective memory throughput of approximately 3.97 gb / s , which is well below the maximum 111.9 gb / s of the gtx 260 . to compute the computation throughput in flops ( floating - point operations per second ) , we first decompile the cuda program using the decuda software . by inspecting the resulting codenote that this does not include any instructions needed for interpolation , since we are using the dedicated texture filtering hardware for this purpose . the algorithm performs a total of 25620484096 = 2,147,483,648 floating - point operations , giving us a computational throughput of roughly 13 gflops . again , this is well below the specified maximum of the gtx 260 , which is 715 gflops . since neither the memory throughput nor the computational throughput is close to the specified maximum , we need to determine the limiting factor in a different way . we first rule out the computational throughput as the limiting factor by replacing the current second - order runge - kutta ( rk2 ) ode solver by a simple euler solver . this does not reduce the amount of data transferred between device memory and multiprocessors , but it does reduce the number of floating - point operations per integration step from 256 to 195 . this , however , does not significantly impact the running time ( 165.133 ms for rk2 versus 165.347 ms for euler ) , indicating that the computational throughput ( i.e. , processor load ) is not a limiting factor in our case . to prove that the memory throughput is indeed the limiting factor , we need to reduce the amount of data read in each integration step , without changing the number of instructions . we do so by using the knowledge that the four input tensors of our synthetic data set share a number of duplicate values . by removing some ofthe redundant reads , we can reduce the memory requirements of each thread , without compromising the mathematical correctness of the algorithm . , we can conclude that the performance of our algorithm is limited by the memory throughput , despite the actual throughput being significantly lower than the theoretical maximum of the gtx 260 . possible explanations for this discrepancy are listed in section 6 . to evaluate the performance of our cuda implementation , we compare its running times to those of a c++ implementation of the same algorithm running on a modern cpu . in order to fully explore the performance gain , we use four different cuda - supported gpus : the quadro fx 770 m , the geforce 8800 gt , the geforce gtx 260 , and the geforce gtx 470 . it should be noted that our cuda implementation was developed for the gtx 260 and was not modified for execution on the other gpus . in particular , this means that we did not optimize our algorithm to make use of the improved cuda features of the more recent gtx 470 gpu . the cpu running the c++ implementation is an intel core i5750 , which has four cores , with a clock speed of 2.67 ghz . in terms of bothdate of release and price segment , the i5750 ( released in fall 2009 ) is closest to the gtx 470 ( spring 2010 ) ; at the time of writing , both are considered mid - to high - range consumer products of the previous generation . for this benchmark , we use a brain dti image with dimensions of 12812830 voxels . seed points are placed in a small , two - dimensional region of 22 by 4 voxels , located in a part of the corpus callosum . an approximation of the seed region , as well as the resulting fibers , is shown in figure 8 . this test thus closely mimics a real - life application of the ray - tracing algorithm , as demonstrated in figure 8 . our c++ implementation of the algorithm features support for multiple threads of execution ( multithreading ) , which allows it to utilize the parallelism offered by the cpu 's four cores . we assign s / n seed points to each cpu thread , thus having each thread compute s / n fibers . we have measured the running times of this cpu implementation for several different values of n , and with s set to 4096 points . , we can conclude that parallelizing the cpu implementation ( using essentially the same fiber - level parallelism as for our gpu implementation ) can reduce the running times by a factor of roughly 4.5 . the fact that the performance increases for n larger than the number of cores can be attributed to the fact that a cpu core can switch to a different thread when the active thread is waiting for data from the main memory of the pc . from figure 7 , we can also conclude that 64 threads is the best configuration for this algorithm and this cpu . we performed the same benchmarking experiment on the four cuda - enabled gpus , and we compared the running times to those of the best cpu configuration . the results for this test are shown in table 3 . from the results , we can conclude that our cuda implementation significantly reduces the running time of the ray - tracing algorithm . even on a mid - range gpu for laptops like the fx 770 m , the running timeis reduced by a factor of roughly two times . using a high - end , recent gpu like the gtx 470 , we are even able to achieve a speed - up factor of 40 times , which greatly increases the applicability of the algorithm . the differences in speed - up factors between the gpus can be explained in part by the differences in bandwidth which was identified as the limiting factor in section 5.2 and by the number of processors . in previous sections , we described a cuda implementation of a geodesic fiber tracking method . this cuda program uses the knowledge that fibers can be computed independently of one another to parallelize these computations , thus reducing running times by a factor of up to 40 times , compared to multithreaded cpu implementations of the same algorithm . while the algorithm does allow for meaningful parallelization , we do note two problems that make full exploitation of the parallelism offered by the gpu challenging . the algorithm requires a large amount of internal storage ; between the four input tensors , the christoffel symbol , and the position and direction of the fiber , even the most efficient version of our implementation still required 43 registers per thread , while typical values for cuda algorithms are between 8 and 32 . more importantly , the algorithm requires a large amount of data transfer , and as a result , the memory throughput becomes its limiting factor . this problem is far from trivial to solve , and while some options do exist , they all have their own downsides . ( 1 ) reducing the number of bits per input value would lower the required memory throughput , but comes at the cost of reduced accuracy . ( 2 ) allowing fibers to reuse the input data used for interpolation greatly increases the size of the kernel and does not work with texture - filtering interpolation , the use of which has been shown to be very beneficial in our case . ( 3 ) sharing the input data between threads in one multiprocessor requires some sort of spatial coherence between the fibers , which is extremely difficult to guarantee . reducing the number of bits per input value would lower the required memory throughput , but comes at the cost of reduced accuracy . allowing fibers to reuse the input data used for interpolationgreatly increases the size of the kernel and does not work with texture - filtering interpolation , the use of which has been shown to be very beneficial in our case . sharing the input data between threads in one multiprocessor requires some sort of spatial coherence between the fibers , which is extremely difficult to guarantee . as noted , the memory throughput between the device memory and the multiprocessors is the limiting factor for our performance . however , as noted in section 5.2 , the actual throughput is well below the theoretical maximum of the device . most random - access memory ( ram ) configurations experience a certain overhead when subsequent reads access different parts of a data range . since a low spatial locality of the seed points will lead to such scattered access pattern , this overhead may explain our relatively low memory throughput . according to cuda documentation , texture readshave been optimized for 2d spatial locality , presumably using a space - filling curve . the throughput of the texture fetching and filtering units may become a limiting factor when large numbers of voxels are involved . the documentation of the gtx 260 states that it should be able to process 36.9 billion texels per second , while our implementation only loads 39 billion bytes ( of multibyte texels ) per second . however , this figure is based on 2d bilinear interpolation , while we use 3d trilinear interpolation . we expect the first point to be the main contributing factor , though we have not conducted experiments to either prove or disprove this hypothesis . the gpu - based acceleration of the geodesic ray - tracing algorithm for dti is a useful technique , but its implementation poses several challenges . part of the problem in accelerating numerical integration algorithms such as the one under discussion in the paper is that it almost inevitably introduces unpredictable memory access patterns , while existing cuda algorithms generally use access patterns that are more regular and predictable , and thus easier to optimize . this is a fundamental problem without an easy solution , and one that is not restricted to cuda - enabled gpus , but applies to other parallel platforms as well . still , despite our implementation achieving suboptimal performance , we do believe that its significant speed - up factor of up to 40 times , coupled with the low cost and high availability of cuda - enabled hardware , makes it a practical solution to the computational complexity of the geodesic ray - tracing algorithm for fiber tracking , and a good starting point for future acceleration of similar algorithms . in this paper , we discussed the gpu - based acceleration of a geodesic ray - tracing algorithm for fiber tracking for dti . one of the advantages of this algorithm is its ability to find multivalued solutions , that is , multiple possible connections between regions of the white matter . however , the high computational complexity of the algorithm , combined with the fact that we need to compute a large amount of trajectories if we want to find the right connection , makes it slow compared to similar algorithms . to overcome this problem , we accelerated the algorithm by implementing a highly parallel version on a gpu , using nvidia 's cuda platform . we showed that despite the large kernel size and high memory requirements of this gpu implementation , we were able to speed up the algorithm by a factor of up to 40 . this significant reduction in running time using cheap and widely available hardware greatly increases the applicability of the algorithm . aside from further optimization of our current gpu implementation , with the aim of further reducing its running time , we identify two possible extensions of the work presented in this paper . at the moment , the computed fibers are downloaded back to the cpu , where they are postprocessed and subsequently visualized . a more direct approach would be to directly visualize the fibers computed by our algorithm , using the available rendering features of the gpu . if we can also implement the necessary postprocessing steps in cuda , we can significantly reduce the amount of memory that needs to be transferred between the cpu and the gpu , thus accelerating the complete fiber tracking pipeline . the region - to - region connectivity method is a valuable application of the geodesic ray - tracing algorithm . this method introduces three extra steps : ( 1 ) computing a suitable connectivity measure , either while tracking the fibers or during a post - processing step , ( 2 ) filtering the computed fibers through a target region , and ( 3 ) sorting the remaining fibers according to their connectivity measure , showing only those fibers with high cm values . these three steps have currently been implemented on a cpu , but implementing them on a gpu can reduce the overall processing time of the fiber tracking pipeline , as noted above . the dti model is limited in its accuracy by its inability to model crossing fibers . high angular resolution diffusion imaging ( hardi ) aims to overcome this limitation by measuring and modeling the diffusion in more directions . an extension of the algorithm presented in section 2.3 which uses hardi data rather than dti data would theoretically be more accurate , particularly in complex areas of the white matter . such an extension may , for example , be realized by using the finsler metric tensor ( which depends both on the position and local orientation of the fiber ) , rather than the riemannian metric tensor . while the extended algorithm for hardi would likely be more complex in terms of both number of computations and amount of required memory , a cuda - based acceleration using the parallelization principles presented in this paper will still be significantly faster than any cpu implementation . we note that , while these extensions would be valuable additions , the current cuda implementation already provides a practical and scalable solution for the acceleration of geodesic ray - tracing .\noutput:\n" }, { "from": "agent", "value": "diffusion tensor imaging ( dti ) allows to noninvasively measure the diffusion of water in fibrous tissue . by reconstructing the fibers from dti data using a fiber - tracking algorithm , we can deduce the structure of the tissue . in this paper , we outline an approach to accelerating such a fiber - tracking algorithm using a graphics processing unit ( gpu ) . this algorithm , which is based on the calculation of geodesics , has shown promising results for both synthetic and real data , but is limited in its applicability by its high computational requirements . we present a solution which uses the parallelism offered by modern gpus , in combination with the cuda platform by nvidia , to significantly reduce the execution time of the fiber - tracking algorithm . compared to a multithreaded cpu implementation of the same algorithm , our gpu mapping achieves a speedup factor of up to 40 times ." } ]

[ { "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: foot complications are a major cause of admissions in diabetic patients , and comprise a disproportionately high number of hospital days because of multiple surgical procedures and prolonged length of stay in hospital . foot disorders such as ulceration , infection and gangrene are the most common , complex and costly sequelae of diabetes mellitus . the optimal therapy for diabetic foot ulcers remains ill - defined . saline - moistened gauze has been the standard method ; however , it has been difficult to continuously maintain a moist wound environment with these dressings . this has led to the development of various hydrocolloid wound gels , which provided more consistent moisture retention . refinements in topical ointments have resulted in the addition of various pharmacological agents including growth factors and enzymatic debridement compounds . hyperbaric oxygen therapy and culture skin substitutes are other wound therapies that have been advocated . all these therapies are associated with significant expense and are being utilized in some situations without sufficient scientific evidence demonstrating their efficacy . therefore , the search for an efficacious , convenient and cost - effective therapy continues . negative pressure wound therapy ( npwt ) is a newer noninvasive adjunctive therapy system that uses controlled negative pressure using vacuum - assisted closure device ( vac ) to help promote wound healing by removing fluid from open wounds through a sealed dressing and tubing which is connected to a collection container . the use of sub - atmospheric pressure dressings , available commercially as a vac device , has been shown to be an effective way to accelerate healing of various wounds . till today , very limited data is available on the role of negative pressure dressing in healing of diabetic foot ulcers . therefore , we endeavor to put forward a study to evaluate the role of negative pressure dressing in healing of diabetic foot ulcers using vac device . the present study was done on 30 patients at dayanand medical college and hospital , ludhiana . control group ( b ) : received twice daily dressing changes with saline - moistened gauze . age group 20 - 75 years.ulcer area ranging between 50 cm and 200 cm.diagnosis of diabetes mellitus made by american diabetes association criteria . age 20 years or 75 years.an obvious septicemia.osteomyelitis.wounds resulting from venous insufficiency.malignant disease in a wound.patients being treated with corticosteroids , immunosuppressive drugs or chemotherapy.any other serious pre - existing cardiovascular , pulmonary and immunological disease . wounds of the subjects included in the study underwent initial sharp debridement to remove necrotic tissue and slough as far as possible . after the debridement , foam - based dressing was done over the wounds of the study group under all aseptic conditions . an evacuation tube embedded in the foam was connected to a fluid collection canister contained within a portable vacuum / suction machine [ figures 1 and 2 ] . subatmospheric ( negative ) pressure was applied within a range of 50 mmhg to 125 mmhg intermittently three times a day . weekly cultures were taken from the floor of the ulcers to assess for the bacterial flora . standard antibiotic regimes were administered to all the patients which consisted broad spectrum antibiotics initially and later according to the culture sensitivity report . ulcers were treated until the wound got closed surgically or spontaneously , or until completion of the 56 - days ( 8 weeks ) assessment whichever was earlier . showing application of negative pressure wound therapy showing machine used to create negative pressure complete healing was defined as 100 % wound closure with re - epithelialization or scab with no wound drainage present and no dressing required . at the end of the study period patients were categorized as : complete responders : complete healing of lower limb ulcers.partial responders : 50 % or greater reduction in product of the two longest perpendicular diameters from baseline.noncomplete responders : less than 50 % reduction in the product of the two longest perpendicular diameters from baseline.nonresponders : no reduction in ulcer or increase in ulcer area over base line . partial responders : 50 % or greater reduction in product of the two longest perpendicular diameters from baseline . noncomplete responders : less than 50 % reduction in the product of the two longest perpendicular diameters from baseline . the observations were noted and all results were tabulated and analyzed by using student t - test for age , fasting blood sugar and percentage change in wound size from 1st to 8th week . the appearance of granulation tissue and the primary study end point were tested for significance by applying test . the analysis for time status of woundage group 20 - 75 years.ulcer area ranging between 50 cm and 200 cm.diagnosis of diabetes mellitus made by american diabetes association criteria . age 20 years or 75 years.an obvious septicemia.osteomyelitis.wounds resulting from venous insufficiency.malignant disease in a wound.patients being treated with corticosteroids , immunosuppressive drugs or chemotherapy.any other serious pre - existing cardiovascular , pulmonary and immunological disease . patients being treated with corticosteroids , immunosuppressive drugs or chemotherapy . any other serious pre - existing cardiovascular , pulmonary and immunological disease . wounds of the subjects included in the study underwent initial sharp debridement to remove necrotic tissue and slough as far as possible . after the debridement , foam - based dressing was done over the wounds of the study group under all aseptic conditions . an evacuation tube embedded in the foam was connected to a fluid collection canister contained within a portable vacuum / suction machine [ figures 1 and 2 ] . subatmospheric ( negative ) pressure was applied within a range of 50 mmhg to 125 mmhg intermittently three times a day . weekly cultures were taken from the floor of the ulcers to assess for the bacterial flora . standard antibiotic regimes were administered to all the patients which consisted broad spectrum antibiotics initially and later according to the culture sensitivity report . ulcers were treated until the wound got closed surgically or spontaneously , or until completion of the 56 - days ( 8 weeks ) assessment whichever was earlier . showing application of negative pressure wound therapy showing machine used to create negative pressure complete healing was defined as 100 % wound closure with re - epithelialization or scab with no wound drainage present and no dressing required . at the end of the study period patients were categorized as : complete responders : complete healing of lower limb ulcers.partial responders : 50 % or greater reduction in product of the two longest perpendicular diameters from baseline.noncomplete responders : less than 50 % reduction in the product of the two longest perpendicular diameters from baseline.nonresponders : no reduction in ulcer or increase in ulcer area over base line . partial responders : 50 % or greater reduction in product of the two longest perpendicular diameters from baseline . noncomplete responders : less than 50 % reduction in the product of the two longest perpendicular diameters from baseline . the observations were noted and all results were tabulated and analyzed by using student t - test for age , fasting blood sugar and percentage change in wound size from 1st to 8th week . the appearance of granulation tissue and the primary study end point were tested for significance by applying test . the present study was conducted in a total of 30 patients aged between 20 and 75 years of age , of either sex , having ulcer area ranging between 50 and 200 cm and fulfilling the diagnostic criteria of diabetes mellitus made by american diabetes association . the mean age of patients in group a was 61.337.63 years and in group b was 55.4011.54 years . the age distribution was comparable and statistically insignificant in both the groups ( p 0.10 ) . in group a , 80 % of the patients were males whereas 20 % were females while in group b 86.67 % of the patients were males and 13.33 % were females . at first weekit was observed that all the patients in group a and b had discharge from the wound . the discharge kept on decreasing over the period of observation in both the groups ; however , group a subjects had faster rate of disappearance of discharge . wound discharge was present in only 13.33 % of patients in 7th and 8th week in group a as compared to 33.33 % and 26.67 % in group b. from the study it was observed that during the first week granulation tissue was absent in 4 patients ( 26.67 % ) in group a and 10 patients ( 66.67 % ) in group b. it was seen that granulation tissue appeared at 2nd week in three out of four patients ( 75 % ) and 4th week in the remaining 1 ( 25 % ) patient in group a ( plate 4 ) . the appearance of granulation tissue in patients of group b was at 2nd , 4th and 5th week in three ( 30 % ) , 3 ( 30 % ) and two ( 20 % ) patients , respectively . it was also noted that in two ( 20 % ) patients granulation tissue remained absent even at the end of observation period . this suggested early appearance of granulation tissue in patients of group a which was also found to be statistically significant the wound size showed no change in 1 ( 6.67 % ) patient of group a as compared to 3 ( 20 % ) patients of group b. it was also observed that 2 ( 13.33 % ) patients of group b showed increase in wound size . the percentage decrease in the wound size was more in patients of group a as compared to group b. the mean decrease in the wound size in patients of group a was -16.1413.04 cm and that of group b was -5.9814.41 cm . we observed that patients of group a showed rapid clearance of bacterial load as compared to group b. this was suggested by 40 % of the cultures in group a having no growth by 3rd week as compared to 20 % in group b. staphylococcus aureus was the found to be most prominent in patients of group a whereas cultures from group b mostly showed mixed growth and acinetobacter . although statistically the time status of wound closure was comparable in both the groups ( p 0.10 ) , it was seen that the patients in group a showed faster healing as compared to the patients of group b. this was suggested by wounds of 9 ( 5 + 1 + 3 ) ( 60 % ) patients of group a getting closed by the end of 4th week as compared to only 3 ( 0 + 2 + 1 ) ( 20 % ) patients of group b. the patients who underwent below knee amputation were excluded from this analysis . both the groups had received similar treatment for the closure of wound , the most common mode of wound closure being stsg . although statistically the primary study endpoint was comparable in both the groups ( p 0.10 ) , group a promised better outcome ( 80 % complete responders ) as compared to group b ( 60 % complete responders ) . the mean age of patients in group a was 61.337.63 years and in group b was 55.4011.54 years . the age distribution was comparable and statistically insignificant in both the groups ( p 0.10 ) . in groupa , 80 % of the patients were males whereas 20 % were females while in group b 86.67 % of the patients were males and 13.33 % were females . at first week it was observed that all the patients in group a and b had discharge from the wound . the discharge kept on decreasing over the period of observation in both the groups ; however , group a subjects had faster rate of disappearance of discharge . wound discharge was present in only 13.33 % of patients in 7th and 8th week in group a as compared to 33.33 % and 26.67 % in group b.from the study it was observed that during the first week granulation tissue was absent in 4 patients ( 26.67 % ) in group a and 10 patients ( 66.67 % ) in group b. it was seen that granulation tissue appeared at 2nd week in three out of four patients ( 75 % ) and 4th week in the remaining 1 ( 25 % ) patient in group a ( plate 4 ) . the appearance of granulation tissue in patients of group b was at 2nd , 4th and 5th week in three ( 30 % ) , 3 ( 30 % ) and two ( 20 % ) patients , respectively . it was also noted that in two ( 20 % ) patients granulation tissue remained absent even at the end of observation period . this suggested early appearance of granulation tissue in patients of group a which was also found to be statistically significantthe wound size showed no change in 1 ( 6.67 % ) patient of group a as compared to 3 ( 20 % ) patients of group b. it was also observed that 2 ( 13.33 % ) patients of group b showed increase in wound size . the percentage decrease in the wound size was more in patients of group a as compared to group b. the mean decrease in the wound size in patients of group a was -16.1413.04 cm and that of group b was -5.9814.41 cm . we observed that patients of group a showed rapid clearance of bacterial load as compared to group b. this was suggested by 40 % of the cultures in group a having no growth by 3rd week as compared to 20 % in group b. staphylococcus aureus was the found to be most prominent in patients of group a whereas cultures from group b mostly showed mixed growth and acinetobacter . although statistically the time status of wound closure was comparable in both the groups ( p 0.10 ) , it was seen that the patients in group a showed faster healing as compared to the patients of group b. this was suggested by wounds of 9 ( 5 + 1 + 3 ) ( 60 % ) patients of group a getting closed by the end of 4th week as compared to only 3 ( 0 + 2 + 1 ) ( 20 % ) patients of group b. the patients who underwent below knee amputation were excluded from this analysis . both the groups had received similar treatment for the closure of wound , the most common mode of wound closure being stsg . although statistically the primary study endpoint was comparable in both the groups ( p 0.10 ) , group a promised better outcome ( 80 % complete responders ) as compared to group b ( 60 % complete responders ) . the role of negative pressure dressing in healing of diabetic foot ulcers has been proposed as a novel method of manipulating the chronic wound environment in a way that it reduces bacterial burden and chronic interstitial wound fluid , increases vascularity and cytokine expression and to an extent mechanically exploiting the viscoelasticity of peri wound tissues . vac is generally well - tolerated and , with few contraindications or complications , is fast becoming a mainstay of current wound care . hence we planned to use npwt for the treatment and fast healing of diabetic foot ulcers . the demographical profile was statistically studied and found comparable with no significant difference between the groups . the mean age of patients in study group was 61.337.63 years and in control group was 55.4011.54 years which was comparable to the multicenter randomized controlled trial enrolling 342 patients done by blume et al . , who had a mean age of 58 years . the sex distribution was also similar to the above quoted study that had 79 % males . we observed that there was a decreasing trend in the presence of wound discharge in both the groups . however , it was noted that the rate of disappearance of wound discharge was faster in the study group as compared to the control . only 13.33 % of patients in study group had discharge at the end of 7th and 8th week as compared to 33.33 % and 26.67 % of patients in control group , respectively . this could be attributed to the faster rate of wound closure in the study group . in a similar study conducted by tamhankar et al . , in four patients with mesh - related infection after abdominal wall hernia repair which were treated by npwd therapy , it was seen that npwd therapy allows salvage of infected exposed mesh by clearing the purulent discharge promoting granulation tissue formation . application of negative pressure over wound bed allows the arterioles to dilate , so increasing the effectiveness of local circulation , promoting angiogenesis , which assists in the proliferation of granulation tissue . we have also found that the patients on npwd therapy had earlier appearance of granulation tissue . of all the patients who initially did not have granulation tissue , 75 % of those in the study group promised its appearance by the end of 2nd week as compared to 30 % in the control group and this was also found to be statistically significant ( p 0.05 ) . shrestha et al . , in their prospective study of nine patients of renal transplantation who had developed wound infections following rt , observed progressive reduction in the size of wound and development of healthy granulation tissue in all the cases . we found a statistically significant difference in the percentage change in the wound size between both the groups ( p 0.05 ) . the mean decrease in the wound size was more in the study group ( -16.1413.04 cm ) as compared to the control group ( -5.9814.41 cm ) . , who had observed average decrease of 28.4 % ( 24.3 ) in wound size in the vac group as compared to 9.5 % ( 16.9 ) average increase in wound size in control group . mark eginton et al . , had also observed that the wound volume and depth decreased significantly in vac dressings as compared to moist gauze dressings ( 59 % vs. 0 % and 49 % vs. 8 % , respectively ) . we observed that patients of study group showed rapid clearance of bacterial load as compared to control group . this was suggested by 40 % of the cultures in study group having no growth by 3 week as compared to 20 % in control group . the decrease in the bacterial load could have been attributed to the antibiotic regimes administered during the study . however , s. aureus was the found to be most prominent in study group whereas cultures from control group mostly showed mixed growth and acinetobacter . , who had observed that nonfermentative gram - negative bacilli showed a significant decrease in vacuum - assisted closure - treated wounds , whereas s. aureus showed a significant increase in vac - treated wounds . although statistically the time status of wound closure was comparable in both the groups ( p 0.10 ) , it was seen that the study group showed faster rate of wound closure as compared to control group . mccallon et al . , also observed satisfactory healing in vac group in 22.817.4 days , compared to 42.832.5 days in control group . the endpoint taken was a granulated wound or a wound ready for skin grafting or healing by secondary intention spontaneously whichever was earlier . both the groups had received similar treatment for the closure of wound , the most common mode of wound closure being stsg [ figures 3 and 4 ] . it was also observed that the failure rate was higher in patients of control group as compared to study group . , who had observed that npwt delivered by vac device was safe and effective treatment for complex diabetic foot wounds and could lead to higher proportion of healed wounds , faster healing rates and potentially fewer re - amputations than standard care . , have also reported overall progressively increasing wound debridementdepth and amputation rates in control groups ; however the same increasing trend didnot occur in the npwt group . diabetic ulcer treated with negative pressure wound therapy postoperative picture of the healed ulcer at the end of the study , although the primary endpoint was statistically comparable in both the groups ( p 0.10 ) , the study group promised a better outcome ( 80 % complete responders ) as compared to the control group ( 60 % complete responders ) [ table 1 ] . analyzing the results of our study , we opine that npwt has a definitive role in promotion of proliferation of granulation tissue , reduction in the wound size , rapid clearing of the wound discharge and bacterial load . our data demonstrates that negative pressure wound dressings decrease the wound size more effectively than saline gauze dressings over the first 4 weeks of therapy . it is suggested that npwt is a cost - effective , easy to use and patient - friendly method of treating diabetic foot ulcers which helps in early closure of wounds , preventing complications and hence promising a better outcome .\noutput:\n" }, { "from": "agent", "value": "introduction : foot disorders such as ulceration , infection and gangrene are the most common , complex and costly sequelae of diabetes mellitus . [ 13 ] even for the most superficial wounds , treatment is often difficult with poor healing responses and high rates of complications . the purpose of this study is to compare the rate of ulcer healing with the negative pressure dressing technique to conventional moist dressings in the treatment of diabetic foot ulcers.materials and methods : the study was conducted on 30 patients , which were divided into two groups . one group received negative pressure dressing while other group received conventional saline moistened gauze dressing . results were compared for rate of wound healing.results : there was a statistically significant difference in the rate of appearance of granulation tissue between the two groups ; with granulation tissue appearing earlier in the study group . the study group promised a better outcome ( 80 % complete responders ) as compared to the control group ( 60 % complete responders ) . conclusions : negative pressure wound therapy has a definitive role in healing of diabetic foot ulcers ." } ]

[ { "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 66 - year - old male patient arrived at the emergency room of kangwon national university hospital . he was rescued after being jammed between an excavator basket and a wall with some stacked material for 5 minutes . when the patient arrived , the vital signs were stable except the respiratory rate : blood pressure 121/71 mmhg , heart rate 90 beats per minute ( bpm ) , respiratory rate 30 breaths per minute , body temperature 36.9 c , and o2 saturation 94 % . the patient complained of severe pain on the whole left side of his body down to the waist and on the right chest wall . according to the plain radiography and the computed tomography performed in the emergency room , the patient had multiple rib fractures ( right , 7th and 8th ; left , 3rd to 12th ) , hemothorax on both sides ( left dominant ) , left scapular fracture , liver laceration , retro - peritoneal hematoma , and transverse process fracture of the thoracic and lumbar spine .1 ) . there was no special complication during the chest tube insertion , and the initial drainage was approximately 200 ml . there was bloody drainage during the chest tube insertion ; however , it became serous and the patient was transferred to the general ward on the next day . on the 4th post - trauma day , the patient complained of acute pain radiating in the left rear direction . about 400 ml of bloody drainage was found at the collecting bottle at the same time . when the patient complained of pain , he became drowsy as the blood pressure decreased to 70/50 mmhg ; however , the blood pressure became 100/70 mmhg after the infusion of 300 ml of isotonic saline . although the vital signs became stable with a heart rate of 71 beats per minute , respiratory rate of 24 breaths per minute , body temperature of 36.6 c , and o2 saturation of 99 % , bloody drainage of 100 ml or more hourly continued . a fluid resuscitation was done through the intravenous infusion of vitamin k1 and tranexamic acid . then , plain radiography and computed tomography were performed . from the results of plain radiography and chest computed tomography , we observed that the left hemothorax had increased . at the abdominal computed tomography , a portion of laceration at the liver improved ; however , it was decided to perform further exploration on the basis of the judgment that there was a possibility of major bleeding because the retro - peritoneal hematoma increased ( fig .2 ) . at 0:00 ( midnight ) on the 5th post - trauma day , the patient was transferred to an operating room . after the insertion of the right radial arterial line and the right internal jugular venous central line under general anesthesia , a drape was performed while the patient was in the right lateral decubitus position . when a thoracoscope was inserted after removing the existing chest tube , a huge amount of pleural hematoma was found . the 2nd port was made at the intersection of the 4th intercostal space and the anterior axillary line , and the 3rd port was made at the intersection of the 8th intercostal space and the posterior axillary line . the 3rd port was elongated by 8 cm for bleeding control and hematoma evacuation during one - lung ventilation . when the hematoma was removed through the 3rd port under the assistance of a thoracoscope , it was possible to find that a fractured fragment of the 7th rib remained in the intra - thoracic cavity after penetrating the parietal pleura with its sharp edge . it was believed that the bleeding originated from the damage of the aorta adventitia inflicted by the fractured rib segment . the sharpness of the rib was dulled by a bone file , and the aorta was repaired by a 2 - point interrupted suture using 4 - 0 prolene ( fig . other than this , there was no conspicuous damage at the pleura , diaphragm , lung , or parenchyma . chest tubes were inserted at the 1st and the 2nd ports , and the operation was completed with routine closure . the patient was checked for stable vital signs and chest tube drain status in the recovery room . around 4:30 a.m. , the patient was transferred to the general ward after extubation . multiple rib fracture is quite common in blunt chest trauma patients , and it is a major indicator suggesting solid - organ damage in the thoracic cavity or the peritoneal cavity . the aorta injury caused by the fractured rib fragment is a major sign of a blunt chest trauma patient ; however , the actual occurrence of such an injury is very rare . this case is judged as a case in which the aorta wall was damaged and the sharp margin of the fractured rib caused continuous irritation . according to oconor et al . , only 15 % of patients with aorta damage at the time of injury can survive until they arrive at a hospital . on the other hand , some delayed injuries caused by the fractured rib fragment are found after few days depending on the case . repaired the impinging of the descending thoracic aorta wall by the fractured 5th rib during a motor vehicle collision on the 3rd post - trauma day . kano et al . performed the replacement of an ascending thoracic aorta on the 11th post - trauma day ( although it was a psychological problem of the patient ) . there was also a case in which the patient returned home from the emergency room on the injury date because there were no symptoms other than rib fracture ; however , a delayed injury was found on the 4th post - trauma day when the patient visited the clinic due to pain . the mechanism of such delay is not clear ; however , it was suggested that the penetration of vessels had happened at the time of injury but was immediately clotted ; then , the clot was dissolved after a few days . alternatively , it was suggested that there could have been a new laceration caused by the physical movement of the patient . suggested a video - assisted resection of the fractured fragment to prevent the descending thoracic aorta injury . the patient in the case of this paper also had been generally stable and an acceptable quantity of chest tube drainage . he had been transferred to the general ward , but a bleeding complication occurred 2 days after his transfer to the general ward . therefore , even in the case of multiple fractures of the ribs without any external injury , a secondary delayed injury is possible depending on the part of fracture or the shape of the fractured plane . it should be remembered that the delayed injury can have fatal results depending on the damaged part .\noutput:\n" }, { "from": "agent", "value": "a 66 - year - old male patient arrived at the emergency room with a crush injury to his chest . multiple rib fractures , hemothorax on both sides , left scapular fracture , liver laceration , and retroperitoneal hematoma were found upon the radiologic examination . after closed thoracostomy , the patient had been initially admitted to the intensive care unit , but he was transferred to the general ward on the next day . on the 4th post - trauma day , the patient complained of severe pain and there was bloody drainage through the chest tube . this case is an exploration with the consideration of the possibility of major bleeding and the subsequent repair of the descending thoracic aorta . this case is regarded as a case in which the aorta wall was damaged as the sharp margin of the fractured ribs caused continuous irritation ." } ]

[ { "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: mutism is defined as an inability or unwillingness to speak , resulting in the absence or marked paucity of verbal output . it is a common presenting symptom seen in various disorders , including psychiatric as well as medical disorders . though , it often is the main focus of clinical attention , both for the patients and the treating physicians , it rarely presents as an isolated disability and often occurs in association with other disturbances in behavior , thought processes , affect , or level of consciousness . despite its association with a variety of neuropsychiatric disorders , mutism has received relatively little attention in the psychiatric literature . mutism occurs in a number of conditions , both functional and organic , and a proper diagnosis is important for the management . we hereby present three cases , who presented with mutism as the presenting symptom and the differential diagnosis and management issues related to these cases are discussed . the literature on mutism , including psychiatric , neurologic , toxic - metabolic , and drug - induced causes , is also selectively reviewed . a 26 - year - old unmarried male educated upto high school presented with abrupt onset progressive complaints of not speaking at all and decreased oral intake for the past 2 days . this was also associated with anxiety symptoms and hiccups that would occur in episodes for hours together . there was no other significant history suggestive of any organicity or psychosis , mood disorder , or any history of substance use . the patient had past history of an episode of acute stress reaction with mutism around 7 years back when he witnessed murder of his friend . also , he would have episodes of mutism in between lasting few hours to 1 day around three to four times in the last 3 years . positive findings in the mental status examination ( mse ) were that the patient was following commands given to him , he would respond in non - verbal manner or by writing , his eyes were open and movements were normal , he would cough and clear throat when asked to do so , would have hiccups ( around 20 times in interview of around 30 min ) , and his psychomotor activity ( pma ) was decreased . a diagnosis of dissociative ( conversion ) disorder - motor type was made and the patient was started on sertraline 50 mg per day along with chlorpromazine 100 mg per day . he was engaged in supportive psychotherapy and suggestion under pentothal was given and patient showed improvement in symptoms . he was subsequently discharged and had been maintaining well for the past 9 months of follow up . a 29 - year - old unmarried male was brought by police personnel with acute onset complaints of not speaking for 9 and a half months and history of irrelevant talks for 2 weeks associated with inability to speak in between . the patient had been under trial for the last 3 years for alleged charge of rape and murder . he would ask for his daily requirements by gestures / writing down . he would however maintain his routine daily chores and his vegetative functions were maintained . mse revealed a young male with little speech output and occasional irrelevant talks in between . on formal questioning , he reported sadness of mood but did not reply to other questions asked . a provisional diagnosis of depressive stupor versus dissociative stupor was kept and started on imipramine 50 - 125 mg per day along with risperidone 2 mg per day and lorazepam 1.5 mg per day in divided doses . lorazepam 4 mg was given on stat basis , with no improvement in his symptoms . he would speak out of the context and would start quarreling with jail inmates for no apparent reason . history from patient 's father was also taken and no pervious history of psychiatric illness or substance use other than tobacco was obtained . , it was observed that the patient had rashes present on dorsum of left hand . mse revealed that eye contact could be established but not maintained , decreased pma , his speech was decreased in output but was clear and comprehensible , his mood was sad but affect appeared euthymic with full range as shown by facial expressions . he would also on occasions give approximate answers to various questions asked ( e.g. date : said 10th instead of 9th , month : said december instead of november , ) . though , he would talk irrelevantly and would give wrong / approximate answers when talked too . information from collateral sources revealed that he was told to behave in this manner to plead his case . skin opinion was taken and a diagnosis of factitious dermatitis was made which further supported our diagnosis . a 35 - year - old married male was brought by police personnel with chief complaints of not speaking for the last 3 months . the patient had been under trial for the last 6 months for the alleged charge of setting fire in a cowshed . he would however ask for food by non - verbal communication / gestures and would perform all his daily chores normally as reported . history reviewed from wife and elder brother reveled history of 18 years history characterized by violent abusive behavior , wandering behavior , irritability , decreased sleep , restlessness , muttering to self , and at times reporting that other would harm him , associated with withdrawn behavior and socio - occupational dysfunction . on one occasion , he became mute also and did not talk for a period of around 4 months associated with sadness of mood and decreased interest in surroundings .6 months back , he had symptoms of muttering to self , would often roam about naked and get irritable on minor issues . mse revealed decreased pma , rapport not established , eye to eye contact could not be maintained , he was mute and would communicate nonverbally appropriately . a diagnosis of schizophrenia was entertained , and he was started on risperidone 6 mg per day and lorazepam 4 mg per day . a 26 - year - old unmarried male educated upto high school presented with abrupt onset progressive complaints of not speaking at all and decreased oral intake for the past 2 days . this was also associated with anxiety symptoms and hiccups that would occur in episodes for hours together . there was no other significant history suggestive of any organicity or psychosis , mood disorder , or any history of substance use . the patient had past history of an episode of acute stress reaction with mutism around 7 years back when he witnessed murder of his friend . also , he would have episodes of mutism in between lasting few hours to 1 day around three to four times in the last 3 years . positive findings in the mental status examination ( mse ) were that the patient was following commands given to him , he would respond in non - verbal manner or by writing , his eyes were open and movements were normal , he would cough and clear throat when asked to do so , would have hiccups ( around 20 times in interview of around 30 min ) , and his psychomotor activity ( pma ) was decreased . a diagnosis of dissociative ( conversion ) disorder - motor type was made and the patient was started on sertraline 50 mg per day along with chlorpromazine 100 mg per day . he was engaged in supportive psychotherapy and suggestion under pentothal was given and patient showed improvement in symptoms . he was subsequently discharged and had been maintaining well for the past 9 months of follow up . a 29 - year - old unmarried male was brought by police personnel with acute onset complaints of not speaking for 9 and a half months and history of irrelevant talks for 2 weeks associated with inability to speak in between . the patient had been under trial for the last 3 years for alleged charge of rape and murder . he would ask for his daily requirements by gestures / writing down . he would however maintain his routine daily chores and his vegetative functions were maintained . mse revealed a young male with little speech output and occasional irrelevant talks in between . on formal questioning , he reported sadness of mood but did not reply to other questions asked . a provisional diagnosis of depressive stupor versus dissociative stupor was kept and started on imipramine 50 - 125 mg per day along with risperidone 2 mg per day and lorazepam 1.5 mg per day in divided doses . lorazepam 4 mg was given on stat basis , with no improvement in his symptoms . cat scan head plain and contrast was also normal . on evaluation , he would follow simple commands and was able to write properly on persuasionhe would speak out of the context and would start quarreling with jail inmates for no apparent reason . history from patient 's father was also taken and no pervious history of psychiatric illness or substance use other than tobacco was obtained . , it was observed that the patient had rashes present on dorsum of left hand . mse revealed that eye contact could be established but not maintained , decreased pma , his speech was decreased in output but was clear and comprehensible , his mood was sad but affect appeared euthymic with full range as shown by facial expressions . he would also on occasions give approximate answers to various questions asked ( e.g. date : said 10th instead of 9th , month : said december instead of november , ) . though , he would talk irrelevantly and would give wrong / approximate answers when talked too . information from collateral sources revealed that he was told to behave in this manner to plead his case . skin opinion was taken and a diagnosis of factitious dermatitis was made which further supported our diagnosis . a 35 - year - old married male was brought by police personnel with chief complaints of not speaking for the last 3 months . the patient had been under trial for the last 6 months for the alleged charge of setting fire in a cowshed . he would however ask for food by non - verbal communication / gestures and would perform all his daily chores normally as reported . history reviewed from wife and elder brother reveled history of 18 years history characterized by violent abusive behavior , wandering behavior , irritability , decreased sleep , restlessness , muttering to self , and at times reporting that other would harm him , associated with withdrawn behavior and socio - occupational dysfunction . on one occasion , he became mute also and did not talk for a period of around 4 months associated with sadness of mood and decreased interest in surroundings .6 months back , he had symptoms of muttering to self , would often roam about naked and get irritable on minor issues . mse revealed decreased pma , rapport not established , eye to eye contact could not be maintained , he was mute and would communicate nonverbally appropriately . a diagnosis of schizophrenia was entertained , and he was started on risperidone 6 mg per day and lorazepam 4 mg per day . gradually the patient started showing improvement in symptoms . some of these besides mutism are as follows : aphonia : defined as the absence of definable laryngeal tone i.e. loss power of vocal chords to adduct.aphasia : this is a disorder of the content of speech , seen generally in organic conditions and occasionally as gargon aphasia in schizophreniadysarthria : a motor speech disorder characterized by difficulty in articulation of speech . any of the speech subsystems ( respiration , phonation , resonance , prosody , articulation and movements of jaw and tongue ) can be affected . aphonia : defined as the absence of definable laryngeal tone i.e. loss power of vocal chords to adduct . aphasia : this is a disorder of the content of speech , seen generally in organic conditions and occasionally as gargon aphasia in schizophrenia dysarthria : a motor speech disorder characterized by difficulty in articulation of speech . any of the speech subsystems ( respiration , phonation , resonance , prosody , articulation and movements of jaw and tongue ) can be affected . one important aspect in case b was that one should keep a possibility of malingering in such group of patients . though case c was also brought by police personnel and was under trial , he had past history of psychotic illness and also his crime was not that serious / grave as compared to case b. the points favoring our diagnosis in respective cases have been summarized in table 1 . besides psychiatric causes , there are other many causes of mutism . differential diagnosis of mutism regarding the frequency of various causes of mutism , besides case reports describing mute patients , there are few studies that report a series of patients presenting with mutism and describing various diagnostic categories . some of these studies are summarized in table 3 . one must perform a thorough physical and systemic examination to rule out organic causes for mutism . also , at times , observation for some time period may be warranted and should be done to reach final diagnosis . the utility of pentothal interview in some cases can be therapeutic also as in our case a. besides being a useful tool to differentiate organic from functional conditions , it can be used to give suggestions and thus help in the immediate management of dissociative disorders . to conclude , it is important to recognize the correct cause for proper management of mutism . though our cases had psychiatric cause for mutism , one must have a high index of suspicion and look for various other non - psychiatric causes for mutism , as this will decide the management and prognosis of the patient .\noutput:\n" }, { "from": "agent", "value": "mutism , defined as an inability or unwillingness to speak , resulting in an absence or marked paucity of verbal output , is a common clinical symptom seen in psychiatric as well as neurology outpatient department . it rarely presents as an isolated disability and often occurs in association with other disturbances in behavior , thought processes , affect , or level of consciousness . it is often a focus of clinical attention , both for the physician and the relatives . mutism occurs in a number of conditions , both functional and organic , and a proper diagnosis is important for the management . we hereby present three cases , who presented with mutism as the presenting symptom and the differential diagnosis and management issues related to these cases are discussed . the authors also selectively reviewed the literature on mutism , including psychiatric , neurologic , toxic - metabolic , and drug - induced causes ." } ]

[ { "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 patient with a solitary kidney , cysteine stones , and recurrent ureteral strictures underwent robot - assisted laparoscopic ureterectomy with ileal ureter formation . using a transperitoneal , 4 - port robotic approach , we removed the strictured ureter and created an ileal ureter . the ileal - pyelo and ileal - vesical anastomoses were performed using the robotic system . operative time was 9 hours with negligible blood loss , and the patient was discharged after 5 days . a cystogram at 10 days demonstrated patent anastomoses without extravasation . the patient continues to do well 48 months later . robot - assisted laparoscopic ileal ureter replacement is feasible with excellent long - term outcome . in patients who require complex ureteral reconstruction , one surgical option is the creation of an ileal ureter substitution , in which a segment of diseased ureter is removed and substituted with an isoperistaltic segment of ileum . in the appropriate patient , outcomes from this procedure are good . based on the long - term robotic and advanced laparoscopic experience at our institution in both urologic and colorectal surgery , we felt that use of the da vinci robotic system ( intuitive surgical , inc , sunnyvale , ca ) in this procedure may show benefit over the conventional laparoscopic or open technique . a search of the english language medical literature since 1950 did not find any reports of a robotic - assisted laparoscopic ileal ureter creation . here , we describe our technique and 48 - month follow - up . a 39 - year - old man with a solitary left kidney and cysteine stones had undergone 27 procedures including stents , ureteroscopies , and percutaneous nephrolithotomies over 18 months . he was on maximal medical therapy to prevent stone formation and was otherwise healthy with a serum creatinine of 1.3 mg / dl . the patient opted for a stone chute with ileal ureter replacement and chose the robotic - assisted approach after an extensive preoperative discussion of the surgical options , risks , and benefits . the patient was secured to the table in a 45 - degree , left - flank - up position . a hasson trocar was placed periumbilically and used for the robotic camera port , specimen removal , and the bowel anastomosis . three 8 - mm da vinci robotic trocars were placed ; ports 1 and 2 were used for the superior dissection and anastomosis while ports 1 and 3 were used for the inferior dissection and anastomosis ( figure 1 ) . port placement for robotic ileal ureter creation : a 12 - mm trocar was placed at the umbilicus with a hasson technique ( h ) . though significant peri - ureteral inflammation was present , the ureter was identified crossing the iliac vessels . after dissecting the ureter as far superiorly as possible , the robot was repositioned to perform the remaining superior dissection . a 5 - mm , 0 - degree lens was placed through port 2 , and the specimen was removed with a retrieval bag inserted through the hasson trocar . using standard laparoscopic instruments and a harmonic scalpel , an appropriate length of ileum was selected and transected using a laparoscopic stapling device . the mesentery was incised with a harmonic scalpel to allow adequate mobilization , and the ileum was swung laterally . two long 0 silk sutures were placed on each end of the bowel and clipped together to allow for easier identification for the bowel anastomosis . a dyed and undyed 20 monocryl on an sh needle ( ethicon , cincinnati , oh ) were tied together , and a running ileal - pyelo anastomosis was performed as described for urethral - vesical anastomosis after radical prostatectomy . after completing the posterior portion of the anastomosis , a 0.038 guidewire was passed through the ileal segment , over which an 8fr , 26 - cm double jj stent was passed . a cystotomy was performed in the superior - lateral bladder , and the mucosa was everted with interrupted 30 vicryl on an rb needle ( ethicon , cincinnati , oh ) . a jackson - pratt drain was placed near each anastomosis and brought out through ports 1 and 3 ( figure 2 ) . the 5 - mm , 0 - degree lens was again passed into port 2 and the previously placed ileal sutures were grasped through the hasson trocar . the bowel was brought out through this site , and bowel continuity was restored using stapling devices . two 10 - mm jackson - pratt drains are placed through the 8 - mm robotic ports 1 and 3 . he has not had any episodes of obstruction or renal colic and continues to do well 48 months after surgery . the primary indication for ileal ureter replacement is lengthy ureteral injury precluding simple reimplantation or a boari flap . the only alternatives for most patients requiring ileal ureter are a permanent nephrostomy tube , autotransplantation , and nephrectomy . given his solitary kidney and history of cysteine stones , laparoscopic techniques are being increasingly utilized for reconstructive procedures , such as radical prostatectomy and cystectomy . with experience , this technology is being applied to an expanding number of procedures . to our knowledge , robotic - assisted laparoscopic surgery offers several advantages over conventional laparoscopic surgery and is ideally suited for longer , complex reconstructive procedures . the robotic system offers a 3 - dimensional visualization with magnification for the surgeon , who can control camera position . the surgical instruments have increased degrees of freedom that facilitate the surgeon 's ability to perform complex maneuvers in a tight space without tremor or fatigue . these factors also decrease estimated blood loss , incision length , hospital length of stay , postoperative pain , and complication rate compared with open or laparoscopic surgery . although the large surgical field required for this procedure may seem to preclude the robotic approach , our technique demonstrates that the same ports can be used with changes in the robotic position to safely complete the surgery . this surgery was done prior to the introduction of the newer da vinci - s system , but either system could be used today . despite the advantages of robotics , the procedure was lengthy for several reasons . identification of the ureter was difficult due to severe retroperitoneal inflammation , which was not unexpected given the patient 's stone history and would have also complicated open surgery . lastly , surgeons and nurses were performing a new procedure , and the learning curve for laparoscopic procedures has been demonstrated to be significant . times for this case were similar to times for reported laparoscopic cases . with advancing robotic experience , some of these drawbacks can be expected to improve . the robot - assisted approach achieved the goals of traditional ileal ureter replacement , with maintenance of renal function and decreased stone formation , along with the usual benefits of a minimally invasive approach . because ileal ureter replacement is not a commonly performed procedure , it is unlikely a prospective comparison of the open and laparoscopic approach will be forthcoming . however , robot - assisted laparoscopic ileal ureter replacement appears to be a reasonable alternative to the open approach in the appropriate patient .\noutput:\n" }, { "from": "agent", "value": "background and objectives : a patient with a solitary kidney , cysteine stones , and recurrent ureteral strictures underwent robot - assisted laparoscopic ureterectomy with ileal ureter formation.methods : using a transperitoneal , 4 - port robotic approach , we removed the strictured ureter and created an ileal ureter . the ileal - pyelo and ileal - vesical anastomoses were performed using the robotic system . an extracorporeal bowel anastomosis was performed using stapling devices . operative time was 9 hours with negligible blood loss , and the patient was discharged after 5 days.results : a cystogram at 10 days demonstrated patent anastomoses without extravasation . the patient continues to do well 48 months later.conclusion : robot - assisted laparoscopic ileal ureter replacement is feasible with excellent long - term outcome ." } ]

[ { "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 first commercially successful electronic games ( eg ) were developed in the 1970s for entertainment and played in arcades , but they soon found their way into homes . almost simultaneously , health and mental health care providers started using computer and video games as part of therapy and others began developing egs for psychotherapy ( egp ) . recent estimates of the prevalence of computer and video game play in america range from 59 % to 63 % . current technology provides therapists with many new opportunities of intervening with our clients . with smart devices that are carried with us , using the internet , e - mail , and social media , we are able to gather information and disseminate information in ways that are less time - consuming , more interesting , and more readily available . examples include online forms , multimedia - presented decision trees , and long distance and / or virtual modes of communication . with advanced graphic and audio - visual performance , we are able to create virtual multisensory environments and audio - visual representation of our imaginary worlds . we review the use of eg in therapy , both electronic games for psychotherapy ( egp ) , also called serious games , developed primarily for therapeutic purposes , and electronic games for entertainment ( ege ) , also called off - the - shelf games , developed primarily for leisure purposes but used as a therapeutic tool . preliminary evidence supports the use of these methods , although more empirical work is needed . different approaches to game use and development can be undertaken to devise interventions , but egp and ege have potential to be applied to a wide range of health and mental health issues and settings . egp and ege have been used in health promotion and to improve physical and psychosocial functioning of patients . both types of games may be used to increase motivation , attention / engagement , knowledge , or physical efficacy ; to allow for physical activity , practice , or immediate feedback ; and to provide therapeutic imagery and emotional expression . comprehensive reviews indicate that egp have been used successfully to improve diet and physical activity in children , and ege for chemotherapy - related nausea , preoperative anxiety , fitness , physical therapy , and cognitive rehabilitation . describe the use of imagery in a first - person shooter game to allow patients with brain tumors to experience an imagined immune response to the tumors . in a randomized clinical trial ( rct ) , significant reductions were noted by the authors in depression , anxiety , anger , and disruptive behavior and increases in self - concept , with significant advantages of the intervention over the control in all areas . eg which have gross motor interfaces , such as the dance dance revolution dance mat , wiimote , and xbox kinect , provide physical challenge and a greater variety of physical operations when compared to games with conventional controllers . use of eg with gross motor interfaces has become one of the standard treatments in rehabilitation therapies to increase fitness , and sedentary games increase health - related knowledge and encourage pro - health behaviors . they have been used with demonstrated efficacy with children and adults , including elderly adults , in community , rehabilitation , and long - term care settings to increase overall physical fitness and physical and functional capabilities , reduce pain , and improve aspects of cognitive function , with diagnoses including traumatic brain injury , stroke , huntington s disease , and multiple sclerosis . although a number of investigations consist of pilot and feasibility studies , eg interventions have also been found to improve psychosocial functioning with medical populations , including reducing disfigurement - related distress , stress management , self - confidence , socialization , and quality of life . one pilot study failed to find these effects , however , and in one study , benefits of walking outside on well - being were superior to those associated with wii fit activity , although both groups improved . when using computerized cognitive behavior therapy ( ccbt ) with medical patients , some subjects found the intervention too impersonal . gamelab , a protocol for group therapy tailoring different aspects of game play to individual patient goals , is an example of using eg in a group format with children as treatment for acquired brain injury . although outcomes are encouraging using eg for cognitive stimulation and retraining , bisoglio et al . urge caution in concluding that cognition is meaningfully enhanced by various types of video games , because insufficient rigor has been applied to the investigations . in particular , bisoglio et al . assert that magnitudes of effect , expectancy effects , statistical interactions , and causal models should be examined . these concerns should be noted overall when evaluating the potential for eg in mental health and health care settings . most approaches to incorporating technology into the therapist s office use games or programs specifically designed to serve one or more therapeutic needs . computer - assisted cognitive behavior therapy ( ccbt ) includes computer - delivered information and interventions designed to implement established treatment models . in some cases , a specific game is developed or the interventions exhibit a game - like quality , but some elements may be less interactive , such as video demonstrations or relaxation inductions . for example , online self - help for anxiety disorders and handheld devices with diaries and prompting for individuals with obsessive compulsive disorder have been shown to facilitate cbt . in a systematic review of the use of technology in treating various anxiety disorders and depression , newman et al . concluded that computer - assisted treatment is effective overall and suggested that compliance might be maximized through more therapist exposure . mohr et al . remarked that the serious game movement is finding entertaining games being designed for therapeutic purposes , especially in the field of mental health ( egp ) . in a meta - review of the use of egp in treating depression , support was found for the use of egp , specifically moodgym , beating the blues , and colour your life , in enhancing cbt for depression . they also suggested egp could be cost - effective for therapists . in a similar review , moodgym was compared with two other games , beating the blues and good days ahead . good days ahead incorporates moderate therapist involvement , whereas the other two games had little to none , and had been compared to an established intervention , representing treatment as usual ( tau ) . these concerns about methodology are consistent with many in virtual reality ( vr ) and egp research , the absence of controlled clinical trials and non - significant findings in comparisons with more traditional techniques . used an rct approach to look at the effectiveness of sparx , an egp aimed at adolescents struggling with depression . sparx is a self - directed game in which clinicians provide initial contact and a phone follow up after a month , and clients are encouraged to contact the therapist if no improvement is noted . sparx was found to be effective but not superior to tau , as demonstrated by a decrease in depressive symptoms by 30 % on a children s depression rating scale . although perhaps not a true egp , a pilot study using a game - like presentation of ccbt for anxiety in children demonstrated changes in anxiety and remission of symptoms . in addition to anxiety and mood disorders , egp have been developed to enhance psycho - education , attitude change , relaxation , pain management , social skills , problem - solving skills , emotional modulation , self - control skills , motivation , and therapist - client interaction . of 11 egp , five were found to have been systematically assessed for effectiveness : re - mission , personal investigator , treasure hunt , play attention , and one unnamed game . the authors concluded that egp can be effective in increasing compliance , learning , and behavior and affective change . playmancer , an egp designed to help individuals with impulse - related disorders , was found to be well accepted by the users , seemed to be a good format in which to work on attitudes and emotions , and to make it feasible to apply techniques that tend to be difficult to apply such as controlled intensive exposure , immediate positive and negative reinforcing , complex biofeedback approach , and real time monitoring of physiological - emotional reactionsvirtual reality exposure therapy ( vret ) uses vr to expose clients to sources of stress and / or anxiety in a manner that is realistic enough to be visceral within the relative safety of the therapist s office . performed a quantitative meta - analysis comparing treatment of anxiety disorders using vret , traditional cbt , and traditional behavioral therapy ( bt ) . anxiety disorders examined included fear of flying , panic disorder / agoraphobia , social phobia , arachnophobia , acrophobia , and ptsd . the eight studies of comparing vret to waitlist control at post treatment demonstrated significant improvement for both cbt and bt , and medium to large effect sizes . in a systematic review of ten experimental studies using vret in combination with cbt in the treatment of ptsdmethodological concerns of the studies included small sample size and concerns about randomized treatment assignment . the authors suggested that vret might be of particular value with patients who respond better to the more immersive qualities of vr . in a more recent review of rcts to explore the effectiveness of vret in the treatment of ptsd , similar to other exposure - based interventions for ptsd despite low sample sizes and some challenges in standardization . although the authors suggest that vret might provide treatment in a less stigmatizing manner and a more controlled yet immersive delivery than traditional exposure , they suggested that this has not been verified experimentally . in a line of research exemplifying the diffuse boundary between egp and ege , some researchers are using off - the - shelf gaming hardware such as the xbox kinect to measure body movement in a virtual reality world , laptop computers with built - in webcams to assess facial movement and to explore expression of emotions within an egp as treatment for pain - related fear and disability in chronic pain , and facial recognition for children with autism spectrum disorder . avatars combined with voice alteration programs are being used to assist an individual suffering from auditory hallucinations by offering a visual and interactive perspective on their hallucinations . goh et al . recommended that game designers take into account relevant attributes of the client ; gender , age , developmental sophistication , ethnicity , and social economic status affect the individual 's response to the eg ; diagnoses and treatment objectives guide the style of the eg to be designed . for example , specific treatment objectives such as attention / focus may be aligned with a question - and - answer style game or likewise behavior modification and communication with simulation games and virtual reality . other examples of treatment objectives were control , reading / learning facts , sensory response , and social skills . these had been aligned to problem - solving , drill and practice , virtual reality , matching games , and virtual reality genres , respectively . other points of interest included degree of realism / level of immersion , management of goal direction , and motivation / challenge in game play . although the writers offered research examining these various characteristics of game design , they caution that much of the research has focused on games individually and have not addressed the overall constructs of game design as they apply to all games . the writers also point out that current research seems to focus less on the effectiveness of the games and more on playability and acceptability . although games and other electronic interventions may be designed for specific therapeutic purposes , games that are commercially available provide an incredible variety of interfaces and experiences that can be used as an adjunct to therapy . in fact , despite concerns about their use , ege have been shown to have a number of positive effects . the first study to discover the positive effects of playing ege included commercially produced games as a control for biofeedback . playing ege was as effective as biofeedback for reducing impulsivity , increasing personal influence , and improving one s self - concept . recent research and reviews of ege identified four general areas of beneficial effects : cognitive , motivational , emotional , and social . benefits included increased speed and accuracy of attention and visual special abilities improved learning and memory , executive functions , problem - solving skills and creativity . emotional benefits of using ege included improved mood or increases in positive emotion and adaptive regulation strategies for managing negative emotions like anger , anxiety , and sadness . finally , granic et al . noted the social benefits of ege included increased cooperation , support , and helping behaviors and civic engagement . ege has been investigated as an adjunct to individual and group psychotherapy , primarily in behavioral or talk therapy with children or adults with developmental delays . a variety of commercially produced games are appropriate to use , and granic et al . provided a helpful framework for describing games along two general dimensions : level of complexity and extent of social interaction . any game may be classified as more or less social and more or less complex along the two axes , in order to determine how they might facilitate particular therapeutic goals ( table 1 ) . table 1examples of games designated by level of complexity and social involvementdesignationgame stylegame examplescomplex and socialmultiplayer shooterhalo , call of dutymultiplayer action - adventuregrand theft auto , assassins creedon - line role playingrunescape , world of warcraftmultiplayer sandboxminecraft , half - life 2complex and nonsocialsolo role playingskyrim , final fantasysolo sportfifa , nhl14solo fightingstreet fighter , mortal kombatsimple and socialracingmario kart , need for speedrhythmrock band , guitar heropartywii party , mario partysimple and nonsocialpuzzlecandy crush , bejeweledplatformsuper mario bros . examples of games designated by level of complexity and social involvement adapted from granic et al . one of the earliest studies using ege in behavioral therapy taught social skills to three autistic boys aged 17 , 18 , and 20 . in a remarkably creative research design , the authors attempted to increase the frequency of appropriately initiated social interactions with neurotypical peers during classroom breaks in an outdoor courtyard of a public high school . the therapists trained the subjects to play the games and to approach and greet , offer to play , engage in reciprocal play , and signal the end of the interaction using three different items : a pack of gum , a sony walkman , and a handheld gaming device with pac - man or galaxian . the sony walkman was the most effective adjunct in terms of time spent interacting by the students with mental retardation , and the video game was the most effective item for the higher - functioning student . in a more recent case example , therapists used ege in individual behavior therapy with three boys and one girl between the ages of 9 and 12 diagnosed with autism , who had fine motor skills adequate to manipulate the game controller . the therapists role was to perform a set of interventions including video and in - vivo modeling . the treatment objective was to teach a common leisure skill using the play station 2 console to play guitar hero , a simple - social rhythm game . subjects time on task increased significantly after the training and were able to play the game with at least 70 % accuracy , indicating that training was effective in teaching young children with autism a generalized repertoire of an age - appropriate leisure skill , playing a video game ( p. 366 ) . one of the first reports of using ege as an adjunct in individual talk therapy was a case study of a 7 - year - old boy who presented with anxiety secondary to his parents divorce . in addition to traditional psychotherapeutic methods including giving advice , providing emotional support , and encouraging behavior change , allen utilized the experiences in the game and applied them to the patient s real - life problems ( p. 332 ) . treatment outcomes included self - confidence , a sense of mastery , more willingness to accept responsibility and less stigma about having been in therapy ( p. 333 ) . his choice of platform was a personal computer , and the game he chose was ultima , a simple - nonsocial role - playing game ( rpg ) . gardner presented case studies on three children : a 5 - year - old boy with disruptive behavior in school , a 10 - year - old girl with anxiety , and a 7 - year - old boy with an autism spectrum disorder . gardner described one of his roles with the disruptive child as making , ( 1 ) if - then statements for the moment ( e.g. , if you throw the controller , it s cool off time ) and ( 2 ) generalizing statementshis roles with the remaining two children included having them watch him play , physically modeling play ( therapist placed his fingers over j s and together they played the gamep . 669 ) , encouraging play by providing hints and prompts , and like allen , discussing experiences in the game and generalizing them to others and self . the treatment objectives were improved coping skills for the anxious child and moving the child with developmental deficits from rigid behavior patterns to more flexible ones . the choice of game for the boys was super mario brothers , a simple - nonsocial platform game ; for the female client , gardiner selected jeopardy ( simple - nonsocial puzzle game ) to address performance anxiety in school and legend of zelda ( simple - nonsocial adventure game ) for separation anxiety . favelle described using ege in a residential treatment facility for adolescents who were aggressive and who had poor social problem solving skillslike allen and gardner , he utilized experiences in the game and applied them to real life . the platform used was a pc and two complex - nonsocial role playing games : the wizard and the princess and alter ego . according to friedberg , cognitive - behavioral approaches using ege are the latest stage in the evolution of cbt because of their appeal to clients , standardization , and availability . research on game - based cbt ( gb - cbt ) may provide a good model for the use of and research on ege . gb - cbt is an empirically supported approach to treatment of childhood trauma survivors that uses developmentally appropriate games ( dag ) , but not eg . gb - cbt uses games in group and individual therapy to facilitate the processing of traumatic memories , acquisition of social and emotional management skills , and group cohesion . based on this example , future work on ege should investigate empirically validated strategies and techniques , provide manuals with skill areas and menus of games , clearly defined goals and incentives , and experiential learning that provides opportunities for receiving corrective feedback . clinicians can establish a therapeutic environment , which promotes skill development , minimizes behavioral difficulties , and provides a positive , pleasant and motivating atmosphereone of the first published accounts of using ege for group therapy used a group mystery game ( where in the world is carmen sandiego ) to assess and enhance social skills through modeling . a more recent study using ege in group therapy focused on social skills eight of the participants had asd diagnoses , and one was diagnosed with adhd and social skills deficits . a 10 - week teaching interaction procedure similar to behavioral skills training was used , with the therapist and participants defining the targeted skill , followed by clinician modeling and participant dyads role - playing the targeted skills . the intervention targeted three skills : giving compliments , taking turns , and making a positive postgame comment . the platform was a nintendo wii with wii sports , a simple - social sports game . the targeted skills significantly improved across baseline and training phases and generalized to different video games and actual sports . the authors noted that the wide availability of such [ electronic gaming ] technology may allow for greater transportability of interventions across settings ( p. 303 ) . egp and ege have been used in health promotion and to improve physical and psychosocial functioning of patients . both types of games may be used to increase motivation , attention / engagement , knowledge , or physical efficacy ; to allow for physical activity , practice , or immediate feedback ; and to provide therapeutic imagery and emotional expression . comprehensive reviews indicate that egp have been used successfully to improve diet and physical activity in children , and ege for chemotherapy - related nausea , preoperative anxiety , fitness , physical therapy , and cognitive rehabilitation . describe the use of imagery in a first - person shooter game to allow patients with brain tumors to experience an imagined immune response to the tumors . in a randomized clinical trial ( rct ) , significant reductions were noted by the authors in depression , anxiety , anger , and disruptive behavior and increases in self - concept , with significant advantages of the intervention over the control in all areas . eg which have gross motor interfaces , such as the dance dance revolution dance mat , wiimote , and xbox kinect , provide physical challenge and a greater variety of physical operations when compared to games with conventional controllers . use of eg with gross motor interfaces has become one of the standard treatments in rehabilitation therapies to increase fitness , and sedentary games increase health - related knowledge and encourage pro - health behaviors . they have been used with demonstrated efficacy with children and adults , including elderly adults , in community , rehabilitation , and long - term care settings to increase overall physical fitness and physical and functional capabilities , reduce pain , and improve aspects of cognitive function , with diagnoses including traumatic brain injury , stroke , huntington s disease , and multiple sclerosis . although a number of investigations consist of pilot and feasibility studies , eg interventions have also been found to improve psychosocial functioning with medical populations , including reducing disfigurement - related distress , stress management , self - confidence , socialization , and quality of life . one pilot study failed to find these effects , however , and in one study , benefits of walking outside on well - being were superior to those associated with wii fit activity , although both groups improved . when using computerized cognitive behavior therapy ( ccbt ) with medical patients , some subjects found the intervention too impersonal . gamelab , a protocol for group therapy tailoring different aspects of game play to individual patient goals , is an example of using eg in a group format with children as treatment for acquired brain injury . although outcomes are encouraging using eg for cognitive stimulation and retraining , bisoglio et al . [ 25 ] urge caution in concluding that cognition is meaningfully enhanced by various types of video games , because insufficient rigor has been applied to the investigations . in particular , bisoglio et al . assert that magnitudes of effect , expectancy effects , statistical interactions , and causal models should be examined . these concerns should be noted overall when evaluating the potential for eg in mental health and health care settings . most approaches to incorporating technology into the therapist s office use games or programs specifically designed to serve one or more therapeutic needs . computer - assisted cognitive behavior therapy ( ccbt ) includes computer - delivered information and interventions designed to implement established treatment models . in some cases , a specific game is developed or the interventions exhibit a game - like quality , but some elements may be less interactive , such as video demonstrations or relaxation inductions . for example , online self - help for anxiety disorders and handheld devices with diaries and prompting for individuals with obsessive compulsive disorder have been shown to facilitate cbt . in a systematic review of the use of technology in treating various anxiety disorders and depression , newman et al . concluded that computer - assisted treatment is effective overall and suggested that compliance might be maximized through more therapist exposure . mohr et al . remarked that the serious game movement is finding entertaining games being designed for therapeutic purposes , especially in the field of mental health ( egp ) . in a meta - review of the use of egp in treating depression , support was found for the use of egp , specifically moodgym , beating the blues , and colour your life , in enhancing cbt for depression . they also suggested egp could be cost - effective for therapists . in a similar review , moodgym was compared with two other games , beating the blues and good days ahead . good days ahead incorporates moderate therapist involvement , whereas the other two games had little to none , and had been compared to an established intervention , representing treatment as usual ( tau ) . these concerns about methodology are consistent with many in virtual reality ( vr ) and egp research , the absence of controlled clinical trials and non - significant findings in comparisons with more traditional techniques . merry et al . used an rct approach to look at the effectiveness of sparx , an egp aimed at adolescents struggling with depression . sparx is a self - directed game in which clinicians provide initial contact and a phone follow up after a month , and clients are encouraged to contact the therapist if no improvement is noted . sparx was found to be effective but not superior to tau , as demonstrated by a decrease in depressive symptoms by 30 % on a children s depression rating scale . although perhaps not a true egp , a pilot study using a game - like presentation of ccbt for anxiety in children demonstrated changes in anxiety and remission of symptoms . in addition to anxiety and mood disorders , egp have been developed to enhance psycho - education , attitude change , relaxation , pain management , social skills , problem - solving skills , emotional modulation , self - control skills , motivation , and therapist - client interaction . of 11 egp , five were found to have been systematically assessed for effectiveness : re - mission , personal investigator , treasure hunt , play attention , and one unnamed game . the authors concluded that egp can be effective in increasing compliance , learning , and behavior and affective change . playmancer , an egp designed to help individuals with impulse - related disorders , was found to be well accepted by the users , seemed to be a good format in which to work on attitudes and emotions , and to make it feasible to apply techniques that tend to be difficult to apply such as controlled intensive exposure , immediate positive and negative reinforcing , complex biofeedback approach , and real time monitoring of physiological - emotional reactions [ 35 , p. 371 ] . virtual reality exposure therapy ( vret ) uses vr to expose clients to sources of stress and / or anxiety in a manner that is realistic enough to be visceral within the relative safety of the therapist s office . opris et al . performed a quantitative meta - analysis comparing treatment of anxiety disorders using vret , traditional cbt , and traditional behavioral therapy ( bt ) . anxiety disorders examined included fear of flying , panic disorder / agoraphobia , social phobia , arachnophobia , acrophobia , and ptsd . the eight studies of comparing vret to waitlist control at post treatment demonstrated significant improvement for both cbt and bt , and medium to large effect sizes . in a systematic review of ten experimental studies using vret in combination with cbt in the treatment of ptsdmethodological concerns of the studies included small sample size and concerns about randomized treatment assignment . the authors suggested that vret might be of particular value with patients who respond better to the more immersive qualities of vr . in a more recent review of rcts to explore the effectiveness of vret in the treatment of ptsd , vret provided a robust positive effect similar to other exposure - based interventions for ptsd despite low sample sizes and some challenges in standardization . although the authors suggest that vret might provide treatment in a less stigmatizing manner and a more controlled yet immersive delivery than traditional exposure , they suggested that this has not been verified experimentally . in a line of research exemplifying the diffuse boundary between egp and ege , some researchers are using off - the - shelf gaming hardware such as the xbox kinect to measure body movement in a virtual reality world , laptop computers with built - in webcams to assess facial movement and to explore expression of emotions within an egp as treatment for pain - related fear and disability in chronic pain , and facial recognition for children with autism spectrum disorder . avatars combined with voice alteration programs are being used to assist an individual suffering from auditory hallucinations by offering a visual and interactive perspective on their hallucinations . recommended that game designers take into account relevant attributes of the client ; gender , age , developmental sophistication , ethnicity , and social economic status affect the individual 's response to the eg ; diagnoses and treatment objectives guide the style of the eg to be designed . for example , specific treatment objectives such as attention / focus may be aligned with a question - and - answer style game or likewise behavior modification and communication with simulation games and virtual reality . other examples of treatment objectives were control , reading / learning facts , sensory response , and social skills . these had been aligned to problem - solving , drill and practice , virtual reality , matching games , and virtual reality genres , respectively . other points of interest included degree of realism / level of immersion , management of goal direction , and motivation / challenge in game play . although the writers offered research examining these various characteristics of game design , they caution that much of the research has focused on games individually and have not addressed the overall constructs of game design as they apply to all games . the writers also point out that current research seems to focus less on the effectiveness of the games and more on playability and acceptability . although games and other electronic interventions may be designed for specific therapeutic purposes , games that are commercially available provide an incredible variety of interfaces and experiences that can be used as an adjunct to therapy . in fact , despite concerns about their use , ege have been shown to have a number of positive effects . the first study to discover the positive effects of playing ege included commercially produced games as a control for biofeedback . playing ege was as effective as biofeedback for reducing impulsivity , increasing personal influence , and improving one s self - concept . recent research and reviews of ege identified four general areas of beneficial effects : cognitive , motivational , emotional , and social . benefits included increased speed and accuracy of attention and visual special abilities improved learning and memory , executive functions , problem - solving skills and creativity . emotional benefits of using ege included improved mood or increases in positive emotion and adaptive regulation strategies for managing negative emotions like anger , anxiety , and sadness . finally , granic et al . noted the social benefits of ege included increased cooperation , support , and helping behaviors and civic engagement . ege has been investigated as an adjunct to individual and group psychotherapy , primarily in behavioral or talk therapy with children or adults with developmental delays . a variety of commercially produced games are appropriate to use , and granic et al . provided a helpful framework for describing games along two general dimensions : level of complexity and extent of social interaction . any game may be classified as more or less social and more or less complex along the two axes , in order to determine how they might facilitate particular therapeutic goals ( table 1 ) . table 1examples of games designated by level of complexity and social involvementdesignationgame stylegame examplescomplex and socialmultiplayer shooterhalo , call of dutymultiplayer action - adventuregrand theft auto , assassins creedon - line role playingrunescape , world of warcraftmultiplayer sandboxminecraft , half - life 2complex and nonsocialsolo role playingskyrim , final fantasysolo sportfifa , nhl14solo fightingstreet fighter , mortal kombatsimple and socialracingmario kart , need for speedrhythmrock band , guitar heropartywii party , mario partysimple and nonsocialpuzzlecandy crush , bejeweledplatformsuper mario bros . , donkey kongadventurelegend of zelda , tomb raideradapted from granic et al . [ 45 ] examples of games designated by level of complexity and social involvement adapted from granic et al . one of the earliest studies using ege in behavioral therapy taught social skills to three autistic boys aged 17 , 18 , and 20 . in a remarkably creative research design , the authors attempted to increase the frequency of appropriately initiated social interactions with neurotypical peers during classroom breaks in an outdoor courtyard of a public high school . the therapists trained the subjects to play the games and to approach and greet , offer to play , engage in reciprocal play , and signal the end of the interaction using three different items : a pack of gum , a sony walkman , and a handheld gaming device with pac - man or galaxian . the sony walkman was the most effective adjunct in terms of time spent interacting by the students with mental retardation , and the video game was the most effective item for the higher - functioning student . in a more recent case example , therapists used ege in individual behavior therapy with three boys and one girl between the ages of 9 and 12 diagnosed with autism , who had fine motor skills adequate to manipulate the game controller . the therapists role was to perform a set of interventions including video and in - vivo modeling . the treatment objective was to teach a common leisure skill using the play station 2 console to play guitar hero , a simple - social rhythm game . subjects time on task increased significantly after the training and were able to play the game with at least 70 % accuracy , indicating that training was effective in teaching young children with autism a generalized repertoire of an age - appropriate leisure skill , playing a video game ( p. 366 ) . one of the first reports of using ege as an adjunct in individual talk therapy was a case study of a 7 - year - old boy who presented with anxiety secondary to his parents divorce . in addition to traditional psychotherapeutic methods including giving advice , providing emotional support , and encouraging behavior change , allen utilized the experiences in the game and applied them to the patient s real - life problems ( p. 332 ) . treatment outcomes included self - confidence , a sense of mastery , more willingness to accept responsibility and less stigma about having been in therapy ( p. 333 ) . his choice of platform was a personal computer , and the game he chose was ultima , a simple - nonsocial role - playing game ( rpg ) . gardner presented case studies on three children : a 5 - year - old boy with disruptive behavior in school , a 10 - year - old girl with anxiety , and a 7 - year - old boy with an autism spectrum disorder . gardner described one of his roles with the disruptive child as making , ( 1 ) if - then statements for the moment ( e.g. , if you throw the controller , it s cool off time ) and ( 2 ) generalizing statementshis roles with the remaining two children included having them watch him play , physically modeling play ( therapist placed his fingers over j s and together they played the gamep . 669 ) , encouraging play by providing hints and prompts , and like allen , discussing experiences in the game and generalizing them to others and self . the treatment objectives were improved coping skills for the anxious child and moving the child with developmental deficits from rigid behavior patterns to more flexible ones . the choice of game for the boys was super mario brothers , a simple - nonsocial platform game ; for the female client , gardiner selected jeopardy ( simple - nonsocial puzzle game ) to address performance anxiety in school and legend of zelda ( simple - nonsocial adventure game ) for separation anxiety . favelle described using ege in a residential treatment facility for adolescents who were aggressive and who had poor social problem solving skillslike allen and gardner , he utilized experiences in the game and applied them to real life . the platform used was a pc and two complex - nonsocial role playing games : the wizard and the princess and alter ego . according to friedberg , cognitive - behavioral approaches using ege are the latest stage in the evolution of cbt because of their appeal to clients , standardization , and availability . research on game - based cbt ( gb - cbt ) may provide a good model for the use of and research on ege . gb - cbt is an empirically supported approach to treatment of childhood trauma survivors that uses developmentally appropriate games ( dag ) , but not eg . gb - cbt uses games in group and individual therapy to facilitate the processing of traumatic memories , acquisition of social and emotional management skills , and group cohesion . based on this example , future work on ege should investigate empirically validated strategies and techniques , provide manuals with skill areas and menus of games , clearly defined goals and incentives , and experiential learning that provides opportunities for receiving corrective feedback . clinicians can establish a therapeutic environment , which promotes skill development , minimizes behavioral difficulties , and provides a positive , pleasant and motivating atmosphere ( p. 1 ) . one of the first published accounts of using ege for group therapy used a group mystery game ( where in the world is carmen sandiego ) to assess and enhance social skills through modeling . a more recent study using ege in group therapy focused on social skills . eight of the participants had asd diagnoses , and one was diagnosed with adhd and social skills deficits . a 10 - week teaching interaction procedure similar to behavioral skills training was used , with the therapist and participants defining the targeted skill , followed by clinician modeling and participant dyads role - playing the targeted skills . the intervention targeted three skills : giving compliments , taking turns , and making a positive postgame comment . the platform was a nintendo wii with wii sports , a simple - social sports game . the targeted skills significantly improved across baseline and training phases and generalized to different video games and actual sports . the authors noted that the wide availability of such [ electronic gaming ] technology may allow for greater transportability of interventions across settings ( p. 303 ) . in our survey of the research , electronic methods , including games and other types of computer - assisted therapies , have been shown to be equivalent but not superior in efficacy for a wide variety of medical health and mental health issues , in group , individual , and self - guided treatment . there is evidence that some electronic methods are more acceptable , enjoyable , or engaging than tau and that greater therapist engagement may be associated with better outcomes . methodological limitations include the predominance of quasi - experimental , pre - post designs , and case studies . particularly for ege , more exploration is needed into the efficacy of the use of commercially produced games , although it could be argued that games would simply be incorporated into an already evidence - based framework , such as cbt . the mechanisms of action for the use of video games in psychotherapy have been explored by various theorists and include attention , distraction , problem - solving , feedback , emotional expression , socialization , and exposure , but future studies should verify these actions relationship to outcomes . provide a strong framework that could facilitate game selection once parameters have been determined . the area of therapeutic eg is promising , despite the need for more rigorous outcome studies . if , as has been suggested here , electronic methods produce similar results and are more acceptable than established treatments to clients , or to a subset of clients , their utility will be established based on ability to effectively serve a broader range of the population . egp have the advantage of being tailored to specific client groups , diagnoses , and settings and are more standardized , but are relatively expensive to produce and must be specifically updated . when used at home , they are more specifically designed to retain their therapeutic effects . in order to benefit the client , the video games must be designed or chosen not only to serve a therapeutic purpose but also to be engaging and appropriate to the clients physical , cognitive , and emotional abilities as well as their age , gender , culture , and ses . ege , using off - the - shelf games , are easier and less expensive to acquire and update , provide a much larger set of options , and are generally more preferred by children and adolescents . ege s disadvantages include possible parental objections , the potential for unhelpful distraction , and the potential for game producers to eliminate features that facilitate the therapeutic aspects of play . for example , many of the xbox and xbox 360 games allowed up to four people to play on one console , which facilitated use in group therapy . the newer versions of many of the games require one console per player , and only a few allow two players per console . ege require more engagement by the therapist , in general , which may have other benefits , and when played at home may produce positive effects , but are less targeted in this regard . in a commentary on the adoption of the use of computers in psychotherapy by therapists , barrett and gershkovich raise six clinical , legal , and economic concerns : ( 1 ) the challenge of keeping up with advances in technology , ( 2 ) the potential detriment of computer - assisted technology to the therapeutic relationship , ( 3 ) time requirements for the therapist and compensation for that time in a significantly different format , ( 4 ) the potential for clients to access interventions not appropriate for them when online interventions are made openly available to the community , ( 5 ) implications of the decrease of face - to - face interaction between the client and therapist , including informed consent and assessment of dangerousness towards self or others , and ( 6 ) potential changes in content , maintenance , and confidentiality of records . the authors have a variety of computer - based and console - based games , some in the waiting room and some in practitioners offices . we also have handheld gaming devices like the nintendo 3ds and tablets like the ipad and nook in our individual offices . with respect to the waiting room , the consoles and games are kept in a separate room to minimize damage and prevent children from playing age - inappropriate games . in using ege for groups , we use games that allow as many clients to participate as possible ; for a single console , the best option at this time is the wii u with up to five players at a time ; for multiple consoles , three xbox 360 consoles can accommodate up to 12 players at a time . clients may bring a game to session or , with parent permission , play one of our games . manufacturer s recommendations , parent feedback , and clinical expertise allow us to select games and tailor game play based on client age , cognitive functioning diagnosis , presenting problem , and level of skill . games with graphic violent or sexual content should be avoided , and all content must be selected with an appreciation for not only the age but also the maturity of the client . co - play with family members in family sessions and peers in groups allows for teaching social skills . complex games matched to the developmental level provide adequate challenge and help build frustration tolerance . simple social or nonsocial games can be used to break tension , provide distraction , and maintain adherence to therapy . one of the authors devised a specific world in minecraft which requires group members to engage in cooperative play in order to achieve a series of objectives . research on the inappropriate use of ege indicates that the amount of time gaming and the length of gaming sessions are related to the likelihood of social - emotional and educational problems , whereas playing with children and encouraging social play were key protective factors . parents should be encouraged to play eg with their children to monitor their play for duration and content and to encourage them to play with friends , preferably in person rather than online . this is particularly important for clients for whom socialization and social skills are therapeutic goals . parents should also be reminded that although games with sexual , violent , or otherwise objectionable content are commercially available , and despite research calling into question the extent of potential harm , in particular aggression and violence , they should be used with care especially by children and adolescents . in summary , eg and other technologies can provide effective , efficient , and appealing interventions for a variety of clients . the psychotherapeutic use of ege as an adjunct to individual or group therapies has a long tradition that is consistent with play and group therapy in general , although considerably less empirically researched than the latter . egp is a growing area with a large number of games with varying levels of specificity . with smart devices that are carried with us , using the internet , e - mail , and social media , we are able to gather and disseminate information in ways that are less time - consuming , more interesting , and more readily available . with advanced graphic and audio - visual performance , we are able to create virtual multisensory worlds in order to expose clients to important stimuli in a safe manner without limiting ourselves to the physics or logistics of the real world . the use of eg may allow us to engage our clients in a way that is not only more appealing to many clients , especially children and adolescents , but also with demonstrated efficacy . the authors have a variety of computer - based and console - based games , some in the waiting room and some in practitioners offices . we also have handheld gaming devices like the nintendo 3ds and tablets like the ipad and nook in our individual offices . with respect to the waiting room , the consoles and games are kept in a separate room to minimize damage and prevent children from playing age - inappropriate games . in using ege for groups , we use games that allow as many clients to participate as possible ; for a single console , the best option at this time is the wii u with up to five players at a time ; for multiple consoles , three xbox 360 consoles can accommodate up to 12 players at a time . clients may bring a game to session or , with parent permission , play one of our games . manufacturer s recommendations , parent feedback , and clinical expertise allow us to select games and tailor game play based on client age , cognitive functioning diagnosis , presenting problem , and level of skill . games with graphic violent or sexual content should be avoided , and all content must be selected with an appreciation for not only the age but also the maturity of the client . co - play with family members in family sessions and peers in groups allows for teaching social skills . complex or simple social games would be used in these settings . complex games matched to the developmental level provide adequate challenge and help build frustration tolerance . simple social or nonsocial games can be used to break tension , provide distraction , and maintain adherence to therapy . one of the authors devised a specific world in minecraft which requires group members to engage in cooperative play in order to achieve a series of objectives . research on the inappropriate use of ege indicates that the amount of time gaming and the length of gaming sessions are related to the likelihood of social - emotional and educational problems , whereas playing with children and encouraging social play were key protective factors . parents should be encouraged to play eg with their children to monitor their play for duration and content and to encourage them to play with friends , preferably in person rather than online . this is particularly important for clients for whom socialization and social skills are therapeutic goals . parents should also be reminded that although games with sexual , violent , or otherwise objectionable content are commercially available , and despite research calling into question the extent of potential harm , in particular aggression and violence , they should be used with care especially by children and adolescents . in summary , eg and other technologies can provide effective , efficient , and appealing interventions for a variety of clients . the psychotherapeutic use of ege as an adjunct to individual or group therapies has a long tradition that is consistent with play and group therapy in general , although considerably less empirically researched than the latter . egp is a growing area with a large number of games with varying levels of specificity . with smart devices that are carried with us , using the internet , e - mail , and social media , we are able to gather and disseminate information in ways that are less time - consuming , more interesting , and more readily available . with advanced graphic and audio - visual performance , we are able to create virtual multisensory worlds in order to expose clients to important stimuli in a safe manner without limiting ourselves to the physics or logistics of the real world . the use of eg may allow us to engage our clients in a way that is not only more appealing to many clients , especially children and adolescents , but also with demonstrated efficacy .\noutput:\n" }, { "from": "agent", "value": "therapists and patients enjoy and benefit from interventions that use electronic games ( eg ) in health care and mental health settings , with a variety of diagnoses and therapeutic goals . we reviewed the use of electronic games designed specifically for a therapeutic purpose , electronic games for psychotherapy ( egp ) , also called serious games , and commercially produced games used as an adjunct to psychotherapy , electronic games for entertainment ( ege ) . recent research on the benefits of eg in rehabilitation settings , egp , and ege indicates that electronic methods are often equivalent to more traditional treatments and may be more enjoyable or acceptable , at least to some consumers . methodological concerns include the lack of randomized controlled trials ( rct ) for many applications . suggestions are offered for using eg in therapeutic practice ." } ]

[ { "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 myeloid leukemia ( cml ) is a myeloproliferative disorder of blood stem cells .1 the causative molecular defect is the bcr - abl protein , which is encoded by the philadelphia chromosome ( ph ) .2 this genetic anomaly arises from an exchange of genetic material between chromosomes 9 and 22 , which results in the fusion of the breakpoint cluster region ( bcr ) and the abelson leukemia virus ( abl ) proto - oncogene .3,4 the resulting gene encodes a constitutively active protein kinase that activates a number of proteins involved in cell - cycle regulation that hasten cell division and affect dna repair .58 imatinib , also known as gleevec ( novartis , basel , switzerland ) , is a selective inhibitor of not only abl but also kit and pdgfr kinases , and exerts significant antileukemic activity in the majority of cml patients . according to the current national comprehensive cancer network ( nccn ) guidelines9 and the european leukemianet ( eln ) recommendations ,10 a response outcome to imatinib therapy is classified as optimal , suboptimal , and failure based on the level of response achieved at various time points throughout the course of treatment using specific hematologic , cytogenetic and molecular criteria . optimal responses proposed by the nccn closely corresponding to the eln recommendations and defined as the achievement of a ccyr after 12 months of imatinib at 400 mg daily . in patients with suboptimal responses to first - line imatinib , the use of high - dose ( 600 or 800 mg / day ) is recommended as an alternative therapeutic option by both the eln and the nccn . failure to achieve any cytogenetic response from standard - dose imatinib after 6 months of therapy or major cytogenetic response and a ccyr after 12 and 18 months of therapy , respectively , are considered treatment failure by the nccn . in such cases , it is recommended that treatment should be changed for a second - generation tyrosine kinase inhibitor ( tki ) . these criteria became particularly important as several kinase targeted therapies with long half - lives were developed for the treatment of patients who fail or are intolerant to imatinib therapy . according to the most recent results from the international randomized study of interferon versus sti571 ( iris ) trial , the estimated overall survival for patients still on imatinib was 85 % at 8 years , or 93 % when only cml - related deaths or deaths prior to stem cell transplant were included . a total of 92 % of the patients were free of disease progression . among those who achieved ccyr , only 3 % progressed during the 8 - year follow - up .11 nevertheless , of the 259 patients receiving imatinib as front - line therapy who had treatment discontinuation , 30 ( 5.4 % ) and 77 ( 13.9 % ) patients stopped their therapy because of intolerance or unsatisfactory therapeutic effect , respectively . the inability of patients to tolerate treatment and the emergence of bcr - abl mutations that reduced the binding affinity of imatinib prompted pharmaceutical research that led to the discovery of several similarly effective , targeted , second generation tkis such as nilotinib ( tasigna , amn107 , novartis , basel , switzerland ) and dasatinib ( sprycel ; bristol - myers squibb , new york , ny ) .1214 evidence from an in vitro study has indicated that nilotinib is 20 times more potent than imatinib against cells expressing the wild - type bcrabl .15 dasatinib is a multi - targeted kinase inhibitor that is structurally unrelated to imatinib and is able to bind and inhibit both the active and inactive conformations of abl , resulting in 100 - to 300-fold higher activity than imatinib for unmutated bcr - abl , and greater inhibition against mutants with high levels of imatinib resistance ( except for t315i and relative insensitivity to f317l ) .1517 dasatinib is generally well tolerated . however , adverse events ( aes ) associated with its use , such as pleural effusions , hemorrhage , and febrile neutropenia have been frequently reported in the advanced stage of the disease ( reviewed by wong18 ) . the nccn guidelines9 recommend that at the onset of grade 3/4 thrombocytopenia ( platelet count 50,000 / mm ) , therapy with dasatinib should be held . once the toxicity has resolved ( platelet count 50,000 / mm ) , dasatinib should be resumed at original starting dose if recovery occurs within 7 days or reduced one dose level if platelet count decreased to 25,000 / mm for more than 7 days . attempts to identify the optimum and effective dose of dasatinib continue and include modification of scheduling , management of toxicity and dose optimization . to determine the optimum administration schedule , the efficacy , response and tolerability of dasatinib has been investigated in several clinical trials . it is now apparent that a scheduled once daily starting dose of 100 mg offers an improved safety profile and shows similar efficacy for patients with chronic phase cml ( cp cml ) compared to a 70 mg twice daily dose .1921 the recommended dosage schedule for patients in the advanced phase of the disease is 140 mg once daily .22,23 however , some intolerant patients may require a dose adjustment from 140 to 100 mg / day or from 100 to 80 mg / day to continue treatment and thus maintain control of their disease . even at a dose of 80 mg / day , some patients require further dose reduction due to substantial toxicities . because of the clinical difficulty posed by this subgroup , we report the effects of an unusually low dosage of dasatinib during the treatment of four patients ( 2 in chronic phase and 2 in accelerated phase ) with proven efficacy almost identical to that seen with conventional dosage . a 31 - year - old man was admitted to our department in march 2008 with leukocytosis ( wbc 88.900 / mm ) and splenomegaly of cml . the patient was treated with imatinib mesylate at 400 mg / day in july 2008 . one month after starting the therapy , the patient developed a grade ( g ) 4 thrombocytopenia ( 8.000 / mm platelets ) with epistaxis and needed a platelet transfusion . the patient had a therapy break of 4 months . in october 2008 , after resolution of thrombocytopenia to the g1 level , he was restarted on a reduced imatinib dose of 300 mg per day , but therapy was again discontinued for thrombocytopenia g3 ( 26.000 / mm platelets ) . in february 2009 , because of severe intolerance to imatinib , dasatinib was started at a dose of 100 mg / day . after 2 weeks of treatment under this therapy , the patient developed a g4 thrombocytopenia . as a result , treatment was suspended until ( march 2009 ) recovery to g1 ( 78.000 / mm ) and then resumed at a dose of 80 mg / day . however , the patient experienced the same side effects one week after restarting dasatinib . the dose was then decreased to 50 mg / day with gradual increase of platelets . in june 2009 , after 4 months of treatment , the patient achieved a ccyr . the patient continued the same dasatinib dose and in july 2009 , the platelet count reached 130.000 / mm and molecular analysis showed a bcr - abl / bcr ratio of 0.01 % indicating that the patient had achieved a major molecular response ( mmr ) . a 46 - year - old male was admitted to our department in july 2008 with cp cml . this patient had two breaks in his imatinib therapy due to the recurring of g 3 thrombocytopenia . after the second break , the patient progressed to ap cml without evidence of mutations in the abl kinase domain . in march 2009 , dasatinib was prescribed to this patient at 140 mg / day and after four weeks of therapy , the patient developed g3 thrombocytopenia , after which we decided to maintain the therapy at a lower dose of 70 mg / day . in june 2009 , after three months of treatment , the patient reached a ccyr and his thrombocytopenia improved to g1 . to achieve mmr , we decided to increase the therapeutic dose to 80 mg / day in may 2010 . by august 2010 , on his last evaluation , this patient s bcr - abl / a 69 - year - old male was admitted to our department in march 2009 with a history of cml , first diagnosed in august 2007 in japan . six months before the referral , he complained of fatigue , weight loss and splenomegaly . a diagnosis of ap cml was confirmed with the appearance of additional chromosomal aberrations besides the ph chromosome ( 47xy , + 8 , t ( 9,22 ) , add ( 13 ) ( q33 ) in 20/20 metaphase analyzed ) and , in march 2009 , imatinib was initiated at a daily dose of 600 mg . after 1 month , the patient experienced g3 neutropenia ( 700 / mm ) and g2 thrombocytopenia ( 62.000 / mm ) . the patient continued imatinib at the same dose with 300 g granulocyte - colony - stimulating factor ( g - csf ) added simultaneously every week to stimulate myelopoiesis . in october 2009 , the patient experienced g3 thrombocytopenia ( 41.000 / mm ) and his bcr - abl / bcr ratio was 7.68 % without any cytogenetic response after 6 months of therapy . at this time , sequencing of the bcr - abl kinase domain revealed no evidence of mutations in the abl kinase domain . based on these results , the patient was , therefore , considered resistant to imatinib and , in november 2009 , was placed on dasatinib at a daily dose of 140 mg . after the first 3 weeks of treatment , dasatinib was reduced to 100 mg / day because of the occurrence of g2 thrombocytopenia ( 61.000 / mm ) . two weeks later , his platelet count dropped to 50.000 / mm . at this time , dasatinib was lowered to a dose of 70 mg in an attempt to maintain a stable platelet count . however , after another 2 weeks , in january 2010 , the patient developed g3 neutropenia ( 900 / mm ) and his platelet count dropped to 26.000 / mm . at this time , the patient s bcr - abl / bcr ratio was 9.87 % . as dasatinib was the only option for the treatment of this patient s disease , it was again reduced to a dose of 50 mg / day with g - csf . in february 2010 , the patient s bcr - abl / bcr ratio was decreased to 0.81 % and his platelet numbers started to increase gradually . as a result , g - csf was stopped and the patient continued dasatinib at the same dose . five months after initiation of dasatinib , in april 2010 , cytogenetic analysis revealed a ccyr and complete disappearance of the initially detected additional chromosomal aberrations . in may 2010 , dasatinib was increased to 60 mg once daily to achieve mmr and no toxicity was noted on follow - up examination . one month later , in june 2010 , the patient achieved mmr , with a transcript ratio of 0.01 % . the patient , a 58 - year - old man , was presented to our hospital in march 2009 with a clinical history of rheumatoid arthritis , hypertension , gastritis and chronic renal failure and undergoing conservative therapy . at presentation , a routine blood count showed leukocytosis with a left shift and physical examination revealed no splenomegaly . a diagnosis of cp cml was made after further laboratory studies and , in april 2009 , imatinib was initiated at a daily dose of 400 mg . after a one month , despite a complete hematological response , the patient s pancreatic enzymes elevated to g1 and then gradually increased in severity to g4 in may 2009 . after a one month period of interruption , imatinib was resumed at the same dose . however , the patient experienced the same side effects again and treatment was permanently discontinued . one month later , the patient s pancreatic enzyme values returned to normal but he lost his hematologic response . at that time , dasatinib was initiated at a dose of 100 mg / day . during follow - up , the patient had two breaks in the dasatinib therapy at a daily dose of 100 mg and 40 mg because of recurring g2 and g4 pancreatitis , respectively . after the second break , a 10 - week interruption , the serum lipase level was returned to normal and dasatinib was reintroduced at a further reduced dose of 20 mg / day taken in combination with pancrelipase ( creon ) capsules . at a subsequent clinic visit , the patient presented with g2 pancreatitis and the treatment schedule and doses were maintained . in february 2010 , the patient underwent a switch to alternate - day dasatinib at dosages of 20 and 40 mg every other day . in march 2010 , after 3 months of taking a lower dosage ( 20 mg / day ) of dasatinib , the patient achieved a ccyr and his bcr - abl / bcr showed a ratio of 0.1 % . the measurement of his transcript was repeated in august 2010 and confirmed the mmr ( bcr - abl / bcr ratio = 0.018 % ) . at that time , the patient had mild pancreatitis with serum lipase level and was scored as grade 1 . a 31 - year - old man was admitted to our department in march 2008 with leukocytosis ( wbc 88.900 / mm ) and splenomegaly of cml . the patient was treated with imatinib mesylate at 400 mg / day in july 2008 . one month after starting the therapy , the patient developed a grade ( g ) 4 thrombocytopenia ( 8.000 / mm platelets ) with epistaxis and needed a platelet transfusion . the patient had a therapy break of 4 months . in october 2008 , after resolution of thrombocytopenia to the g1 level , he was restarted on a reduced imatinib dose of 300 mg per day , but therapy was again discontinued for thrombocytopenia g3 ( 26.000 / mm platelets ) . in february 2009 , because of severe intolerance to imatinib , dasatinib was started at a dose of 100 mg / day . after 2 weeks of treatment under this therapy , the patient developed a g4 thrombocytopenia . as a result , treatment was suspended until ( march 2009 ) recovery to g1 ( 78.000 / mm ) and then resumed at a dose of 80 mg / day . however , the patient experienced the same side effects one week after restarting dasatinib . the dose was then decreased to 50 mg / day with gradual increase of platelets . in june 2009 , after 4 months of treatment , the patient achieved a ccyr . the patient continued the same dasatinib dose and in july 2009 , the platelet count reached 130.000 / mm and molecular analysis showed a bcr - abl / bcr ratio of 0.01 % indicating that the patient had achieved a major molecular response ( mmr ) . a 46 - year - old male was admitted to our department in july 2008 with cp cml . this patient had two breaks in his imatinib therapy due to the recurring of g 3 thrombocytopenia . after the second break , the patient progressed to ap cml without evidence of mutations in the abl kinase domain . in march 2009 , dasatinib was prescribed to this patient at 140 mg / day and after four weeks of therapy , the patient developed g3 thrombocytopenia , after which we decided to maintain the therapy at a lower dose of 70 mg / day . in june 2009 , after three months of treatment , the patient reached a ccyr and his thrombocytopenia improved to g1 . to achieve mmr , we decided to increase the therapeutic dose to 80 mg / day in may 2010 . by august 2010 , on his last evaluation , this patient s bcr - abl / bcr ratio showed 0.8 % . a 69 - year - old male was admitted to our department in march 2009 with a history of cml , first diagnosed in august 2007 in japan . six months before the referral , he complained of fatigue , weight loss and splenomegaly . a diagnosis of ap cml was confirmed with the appearance of additional chromosomal aberrations besides the ph chromosome ( 47xy , + 8 , t ( 9,22 ) , add ( 13 ) ( q33 ) in 20/20 metaphase analyzed ) and , in march 2009 , imatinib was initiated at a daily dose of 600 mg . after 1 month , the patient experienced g3 neutropenia ( 700 / mm ) and g2 thrombocytopenia ( 62.000 / mm ) . the patient continued imatinib at the same dose with 300 g granulocyte - colony - stimulating factor ( g - csf ) added simultaneously every week to stimulate myelopoiesis . in october 2009 , the patient experienced g3 thrombocytopenia ( 41.000 / mm ) and his bcr - abl / bcr ratio was 7.68 % without any cytogenetic response after 6 months of therapy . at this time , sequencing of the bcr - abl kinase domain revealed no evidence of mutations in the abl kinase domain . based on these results , the patient was , therefore , considered resistant to imatinib and , in november 2009 , was placed on dasatinib at a daily dose of 140 mg . after the first 3 weeks of treatment , dasatinib was reduced to 100 mg / day because of the occurrence of g2 thrombocytopenia ( 61.000 / mm ) . two weeks later , his platelet count dropped to 50.000 / mm . at this time , dasatinib was lowered to a dose of 70 mg in an attempt to maintain a stable platelet count . however , after another 2 weeks , in january 2010 , the patient developed g3 neutropenia ( 900 / mm ) and his platelet count dropped to 26.000 / mm . at this time , the patient s bcr - abl / bcr ratio was 9.87 % . as dasatinib was the only option for the treatment of this patient s disease , it was again reduced to a dose of 50 mg / day with g - csf . in february 2010 , the patient s bcr - abl / bcr ratio was decreased to 0.81 % and his platelet numbers started to increase gradually . as a result , five months after initiation of dasatinib , in april 2010 , cytogenetic analysis revealed a ccyr and complete disappearance of the initially detected additional chromosomal aberrations . in may 2010 , dasatinib was increased to 60 mg once daily to achieve mmr and no toxicity was noted on follow - up examination . one month later , in june 2010 , the patient achieved mmr , with a transcript ratio of 0.01 % . the patient , a 58 - year - old man , was presented to our hospital in march 2009 with a clinical history of rheumatoid arthritis , hypertension , gastritis and chronic renal failure and undergoing conservative therapy . at presentation , a routine blood count showed leukocytosis with a left shift and physical examination revealed no splenomegaly . a diagnosis of cp cml was made after further laboratory studies and , in april 2009 , imatinib was initiated at a daily dose of 400 mg . after a one month , despite a complete hematological response , the patient s pancreatic enzymes elevated to g1 and then gradually increased in severity to g4 in may 2009 . after a one month period of interruption , imatinib was resumed at the same dose . however , the patient experienced the same side effects again and treatment was permanently discontinued . one month later , the patient s pancreatic enzyme values returned to normal but he lost his hematologic response . at that time , dasatinib was initiated at a dose of 100 mg / day . during follow - up , the patient had two breaks in the dasatinib therapy at a daily dose of 100 mg and 40 mg because of recurring g2 and g4 pancreatitis , respectively . after the second break , a 10 - week interruption , the serum lipase level was returned to normal and dasatinib was reintroduced at a further reduced dose of 20 mg / day taken in combination with pancrelipase ( creon ) capsules . at a subsequent clinic visit , the patient presented with g2 pancreatitis and the treatment schedule and doses were maintained . in february 2010 , the patient underwent a switch to alternate - day dasatinib at dosages of 20 and 40 mg every other day . in march 2010 , after 3 months of taking a lower dosage ( 20 mg / day ) of dasatinib , the patient achieved a ccyr and his bcr - abl / bcr showed a ratio of 0.1 % . the measurement of his transcript was repeated in august 2010 and confirmed the mmr ( bcr - abl / bcr ratio = 0.018 % ) . at that time , the patient had mild pancreatitis with serum lipase level and was scored as grade 1 . dasatinib is a highly effective targeted therapy in patients with cml who are unresponsive to imatinib , or as an alternative where imatinib is poorly tolerated . as such , it provides a valuable therapeutic option for those patients who are at high risk for disease progression . although dasatinib is generally well tolerated , serious toxicities can occur in some patients , even at a lower recommended dose of 80 mg / day , and can pose particular challenges to clinicians caring for this subgroup of patients . patients intolerant of dasatinib and other tkis are unlike those resistant to therapy ; they often suffer increased treatment interruptions and compromised therapeutic benefits . therefore , to fit an individual s unique profile , adjustment of dose on the basis of the patient s response and tolerability is required . our experience in this short case series demonstrate that dasatinib at a dose well below the minimum recommended dosage has clinical activity associated with only minor toxicity in 4 dasatinib - intolerant patients who had previously experienced imatinib - related hematological ( 3 cases ) and non - hematological complications ( 1 case ) . at the time of initiation of dasatinib therapy , all 4 patients had been initially treated with imatinib as a first - line therapy at either 400 mg / day or 600 mg / day and all but one developed hematological toxicities ( table 1 ) . the same pre - existing complications that occurred during imatinib therapy were observed after crossover to dasatinib . it is possible that the complications manifested in our patients during imatinib therapy may have increased the likelihood of these abnormalities shortly after initiation of dasatinib . alternatively , it is also possible that tkis predisposed our patients to these aes . in all patients , dasatinib , was the only second generation tkis available at that time , had to be reduced to a lower dose because of the dose - limiting toxicity . the mean time to a ccyr in the first 3 patients was 3 and 5.5 months ; similar to durations of 6 months that have been reported previously for standard doses .21,24 administration of dasatinib at a reduced daily dose thus induces remissions in a similar time frame compared with administration of a conventional dosage amount . moreover , under continuous treatment with dasatinib under low dosage , there was progressive improvement of the platelet count in all of our first three patients , with progression to g1 thrombocytopenia ( case 1 and 2 ) and complete normalization ( case 3 ) . although the third patient developed g3 neutropenia with dasatinib , it was easily managed by the weekly administration of g - csf . the myelosupression can occur as a result of a sudden hematopoiesis suppression that was maintained by ph + cells without equilibrium of the reappearance of the ph - cells . the fourth patient developed g4 pancreatitis after being initiated on imatinib mesylate and recurred with the same symptoms after switching to dasatinib even at the lower dose of 40 mg / day . the patient had no risk factors for pancreatitis and was taking no medications known to cause pancreatitis other than imatinib . the reason why it was unlikely for this patient to develop pancreatitis due to cml is because the onset of this complication appeared during the imatinib treatment and then gradually improved upon suspension of therapy . pancreatitis is an extremely rare adverse event which occurs after the use of tkis .23,2529 the pathophysiology of tkis - induced pancreatitis remains speculative , but has been proposed by plandari and colleagues26 to be due either to the inhibition of c - abl , which might interfere with the molecular mechanisms that regulate pancreatic cell death and thus induce pancreatic damage , or to the indirect effect of the drug on the release of calcium from the intracellular acinar stores , which regulate exocrine pancreatic secretion , and may enhance the accumulation of fatty acid inside the pancreatic acinar cell , which disturbs exocytosis . at the time of this report , it is possible that the greater potency of bcr - abl inhibition of dasatinib compared to imatinib contributed to the induction of remissions in our patients . because of its greater potency ( 325-fold ) , it has previously been reported that exposure to low or subnanomolar concentrations of dasatinib is sufficient to commit cell lines expressing bcr - abl to apoptotic cell death .15,16 these results may help to explain the improved tolerability and efficacy observed in our patients . an increasing number of investigators are exploring the use of a lower dose intensity of dasatinib for the treatment of therapy intolerant patients . in one recent study , the frequency and significance of dose reductions and treatment holidays among 280 patients treated with 2nd generation tkis were retrospectively analyzed .30 the results revealed that 176 ( 63 % ) of these patients required treatment interruptions and / or dose reduction at least once during therapy . the authors conclude that lower doses of dasatinib and nilotinib may potentially have similar efficacy in the therapy of cml as standard doses . in another small study , bergeron et al31 investigated pleural and pulmonary complications in 40 patients who received dasatinib ( 70 mg twice daily ) for imatinib resistance or intolerance . dasatinib treatment was interrupted in eight patients , either immediately after diagnosis of lung involvement ( five patients ) , or after a course of diuretics ( three patients ) . after treatment holidays , lung abnormalities were resolved in all cases and did not recur in three out of four patients when dasatinib was reintroduced at a dose of 40 mg twice daily . in addition , breccia et al32 treated a 34 - year - old ph + cml female patient who had a molecular relapse after haploidentical bmt with chronic liver gvhd and was severely intolerant to both imatinib and dasatinib at a standard dose ; she had a cmr to dasatinib at a reduced dose of 20 mg / day without serious adverse events . a recent case report published by yamaguchi et al. 33 described a successful treatment of a 70 - year - old man with cml who developed a megakaryoblastic crisis concomitant with myelofibrosis despite imatinib therapy with dasatinib at a starting dose of 80 mg / day . despite the successful clinical response in these patients , conclusions drawn from this seriesshould be interpreted with caution and considered tentative until experimental studies to define the minimum effective dose and optimal dosing schedule for dasatinib - intolerant patients are carried out . however , our series lend support to previous reports that showed a comparable efficacy of standard and low - dose dasatinib with very minor toxicities ; thus , for patients intolerant to dasatinib at a standard dose , a gradual dose reduction may be tried before drug discontinuation .\noutput:\n" }, { "from": "agent", "value": "we report our experience in 4 patients with chronic myeloid leukemia ( cml ) who had discontinued imatinib as a result of adverse events and had switched to dasatinib . the chronic phase ( n 2 ) and accelerated phase ( n 2 ) cml patients received dasatinib at starting dose of 100 and 140 mg once daily , respectively . reappearance of hematological toxicity was observed in 3 patients and pancreatitis in one patient . treatment was given at a lower dose and patients were followed . the median follow - up was 13 months and the median dose of dasatinib until achievement of complete cytogenetic remission ( ccyr ) was 60 mg daily ( range = 20 to 120 mg ) . all four patients had achieved ccyr at a median of 4 months ( range = 3 to 5 months ) and among them , three had also achieved major molecular remission . we conclude that low - dose dasatinib therapy in intolerant patients appears safe and efficacious and may be tried before drug discontinuation ." } ]

[ { "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: glioblastoma is essentially a pathogenetically heterogeneous tumor , and resent large - scale genomic analyses have allowed molecular subclassification of glioblastomas . recent work has identified a class of small noncoding rna molecules , named microrna ( mirna ) , which regulate a wide spectrum of gene expression in a posttranscriptional manner . more than 1500 precursors and 1921 mature human mirnas have been discovered and registered in mirbase to date , and these mirnas reportedly regulate approximately 30 % of all protein - coding genes . at present , it is predicted that more than half of protein coding genes would be regulated by mirnas . the incorporation of the mature mirna into an effector complex , called rna - induced silencing complex ( risc ) , binds to messenger rna ( mrna ) and can affect the translation and stability of mrna . recent reports have revealed that mirnas play crucial roles in tumorigenesis , angiogenesis , invasion , and apoptosis in various types of tumor . in addition , previous mirna expression profiling may yield more accurate classification of human cancers than mrna expression profiling . a recent large - scale multidimensional analysis of molecular characteristics , the cancer genome atlas ( tcga ) , which includes the expression profiles of mirna as well as dna copy number , gene expression , and dna methylation , has revealed frequent genetic alterations in three critical core pathways . in 2002 , calin first reported the frequent deletions and downregulation of mir - 15 and mir - 16 at chromosome 13q14 in a majority of cases of chronic lymphocytic leukemia ( cll ) and also demonstrated that more than half of mirna genes are located in cancer - associated genomic regions or in fragile sites . in addition , lu et al . reported that the classification of malignant tumors based on mirna expression profiles was more precise than mrna profiles . these findings have facilitated mirna research in the field of oncology . in 2005 , two groups initially reported mirna dysregulation in glioblastoma using microarray analysis . chan et al . identified five upregulated and three downregulated mirnas out of 180 mirnas in glioblastoma , while ciafr et al . also demonstrated nine upregulated and four downregulated mirnas . a common mirna identified by both groups was mir - 21 , which was revealed to act as an antiapoptotic factor . both groups used microarray analysis to identify mirnas , whose expression was altered in glioblastoma . they also investigated the biological function of mir - 128 and mir - 10b , respectively . we subsequently applied the stem - loop reverse transcription - pcr array , which can evaluate mirna expression with sensitivity and specificity superior to microarrays . our study identified 16 mirnas for which expression was significantly altered in glioblastoma ( who grade 4 ) compared with anaplastic astrocytoma ( who grade 3 ) . furthermore , we clearly demonstrated that overexpression of mir - 196a or -196 b is correlated with shorter overall survival among patients with malignant glioma . in the same year , malzkorn et al . also identified 12 upregulated mirnas involved in the malignant progression of gliomas using stem - loop real - time rt - pcr . kim et al . also reported clinical implications of mir - 26 gene amplification in glioblastoma patients by using tcga data . recently , rao et al . performed locked nucleic acid ( lna ) array for a large - scale , genomewide mirna expression profile and identified 55 upregulated and 29 downregulated mirnas in malignant gliomas . more important thing of this study was that a cluster of only 23 mirnas was sufficient to distinguish glioblastoma from anaplastic astrocytoma with an accuracy of 95 % . identified a ten - mirna expression signature , which could predict overall survival of glioblastoma patients . more recently , combination of mrna and mirna expression profiling signature identified five glioblastoma subclasses . in this paper , mirnas dysregulated , which were identified by recent global studies for glioblastomas , were summarized ( table 1 ) . each report has demonstrated several mirnas , whose expression was significantly altered in glioblastoma compared with normal brain tissues or lower - grade gliomas . taken together ,52 upregulated mirnas and 33 downregulated mirnas have been reported by seven global studies published between 20052010 ( table 1 ) . . one of the causes of this diversity is the difference of methodology , platform , and control samples . consequently novel mirnas , of which more than three studies confirmed aberrations , were only four mirnas ( mir - 21 , mir - 10b , mir - 128 - 1 , and mir - 128 - 2 ) . in fact , newly identified mirnas have not been elucidated in previous analysis ; however , the number of concordance among these studies is extremely small . it would be better to say that these four mirnas may be consistently important in glioblastomas . one of the most common mirnas identified by recent studies of gliomas , mir - 21 has been revealed to act as an anti - apoptotic factor that targets a network of p53 , transforming growth factor ( tgf ) - , and mitochondrial apoptosis tumor suppressor genes in glioblastoma cells . overexpressed mir - 21 is a unique mirna , whose overexpression is identified in a large number of cancers investigated to date . essentially , medina et al . first demonstrated that tumors addicted to oncomirs by using an in vivo model of mir -21-induced pre - b - cell lymphoma . this result has facilitated the research elucidating the potential application as therapeutic targets in cancer . our data revealed that mir - 21 expression is significantly higher in glioblastoma than anaplastic astrocytoma ( 3.6 fold ) ; however , the expression did not affect patients ' outcome . the important point to note is that mir - 21 is only one mirna , whose overexpression is identified in all of the recent reports . we have already reported a significant association between high expression of mir - 196 and shorter overall survival among glioblastoma patients . expression of mir - 196a and mir - 196b is extremely high compared with other overexpressed mirnas in glioblastoma , so both of these two mirnas are considered to be associated with the malignant transformation of gliomas . our data also showed correlations between overexpression of mir - 196 and shorter overall survival with malignant gliomas . the characteristic of mir - 196 is the location in the vicinity of homeobox ( hox ) clusters within the genome of vertebrate genomes . three mir - 196 genes have been identified ; mir - 196a - 1 located on chromosome 17 ( 17q21 .32 ) at hoxb cluster , mir - 196a - 2 located on chromosome12 ( 12q13 .13 ) at hoxc cluster , and mir - 196b is located on chromosome 7 ( 7p15 .2 ) at hoxa cluster . interestingly , another mirna involved in the hox cluster , mir - 10b , appears strongly upregulated in glioma . recent reports have also indicated clinical implications of hox genes in glioblastoma , so the implications of mirna dysregulations in hox clusters should be clarified for glioblastomas . the function of mir - 196 is , however , more complicated , since the targets of mirna usually number more than one hundred . another target of mir196a , annexin a1 ( anxa1 ) , has also been implicated in glioblastoma as a mediator of apoptosis and an inhibitor of cell proliferation . previous study , which evaluated mirna expression in human cancer cell lines , also showed overexpression of mir - 196 in glioblastoma cell lines . however , lakomy et al . reported an association opposite to our finding between mir - 196b expression and clinical outcome , indicating another important aspects . further investigation is necessary to elucidate the clinical implications and biological functions of mir - 196 in malignant gliomas . upregulation of mir - 10b is one of the common aberrations in glioblastoma , which is identified by several recent reports ( table 1 ) . importantly , mir - 10b is overexpressed in the vast majority of glioblastoma , whereas it is not detected in normal brain . previous reports showed that mir - 10b was overexpressed in breast cancer and regulated invasion and metastasis by targeting hoxd10 . reported that the expression of rhoc and upar was correlated with mir - 10b expression level and lead to multifocal and dissemination of glioblastoma . . demonstrated that in glioblastoma mir - 10b regulated cell cycle and programmed cell death via regulation of bim , tfap2c , p16 , and p21 but not hoxd10 and was significantly associated with patients ' survival . in glioblastoma , the function of mir - 10b appeared to be different from breast cancer . godlewski et al . identified downregulation of mir - 128 in glioblastoma compared with adjacent brain , leading to a reduction in self - renewal of glioma stem cells via bmi - 1 downregulation . that report was the first demonstration of an association between mirna and stem - cell properties in glioma . in addition , tcga revealed that mir - 128 expression is lower in high - grade gliomas than in low - grade gliomas . a recent study revealed that reduced mir - 128 levels are associated with dedifferentiation and aggressiveness of malignant gliomas via egfr / pdgf / akt signaling . interestingly , mir - 128 is enriched in brain , and associated with terminally differentiated neuron . verhaak et al . have revealed that mir - 128 was repressed in glioblastoma classified the aggressive / dedifferentiated tumor subtype . mir - 128 has been shown to be able to repress the growth of glioma initiating cell in vivo . these findings support that mir - 128 has a potential to achieve its therapeutic effect by suppressing proliferation and enhancing differentiation of glioma initiating cells . two classifications based on mrna expression profiles have been reported in recent year , and both identified one of the subclasses as showing an expression signature resembling that of a proneuralhowever , the other subclasses of glioblastomas have shown little association with neural differentiation , and disagreement remains regarding the relationship of the subclasses to clinical outcomes . establishment of more accurate diagnostic and therapeutic strategies based on pathogenetic subclassification is obviously clinically important . recent attempts at mirna expression profiling may show the way toward more accurate classifications of human cancers than mrna expression profiling . furthermore , the recent large - scale multidimensional analysis of molecular characteristics , tcga , which includes expression profiles of mirna along with dna copy number , gene expression and dna methylation , has revealed frequent genetic alterations in three critical core pathways . in fact , kim et al . identified five clusters of glioblastoma based on mirna expression profiles , which appeared to predict clinical outcomes more precisely than mrna profiles . expression profiles using mirna are useful for subclassification of glioblastoma and could identify novel therapeutic targets . since the introduction of temozolomide ( tmz ) as standard chemotherapy , concomitant tmz and radiotherapy have improved both progression - free survival and overall survival in patients with gbm . however , the clinical prognosis of patients with gbm remains poor , with a median overall survival of only 14.6 months . the cancer stem cell ( csc ) hypothesis , that tumors are driven by a subpopulation of tumor cells with stem cell - like properties , may provide new insights into the radio - and chemo - resistance of gbm . based on this hypothesis , some therapies in which shrink tumors show reduced diameter might not be associated with improved rates of cure if cscs fail to be eliminated , and the therapies targeting cscs should prove clinically more effective . recently , some mirnas have been reported to contribute to csc properties and cancer heterogeneity . in addition to mir - 128 described above , mir - 124 , -137 , -34 a , and -326 have been reported to play roles in the maintenance of csc properties . the identification of mirnas thus adds another layer of gene expression associated with gliomagenesis and maintenance of csc properties via regulation of targeted signaling pathways . the regulation of aberrant mirnas could affect not only conventional radio - and chemo - therapy , but also the sensitivity to molecular target therapy . further study of mirnas function in csc may lead to novel treatment strategies for gbm patients . consideration of the therapeutic application of mirnas suggests two putative options : inhibition of oncogenic mirnas and replacement of tumor - suppressor mirnas . however , mirna - based therapy could be more practical than gene therapy , since mirna is a substantially small molecule . in conclusion , mirna appears to offer a crucial biomarker not only as a diagnostic marker , but also as a target for molecular therapies . the mirna approach to therapy could thus achieve modest changes for multiple genes and may prove more effective than current molecular targeted therapies to target single gene within an oncogenic signaling pathway . molecular - targeted therapy based on mirna expression in cscs has the potential to allow more personalized and effective treatment strategies in the not - too - distant future .\noutput:\n" }, { "from": "agent", "value": "microrna ( mirna ) is a new class of small noncoding rna molecules that regulate a wide spectrum of gene expression in a posttranscriptional manner . mirnas play crucial roles in tumorigenesis , angiogenesis , invasion , and apoptosis for various types of tumor . recent studies have identified dysregulation of specific mirnas in malignant gliomas . global expression profiling of mirnas has revealed several mirnas clinically implicated in human glioblastomas . some mirnas are clearly associated with clinical outcome and chemo - and radio - therapy resistance in these tumors . furthermore , mirnas also regulate specific signaling pathways , including the critical core pathways in glioblastoma . as a result , mirnas have the potential to affect the responses to molecular - targeted therapies . more recent studies have revealed that mirnas might be associated with cancer stem cell properties , affecting tumor maintenance and progression . recent investigation have revealed that mirnas are not only biological markers with diagnostic implications , but also one of the most promising treatment targets in human glioblastoma . herein , we summarized the novel insights of mirnas into human malignant gliomas ." } ]

[ { "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: four years after food and drug administration ( fda ) approval , the first oral treatment for relapsing forms of ms , fty720 , is showing good efficacy for managing morbidity and the progression of active disease . therapeutically , the benefit afforded by fty720 in managing symptoms of relapsing - remitting ms appears largely dependent on s1p1 - dependent modulation on immune blood cells , neurons , astrocytes and endothelia , all mediated by its active phosphorylated fty720 - p ( s1p - mimic , figure 1 ) product . in 1996 , closely following its synthesis , fty720 demonstrated efficacy in preventing transplant rejection across animal models due to its potent immunosuppressive action . it later became discontinued for that indication based on findings that fty720 did not afford additional benefit to standard of care therapy . findings that s1p1 modulation was the driving force behind fty720 's efficacy and that the fty720 - mediated sequestration of circulating lymphocytes , or immune modulation ( correlated with positive therapeutic outcomes ) , has prompted the search for second - generation compounds . these compounds either have a structural similarity to the fty720 prodrug backbone , or are newer , directly acting modulators having chemically optimized aromatic backbones and a higher selectivity window for s1p1 over s1p3 , while still having s1p5 activity ( figure 2 and table 1 ) . the other difference between the newer class modulators and fty720 appears to be in the time course of immunosuppression , with the newer compounds having shorter half - lives and a shorter duration of lymphopenia , in contrast to the long - lasting fty720 actions . in addition , the therapeutic efficacy of the newer compounds appears to correlate well with the lymphocyte reduction mechanism ( s ) first defined by fty720 . in ms , there are several s1p receptor modulators being tested , such as siponimod , krp - 203 , cs - 0777 , and rpc - 1063 . siponimod is an oral , second - generation s1p1 / 5 modulator in phase 3 development for secondary progressive ms . the results from the bold siponimod study , an adaptive dose - ranging phase 2 study , were published in 2013 and showed that , compared to placebo , siponimod reduced brain magnetic resonance imaging ( mri ) lesions and relapses by up to 80 % in relapsing - remitting ms . phase 3 development of siponimod in secondary progressive ms started in 2012 , and results should be available in 2017 . this article will highlight key preclinical findings of immunomodulators with a high selectivity window for s1p1 and / or s1p5 in support of furthering available treatment options in various autoimmune conditions . a ) sphingosine is a substrate for two long - chain base kinases , sphingosine kinase 1 and 2 ( sphk1 and sphk2 ) , which phosphorylate sphingosine on its primary hydroxyl group generating s1p . s1p accumulation in distinct intracellular environments also mediates a variety of biological processes through non - receptor - mediated mechanisms . these processes include a role for sphk2 - generated s1p in the apoptosis of lymphoid cells and sphk2 - mediated s1p formation and s1p binding to the histone deacetylases hdac1 and hdac2 to control gene transcription . s1p can also be degraded intracellularly by dephosphorylation to sphingosine , or being diverted from lysolipid metabolism by degradation to phosphatidylethanolamine and hexadecanal by s1p lyase . b ) circulating s1p binds to and activates five high - affinity g protein - coupled receptors ( gpcrs ) , s1p1 - 5 . unlike sphingosine phosphorylation , fty720 phosphorylation appears to be exclusively mediated by sphk2 whereas the dephosphorylation of fty720 - p has been shown to involve both lipid phosphate phosphatase 3 and 1a . fty720 - p is able to bind with high nanomolar affinity to all s1p receptors , except s1p2 . in addition to s1p receptors , the prodrug has been found to target cytosolic phospholipase a2 ( cpla2 ) , sphingosine lyase , and transient receptor potential cation channel ( trp7 ) and while these other interactions may not prove critical in the regulation of lymphocyte sequestration by fty720 , they may play a role in its tolerability and potential side effects following long - term , broad exposure in patients . structures of the endogenous ligand s1p , the non - selective s1p1 ,3 - 5 receptor modulator pro - drugs fty720 and aal - r , the s1p1 / 4/5 modulator prodrug krp - 203 , and the s1p1 / 5 modulators ceralifimod , ponesimod , siponimod , cym - 5442 and rp - 001 . av - block , atrioventricular block ; fev , forced expiratory volume ; ms , multiple sclerosis ; rr - ms , relapsing - remitting ms ; sp - ms , secondary progressive multiple sclerosis ; s1p , sphingosine -1-phosphate ; uc , ulcerative colitis . first - line corticosteroidal therapy and sulfasalazine ameliorate intestinal inflammation but have substantial toxicity . suppressing local inflammation to the intestine by conventional 5 - aminosalicylic acids ( 5 - asa ) therapeutics reduces andsecond - line anti - tumor necrosis factor alpha ( tnf - ) monoclonal antibodies , though safer than conventional immunosuppressants , are another option , yet can lose effectiveness over time , and can predispose certain patients to potentially fatal opportunistic infections . s1p receptor modulatory strategies have been evaluated in animal models of ibd in the past . data using fty720 and krp - 203 , and later backed by the ono - 4641 prototype w - 061 ( s1p1 / 5 modulator of unpublished structure ) , show effectiveness for alleviating multiple aspects of chronic intestinal inflammation . krp - 203 is a s1p1 / 4/5 agonist prodrug with a molecular structure resembling fty720 . like fty720 , krp - 203 sequesters circulating lymphocytes in secondary lymphoid organs in mice , and was first shown to prolong skin and heart allograft survival and significantly attenuate chronic rejection . the efficacy of krp - 203 was assessed in the validated il -10-deficient mouse model of human ibd . il - 10 knockouts develop distal small bowel inflammation spontaneously and display hallmark ibd histolopathological findings due to immune cell recruitment to the mucosa , enhanced production of t helper ( th ) - 1 cytokines , resulting in the disruption of the mucosal barrier , low body weight and poor survival . song et al . reported that krp - 203 administration to il - 10 knockout mice reduced mortality once the disease had been established . both acute , 7 - day , and chronic , 28 - day , daily krp - 203 protocols reduced histological scores in the colon and prevented weight loss vs. vehicle - treated controls . a decreased recruitment of lymphocytes to the colonic lamina propria in the krp - 203 group correlated with the survival benefit and the immunohistological findings . a separate study using w - 061 reported reduced inflammation to the distal colon of mice that underwent chemical dextran sodium sulfate ( dss ) - induced colitis . w - 061 administration in this model reduced cellular infiltration to the colonic lamina propria , with associated reductions in th17 and th1 cytokines as measured in cultured cd4 - t cells isolated from the w - 061 treated group at study end . w - 061 also prevented mucosal thickness and mucin depletion induced by dss , relative to vehicle treatment . the results with krp - 203 and w - 061 are promising and recapitulate some of the findings of fty720 in animal models of ibd . fty720 at low 0.3 mg / kg dose was effective in preventing body weight loss in the dss colitis model and the cd4 + cd62l + t cell transfer models of colitis . in addition , therapeutic efficacy of fty720 was reported in the 2,4,6 - trinitrobenzenesulfonic acid ( tnbs ) inflammatory colitis model , whereby drug treatment led to the dampening of il - 12p70 and subsequent th1 pro - inflammatory cytokines , while simultaneously inducing the functional activity of cd4 + cd25 + regulatory t cells . this indicates that , besides migration and the homing of lymphocytes to secondary lymphoid organs via s1p1 , fty720 can also influence cytokine effector function directly , as was shown by the prophylactic and therapeutic efficacy of fty720 in the th2 - mediated oxazolone - induced colitis model in balb / c mice . another class of s1p1 modulator , rpc - 1063 ( of unpublished structure , but of similar backbone to rp - 001 , figure 2 ) , is being currently tested worldwide as an oral therapeutic in phase 2 clinical trials of uc . in healthy subjects , rpc - 1063 has shown no qtc interval alterations , and is additionally being evaluated in phase 3 trials in relapsing - remitting ms . fty720 has been compared against methylprednisolone in the mlr / lpr experimental autoimmune lupus mouse model , which has a mutation in t cell - dependent immune dysfunction with human - like sle phenotype . the clinical goal of therapy relies on suppressing the renal complications , or lupus nephritis that leads the mortality index in sle . genetically modified mrl / lpr mice have a mutational deficit in the fas - mediated apoptosis of lymphoid cells , and spontaneously develop severe glomerulonephritis , vasculitis and tubular atrophy , replicating some of the clinical features of the human disease . proteinuria , microscopic deposition of anti - double stranded dna antibodies with complement contribution are strong markers of kidney malfunction in mlr / lpr mice , as well as in patients with sle . okazaki et al . reported on survival , disease biomarkers , apoptotic indexes , and immune cellularity in mrl / lpr mice treated with fty720 or methylprednisolone . fty720 and the steroid showed survival protection vs. controls , with reduced igg glomerular complex deposition consistent with the survival advantage . notably , fty720 treated mlr / lpr mice had drug - induced apoptotic destruction of a double - negative t cell population that is inherently dysregulated in this model . while the paper did not report on histopathology , wenderfer et al. showed histological findings after a 12 - week 6 mg / kg krp - 203 daily dosing study in mlr / lpr mice . drug treatment increased survival only at therapeutic dosing , inhibiting glomerulonephritis , vasculitis and tubular atrophy . there was also decreased proteinuria by krp - 203 , although no differences in serum anti - double stranded dna iggs titers were noted . findings that krp - 203 , like fty720 , promoted dose - dependent apoptosis in double - negative t cells in mlr / lpr mice strongly support the argument that s1p receptor targeting efficacy , in this model , is mostly dependent on fas - independent pathway apoptosis . the selective s1p1 / 3/5 modulator ponesimod has successfully met the primary endpoint of efficacy and safety in patients with moderate to severe chronic plaque psoriasis . the proportion of patients with at least 75 % improvement in psoriasis area and severity index ( pasi ) from baseline ( pasi75 ) at week 16 was determined in a double - blind , placebo - controlled study consisting of 326 patients . with ponesimod 20 mg daily , nearly half of patients improved by at least 75 % at week 16 ( p 0.0001 vs. placebo ) . doubling the dose improved the outcome by at least 75 % in patients at week 16 ( p 0.0001 vs. placebo ) , whereas only 13.4 % of the placebo group improved by 75 % . safety and tolerability data from this study were consistent with the safety profile of ponesimod observed in the past , including a phase 2 study in ms . as expected of s1p receptor modulators , there was a transient bradycardia and , less frequently , a transient effect on atrioventricular conduction . dyspnea andthese results suggest that ponesimod could become a first in its class , oral therapeutic for treating psoriasis , although it has been discontinued as a potential ms therapeutic . early studies of acute viral lung pathogenesis , using the wsn strain of the influenza a virus , demonstrated that compounds targeting multiple s1p receptor subtypes suppressed the cytokine response during infection . specifically , the results demonstrated that intratracheal but not intraperitoneal administration of aal - r , an fty720 analog ( table 1 ) , to infected mice reduced mortality and the accumulation and proliferation of activated cd8 + - t cells into the lung . subsequent studies with cym - 5442 and rp - 001 , compounds designed to target only the s1p1 subtype , also significantly reduced morbidity and mortality in mice infected with the highly virulent human isolate of pandemic 2009 h1n1 . the authors proposed that these compounds increased survival by blunting and not abolishing excessive cytokine production often associated with certain virus strains . a follow up animal study using ferrets , a relevant model used in influenza research due to its human - like mode of airway viral propagation and ability to develop symptoms seen in humans , were performed using the s1p1 - specific agonist rp - 002 . the study demonstrated that agonism of the s1p1 receptor down - regulated and controlled the overly robust innate inflammatory response while minimally altering viral replication . gavage administration of rp - 002 to h1n1 : 2009 infected ferrets significantly reduced mortality as compared to vehicle - administered controls . additionally , the survival benefit in the ferret study was improved upon co - administration of rp - 002 with the neuraminidase inhibitor oseltamivir . the authors concluded that rp - 002 and oseltamivir as combined therapy conferred maximal protection by blunting both the immune pathology and viral replication . the mechanism used by the s1p1 receptor to modulate cytokine secretion and subsequent morbidity remains unknown . future studies should examine whether the s1p1 receptor directly modulates toll - like receptor - 7 ( tlr - 7 ) . it is feasible that both of these transmembrane proteins reside in the same subcellular compartment and upon s1p1 agonism whether a transient disruption of tlr - 7 's microdomain occurs . this disruption may result in the abrogation of tlr - 7 signaling through the canonical myd88 - irf - 7 pathway . since this pathway is chemically tractableoverall , the data is promising in defining a proof - of - concept mechanism and should be carefully explored as an option to dampen excessive host innate immune collateral damage from highly pathogenic viruses . early studies of acute viral lung pathogenesis , using the wsn strain of the influenza a virus , demonstrated that compounds targeting multiple s1p receptor subtypes suppressed the cytokine response during infection . specifically , the results demonstrated that intratracheal but not intraperitoneal administration of aal - r , an fty720 analog ( table 1 ) , to infected mice reduced mortality and the accumulation and proliferation of activated cd8 + - t cells into the lung . subsequent studies with cym - 5442 and rp - 001 , compounds designed to target only the s1p1 subtype , also significantly reduced morbidity and mortality in mice infected with the highly virulent human isolate of pandemic 2009 h1n1 . the authors proposed that these compounds increased survival by blunting and not abolishing excessive cytokine production often associated with certain virus strains . a follow up animal study using ferrets , a relevant model used in influenza research due to its human - like mode of airway viral propagation and ability to develop symptoms seen in humans , were performed using the s1p1 - specific agonist rp - 002 . the study demonstrated that agonism of the s1p1 receptor down - regulated and controlled the overly robust innate inflammatory response while minimally altering viral replication . gavage administration of rp - 002 to h1n1 : 2009 infected ferrets significantly reduced mortality as compared to vehicle - administered controls . additionally , the survival benefit in the ferret study was improved upon co - administration of rp - 002 with the neuraminidase inhibitor oseltamivir . the authors concluded that rp - 002 and oseltamivir as combined therapy conferred maximal protection by blunting both the immune pathology and viral replication . the mechanism used by the s1p1 receptor to modulate cytokine secretion and subsequent morbidity remains unknown . future studies should examine whether the s1p1 receptor directly modulates toll - like receptor - 7 ( tlr - 7 ) . it is feasible that both of these transmembrane proteins reside in the same subcellular compartment and upon s1p1 agonism whether a transient disruption of tlr - 7 's microdomain occurs . this disruption may result in the abrogation of tlr - 7 signaling through the canonical myd88 - irf - 7 pathway . since this pathway is chemically tractableoverall , the data is promising in defining a proof - of - concept mechanism and should be carefully explored as an option to dampen excessive host innate immune collateral damage from highly pathogenic viruses . the remarkable impact of therapeutic modulation of the s1p - s1pr1 axis reflects the multi - point interdiction of autoimmune pathogenesis . by blunting but not abolishing immune protection , these therapies provide unprecedented efficacy in ms and uc with a tolerability window that enhances the possibilities of treating autoimmune diseases with fewer infectious complications . because disease relapse is clinically unpredictable , and especially difficult to treat in certain patients , evaluation of s1p receptor modulatory therapies needs to be thoroughly explored in additional pre - clinical studies . underlying the disease is a chronic and progressive state of local inflammation known to alter the metabolism of pathway ( s ) regulating s1p levels . for instance , intestinal biopsy samples in patients with uc reveal a deregulated metabolic pathway whereby sphingosine kinase 1 ( sphk - 1 ) and s1p phosphohydrolase - 1 ( sph - ppase ) are upregulated and sphingosine 1 - phosphate lyase ( spl ) is downregulated ( figure 1 ) , leading to high local tissue s1p concentration . sphk - 1 upregulation in humans is consistent with a key role of sphk1 in promoting murine intestinal inflammation and colitis - associated cancer via hyperactive intestinal nuclear factor - b ( nf - kb ) - signal transducer and activator of transcription 3 ( stat - 3 ) signaling . one important question is whether s1p1 modulation alone would be sufficient to clinically reduce fully active intestinal disease , or whether it may be indicated as maintenance therapy . the other question is whether global immunomodulation by s1p1 selective or s1p1 / 5 selective compounds may be contraindicated with adjunct therapeutics of ibd , as shown with tnf - blockers and other immunomodulators . the uc touchstone phase 2 clinical trial results demonstrated the medically significant efficacy of daily 1 mg rpc1063 . the study enrolled 199 patients split into three arms , placebo , low dose ( 0.5 mg ) and high dose ( 1.0 mg ) . at 8 weeks of treatment , induction of clinical remission reported by standard mayo scoring , was 16.4 % ( p 0.05 ) of the patients on the 1 mg dose as compared to 6.4 % on placebo . whether human genetic factors are involved that would alter the predisposition for such sphk - 1 pathways in uc and colitis - associated cancer needs to be investigated , and whether s1p1 and or s1p1 / 5 modulator therapy can dampen inflammation - promoting colitis - associated cancer is not known . nevertheless , s1p1 modulations of lymphocyte trafficking and cytokine production strategies represent a good opportunity to reduce intestinal inflammation in ibd and provide a steroid alternative to chronic use . hugh rosen is a scientific co - founder and scientific advisory board member of receptos and has a significant financial interest in the company .\noutput:\n" }, { "from": "agent", "value": "development of sphingosine -1-phosphate receptor 1 ( s1p1 ) modulators to dampen inflammation and its sequelae is becoming increasingly promising for treating medical conditions characterized by significant immunopathology . as shown by the non - selective s1p receptor modulator fty720 ( fingolimod [ gilenya ] ) in the treatment of relapsing - remitting multiple sclerosis ( ms ) , the ability to use s1p1 modulation to precisely block immune cell traffic immunomodulation while maintaining immunosurveillance , has opened therapeutic opportunities in various other immune - derived chronic pathologies , including inflammatory bowel disease ( ibd ) , lupus , psoriasis , as well as , potentially , in early acute viral respiratory infection . proof - of - concept studies across validated animal models with s1p receptor modulators highly selective for s1p1 , such as baf - 312 ( siponimod ) , krp - 203 , ono - 4641 ( ceralifimod ) , ponesimod and rpc - 1063 , and emerging clinical trials for safety and efficacy in humans , particularly in ms , ulcerative colitis ( uc ) and psoriasis , have set the stage for us to consider additional testing in various other autoimmune diseases ." } ]

[ { "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: during the process of infection , after the engagement of innate immunity into the defence system , adaptive immunity is activated . the principal effectors of cellular immunity are t lymphocytes , while the principle effectors of humoral immunity are b lymphocytes . the activation of adaptive immunity is mediated by the production of antibodies by b lymphocytes that are able , for example , to block the adhesion of pathogens on mucosal surfaces , agglutinate bacteria , or to neutralise pathogens in blood circulation and subsequently activate complement . the antigens are then eliminated by t cells or in concert with specific antibodies further produced by b cells . abnormal cell - mediated immunity , including changes in main immunoglobulins as well as their subclasses that play a specific role in the immune response cascades , namely , igg subclasses igg1 and igg3 are complement activators via their binding to the protein antigens of the pathogens . igg2 usually mediates immune response to polysaccharide ( bacterial ) antigen and opsonisation of encapsulated bacteria . subclass igg4 binds to protein antigens of gram - positive bacteria and activates phagocytic cells . igg subclass deficiencies lead to the alteration of immune defence against microbial pathogens and thus increase the risk of repeated infections . the immune system has been studied in patients with diabetes mellitus but with conflicting results . in the face of chronic hyperglycaemia ( predominantly of more than 10mmol / l ) , alterations of several steps of phagocytosis including oxidative burst and occasionally abnormalities of selected lymphocyte subpopulations as well as immunoglobulins have been described in both in vivo and in vitro studies . therefore , we could hypothesised that the impairment of immune system function could be present also in patients with diabetic foot ulcers ( dfus ) , in whom infection related complications occur quite frequently and could lead to lower limb amputation . in our previous study , we investigated possible changes of the immune system in patients with chronic dfus . the results of this study revealed mild immunological changes characterised by the activation of the inflammatory response such as increased leucocyte and neutrophil counts , crp , and iga levels . however , more serious immunodeficiencies of adaptive or innate immunity have not been observed in such risk group of diabetic patients to date . the aim of our current study was to analyse in detail the presence of possible immunological abnormalities in humoral as well as in cell - mediated immunity in patients with more severe , chronically infected dfus and the potential relationship between immunological alterations and glycaemic control . in addition , we analysed differences in selected immune parameters between the patients with ulcers infected by sensitive pathogens and those infected by resistant bacterial strains recruited presumably from repeated chronic infections and antibiotic therapy in whom we hypothesised an immunocompromisation .68 patients with type 1 and type 2 diabetes mellitus aged between 30 and 70 years with infected dfus were consecutively included into our cross - sectional study . control group was formed by 34 patients matched by age , gender , and type of diabetes but without a history of diabetic foot disease . we included those patients with dfus who had been treated according to current guidance by the iwgdf in our out - patient foot clinic for their dfus for at least six weeks , were classified as texas ii - iii / b - d , and had mild or moderate infection as defined by the pedis system . the presence of infection was confirmed by clinical findings and / or elevated laboratory markers of inflammation ; osteomyelitis was defined clinically , by x - ray , positive microbial findings , and / or laboratory signs of infection . before inclusion , patients with dfus had to have at least two positive wound cultures from swabs taken from the deep tissue after local debridement . resistance to antibiotics was tested by sets of antibiotics composed on the basis of previous analysis of resistance at the institute for clinical and experimental medicine and upon the recommendations of the national reference laboratory on antibiotics , national institute of health , prague , czech republic . microbial resistance to different types of antibiotics was determined by disc diffusion test . minimum inhibitory concentration ( mic ) was evaluated only in special cases by broth microdilution testing on microplates or by using the gradient method ( e - test ) . resistant pathogens were defined as those resistant to all oral antibiotics or produced enzymes causing microbial resistance such as esbl ( broad - spectrum beta - lactamase ) , ampc ( beta - lactamase c ) , and mec gen . our department of clinical microbiology works with eucast methodology to interpret the results of sensitivity using clinical breakpoints according to the current version . to identify resistance phenotypes ( determination of resistant / sensitive pathogens ) we also used methods developed by the national reference laboratory on antibiotics , national institute of health , prague , czech republic . patients with critical limb ischemia ( doppler ankle / brachial index 0.6 and / or doppler toe pressure 50 mmhg and / or transcutaneous oxygen pressure ( tcpo2 ) 30 mmhg and / or advanced arterial stenosis or occlusion requiring endovascular / surgical revascularisation based on invasive arterial assessment , angiography , ct - , or mr - angiography ) , with no option critical limb ischemia , advanced renal insufficiency ( based on chronic kidney disease classification of 4th and 5th stage ) , active cancer , signs of acute infection , treatment with corticosteroids or other immunosuppressive drugs , post - organ transplant , with known immune dysfunction , hepatic failure , or malnutrition were excluded . all patients with infected chronic dfus included into our study were further divided into two subgroups : patients from whom sensitive microbial strains were isolated ( subgroup s , n = 50 ) and those from whom resistant microbes ( subgroup r , n = 18 ) were isolated on at least one occasion . these subgroups did not differ significantly in age , tcpo2 , type and duration of dfus , the incidence of osteomyelitis , or dfus characteristics ( depth , area ) . the following were measured in all participants : blood glucose level ( by spectrophotometry ; abbott architect , usa ) , creatinine ( detected enzymatically ; abbott architect , usa ) , and glycosylated haemoglobin ( hba1c : normal values 2042 mmol / mol ; by hplc method ; tosoh g8 , japan ) . from laboratory markers of infectionwere assessed crp ( determined turbidimetrically ; abbott architect , usa ) , procalcitonin ( by electrochemiluminescence ; eclia , cobac 6000 , roche , switzerland ) , and blood cell counts ( by spectrophotometry ; sysmex , japan ) . complements represented by c3 , c4 ( by immunonephelometry ; abbott architect , usa ) , the absolute amounts and percentages of nk cells ( cd16 / 56 + cells ) , and cd14 + hla - dr cells ( monocytes , which serve as an important prognostic factor for the progression of an infection , especially in septic stage ) were measured . nk cells and cd14 + hla - dr cells were determined together with subpopulations of lymphocytes ( see below ) by flow cytometry . phagocytosis was defined by the percentage of phagocytic cells and fagsi ( phagocyte stimulation index ) . phagocytic activity of granulocytes was tested by measuring the respiratory ( oxidative ) burst after their stimulation with e. coli bacteria in human heparinized whole blood using flow cytometry . cd3 + , cd4 + , cd8 + , naive inactive ( cd4 + cd45ra + cd62l + ) , memory inactive ( cd4 + cd45racd62l + ) , naive effector ( cd4 + cd45ra + cd62l ) and memory effector cd4 + t lymphocytes ( cd4 + cd45racd62l ) and naive inactive ( cd8 + cd45ra + cd62l + ) , memory inactive ( cd8 + cd45racd62l + ) , naive effector ( cd8 + cd45ra + cd62l ) , and memory effector cd8 + t lymphocytes ( cd8 + cd45racd62l ) were assessed by flow cytometry . also we assessed their indexes counted as naive / memory cells . during flow cytometry venous blood samples were collected into sterile tubes containing edta . lymphocytes from peripheral blood ( 100 l ; approximately 110 cells ) were labelled with a 4 - color monoclonal antibody panel cyto - stat tetrachrome cd45 - fitc ( clone : b3821f4a ) / cd56 - rd1 ( clone : n901 / nkh1 ) / cd19 - ecd ( clone : j3 - 119 ) / cd3 - pc5 ( clone : ucht1 ) + cd16 - pe ( clone : 3g8 ) and cd45 - fitc ( clone : b3821f4a ) / cd4 - rd1 ( clone : sfci12t4d11 ) / cd8 - ecd ( clone : sfci21thy2d3 ) / cd3 ( clone : ucht1 ) ( all beckman coulter , brea , ca ) . the specific antibody panels used for t effector cells consisted of anti - cd4 - pe ( clone : 13b8 .2 ) , anti - cd8 - pc7 ( clone : sfci21thy2d3 ) , anti - cd62l - pc5 ( clone : dreg56 ) , and anti - cd45ra - fitc ( clone : alb11 ) ( all beckman coulter , brea , ca ) . the specific antibody panels used for activation of cd14 + cells consisted of anti - cd14 ( clone : rm052 ) and anti - hla - dr - pe ( clone : immu357 ) ( beckman coulter , brea , ca ) . following staining , samples were analysed using an fc 500 flow cytometer ( beckman coulter ) with cxp and kaluza software ( beckman coulter ) . serum levels of immunoglobulins ( igm , iga , and igg , diagnosed by immunoturbidimetry ; abbott architect , usa ) and igg subclasses ( determined by immunonephelometry ; immage / immage 800 , beckman coulter , usa ) were also measured . in addition to this , we also compared the number of patients with deficits , particularly in igg subclasses . deficiencies were defined as serum levels of certain immunoglo - bulin or its subclass below physiological ranges that were determined by several studies and the producer beckman coulter . the characteristics of patients , laboratory markers of infection , and selected measures of innate and adaptive immunity , including lymphocyte subpopulations and igg subclasses , were compared between the study groups and subgroups . descriptive data were presented as means sd ; differences between all study groups were determined using t - test , mann whitney test , and multiple comparisons for kruskal - wallis test . the spearman rank correlation coefficient was used to determine any significant correlation between assessed data . patients with infected dfus did not differ significantly in basic characteristics from the diabetic controls apart from higher serum creatinine levels ( table 1 ) . study patients with dfus had median of dfu duration 7.5 months ( range 1.548 months ) and median of ulcer area 1 cm ( range 0.0443.4 cm ) .66.2 % of patients had dfus of texas classification iib / d and 33.8 % of texas classification iiib / d . total numbers of leukocytes ( 7.71.9 versus 8.52.410 / l ; ns ) , neutrophils ( 5.11.5 versus 5.31.810 / l ; ns ) , and other laboratory markers of infection instead of crp ( table 1 ) did not differ significantly between patients with dfus and diabetic controls . there were no changes in measures of innate immunity except for lower absolute numbers of nk cells between the two study groups ( table 2 ) . differences were observed predominantly in measures as of cellular as of humoral branch arm of adaptive immunity . reductions of percentages and absolute values of total lymphocytes and decreased absolute numbers of almost all types of lymphocytes subpopulations including b lymphocytes , cd4 + , cd8 + t lymphocytes , and their effector and memory cells ( table 3 ) as well as changes in humoral immunity were found in patients with infected dfus ( table 4 ) . from the evaluated immunological measures only igg2 ( r = 0.2008 ; p 0.05 ) and igg3 ( r = 0.1972 ; p 0.05 ) significantly negatively correlated with hba1c . patients infected by resistant pathogens differed significantly from those infected by sensitive microorganisms in the percentage of basophils ( 0.430.24 versus 0.660.3810 / l ; p 0.01 ) . other measures of inflammation did not differ significantly between the study subgroups except a significantly higher percentage of nk cells in subgroup r ( 16.67.5 versus 12.35.7 ; p 0.01 ) compared to subgroup s. moreover , subgroup r did not reach high levels of iga ( 3.071.15 versus 3.741.35 g / l ; ns ) , igg ( 11.013.01 versus 12.693.16 g / l ; p 0.05 ) , and igg1 ( 6.492.13 versus 6.982.22 g / l ; ns ) in contrast to subgroup s that differed significantly in mentioned parameters compared to diabetic controls ( figure 1 ) . subgroup r was characterised by significantly lower levels of igg4 compared to subgroup s and diabetic controls ( 0.290.25 versus 0.540.43 and 0.430.38 there were no significant differences in deficits of each immunological subclass between the study groups ( table 4 ) , except a trend to higher igg2 subclass deficiency shown in patients with infected dfus compared to diabetic controls ( 22 versus 15 % ) . in our study , we focused on the evaluation of systemic immunity changes to determine the occurrence of immune deficiencies at the level as of innate as of adaptive immunity . we aimed to clarify whether some patients with any kind of immunodeficiency exist among those treated for nonhealing chronically infected wounds . it could help in several cases potentially explain the prolonged dfus healing and inadequate inflammatory response to local infection . we did not assess any immune parameters or mediators at the local level since their concentrations could be modified by a variety of factors including , for example , the mild forms of peripheral arterial disease or previous applications of biological active local dressings . the main findings in patients with chronically infected dfus were the significantly reduced percentages and absolute numbers of lymphocytes in contrast to diabetic controls without dfus . we could explain the lower serum levels of lymphocytes by a previously described impairment of immune system at the level of lymphoid stem cells or mesenchymal cells or other factors including stress , age , and possibly diabetes mellitus alone . such factors could induce dysregulations of cytokine production and glycation of specific proteins may be behind the control of production and differentiation of lymphocytes . moreover , decreased numbers of lymphocytes in patients with chronically infected dfus could be related to an immunological pressure in which bacterial infection induces a production of polymorphonuclear cells potentially leading to relative suppression or increased apoptosis of lymphocytes as was described by arya et al . . nevertheless , we did not find higher levels of neutrophils in our patients with dfus . the reduced number of lymphocytes seen in our study in patients with the dfus was associated with a decline in the absolute numbers of almost all subpopulations of lymphocytes including t - helper , cytotoxic lymphocytes , b lymphocytes and naive , memory inactive , and effector cells as of cd4 + as ofcd8 + t lymphocytes . similar findings have been demonstrated in experimental animal models and also in healthy individuals under conditions of acutely induced hyperglycaemia , which led not only to lymphopenia but also to a decline of subpopulations of lymphocytes including cd3 + , cd4 + , and cd8 + t lymphocytes . in our study , however , correlations between blood glucose levels or hba1c and subpopulations of lymphocytes were not seen . naive cells are defined by the expression of cd45ra antigen , which is present on the surface of approximately 50 % of t lymphocytes . t lymphocytes expressing on their surface the cd45ro antigen are antigen activated cells ( memory cells ) . ( cd4 + ) . during the activation of t lymphocytes ( i.e. , due to infection ) , the expression of cd45ra decreases simultaneously with the increase of the expression of cd45ro isoforms . the rise of effector cells , particularly cd8 + effector memory cells , together with the lower indexes of naive / memory cells should be seen during the infection . however , we observed neither increased counts of effector cells nor decreased indexes in patients with diabetes and chronic infection within the diabetic foot . we could speculate that the appropriate activation of selected types of lymphocytes does not occur due to the long - lasting depletion of the immune system by repeated and / or chronic infections . other significant changes that were found in our study were alterations in the humoral arm of the adaptive immune system , in immunoglobulins levels . in addition to elevated serum levels of total iga and igg , patients with dfus had in comparison to diabetic controls significant differences in igg subclasses , specifically increased levels of igg1 and igg3 suggesting activation of immune system by inflammation . both molecules serve as complement activators via binding to the protein antigen of the pathogen . therefore , the elevation of their values is not surprising in infection , although it has not been previously described in patients with chronically infected dfus . since a response to bacterial infectioncould be altered in patients with dfus , especially in the presence of immunoglobulin deficiencies particularly in igg subclasses , we have also focused on their detection . a high number of patients from both study groups showed igg2 deficiencies ( defined as serum levels below 2.42 g / l ) , exceeding 1520 % . in the general population , although the most common selective deficit of igg subclasses is an igg2 deficit , however real prevalence data are unavailable . the occurrence of igg subclass deficiencies in the diabetic population , even in patients with dfus , has not been previously described . since igg2 plays an important role in the inflammatory cascade due to the ability to opsonise bacteria , its deficiency may contribute to an increased risk of infection . detected deficits of igg2 subclasses could possibly be secondary to diabetes , since serum levels of igg2 and also igg3 in our study negatively correlated with glycaemic control . we could thus hypothesise that reduced production or greater degradation of immunoglobulins as glycoproteins may be related to their glycation ( b lymphocytes were reduced but their absolute numbers did not correlate with diabetes control ) . conversely , deficits of certain immunoglobulin subclasses could be also caused by long - lasting consumption of them during chronic bacterial load . this theory is supported by the finding of decreased levels of igg and predominantly of igg4 subclasses in the patients repeatedly infected predominantly by resistant pathogens . looking at the possible alterations of the immune system in patients infected by resistant pathogens , we did not find the marked deficits of immune system that we initially supposed in such cohort in contrast to patients infected by sensitive microorganisms . differences were seen predominantly in humoral immunity in the patients with resistant pathogens , in whom the serum levels of individual immunoglobulins and even igg subclasses did not reach the levels detected in patients infected by sensitive microorganisms . in fact , igg4 values were significantly lower , less than half of those found in the subgroup with sensitive pathogens and diabetic controls . we speculate that patients with dfus infected by resistant pathogens have a predisposition to the long persistence of these bacteria possibly due to insufficiently activated humoral immunity , which in turn leads to reduced opsonisation , activation of cell - mediated immunity , and reduced elimination of pathogens by the immune system . our study did not show significant alterations of the immune system at the level of innate immune system including measures of phagocytosis . no changes were found in values of c3 , which is usually reduced during infection due to its consumption or hyperglycaemia . lower absolute numbers of nk cells in our study in patients with dfus were probably given by lower values of total lymphocytes . significantly increased laboratory markers of infection in patients with infected dfus are closely related to physiologically stimulated immune response to inflammation . this confirms the results of other studies , which have not demonstrated dramatic increase of inflammation in patients with dfus despite the presence of infectious complications including osteomyelitis . in our studyonly slightly elevated crp levels up to 10 mg / l ( detected in 33/68 , 49 % , of patients with the dfus versus 5/34 , 15 % , of diabetic controls ; p 0.01 ) , and more than half of the patients actually had crp levels within the normal range . elevated serum procalcitonin has been suggested to be a better predictor for the presence of infection or osteomyelitis than the other laboratory markers of inflammation , except crp . however , we did not find significant abnormalities in procalcitonin levels . from other laboratory markers of infection , the numbers of neutrophils were not significantly increased in our patients with dfus , and this finding is in accordance with other studies . based on the above data , we could surmise that a significant activation of systemic inflammatory immune response does not occur in patients with infected chronic dfus as could be expected in the case of inflammation including osteomyelitis . we conclude that in this group of patients with infected chronic dfus mild activation of a systemic inflammatory response and significantly reduced numbers of lymphocytes , including nearly all of their subpopulations , were found . there was no evidence , however , of their activation , especially an increase of effector cells or reduction of appropriate subpopulations indexes ( naive / memory cells ) as may have been expected . in patients with infected dfuswe further demonstrated abnormalities of the humoral components of immunity particularly at the level of igg subclasses combined with a relatively high incidence of their deficits , especially of igg2 . changes in igg subclasses were more prevalent in patients whose dfus were infected by resistant pathogens . we did not include into our study patients with noninfected diabetic foot ulcers since they represent only a minority group of our complicated patients with the diabetic foot in our foot clinic which provides a comprehensive care for patients from the whole republic , other centers , transplant and immunocompromised patients , and so forth . in our previous study we focused on possible changes of innate or adaptive immunity and compared these results among patients with diabetic foot ulcers ( without clinically relevant infection ) , diabetic controls , nondiabetics with leg ulcers , and healthy volunteers with no largely significant differences . therefore , we tried to select a group of patients with chronically infected nonhealed diabetic foot ulcers , where potential changes of the immune system will be more remarkable in contrast to match control group of diabetic patients . the results of our study showed that there are not major abnormalities of systemic immunity , and only certain deficits mainly at the level of lymphocytes subpopulations and immunoglobulin subclasses are present . its effectiveness may be further reduced at the local level due to a number of factors , including the possible coexistence of mild capillary ischemia contributing to the development of dfus that could lead to worse migration of effector cells to the target destination . we recommend performing more detailed immunological investigations in patients with dfus with recurrent or chronic infectious complications particularly caused by resistant pathogens . these tests should focus on the determination of cell - mediated and humoral immunity , concretely on lymphocyte subpopulations and igg subclasses .\noutput:\n" }, { "from": "agent", "value": "the aim of our study was to analyse immune abnormalities in patients with chronic infected diabetic foot ulcers ( dfus ) especially those infected by resistant microorganisms . methods . 68 patients treated in our foot clinic for infected chronic dfus with 34 matched diabetic controls were studied . patients with infected dfus were subdivided into two subgroups according to the antibiotic sensitivity of causal pathogen : subgroup s infected by sensitive ( n = 50 ) and subgroup r by resistant pathogens ( n = 18 ) . selected immunological markers were compared between the study groups and subgroups . results . patients with infected chronic dfus had , in comparison with diabetic controls , significantly reduced percentages ( p < 0.01 ) and total numbers of lymphocytes ( p < 0.001 ) involving b lymphocytes ( p < 0.01 ) , cd4 + ( p < 0.01 ) , and cd8 + t cells ( p < 0.01 ) and their naive and memory effector cells . higher levels of igg ( p < 0.05 ) including igg1 ( p < 0.001 ) and igg3 ( p < 0.05 ) were found in patients with dfus compared to diabetic controls . serum levels of immunoglobulin subclasses igg2 and igg3 correlated negatively with metabolic control ( p < 0.05 ) . a trend towards an increased frequency of igg2 deficiency was found in patients with dfus compared to diabetic controls ( 22 % versus 15 % ; ns ) . subgroup r revealed lower levels of immunoglobulins , especially of igg4 ( p < 0.01 ) in contrast to patients infected by sensitive bacteria . the innate immunity did not differ significantly between the study groups . conclusion . our study showed changes mainly in the adaptive immune system represented by low levels of lymphocyte subpopulations and their memory effector cells , and also changes in humoral immunity in patients with dfus , even those infected by resistant pathogens , in comparison with diabetic controls ." } ]

[ { "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 analysis is based on a cohort of workers in the swedish construction industry who participated in health examinations between 1971 and 1993 . the examinations were free of charge and offered all constructions workers in the country according to an agreement between unions and employers associations . as previously described , some data from the examinations , as , for example , smoking habits and job title , were computerized .12 the job titles were merged to 22 major groups by technical staff in the industry in the mid-1970s . the computerized register of construction workers who had participated in health examinations was reorganized in 1990s , and persons who could not be identified in official registers were excluded ( 0.1 % ) . about 5 % workers of the cohort were women ( n = 19,418 ) , and most have not been heavily exposed to asbestos and they were excluded in the analysis . men who were younger than 15 years ( n = 1 ) or older than 65 years ( n = 1725 ) at the first examination were excluded because very young persons rarely were hired by the industry and the age of retirement has been 65 years since 1976 . incident cases of lung cancer or pleural mesothelioma were found from a linkage with the swedish cancer register . year of death and emigration were collected from a linkage with official swedish registries . in the analysis , we used information from the first health examination about job title and started the follow - up the year after the first examination . the linkage with registers was from january 1 , 1971 , through december 31 , 2011 . person - years were calculated for each individual from the year after the first health examination , until 2011 , death , emigration , or occurrence of cancer ( lung cancer and mesothelioma , respectively ) . the relative risks ( rrs ) were calculated by the poisson regression [ log ( number of cases group k ) = ak * exposure + bi * age - group + cj * smoking habits + log ( person - years group k ) , where age - group and smoking habits are categorical variables and log ( person - years ) is an offset variable ; exposure is 0 for the reference group and 1 for the exposed group k ; rrk = exp ( ak ) ] using the incidence rate in the low - exposed group in the latest time period ( 2001 to 2011 ) as reference group . standard incidence ratios ( sirs ) were calculated from national statistics of incidence rates stratified for sex , age , and calendar year . to estimate the exposure to asbestosthis analysis was restricted to ages between 40 and 84 years and adjusted for age ( 5 - year classes ) and birth cohort ( 10 - year classes ) according to the distribution of person - years among salaried employees . very old persons ( 85 + years ) were excluded because diagnosis may have less precision in very high ages . * per 100,000 person - years ( adjusted to age and birth cohort ) . persons born in 1955 or later were excluded in the analysis because they started to work in the mid-1970s or later when there was a considerable decrease in the use of asbestos . we restricted the analysis to men who had been examined between 1971 and 1980 because the use of asbestos decreased rapidly in the mid-1970s . in the analysis of lung cancer , we considered only person - years between 40 and 74 years because lung cancer is rare before the age of 40 years . the decision to exclude men who are 75 years orthe smoking habits were classified into nonsmokers , ex - smokers , moderate smokers ( less than 15 cig / day , less than 8 cigars or 100 g or more pipe tobacco / week ) , and heavy smokers from the first health examinations . if data were missing at the first examination , smoking habits from the second or third examination were used if available . we stratified the analysis of lung cancer in the following four decades : 1972 to 1980 , 1981 to 1990 , 1991 to 2000 , and 2001 to 2011 . standard incidence ratios for lung cancer were calculated from national incidence rates adjusting for age - group and calendar year ( table 3 ) using a poisson distribution to calculate 95 % confidence intervals ( cis ) . * relative risk ( 95 % ci ) , estimated from the poisson regression analysis adjusted for age and smoking habits ( for details , see the materials and methods section ) . standard incidence ratio ( 95 % ci ) based on national incidence rates , adjusted for sex , age , and calendar year . ci , confidence intervals ; rr , relative risk ; sir , standard incidence ratio . , cary , nc ) was used for the poisson regression analyses using the wald statistics to estimate 95 % ci . this study was approved by the regional ethical review board ( 2010/326 - 32 m ) . to estimate the exposure to asbestos , we calculated the incidence of pleural mesothelioma in the occupational groups . this analysis was restricted to ages between 40 and 84 years and adjusted for age ( 5 - year classes ) and birth cohort ( 10 - year classes ) according to the distribution of person - years among salaried employees . this analysis included 249,060 men ( table 1 ) . very old persons ( 85 + years ) were excluded because diagnosis may have less precision in very high ages . * per 100,000 person - years ( adjusted to age and birth cohort ) . persons born in 1955 or later were excluded in the analysis because they started to work in the mid-1970s or later when there was a considerable decrease in the use of asbestos . we restricted the analysis to men who had been examined between 1971 and 1980 because the use of asbestos decreased rapidly in the mid-1970s . in the analysis of lung cancer , we considered only person - years between 40 and 74 years because lung cancer is rare before the age of 40 years . the decision to exclude men who are 75 years orthe smoking habits were classified into nonsmokers , ex - smokers , moderate smokers ( less than 15 cig / day , less than 8 cigars or 100 g or more pipe tobacco / week ) , and heavy smokers from the first health examinations . if data were missing at the first examination , smoking habits from the second or third examination were used if available . we stratified the analysis of lung cancer in the following four decades : 1972 to 1980 , 1981 to 1990 , 1991 to 2000 , and 2001 to 2011 . standard incidence ratios for lung cancer were calculated from national incidence rates adjusting for age - group and calendar year ( table 3 ) using a poisson distribution to calculate 95 % confidence intervals ( cis ) . * relative risk ( 95 % ci ) , estimated from the poisson regression analysis adjusted for age and smoking habits ( for details , see the materials and methods section ) . standard incidence ratio ( 95 % ci ) based on national incidence rates , adjusted for sex , age , and calendar year . ci , confidence intervals ; rr , relative risk ; sir , standard incidence ratio . , cary , nc ) was used for the poisson regression analyses using the wald statistics to estimate 95 % ci . this study was approved by the regional ethical review board ( 2010/326 - 32 m ) . men in jobs with incidence rates of pleural mesothelioma more than 10 per 100,000 person - years were classified as heavy exposed to asbestos , those with an incidence between 5.0 and 9.9 as medium exposed , and those less than 5.0 as low exposed ( table 1 ) . there were in total 2835 cases of lung cancer included in the analysis ( table 2 ) . during the 1970s , the risk of lung cancer was increased in groups with heavy or medium asbestos exposure as expected , whereas from the 1990s the risk for lung cancer was similar between the exposure groups ( table 3 and fig . the rrs are compared with the risk in the low - exposed group in the last decade ( 2001 to 2011 ) . the risk of lung cancer in the low - exposed group did not show any clear change over the decades , whereas the rrs in heavy - and medium - exposed groups showed a declining risk . for example , the rr for heavy - exposed workers decreased from 1.74 in 1972 to 1980 to 0.94 in 2001 to 2011 . the incidence rates of lung cancer among the construction workers have also been compared with the incidence rates in the general population adjusted for age and time period and are shown as sir . the sirs show a similar time pattern , that is , a declining sir in heavy - and medium - exposed groups . the sirs were not adjusted to smoking habits , and an sir less than 1 may indicate lighter smoking habits among the construction workers than in the general population . the relative risk of lung cancer according to time period and exposure level . this study shows that the risk of lung cancer was dependent on exposure to asbestos in the 1970s because those with high exposure had a higher risk than those with low exposure . nevertheless , when about 20 years have elapsed since last exposure , there was similar risk for lung cancer among those with high and low exposures ( fig .2 ) . this is a similar time pattern as for lung cancer caused by tobacco smoking , where the risk after about 10 years starts to decrease in ex - smokers compared with current smokers and continues to decrease during several decades .13,14 our findings are similar to some other studies . a swedish study of shipyard workers , mainly exposed to chrysotile , did not show any increased risk of lung cancer 7 to 15 years after the cessation of asbestos even though the pleural mesothelioma incidence was high . nevertheless , the power was low and an elevated risk could not be excluded .10 an italian study of chrysotile and crocidolite cement workers found that the risk of lung cancer was significantly decreased 15 + years since last exposure compared with 3 to 15 years after last exposure ( 15 to 30 years rr = 0.70 ; 30 + years rr = 0.56 ) .9 nevertheless , the risk was also lower during the first 3 years after the exposure had ended ( rr = 0.38 ; 95 % ci , 0.22 to 0.65 ) . the authors pointed out that there were no other asbestos factories in the area after the plant closed in 1986 , which they considered made asbestos exposure among the workers unlikely thereafter . a german case control study conducted in 1988 to 1996 showed that the odds ratio declined to half after 20 years or more after last exposure compared with 0 to 19 years after exposure .8 another italian study of textile workers , heavy exposed to various types of asbestos including crocidolite , studied lung cancer in subjects younger than 80 years . it showed that the rr for lung cancer was significantly increased in three periods after last employment ( less than 15 , 15 to 25 and 25 + years since last employment , standardized mortality ratio : 302 , 363 , and 278 , respectively ) .15 it is not known if the factory workers took another asbestos - related job after leaving the plant . it is a prospective study , where the information about exposure is not dependent on estimations from the workers . the exposure assessment is based on occupational title , and there may be some nondifferential misclassification , which may decrease the difference in risk between the groups . the incidence of pleural malignant mesothelioma is almost entirely caused by exposure to asbestos and should be a good marker of asbestos exposure . nevertheless , amphiboles have a higher potency to cause mesotheliomas than chrysotile , whereas the difference in potency for causing lung cancer is less clear .16 chrysotile has been the major asbestos used in swedish construction industry . if some occupational groups had more exposure to amphiboles , and we use mesothelioma as a marker of total exposure to asbestos , such groups ' total exposure to asbestos would be overestimated . spraying of asbestos usually meant the use of amosite and insulators was the group spraying asbestos , meaning that the total exposure of asbestos could be overestimated . it is , however , a rather small group , and exclusion of them from the analysis did not substantially change the results . we do not know the exact time when every worker stopped being exposed to asbestos , which also may contribute to some nondifferential misclassification . if workers who got lung cancer end exposure to asbestos at the time of diagnosis , there is a linkage between disease and cessation of exposure . nevertheless , it is a small proportion of workers who got the diagnosis , and the bias will be small . the smoking habits were similar in the exposure groups , 29 % to 32 % were nonsmokers , 21 % ex - smokers , 35 % to 36 % moderate smokers , and 11.5 % to 13.5 % heavy smokers , which decrease the risk of residual confounding after adjustment in analyses for smoking habits . they were determined at the first health examination and may have changed over time . if the smoking habits changed differently over time between exposure categories , it may cause bias . although we can not exclude such bias , we consider it less likely because most workers have similar socioeconomic background , were subject to similar antismoking campaigns , and had similar access to health care . there are also exposure to other lung carcinogens in the construction industry , for example , diesel exhaust and silica . if exposure to such agents has changed differently over time in persons with low - and high - exposure asbestos , it may introduce bias . nevertheless , we think that this is less probably because groups with high exposure to asbestos have rather low exposure to silica and diesel exhausts compared with some occupational groups with low exposure to asbestos . the workers in the swedish construction industry have mainly been exposed to chrysotile . also , amosite has been used to some extent , for example , for spray insulation . amphiboles seem to have a higher potency than chrysotile to cause mesothelioma , but it is less clear if there is any different potency to cause lung cancer .16 some studies of humans and animals have indicated that inhaled chrysotile has shorter retention in the lungs than amphiboles .17,18 we can not separately analyze workers with exposure to different types of asbestos , and it is not possible to draw conclusions if the risk of lung cancer in workers with a heavy exposure to amphiboles has another time pattern after cessation of exposure . thus , the time pattern of lung cancer risk in workers exposed to asbestos is different from the pattern of pleural mesothelioma . the clearance of the fibers may be faster than for fibers that have reached the pleura . smoking interacts with asbestos in causing lung cancer , but the risk for mesothelioma is similar for smokers and nonsmokers . the mechanisms by which asbestos cause lung cancer are not established . it seems to cause lung cancer both with and without concomitant exposure to tobacco smoke . experiments in animals have indicated genotoxicity at very high doses , but other mechanisms may be more important at lower exposure , for example , epigenetic mechanisms and enhancing the delivery of polycyclic aromatic hydrocarbons into cells .19 tobacco smoking and asbestos interact as causes of lung cancer .20 a possible mechanism for this interaction is that asbestos enhance the transport of tobacco carcinogens as polycyclic aromatic hydrocarbons into the cell . this interaction may decrease when the exposure to asbestos stops because chrysotile fibers are more rapidly cleared from the lungs . the finding that the risk of lung cancer is similar between the groups 20 years after the exposure has ended has implication for future epidemiological studies of lung cancer . if there are similar time patterns also for other lung carcinogens , the risk may be underestimated if the analysis is not adjusted for time since last exposure . because lung cancer incidence increases by age . a modest increased risk during or shortly after exposure may then be difficult to detect because the majority of cases will occur long time after the exposure has ended . this study shows that workers with an increased risk of lung cancer during high exposure to asbestos have similar risk as low - exposed workers 20 years after the exposure has ended , but their risk of mesothelioma is still higher 20 years later . this indicates that the mechanisms of carcinogenicity for asbestos are different for lung cancer and mesothelioma .\noutput:\n" }, { "from": "agent", "value": "objective : to study the risk of lung cancer in heavily asbestos - exposed workers after the exposure to asbestos has ended.methods : lung cancer was studied in a cohort of 189,896 swedish construction workers through a linkage with the swedish cancer registry . asbestos exposure was estimated by the incidence of malignant mesothelioma in the occupational group.results : there were in total 2835 cases of lung cancer . workers with heavy exposure to asbestos had an increased risk of lung cancer ( relative risks = 1.74 ; 95 % confidence interval , 1.25 to 2.41 ) before exposure ended and a similar risk to those with low exposure 20 years after the exposure had ceased ( relative risks = 0.94 ; 95 % confidence interval , 0.77 to 1.15 ) . conclusions : workers with heavy exposure to asbestos have a similar risk of lung cancer as persons with low or no exposure 20 years after the exposure has ended ." } ]

[ { "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: fracture of dual columns of the acetabulum is the most complicated type of acetabular fracture . posterior - anterior column fixation is considered to be important for joint stability and early mobilization after surgery . ochs et al . investigated screw placement into the anterior column with ct analysis for 260 cadaveric bony hemi - pelvis specimens . chen et al . analyzed 164 cases of three - dimensional ct pelvic data and concluded that there is a sex difference in screw placement into fractured anterior columns . few studies have focused on a fixation model involving fractured posterior - anterior columns of the acetabulum . thus , we designed a plate - screw fixation model for fractured columns of the acetabulum ( figure 1 ; patent no . this model is divided into 3 parts : the reconstructive plate , which acts to fix the anterior column fracture ; the square plate , which is used to support the fracture of the square area ; and the third part is a lag screw for the posterior column , which is the key point of our design because the entry point of the lag screw determines the implant of the guide plate as well as the direction of the screw holes . we first used the modified stoppa approach for measuring the reference point , which can improve the entry point and angle of the lag screw , thus providing an anatomic basis for accurate placement of the screw . after cadaveric research , the comprehensive studies on the placement of the model and entry point of the lag screw of the acetabulum were measured by computed tomography ( ct ) images in healthy adults . the ethics board review of south medical university ( guangzhou , china ) approved the study after a thorough investigation and verification . nineteen recently embalmed adult bony hemi - pelvis specimens were obtained from the anatomy department of south medical university . all of the specimens had complete integrity and there were no deformities or fractures based on visual inspection and an x - ray study . the surgical field of vision was marked by the modified stoppa approach in the hemi - pelves ( figure 2 ) . the screw was inserted in a retrograde motion on the minimum of the ischial tuberosity ( figure 3 ) . a screw , 3.5 mm in length , was inserted parallel to the posterior line of the ischiadic ramus . the distance between the entry point and the vertical line of the arcus marginalis ( op ) , and distance between the apex - q of the greater sciatic notch and the vertical line of the arcus marginalis ( pi ) were measured ( figure 4 ) . after projecting the line of the screw on an - square , the angle of the screw placement direction and the - square ( ) the angle of the screw placement direction and the arcus marginalis ( ) were measured ( figure 4 ) . the distance between the entry point and the front line of the sacroiliac joint may exhibit a sex difference , thus the distance between the ischiadic spine and the posterior inferior iliac spine was also measured . according to the data obtained from the cadaveric study , we selected 50 healthy adults ( 30 males and 20 females ; age range , 25 ~ 69 years ; mean age , 46.4 years ) in this study . the data was collected by ct scan ( 16 - slice multidetector scanner [ slice thickness , 1.25 mm ] ; ge , [ fairfield , connecticut ] , usa ; ) . after data screening , the specimens that included deformities , fractures , tumors , osteoporosis , or incomplete scanning were excluded . format and imported to mimics 10.01 ( materialise , [ leuven ] , belgium ) for measurement . the threshold value was set with bone ct , and three - dimensional reconstruction was performed by region growth . the screw hole had a 2.5 mm radius , with a supplementary hole 1 cm from the screw hole . the 3 - dimensional reconstruction images of the hemi - pelvis specimens were rotated laterally and the square area was fully exposed . a line was drawn along the posterior border of the ischiadic ramus and extended to cross the arcus marginalis at point i. anterior to this point was the placement area of the guide module , which was 3 cm in length and 1.5 cm in width . a 6.5 - mm screw was placed in the posterior column of the acetabulum from the iliac fossa to the tuberosity of the ischium . the entry point of the posterior column was 15.27 mm from the anterior aspect of the sacroiliac joint and 13.62 mm from the arcus marginalis . thus , the entry point of the posterior column was guaranteed in the placement area of the guide module . a 3 - mm radius cylinder was virtually placed in the hemi - pelvis using mimics - cad . then , both ends of the cylinder were extended and crossed out of the iliac fossa and tuberosity of the ischium . the distance between the out - point , o , and the arcus marginalis , op , as well as the length of the screw hole and posterior border of the guide module , pi , were measured ( figure 5 ) . all the hemi - pelvis specimens were placed with screws virtually and the entry points were all guaranteed in the placement area of the guide module ( figure 6 ) . because the placement area of the guide module , the fossa iliaca was parallel to the undersurface of the guide module ; the relative position between the cylinder and the placement area was the direction of the locking screw . the relative position can be determined by and . these 2 angles were measured using the rp slice module of mimics ( figure 7 ) . the corresponding data were analyzed using spss ( statistical program for social sciences , version 20.0 ; spss , inc . , the ethics board review of south medical university ( guangzhou , china ) approved the study after a thorough investigation and verification . nineteen recently embalmed adult bony hemi - pelvis specimens were obtained from the anatomy department of south medical university . all of the specimens had complete integrity and there were no deformities or fractures based on visual inspection and an x - ray study . the surgical field of vision was marked by the modified stoppa approach in the hemi - pelves ( figure 2 ) . the screw was inserted in a retrograde motion on the minimum of the ischial tuberosity ( figure 3 ) . a screw , 3.5 mm in length , was inserted parallel to the posterior line of the ischiadic ramus . the distance between the entry point and the vertical line of the arcus marginalis ( op ) , and distance between the apex - q of the greater sciatic notch and the vertical line of the arcus marginalis ( pi ) were measured ( figure 4 ) . after projecting the line of the screw on an - square , the angle of the screw placement direction and the - square ( ) the angle of the screw placement direction and the arcus marginalis ( ) were measured ( figure 4 ) . the distance between the entry point and the front line of the sacroiliac joint may exhibit a sex difference , thus the distance between the ischiadic spine and the posterior inferior iliac spine was also measured . according to the data obtained from the cadaveric study , we selected 50 healthy adults ( 30 males and 20 females ; age range , 25 ~ 69 years ; mean age , 46.4 years ) in this study . the data was collected by ct scan ( 16 - slice multidetector scanner [ slice thickness , 1.25 mm ] ; ge , [ fairfield , connecticut ] , usa ; ) . after data screening , the specimens that included deformities , fractures , tumors , osteoporosis , or incomplete scanning were excluded . format and imported to mimics 10.01 ( materialise , [ leuven ] , belgium ) for measurement . the threshold value was set with bone ct , and three - dimensional reconstruction was performed by region growth . the screw hole had a 2.5 mm radius , with a supplementary hole 1 cm from the screw hole . the 3 - dimensional reconstruction images of the hemi - pelvis specimens were rotated laterally and the square area was fully exposed . a line was drawn along the posterior border of the ischiadic ramus and extended to cross the arcus marginalis at point i. anterior to this point was the placement area of the guide module , which was 3 cm in length and 1.5 cm in width . a 6.5 - mm screw was placed in the posterior column of the acetabulum from the iliac fossa to the tuberosity of the ischium . the entry point of the posterior column was 15.27 mm from the anterior aspect of the sacroiliac joint and 13.62 mm from the arcus marginalis . thus , the entry point of the posterior column was guaranteed in the placement area of the guide module . a 3 - mm radius cylinder was virtually placed in the hemi - pelvis using mimics - cad . then , both ends of the cylinder were extended and crossed out of the iliac fossa and tuberosity of the ischium . the distance between the out - point , o , and the arcus marginalis , op , as well as the length of the screw hole and posterior border of the guide module , pi , were measured ( figure 5 ) . all the hemi - pelvis specimens were placed with screws virtually and the entry points were all guaranteed in the placement area of the guide module ( figure 6 ) . because the placement area of the guide module , the fossa iliaca was parallel to the undersurface of the guide module ; the relative position between the cylinder and the placement area was the direction of the locking screw . the relative position can be determined by and . these 2 angles were measured using the rp slice module of mimics ( figure 7 ) . the corresponding data were analyzed using spss ( statistical program for social sciences , version 20.0 ; spss , inc . , the data for cadaveric specimens are recorded in table 1 and figure 8 . the distance between the out - point , o , andthe arcus marginalis , op , was 0.960.32 cm in females and 0.920.16 cm in males ( p 0.05 ) . the length of the screw hole and posterior border of the guide module , pi , was 0.980.28 cm in females and 0.750.23 cm in males ( p 0.05 ) . for the width of the entry point and the anterior border of the sacroiliac joint , the value was 2.430.66 cm in females and 1.870.26 cm in males ( p 0.05 ) . the distance between the ischiadic spine and posterior inferior iliac spine was 5.740.46 cm in females and 5.160.29 cm in males ( p 0.05 ) . the angle of the screw and the arcus marginalis , , was 59.686.28 in females and 56.753.22 in males ( p 0.05 ) . the angle of the screw and square , , was 41.272.76 in females and 34.312.78 in males ( p 0.05 ) . the length of pi was 1.080.22 cm in females and 0.850.27 cm in males ( mean , 0.980.13 cm ; range , 0.67 ~ 1.56 cm ; p 0.05 ) , and the length of op ( the entry point and arcus marginalis ) was 1.060.29 cm in females and 1.120.24 cm in males ( mean , 1.090.26 cm ; range , 0.70 ~ 1.59 ; p 0.05 ) . the angle of the screw and the arcus marginalis ( ) was 55.334.00 in females and 55 . the angle of the screw and the plate ( ) was 39.212.45 in females and 35.582.31 in males ( p 0.05 ) . the width of the entry point and the anterior border of the sacroiliac joint was 2.210.46 cm in females and 1.980.12 cm in males ( p = 0.51 ) . the distance between the ischiadic spine and posterior inferior iliac spine was 5.490.61 cm in females and 4.860.54 cm in males p 0.001 ) . a comparison of the corresponding data was made between specimens and healthy adults , and there was no significant difference based on sex and side ( p 0.05 ) . the data for cadaveric specimens are recorded in table 1 and figure 8 . the distance between the out - point , o , andthe arcus marginalis , op , was 0.960.32 cm in females and 0.920.16 cm in males ( p 0.05 ) . the length of the screw hole and posterior border of the guide module , pi , was 0.980.28 cm in females and 0.750.23 cm in males ( p 0.05 ) . for the width of the entry point and the anterior border of the sacroiliac joint , the value was 2.430.66 cm in females and 1.870.26 cm in males ( p 0.05 ) . the distance between the ischiadic spine and posterior inferior iliac spine was 5.740.46 cm in females and 5.160.29 cm in males ( p 0.05 ) . the angle of the screw and the arcus marginalis , , was 59.686.28 in females and 56.753.22 in males ( p 0.05 ) . the angle of the screw and square , , was 41.272.76 in females and 34.312.78 in males ( p 0.05 ) . the length of pi was 1.080.22 cm in females and 0.850.27 cm in males ( mean , 0.980.13 cm ; range , 0.67 ~ 1.56 cm ; p 0.05 ) , and the length of op ( the entry point and arcus marginalis ) was 1.060.29 cm in females and 1.120.24 cm in males ( mean , 1.090.26 cm ; range , 0.70 ~ 1.59 ; p 0.05 ) . the angle of the screw and the arcus marginalis ( ) was 55.334.00 in females and 55 . the angle of the screw and the plate ( ) was 39.212.45 in females and 35.582.31 in males ( p 0.05 ) . the width of the entry point and the anterior border of the sacroiliac joint was 2.210.46 cm in females and 1.980.12 cm in males ( p = 0.51 ) . the distance between the ischiadic spine and posterior inferior iliac spine was 5.490.61 cm in females and 4.860.54 cm in males p 0.001 ) . a comparison of the corresponding data was made between specimens and healthy adults , and there was no significant difference based on sex and side ( p 0.05 ) . acetabular fractures , particularly those involving the anterior and posterior columns , remain technically challenging for orthopedic surgeons . dual column fixation is considered to be important for joint stability and early mobilization in surgery . we designed a plate - screw fixation model for both fractured columns of the acetabulum . in this model , an excellent anatomic understanding of the hemi - pelvis can be very useful in determining the screw insertion into the hip joint . thus , an anatomic study was conducted regarding screw fixation in the posterior column of the acetabulum because the placement of the screw determines fixation of the plate - screw model . the angle of screw insertion in the posterior column was improved using a modified stoppa approach , which can expose an area of 1519 mm from the iliac fossa to the arcus marginalis . this area , as well as the distal end of the square , was considered as the penetration plate . to determine the insertion angle , the included angle of square , , and screw , , was measured and the angle of the screw and arcus marginalis , , was measured for assistance . there was no significant sex difference in , while was significantly different . during insertion , the deviation of the screw should be near 34 in males and 41 in females . the data maintained from the cadaveric specimens can support designation of the plate - screw . to assist the design and clinical application of the guide module , the measured parameters were revised with reference to the data obtained from the cadaveric specimens . the reference section of the entry point , the anterior border of the sacroiliac joint , was changed to the intersection point of the arcus marginalis and the extension line of posterior border of the ischiadic ramus . the reason for this revision indicates a significant sex difference by defining the anterior border of the sacroiliac joint as a reference section because the greater sciatic notch is wider in females than males . accordingly , the distance between the anterior border of the sacroiliac joint and the entry point is also wider in females . if the reference section is defined as the intersection point of the arcus marginalis and the extension line of the posterior border of the ischiadic ramus , there is no sex difference . this was approved in ct reconstruction in our study and the distance was approximately 1 cm . the intersection point was closer to the fracture line and was determined by touching the greater sciatic notch in the anterior incision . second , the absolute angle of the horizontal and sagittal planes was revised as the angle of the screw and the placement square , as well as the major axis of the placement square . the horizontal and sagittal planes were difficult to define because of the posture change of the patients . moreover , the ct data may have error when the different postures of patients were adjusted . therefore , the relative angle may help with the design and manufacture of the guide module . as our research demonstrated promising results , we consider that the design may be valuable for safer fixation of bilateral acetabular fractures in peri - operative planning . the major limitation in this study was that we only included a small number of cases based on the design in our study . we will continue to apply this method in larger numbers of healthy adults with dual acetabular fractures . the more comprehensive research on a larger number of cases will be beneficial to confirm the validity and efficiency of this design in clinical practice . in this study , cadaveric specimens and healthy adults were selected to study the entry point and angle of the lag screw . the data of measured parameters obtained in this study , which are consistent , provided an anatomic basis for the designation of the guide module ; therefore , accurate and safe placement of the lag screw into the posterior column of the acetabular fracture is possible .\noutput:\n" }, { "from": "agent", "value": "backgroundthe aim of this study was to provide valid data for a plate - screw fixation model for fractured posterior - anterior columns of the acetabulum.material / methodsnineteen cadaveric bony hemi - pelvis specimens were obtained and 50 healthy adults were enrolled . the modified stoppa approach and computed tomography ( ct ) imaging were used to collect the measured parameter data of the module.resultsthe measured parameter data were as follows : op , 0.960.32 cm in females and 0.920.16 cm in males ( p > 0.05 ) ; pi , 0.980.28 cm in females , and 0.750.23 cm in males ( p > 0.05 ) ; , 59.686.28 in females and 56.753.22 in males ( p > 0.05 ) ; and , 41.272.76 in females and 34.312.78 in males ( p < 0.05 ) . the corresponding ct image data were as follows : pi , 1.080.22 cm in females and 0.850.27 cm in males ( p > 0.05 ) ; op , 1.060.29 cm in females and 1.120.24 cm in males ( p > 0.05 ) ; , 55.334.00 in females and 55 . 503.43 in males ( p > 0.05 ) ; and was 39.212.45 in females and 35.582.31 in males ( p < 0.05 ) . no significant difference with respect to sex and side existed between specimens and healthy adults ( p > 0.05 ) . conclusionsthe measured parameter data obtained in healthy adults and cadaveric specimens provided an anatomic basis for the designation of the guide module , and thus confirmed the accuracy and safety of screw placement in fractured columns of the acetabulum ." } ]

[ { "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: intervertebral discogenic pain is the most common low back pain ( lbp ) and requires extensive medical attention . a study utilized percutaneous intradiscal radiofrequency thermocoagulation ( pirft ) to treat lbp in 1994 . in this study , an electrothermal cannula was placed into the center of the disc , and the device was activated to generate heat . the objective of the technique was to shrink collagen fibrils by coagulating neural and inflammatory tissues of the disc , thus decreasing nociceptive input from the painful disc . however , more recent studies have found that the efficacy of pirft for the treatment of discogenic lbp remains controversial . the available evidence does not support the effectiveness of pirft for the treatment of discogenic lbp . patients do not benefit from the pirft - induced radiofrequency ( rf ) lesion , and the reduction of nociceptive input generated by the single electrode is insufficient to relieve the lbp . recently , bipolar rftc has been developed as an alternative treatment to improve clinical results and decrease adverse events . bipolar rftc has been successfully used to treat plantar fasciotomy , and the successful clinical outcome rate was 87.5 % at 4 weeks following the operation . previous reports , which utilized bipolar rftc for synovial joints such as the sacroiliac joint and the thoracic facet joint , provide evidence that this technique is a more effective mode of treatment . an ex vivo study utilizing porcine spinal tissue samples confirmed that heating the two electrodes simultaneously appeared to coagulate a wider area and potentially achieved better results in less time . based on these findings , we hypothesized that bipolar rftc will be more efficacious than pirft in generating effective rf lesions and decreasing nociceptive input in discogenic lbp patients . in this study , we modified the routine method of pirft by inserting two cannulas into the center and last third of the disc , followed by heating of the two cannulas simultaneously . we observed 23 patients with discogenic lbp over a period of 1 year to evaluate their pain relief and functional improvement . this study was approved by the hospital ethics committee and was registered at the chinese clinical trial registry with the identifier chictr - opc - 15006556 . patients with discogenic lbp who underwent bipolar rftc between october 2013 and may 2015 were enrolled in the study . the rftc devices and cannulas were purchased from cosman medical , burlington , usa . the c - arm fluoroscope was purchased from ge company , pittsburgh , usa . the contrast agent delivery system was purchased from merit medical , utah , usa . iohexol was purchased from ge healthcare as , oslo , norway . patients were included if they met the following criteria : ( 1 ) lbp with or without pseudoradicular referral for at least 6 months ; ( 2 ) lack of satisfactory improvement after adequate conservative therapy ; ( 3 ) concordant pain upon provocative discography in the affected disc but not in the control discs ; ( 4 ) lbp exacerbated by sitting ; ( 5 ) disc height 50 % of the control disc ; ( 6 ) high - intensity zones ( hizs ) in the affected disc detected by magnetic resonance imaging ( mri ) scans ; ( 7 ) single - level disc disease without evidence of additional degenerative changes in other discs ; ( 8 ) the absence of neural compression lesions ; and ( 9 ) normal neurological examination findings . we excluded patients with compressive radiculopathy , an extruded or sequestered disc , calcification of the extruded disc , bony spinal canal stenosis , more than two symptomatic levels , previous surgery at the symptomatic level , severe scoliosis , spondylolisthesis , spinal tumor , fracture , infection , segmental instability , coagulation dysfunction , serious cardiopulmonary dysfunction , drug abuse , psychological issues by exam or history , beck depression inventory 20 , or pregnancy . all provocative discographies were performed under c - arm fluoroscopy in a sterile operating room . thirty minutes before the intervention , the patients were administrated 2 mg midazolam for relaxation and 1 g cefuroxime intravenously for the prevention of discitis . a discogram was performed using a standard posterolateral approach with the two - needle technique ( 19 - gauge outer and 25 - gauge inner ) . under fluoroscopy , the final location of the needle was verified in the center of the discs , and then the needle was connected to a contrast agent delivery system . iohexol ( 2 ml ) was injected into the nuclei at a rate of 0.05 ml / s . the pain visual analog scale ( vas ) score was at least 6 . only patients with concordant pain at the suspicious level , and with no pain or discordant pain at the adjacent levels were included in the study . furthermore , the concordant pain was reproduced by the application of pressure of l 15 psi above the opening pressure . all the procedures were performed under strict aseptic conditions and local anesthesia by two pain physician specialists . the affected discs were selected based on previous discograms and mri analysis . only a single - level disc with both positive provocative discography and hizs on the t2 - weight mrithe proper disc level and placement of the needle were confirmed with an anteroposterior fluoroscopic view , and the depth of the needle was confirmed with a lateral fluoroscopic view . two 20 - gauge 15 cm rf cannulas , each containing a 10 mm active tip , were , respectively , placed inside the disc near the medial border utilizing a facet joint approach and / or a posterolateral oblique approach . the confirmation of the correct positions of the rf needles was monitored by stimulation at 2 hz ( motor stimulation ) and 50 hz ( sensory stimulation ) , which was not expected to produce a response at 2 v. the impedance measurements were lower than 400 . the bipolar rftc was performed at 85c with the two needle electrodes heated simultaneously for 180 s utilizing an rfg - 1a radiofrequency generator ( cosman medical , burlington , usa ) . the patients were prescribed oral antibiotics for 1 day and bed rest for 24 h. the data collection and follow - up were performed before the procedure and at 1 week , 1 month , 3 months , 6 months , and 1 year after the procedure . demographic variables such as age , gender , disease duration , disc level treated , and puncture approach were collected . pain relief , reduction of analgesic dose , and patient satisfaction ( very satisfied , satisfied , or unsatisfied ) were the secondary outcome . satisfied patients included the two groups of patients who reported that they were either very satisfied or satisfied with the procedure . a reduction in the daily dosage of analgesics reduced to 50 % or less was considered to be significant . statistical analysis was performed utilizing the statistical package for the social science version 17.0 ( spss inc . , the wilcoxon rank - sum test was used to evaluate the differences in vas score , odi scores , and morphine equivalents before and after the procedure . this study was approved by the hospital ethics committee and was registered at the chinese clinical trial registry with the identifier chictr - opc - 15006556 . patients with discogenic lbp who underwent bipolar rftc between october 2013 and may 2015 were enrolled in the study . the rftc devices and cannulas were purchased from cosman medical , burlington , usa . the c - arm fluoroscope was purchased from ge company , pittsburgh , usa . the contrast agent delivery system was purchased from merit medical , utah , usa . iohexol was purchased from ge healthcare as , oslo , norway . patients were included if they met the following criteria : ( 1 ) lbp with or without pseudoradicular referral for at least 6 months ; ( 2 ) lack of satisfactory improvement after adequate conservative therapy ; ( 3 ) concordant pain upon provocative discography in the affected disc but not in the control discs ; ( 4 ) lbp exacerbated by sitting ; ( 5 ) disc height 50 % of the control disc ; ( 6 ) high - intensity zones ( hizs ) in the affected disc detected by magnetic resonance imaging ( mri ) scans ; ( 7 ) single - level disc disease without evidence of additional degenerative changes in other discs ; ( 8 ) the absence of neural compression lesions ; and ( 9 ) normal neurological examination findings . we excluded patients with compressive radiculopathy , an extruded or sequestered disc , calcification of the extruded disc , bony spinal canal stenosis , more than two symptomatic levels , previous surgery at the symptomatic level , severe scoliosis , spondylolisthesis , spinal tumor , fracture , infection , segmental instability , coagulation dysfunction , serious cardiopulmonary dysfunction , drug abuse , psychological issues by exam or history , beck depression inventory 20 , or pregnancy . all provocative discographies were performed under c - arm fluoroscopy in a sterile operating room . thirty minutes before the intervention , the patients were administrated 2 mg midazolam for relaxation and 1 g cefuroxime intravenously for the prevention of discitis . a discogram was performed using a standard posterolateral approach with the two - needle technique ( 19 - gauge outer and 25 - gauge inner ) . under fluoroscopy , the final location of the needle was verified in the center of the discs , and then the needle was connected to a contrast agent delivery system . iohexol ( 2 ml ) was injected into the nuclei at a rate of 0.05 ml / s . the pain visual analog scale ( vas ) score was at least 6 . only patients with concordant pain at the suspicious level , and with no pain or discordant pain at the adjacent levels were included in the study . furthermore , the concordant pain was reproduced by the application of pressure of l 15 psi above the opening pressure . all the procedures were performed under strict aseptic conditions and local anesthesia by two pain physician specialists . only a single - level disc with both positive provocative discography and hizs on the t2 - weight mri was chosen . the proper disc level and placement of the needle were confirmed with an anteroposterior fluoroscopic view , and the depth of the needle was confirmed with a lateral fluoroscopic view . two 20 - gauge 15 cm rf cannulas , each containing a 10 mm active tip , were , respectively , placed inside the disc near the medial border utilizing a facet joint approach and / or a posterolateral oblique approach . the confirmation of the correct positions of the rf needles was monitored by stimulation at 2 hz ( motor stimulation ) and 50 hz ( sensory stimulation ) , which was not expected to produce a response at 2 v. the impedance measurements were lower than 400 . the bipolar rftc was performed at 85c with the two needle electrodes heated simultaneously for 180 s utilizing an rfg - 1a radiofrequency generator ( cosman medical , burlington , usa ) . the data collection and follow - up were performed before the procedure and at 1 week , 1 month , 3 months , 6 months , and 1 year after the procedure . demographic variables such as age , gender , disease duration , disc level treated , and puncture approach were collected . pain relief , reduction of analgesic dose , and patient satisfaction ( very satisfied , satisfied , or unsatisfied ) were the secondary outcome . satisfied patients included the two groups of patients who reported that they were either very satisfied or satisfied with the procedure . a reduction in the daily dosage of analgesics reduced to 50 % or less was considered to be significant . statistical analysis was performed utilizing the statistical package for the social science version 17.0 ( spss inc . , the wilcoxon rank - sum test was used to evaluate the differences in vas score , odi scores , and morphine equivalents before and after the procedure . twenty - five patients with concordant pain were enrolled ; however , two of these were lost to follow - up for no identifiable reason . finally , 23 patients with hizs on the t2 - weight mri and positive provocative discography at a single suspicious level were selected . the mean age of the patients who had discogenic lbp was 43.07.8 years . twenty - three patients were subjected to bipolar rftc therapy in l4 / l5 or l5 / s1 spinal levels according to their symptoms and dermatome distribution . patient demographic and clinical data of this study mb : the medial border of the facet joint approach ; pl : the posterolateral oblique approach ; sd : standard deviation . bipolar rftc was performed at l4 / l5 in 7 patients , and at l5 / s1 in 16 patients . considering the evaluation of the imaging data and whether these patients had a pseudoradicular referral , different approaches were adopted . at the l4 / l5 level , five patients with pseudoradicular referral were treated by the median border of the facet joint and the posterolateral oblique ( mb + pl ) approach [ figure 1a and 1b ] , while two patients without pseudoradicular referral were treated by the bilateral median border of the facet joint ( mb + mb ) approach [ figure 1c and 1d ] . at the l5 / s1 level , four patients were treated by the mb + pl approach , and 12 patients were treated by the mb + mb approach . treatment levels and puncture approaches used in this study ( n = 23 ) mb : the medial border of the facet joint approach ; pl : the posteorlateral oblique approach . mb + pl : the median border of the facet joint and posteorlateral oblique approach ; mb + mb : the bilateral median borders of the facet joint approach . the follow - up period was from 1 week to 1 year after the operation . the vas and odi scores at 1 week , 1 month , 3 months , 6 months , and 1 year after procedure were significantly decreased when compared to the baseline ( p 0.05 ) [ figures 2 and 3 ] . bipolar rftc also resulted in a significant change in all secondary measures at all points of follow - up [ table 3 ] . the daily analgesic dose was expressed in morphine equivalents , and bipolar rftc contributed to a significant reduction of analgesic dose [ figure 4 ] . three patients suffered from mild short - term postdural puncture headache ( pdph ) , but the symptom disappeared within 1 week . no serious complications , such as nerve injuries , discitis , and hematoma , occurred in any of the patients . significant differences were found between baseline and 1 week , 1 month , 3 months , 6 months , and 1 year postoperation in the vas score during 1 - year follow - ups . * p 0.05 during comparison of different values with baseline . significant differences were found between baseline and 1 week , 1 month , 3 months , 6 months , and 1 year postoperation in the odi score during 1 - year follow - ups . * p 0.05 during comparison of different values with baseline . secondary outcome measures ( n = 23 , absolute numbers ) significant differences were found between baseline and 1 week , 1 month , 3 months , 6 months , and 1 year postoperation in the morphine equivalents during 1 - year follow - ups . * p 0.05 during comparison of different values with baseline . daily analgesic dose was expressed in morphine equivalents . lbp is one of the most common public health problems , which limits activity , causes significant disability , and creates a heavy social burden . internal disk disruption ( idd ) characterized by degradation of the nucleus and disruption of the inner lamella of the annulus fibrosus is thought to be the major cause of chronic lbp . the diagnosis of discogenic lbp due to idd is difficult and controversial because of a lack of specific features . provocative discography , which aims to reproduce the patients symptoms by stimulating the suspicious disc but not the adjacent discs , is considered to be a main diagnostic test for idd - induced lbp . recently , several studies reported that the presence of hizs in the affected disc on mri scans contributed to the effective diagnosis of discogenic lbp . in our study , patients were selected by provocative discography and hizs in the t2 - weight mri . only patients with single - level temporary pain , minimally invasive techniques have been developed as an alternative to treat discogenic lbp . among those , monopolar rftc uses a grounding pad and an uninsulated cannula to heat surrounding tissue around the exposed tip . however , the effectiveness of traditional monopolar rftc techniques for treatment of discogenic pain is still controversial . a randomized controlled trial performed by barendse et al. found that an rf - induced lesion ( generated by a straight rf probe inserted into the center of the disc and heated to 70c for 90 s ) was not effective in reducing discogenic lbp . ercelen et al . conducted another prospective randomized trial utilizing rf at 80c for 120 s or 360 s and found that the increased duration of pirft failed to improve the effectiveness of treating patients with lbp . the pirft strategy of inserting a single catheter ( monopolar rftc ) into the center of the disc will likely only produce limited tissue destruction surrounding the tip of the treatment cannula . the resulting rf lesion may be limited and heating the center of the nucleus might not destroy enough nociceptive fibers in the annulus . bipolar rftc is emerging as an alternative treatment to improve clinical results and decrease adverse events . in contrast to monopolar rftc , bipolar rftc utilizes two cannulas , which are heated simultaneously and complete the circuit . the large current provides a second site of tissue coagulation , and a wider coagulation area is produced in the intervening tissue . a possible mechanism of bipolar rftc therapy was indicated by a cadaver spine study , which demonstrated that a bipolar rf electrode inserted into the intervertebral disc destroyed a portion of the nucleus pulposis after the application of an rf current . first , david utilized bipolar rftc for the treatment of mid back pain of thoracic facet origin and found that 66 % of patients had a significant pain relief with a mean vas reduction of 80.4 % . second , chronic plantar fasciitis has also been treated with bipolar rftc , which was shown to be an effective and safe surgical option . third , bipolar rftc has been recently described as an alternative treatment for the management of chronic spinal pain syndromes . taken together , these reports suggest that bipolar rftc may be a promising strategy to treat multiple chronic pains . in the present study , we hypothesized that bipolar rftc would generate a more effective rf lesion than monopolar rftc and would result in a greater reduction of nociceptive input for the treatment of discogenic lbp patients . bipolar rftc was performed by inserting two adjacent needles into the periphery of the disc not at the center , respectively , with the last third of the disc most common , aiming at reducing discogenic pain by dealing with the nerve fibers accompanying neovascularization through annular tore . the target was located in the tore annulus fibrosis , where neovascularization displayed hizs on t2 - weight mri . different from monopolar rftc which failed to show remarkable improvement in vas scores , odi scores and global perceived effect , we observed that bipolar rftc resulted in a significant improvement in vas scores , pain relief , analgesic consumption , patient satisfaction , and odi scores . we achieved 50 % pain relief at a 1 - year follow - up in 86.9 % of the patients . similarly , the mean vas scores and mean odi scores at all points of follow - up were significantly reduced after the bipolar rftc treatment ( mean vas score at 1 year = 2.71 ; mean odi score at 1 year = 22.5 ) . the bipolar rftc technique can increase the volume of tissue included within the heating radius of the exposed tips , minimize technical failure due to incomplete coagulation and prolong the duration of relief . thus , heating the two adjacent cannulas simultaneously appears to create a more extensive rf lesion and potentially achieve better outcomes in less time . a previous study has shown that an rf temperature 65c can destroy the nociceptive fibers ( a - delta and c fibers ) which are richly innervated in the superficial annulus of the disc . furthermore , in the degenerated or damaged disc , there is more extensive innervation associated with the centripetal growth of nerve fibers . taken together , bipolar rftc can provide faster pain relief than the traditional monopolar rftc techniques ( pirft ) for patients with discogenic lbp . first of all , the operational skill of the clinician is very important . an experienced pain clinician guided by a standard protocol performed all the punctures in this study . pino et al . evaluated the morphology of the lesions generated with bipolar rf electrodes placed 210 mm apart in egg whites and found that the electrodes should be placed 6 mm apart to create a continuous lesion . third , the rf temperature and the duration of the exposure to the rf electrodes may play important roles in the efficacy of the procedure . the optimal rf temperature and precise duration of the exposure to the rf electrodes remain unknown . what is known is that the coagulation size increased with higher rf temperature and longer exposure . previous research indicated that heat produced a tissue color change at 65c in egg albumin and between 45c and 50c in liver . we performed the bipolar rftc at 85c for the duration of 180 s. future studies include a careful analysis of the temperature and duration required for effective treatment . fourth , the puncture approaches were adopted according to the symptoms , image materials , and the disc level . at the l4 / l5 disc level , the mb + mb approach was adopted for patients without pseudoradicular referral . in contrast , the mb + pl approach was adopted for patients with pseudoradicular referral . at the l5 / s1 disc level , we preferred the mb + mb approach to accommodate a higher iliac crest . only four patients with a lower iliac crest were subjected to the mb + pl approach due to unilateral symptoms . a few studies found that the risk of pdph increased after dural puncture . in our study , three patients suffered from mild short - term pdph , and the symptom disappeared within 1 week . the low incidence of pdph in our study was possibly associated with fewer patient cohorts , fewer females , older age , expert operators , accurate puncture , late mobilization , prophylactic bed rest in the horizontal position , and adequate hydration . it was not a randomized controlled clinical trial , and the sample size was relatively small . we have submitted this report for publication because we found that treatment of discogenic lbp with bipolar rftc is safe and effective . further studies including the comparison between different methods of groups should be carried out to investigate the effectiveness of bipolar rftc in patients with discogenic lbp and the incidence of short - term pdph . in the present study , based on the improved functional capacity , superior pain relief , reduced analgesic dose , decreased pain scores , and increased patient satisfaction , our results suggest that bipolar rftc may be an effective minimally invasive procedure for the treatment of discogenic lbp . this work was supported by a grant from the national natural science foundation of china ( 81401860 ) . this work was supported by a grant from the national natural science foundation of china ( 81401860 ) .\noutput:\n" }, { "from": "agent", "value": "background : the efficacy of percutaneous intradiscal radiofrequency thermocoagulation ( pirft ) for the treatment of discogenic low back pain ( lbp ) remains controversial . however , all the pirft studies utilized monopolar radiofrequency thermocoagulation ( rftc ) . the aim of this study was to investigate the safety and efficacy of bipolar rftc for the treatment of discogenic lbp.methods : a total of 23 patients with discogenic lbp were treated with single - level bipolar rftc . the patients were assessed before the procedure and at 1 week , 1 month , 3 months , 6 months , and 1 year after the procedure . the primary outcome included the visual analog scale ( vas ) score and the oswestry disability index ( odi ) score . the secondary outcome included pain relief , reduction of analgesic dose , and patient satisfaction.results : the vas and odi scores were significantly decreased after bipolar rftc treatment at all time points of follow - up ( p < 0.05 ) . bipolar rftc treatment also resulted in a significant change in all secondary measures , such as pain relief , reduction of analgesic dose , and patient satisfaction . no serious complications or neurological sequelae were observed in any of the patients.conclusions : bipolar rftc treatment can significantly attenuate pain and improve the function of patients with discogenic lbp ." } ]

[ { "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 not synthesized in human body and supplied exclusively in non - vegetarian diet . psychiatric disturbances include apathy , depression , dementia , delirium , delusions , hallucinations , irritability , incoherent speech , and catatonia are commonly reported in adults / elderly . till date , the psychiatric presentations of cobalamin deficiency are reported in four children . second , oral vitamin - b12 monotherapy showed dramatic improvement in psychosis , but relapsed a year later after stopping ; however , author did not mention serum vit - b12 level or other manifestations . third , inadequate dietary intake of vitamin b12 and folate presented as neuropsychiatric changes and megaloblastic anaemia . last , a case of psychotic disorder and thrombotic manifestations of vitamin b12 and folate deficiency . however , there is no report of vegetarian pediatric case presenting solely as psychosis due to dietary deficiency . authors report a first case of dietary deficiency of cobalamin in lacto - vegetarian adolescent presenting solely as schizoaffective disorder without hematological / neurological manifestations . a 13 - year - old lacto - vegetarian class viii boy was presented from lower socioeconomic status with nil significant family and personal history . no past history of gastrointestinal pathology , surgeries , or use of alcohol or proton - pump blockers . patient admitted with 1 week history of mutism , rigidity , immobility , staring look , disturbed sleep , ideas of worthlessness and hopelessness , aimless wandering , guilt , and suicidal ideas . physical examination ( pe ) found no abnormality . on mental status examination ( mse ) , patient had partial mutism , manneristic posture , depressed mood , paranoid delusions , thought echo / broadcast , running commentary , and command hallucinations . complete blood count with peripheral blood smear , blood sugar , renal / liver function test , serum iron , total iron binding capacity , urinary iron binding capacity , transferring , and transferrin saturation were normal . he responded quickly with lorazepam - 6 mg / day ( stopped third day ) , olanzapine - 15 mg / day and sertraline - 50 mg / day , and discharged in 5 days . subsequently patient was asymptomatic , but had functional disability for which aripiprazole 15 mg / day was added and followed up for the next 2 months . then patient relapsed despite good adherence with 1 week history of suspiciousness , hearing voices , over - talkativeness , over - cheerfulness , inflated self - esteem , decreased need for sleep , increased appetite , increased pleasurable activities , and disruptive socio - education . mse revealed inflated self - esteem , over - familiarity , spontaneous over - productive speech , increased psycho - motor activity , elated affect , flight of ideas , thought echo and broadcasting , delusions of persecution and reference , command and commentary second person hallucinations , impaired judgment , and absent insight . sertraline stopped and divalproate sodium - 500 mg / day added along with olanzapine - 15 mg / day and aripiprazole - 15 mg / day . divalproate increased to 1 gm and lithium carbonate 600 mg and haloperidol - 10 mg were added . two days later , patient was re - admitted for worsening of symptoms for evaluation of organicity . no abnormality in magnetic resonance imaging of brain , thyroid function test , and gastric mucosal biopsy by upper gastrointestinal endoscopy was reported . serum cobalamin level was 112 ng / ml ( normal range : 180 to 914 ng / ml ) while serum folate was normal . patient started on alternate days 1 ml intramuscular injection vitcofol ( vitamin b12 = 500 mcg , folate = 15 mg andniacinamide = 200 mg per ml ) for six doses , then 2 ml monthly . patient became asymptomatic soon after second dose of cobalamin and discharged in 1 week . during followups , normal serum cobalamin level was maintained and psychiatric medications tapered and stopped on the 52 day of vitcofol . atypical presentation of case consists of acute onset , fluctuating course of psychotic spectrum initially with catatonia , depressive symptoms , first rank symptoms , ( frs ) , and later as mania , frs , and relapsed soon on medications . patient reached quickly and maintained the premorbid level in the short - term follow - up with only cobalamin supplementation . dietary deficiency of cobalamin associated with psychosis is significant in developing country like india for two reasons . first , the high prevalence of dietary deficiency of cobalaminin indian children , and second , course and prognosis with supplementation is better . this emphasizes the importance of diet history and performing serum cobalamin level as a routine investigation in first episode , atypical presentation , and treatment resistant cases , especially in vegetarian . early diagnosis and treatment of cobalamin deficiency in neuropsychiatry is recommended for following reasons : first , better prognosis is expected if treated in window period to avoid irreversible neuronal injury . second , to avoid treatment resistance and last , finding that high vitamin b12 level is associated with better treatment outcomes . methylene - tetrahydrofolate reductase , an enzyme of cobalamin metabolism , is involved in metabolism of tetrahydrobiopterin and latter is required for synthesis of dopamine and serotonin . short - term followup is a limitation , but , rapid disappearance of florid psychopathology and maintaining pre - morbid level solely on cobalamin supplementation is vital . early diagnosis and treatment of cobalamin deficiency during narrow window period is an opportunity to revert pathophysiology . this highlights the importance of diet history and serum cobalamin level in atypical psychiatric presentations .\noutput:\n" }, { "from": "agent", "value": "cobalamin is an important nutrient . it is not synthesized in human body and supplied only in nonvegetarian diet . its deficiency reported with range of psychiatric disorders . only four pediatric cases have been reported as psychiatric disorders . authors report a case of dietary deficiency of cobalamin presenting solely as schizoaffective disorder without hematological / neurological manifestations . early diagnosis and treatment of cobalamin deficiency is an opportunity to reverse pathophysiology . this case highlights the importance of diet history and serum cobalamin level in atypical psychiatric presentations ." } ]

[ { "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: lipomas are relatively uncommon tumors in the gastointestinal tract , often located in the right colon ( 1 ) . gastric lipomas are even more unusual with approximately 220 cases reported in the literature ( 2 ) . the diagnosis is strongly suggested by abdominal ct scan findings and is confirmed by histology . however , the tumor may sometimes undergo significant inflammatory changes leading to misdiagnosis of this lesion with a well - differentiated liposarcoma ( wdls ) . a 51 - year - old man , in otherwise excellent general health , presented with epigastralgia of recent onset . the patient denied any history of gastrointestinal hemorrhage , nausea , vomiting , change in bowel habits , fevers , or melena . endoscopy revealed a soft , large , ulcerated , submucosal mass in the gastric antrum . multiple biopsies were obtained but were all superficial , showing unspecific inflammation of the gastric mucosa . the abdominal ct scan revealed a round , well circumscribed , low - attenuation , gastric antral mass , measuring approximately 9 cm in diameter ( figure 1 ) . the patient underwent total gastrectomy . abdominal ct scan : a large , low - attenuation gastric mass gross examination of the surgical specimen identified in the antral submucosa , a well - circumscribed , smooth , nodular lesion , measuring 9x7 .5 x5 cm , with a homogeneous , yellow , greasy cut surface . macroscopic features : a well - circumscribed nodular lesion with a yellow , greasy , and cut - surface . histological examination revealed a sub - mucosal tumor , composed of a mature adipocytes proliferation , showing significant variation in cell size ( figure 3 ) , associated to some lipoblasts , in a fibromyxoid background ( figure 4 ) . the tumor is made of an adipocytic proliferation showing a significant variation in cell size , with many branched capillaries in a fibromyxoid background ( hex100 ) . areas of lower cellularity , displaying chronic inflammatory changes and containing bland spindle cells were also noted . the overlying mucosa was ulcerated and the muscularis propria was focally dissociated by the tumor . tumor cells were reactive with anti - hmga2 and did n't express s - 100 protein , cd34 , mdm2 and cdk4 . a cytogenetic study was then performed , showing neither mdm2 nor cdk4 gene amplification on fluorescent in situ hybridization ( fish ) . gastric lipoma is a rare , benign lesion , accounting for only 5 % of gastrointestinal tract lipomas and less than 1 % of all gastric tumors ( 3 ) . they are typically occuring in the fifth or sixth decade of life ( 2 , 3 ) .75 % of gastric lipomas are located in the antrum and are usually submucosal in origin ( 2 ) . when small ( 2 cm ) , lipomas are usually asymptomatic and they are often discovered fortuitously ( 1 , 3 ) . when the tumors are large ( 34 cm ) , patients often present upper gastrointestinal hemorrhage , either chronic or acute , caused by ulceration of the neoplasm ( 1 , 3 ) . abdominal pain andobstructive symptoms are also common , especially if there is endoluminal growth that could cause intussusceptions ( 1 , 3 ) . endoscopically , gastric lipomas typically appear as a soft , sharply defined , submucosal mass , often yellow in color as opposed to the surrounding pink mucosa . typically , 3 clues help to identify these lesions as lipomas on endoscopic examination : the tenting sign , in which the overlying mucosa is easily retracted with the biopsy forceps ; the cushion sign which occurs when the forceps produces a soft , cushioning indentation when applied to the lipoma ; and the naked fat sign produced when fat protrudes through the overlying mucosa after multiple biopsies are performed ( 4 ) . occasionally , the lesion may be associated with a centrally located , superficial ulceration , caused by pressure necrosis . at times , ulceration can be fairly extensive , leading to the false impression of a more aggressive lesion ( 3 , 4 ) . it strongly suggests the diagnosis by showing a well - circumscribed lesion with a uniform , fatty density and an attenuation ranging from 70 to 120 h ( 3 ) . the typical findings of eus reveal the tumor as a hyperechoic neoplasm in the submucosal layer ( 5 ) . standard biopsies are often inadequate because of the submucosal location of the tumor . on gross examination , gastric lipomas appear as solitary , smooth , soft masses , most often more than 2 cm in diameter with an average size of 6.5 cm . on cut surface , they appear bright yellow , round , greasy and encapsulated , unless they have become infracted . large lesions may be ulcerated , like in our patient ( 13 ) . histologically , gastric lipomas are sharply circumscribed tumors , usually surrounded by a thick and fibrous capsule . they are composed of mature adipocytes , relatively uniform in size and lacking cytologic atypia . the tumor is usually centered in the submucosa and often compresses the overlying muscularis mucosae ( 1 , 6 ) . when the tumor is large , there is a progressive tendency for the submucosal mass to extrude into the lumen , leading to traumatic and inflammatory changes and resulting in necrosis , ulceration , and hemorrhage . secondary changes including nuclear hypertrophy , hyperchromasia , fat necrosis , fatty cysts , and foamy macrophages may be observed . the tumor can , in this situation , mimic a wdls ( 3 , 6 , 7 ) . in such situation , diagnosis is difficult and morphological features are insufficient to classify the tumor . cytogenetics and molecular biology offer new powerful tools for differentiating benign and malignant lipomatous tumors . wdls are characterized by giant marker and ring chromosomes , sometimes as a sole finding or occasionally in association with other numerical or structural alterations . the giant marker and ring chromosomes contain amplified sequences of 12q13 - 15 , the site of several genes ( e.g. , mdm2 , gli , sas , cdk4 , and hmgic ) . this structural abnormality results in the consistent amplification of mdm2 and the frequent amplification of the adjacent genes , sas , cdk4 , and hmg1c ( 7 ) . the high specificity and sensitivity of detection of mdm2 and cdk4 amplification in wdls and dedifferentiated liposarcomas have been demonstrated and analysis of these abnormalities using fish or polymerase chain reaction has recently been shown to be an interesting means of identifying and separating wdsl from various benign lipomatous lesions ( 79 ) . the treatment of choice for a symptomatic gastric lipoma is circumferential excision with a clear margin of normal tissue . due to the benign nature of this lesionsimple local enucleation or partial gastric resection is sufficient to remove the lipoma without fear of relapses or malignant degeneration ( 2 ) . cytogenetic procedures are , in these cases , the only means for an accurate diagnosis .\noutput:\n" }, { "from": "agent", "value": "gastric lipoma is a rare tumor , accounting for only 5 % of gastrointestinal tract lipomas and less than 1 % of all gastric tumors . histological diagnosis is usually easy . however , the tumor may sometimes undergo significant inflammatory changes leading to a difficult differential diagnosis with well - differentiated liposarcoma . authors report the case of a 51 - year - old man , presenting with epigastralgia of recent onset . physical exam was unremarkable . endoscopy revealed a large , ulcerated , submucosal , and antral tumor . ct scan showed an antral mass with fat attenuation . the patient underwent a total gastrectomy . macroscopic examination identified in the antral wall a 9 - cm , well - circumscribed , nodular lesion , with a greasy cut surface . on histological examination , the tumor was composed of a mature adipocytes proliferation , showing significant variation in cell size , associated to some lipoblasts . nuclei were sometimes large , irregular , neither with hyperchromasia nor mitosis . diagnosis of a well - differentiated liposarcoma was suspected and molecular cytogenetic analyses showed neither mdm2 nor cdk4 gene amplification on fluorescent in situ hybridization . the diagnosis of lipoma was made . twelve months after surgery , the patient is doing well . in conclusion , differentiating benign from malignant fatty tumors is sometimes difficult in morphologic features . in these cases , cytogenetic procedures are the only means for an accurate diagnosis ." } ]

[ { "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: attachment is a relatively stable emotional bond which is created between child and mother or those with whom an infant regularly interacts . parents responses to the signs of child 's attachment behavior and their availability in stressful situations , provides a safe place and condition for children , based on which , children organize their expectations from the environment . the attachment between child and primary caregiver ( usually mother ) would become internalized and later act as a mental model which is used by the adult person to use as a base for building friendship and romantic relationships ; it can affect the attitudes of people in their adulthood as well . adult attachment styles are subdivided into three categories : ( 1 ) secure : secure people are intimate and comfortable in making relationships , and they are sure that others would like them . ( 2 ) anxious - ambivalent : they have a strong desire for close relationships but also have many concerns of rejection . these people have a negative image of themselves , but a positive attitude toward others . ( 3 ) avoidance : for this group of people , self - reliance is the most valuable issue . hence , it can be said that attachment styles affect other aspects of one 's life and have an impact on persons relationships with other people after childhood . many researchers and authorities have shifted their focus toward the topics such as joy , happiness , life satisfaction , and positive emotions . according to many theories of emotions , one of the six great emotions is happiness ; the six great emotions include surprise , fear , anger , happiness , disgust , and worry . happiness is a type of conception about individual 's own life ; it includes items such as life satisfaction , positive emotions , and mood , lack of anxiety and depression and its different aspects of emotions . when people are satisfied with their living conditions and are frequently experiencing positive and less negative emotions , it is said that they are at high levels of mental health . increased levels of happiness is directly associated with the better status of health , appetite , sleep , memory , family relationships , friendships , family status , and ultimately mental health . the relationship between subjective well - being and emotion regulation with attachment styles in various studies has been explained . despite the important role of medical students in public health and the significance of their happiness which is related to their attachment styles , so far , this research was aimed to assess the relationship between attachment styles and happiness and demographic characteristics of medical students . this descriptive and analytical study was conducted on medical students in kurdistan university of medical sciences , in 2012 . as exclusion criteria , students who were unwilling to fill out a questionnaire and guest studentssince there were five independent variables in the study and it was needed to include 35 samples for each variable in the regression model , the calculated sample size was 175 people ; a total of 200 students were included in the study . samples were chosen through stratified sampling method ( different levels of education ) and each stratum was proportional to the size of each class . to collect the data , after obtaining permission from the ethics committee of kurdistan university of medical sciences , list of all medical students , which was classified by educational level , was obtained from education office . the samples were systematically selected from the list provided by education office ; they were selected in proportion to the number of students in each educational level ( physiopathology , extern , intern level ) . after taking their consent to participate in research and explaining the objectives , questionnaires were given to the participants . the questionnaires were filled out by the students and were collected the same day . before completing the questionnaire ( 47 questions ) , students were assured that all information will be confidential , and they were also asked to answer the questions accurately . they were allowed to ask their questions in case of facing any ambiguity in the questionnaire . this scale is developed by hazan and shaver ( 1987 ) and it has 15 items , with five items for each of the three types of secure attachment , ambivalent attachment , and avoidant attachment style . it is scored from never ( zero ) to almost always ( score = 4 ) . the score of each attachment subscale is obtained by calculating the mean of five items for each subscale . in various studies , the reliability of the questionnaire has been calculated from 0.78 to 0.81 ; moreover , its reliability in iranian culture was tested by boogar et al . , the obtained results for the entire test , the ambivalent , avoidant , and secure attachment styles were 0.75 , 0.83 , 0.81 , and 0.77 , respectively . to measure the happiness variable , the scale has 29 items which is scored on a range of zero to four ; it has five marks including life satisfaction with eight items , self - esteem with seven items , subjective well - being with five items , satisfaction with four items , and positive manner with three items . because two items have a correlation coefficients of 35 % with any of the five other components , they are not included in any of the components , but they are included in the total score . the reliability of this scale among iranian students has been reported to be 0.93 . the collected data were entered into spss version 16 ( ibm , chicago il , usa ) . quantitative data were described using the mean and standard deviation ( sd ) , and string variables were described using frequency and percentage . the correlation between happiness score and attachment style scores were assessed using pearson 's correlation coefficient . the difference between the happiness score and the scores of different attachment styles in each sex were compared using independent tests . the scores for different educational levels were compared using one - way anova . finally , using multiple regressions ( enter method ) , happiness variable as the dependent variable and the score of different attachment styles , gender , educational level , and grade point average ( gpa ) as the independent variables , if applicable , were entered into the model . this scale is developed by hazan and shaver ( 1987 ) and it has 15 items , with five items for each of the three types of secure attachment , ambivalent attachment , and avoidant attachment style . it is scored from never ( zero ) to almost always ( score = 4 ) . the score of each attachment subscale is obtained by calculating the mean of five items for each subscale . in various studies , the reliability of the questionnaire has been calculated from 0.78 to 0.81 ; moreover , its reliability in iranian culture was tested by boogar et al . , the obtained results for the entire test , the ambivalent , avoidant , and secure attachment styles were 0.75 , 0.83 , 0.81 , and 0.77 , respectively . to measure the happiness variable , the scale has 29 items which is scored on a range of zero to four ; it has five marks including life satisfaction with eight items , self - esteem with seven items , subjective well - being with five items , satisfaction with four items , and positive manner with three items . because two items have a correlation coefficients of 35 % with any of the five other components , they are not included in any of the components , but they are included in the total score . this scale is developed by hazan and shaver ( 1987 ) and it has 15 items , with five items for each of the three types of secure attachment , ambivalent attachment , and avoidant attachment style . it is scored from never ( zero ) to almost always ( score = 4 ) . the score of each attachment subscale is obtained by calculating the mean of five items for each subscale . in various studies , the reliability of the questionnaire has been calculated from 0.78 to 0.81 ; moreover , its reliability in iranian culture was tested by boogar et al . , the obtained results for the entire test , the ambivalent , avoidant , and secure attachment styles were 0.75 , 0.83 , 0.81 , and 0.77 , respectively . to measure the happiness variable , the revised oxford happiness inventory was used which had an overall reliability of 0.91 . the scale has 29 items which is scored on a range of zero to four ; it has five marks including life satisfaction with eight items , self - esteem with seven items , subjective well - being with five items , satisfaction with four items , and positive manner with three items . because two items have a correlation coefficients of 35 % with any of the five other components , they are not included in any of the components , but they are included in the total score . the collected data were entered into spss version 16 ( ibm , chicago il , usa ) . quantitative data were described using the mean and standard deviation ( sd ) , and string variables were described using frequency and percentage . the correlation between happiness score and attachment style scores were assessed using pearson 's correlation coefficient . the difference between the happiness score and the scores of different attachment styles in each sex were compared using independent tests . the scores for different educational levels were compared using one - way anova . finally , using multiple regressions ( enter method ) , happiness variable as the dependent variable and the score of different attachment styles , gender , educational level , and grade point average ( gpa ) as the independent variables , if applicable , were entered into the model . the mean ( sd ) of participants age was 22.42 ( 2.45 ) years . of all , 122 students ( 61 % ) were female and 185 persons ( 92.5 % ) were single . a total of 89 students ( 44.5 % ) were in basic sciences educational level and the majority of participants , i.e. , 97 students ( 48.5 % ) had gpa of 1517 [ table 1 ] . the distribution of demographic variables in studied subjects overall , the mean ( sd ) score of happiness was 62.71 ( 17.61 ) , secure attachment style was 11.46 ( 2.56 ) , avoidant attachment style was 9.34 ( 3.32 ) , and ambivalent attachment style was 7.93 ( 3.47 ) . there was no significant relationship between gender and attachment styles , however , the happiness score was 67.2 ( 17.2 ) in men and 59.9 ( 17.36 ) in women , and the difference was statistically significant ( p = 0.005 ) . the avoidant attachment style was 9.48 ( 3.34 ) in singles and 7.6 ( 2.66 ) in married people , and the difference was also statistically significant ( p = 0.03 ) [ table 2 ] . the relationship between gender and marital status of the studied subjects with attachment styles and happiness scores there was no significant relationship between the happiness score and educational level . the score of secure attachment style in students with gpa of 1720 was about 9.91 ( 2.9 ) , which was lower compared to those with lower gpas ( p = 0.051 ) . no significant relationship was observed between happiness score and other attachment styles with students gpas . age was not significantly correlated with happiness scores ( p = 0.797 , r = 0.019 ) . in the multivariate analysis , the relationship between attachment styles and happiness scores were compared and the results showed that after controlling for important factors , the variables of secure attachment style ( p = 0.001 ) , male gender ( p = 0.004 ) , and gpa ( p = 0.047 ) were associated with higher happiness scores ( r = 0.180 ) [ table 3 ] . comparison of the relationship between happiness scores and attachment style and other variables using multiple regression analysisthe most common attachment style among students was secure attachment style that was consistent with the results of other studies . secure attachment style leads to activation of a system which bowlby calls the discovery system . this system allows a person to explore his / her environment and experience its own ability to control the condition . secure attachment gradually creates a sense of mastery and ability to handle frustration , and finally , in the context of a secure attachment relationship , then the person is enabled to reflect his / her emotions and positive beliefs about personal values and effectiveness . positive perfectionism , self - esteem , personal control , greater happiness in relationships better emotional management , less stress , and greater job satisfaction are among the specifications of secure attachment style ; these features may be a positive prognostic factor in medical students who usually endure much stress . in our study , the minimum frequency was observed in ambivalent attachment style ; our finding was similar to other studies . in asgharinejad et al. s study as well as ahadi et al. s study avoidant attachment style was the most common and secure attachment was second common style . due to differences in statistical samples and scales , which have been used in these two studies , these differences can be justified . attachment theory is focused on cognitive schema ; the schema affects the organization of individual 's relations with others and his / her perceptions of the world around . attachments formed in childhood can affect adulthood and the attachment between child and primary caregiver ( usually mother ) is internalized and serves as a mental model . according to the mentioned explanations , we can conclude that attachment styles are formed based on schemas and inner experiences , experiences which obtained through interaction with parents and others over time , the role of these factors is much stronger than the effect of gender alone . according to our results , there was a significant relationship between avoidant attachment style and marital status , and avoidant attachment style was more common among single people than married ; so , avoidant attachment could be a barrier to marriage . finney and noler believe that adults with avoidant attachment style have the same characteristics as those with dismissive attachment style ( self - positive model , others negative , with a low anxiety , and high avoidance ) . people with avoidant attachment styles have a negative attitude toward others and have difficulty in communicating with others and maintaining relationships ; they have a high sense of self - esteem and put low values on close relationships with others , which confirms our findings . the results showed no significant relationship between attachment style and gpa of individuals ; however , secure attachment style was less common in participants with high gpa . individuals with a secure attachment style are better able to interact with the environment , so they are expected to have better educational status , but the results of our study did not confirm this idea . it might be that struggling to get a higher score , sometimes help individual to compensate for a sense of frustration and low self - control . it is also possible that the educational system would create an unhealthy competitive environment and promote negative behaviors such as blind imitation without critical thinking . on the other hand , in our study , it was not determined to which educational level and age range each gpa belongs . in addition , the effects of other factors were not considered , and they have not even been considered in other studies as well , and this is one of the limitations of our study . in sheikhmoonesi et al. s study the average score of subjects in the happiness inventory was 41.23 and the average score of happiness in students of tehran university of medical sciences in 2010 was 47.13 . based on these results , our students had higher levels of happiness which could be due to facilities , the status of their field of study and university , their future career perspectives , and their inner attitudes . on the other hand , the statistical sample size , the age range , and demographic conditions can justify these differences . in our study , secure attachment style was associated with higher happiness scores and this finding was consistent with the findings of other studies . people with secure attachment style are successful in making relationships with others and have positive attitudes about self and others ; the mentioned items are effective in creating higher levels of happiness . researches also show that people with insecure attachment styles are more affected with emotional and psychological challenges and with increasing the feeling of helplessness in the marital relationship , they will be at lower levels of happiness . in a study , girls with secure attachment style , compared with girls with avoidant attachment style , were more satisfied with relationships with their fathers . as another results of our study , there was a significant relationship between happiness scores and gender ; accordingly , the happiness scores in boys was higher than that in girls . in keshavarzet al. s study , contrary to the results of our study , there was a positive relationship between female sex and happiness that could be due to differences in the studied populations . we studied students , while in keshavarz et al. s study , yazd population ( males and females ) were studied . study , no significant relationship was observed between sex and happiness . however , in solymani 's et al . study , men achieved higher scores in subscales of life satisfaction and self - esteem while men had higher scores in a positive manner and inner satisfaction . to interpret these differences , it can be said that working and educational condition , society 's attitudes toward gender , which is strongly influenced by cultural factors , can affect a person 's happiness . in our study , there was a negative correlation between age and happiness scores ; however , this relationship was not significant . in sheikhmoonesi et al. s study the happiness scores in people aged below 22 years were higher than that in people aged more than 22 years . to justify the consistency between the two studies , we can note the similarities in the field of study and age range . in keshavarzet al. s study , older age was associated with greater happiness which could be due to differences in population and age range . in boogaret al. s study , job satisfaction among younger nurses was higher than that in older people . in our studied population , individuals at different ages are not facing the same stressors and expectations ; indeed , the course materials , environmental conditions , and people whom they are communicating with ( professors , personals working in different wards , and patients ) are different at any stage . life satisfaction is not an objective and stable trait , rather it is sensitive to situational changes and is shaped based on individual 's perceptions and perspectives . in multiple regression analysis which was performed with the control of key factors , variables of secure attachment style , gender , and gpa were associated with higher happiness scores . such an analysis has not been carried out in other studies and is one of the strengths of our study . the higher gpa was associated with higher happiness scores and other studies have not addressed this issue . there was higher level of dissatisfaction and expectation among people with lower gpas ; on the other hand , students with higher gpas are dealing with more stress of keeping current situation and they have more competition with others . moreover , mediocre gpa did not indicate higher dissatisfaction , and it might even signify less competitive pressure and family expectations ; this greatly originates from individual 's attitudes and expectations . perfection - seeking individuals may excessively get higher scores , but they are less satisfied and happy . according to our results , the satisfaction score was not significantly associated with educational level which was consistent with the results of sheikhmonesi et al. s study . every educational level brings up different external conditions and stressors which may have different effects depending on the internal characteristics , student 's ability to cope with environment , and individual 's expectation , behavior , and social interaction with others . based on the findings of this study , the most common attachment style was secure attachment style , which could be a positive prognostic factor in medical students , helping them to manage stress . the frequency of avoidant attachment style among single persons was higher than that in married people , which is mainly due to their negative attitude toward others and failure to establish and maintain relationships with others . the variables of secure attachment style , male gender , and average gpa were associated with higher happiness scores these factors can be taken into account while planning for promoting happiness levels in students .\noutput:\n" }, { "from": "agent", "value": "background : attachment theory is one of the most important achievements of contemporary psychology . role of medical students in the community health is important , so we need to know about the situation of happiness and attachment style in these students.objectives : this study was aimed to assess the relationship between medical students attachment styles and demographic characteristics.materials and methods : this cross - sectional study was conducted on randomly selected students of medical sciences in kurdistan university , in 2012 . to collect data , hazan and shaver 's attachment style measure and the oxford happiness questionnaire were used . the results were analyzed using the spss software version 16 ( ibm , chicago il , usa ) and statistical analysis was performed via t - test , chi - square test , and multiple regression tests.results : secure attachment style was the most common attachment style and the least common was ambivalent attachment style . avoidant attachment style was more common among single persons than married people ( p = 0.03 ) . no significant relationship was observed between attachment style and gender and grade point average of the studied people . the mean happiness score of students was 62.71 . in multivariate analysis , the variables of secure attachment style ( p = 0.001 ) , male gender ( p = 0.005 ) , and scholar achievement ( p = 0.047 ) were associated with higher happiness score.conclusion : the most common attachment style was secure attachment style , which can be a positive prognostic factor in medical students , helping them to manage stress . higher frequency of avoidant attachment style among single persons , compared with married people , is mainly due to their negative attitude toward others and failure to establish and maintain relationships with others ." } ]

[ { "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: stemi is caused by an acute occlusion of one of the coronary arteries which leads to cessation of blood flow to the infarct zone and that in turn leads to a series of pathological processes . for decadeshuge efforts were directed towards perfection of therapeutic strategies that can open the occluded vessel , thus allowing restoration of coronary blood flow to the infarct zone . this goal was successfully achieved , first by thrombolytic therapy , and later by primary pci . indeed , when delivered timely , both reperfusion strategies have lead to an improvement in survival and left ventricular ( lv ) function . however , it has gradually become clear from large studies that , even with successful and timely opening of the infarct related artery , variable and sometimes severe degree of lv dysfunction still occurs . this prompted massive research to better understand the complete sequence of the biochemical and pathological processes in ami over the last decades . it may sound paradoxical but restoration of blood flow after a period of occlusion itself appear to cause further myocardial damage , often referred to as re - perfusion injury ( rpi ) . it became quickly clear that it was not enough just to restore blood flow to minimize the infarct size . the resulting heart failure is a major consequence of myocardial infarction with massive epidemiologic and economic impact . the target for the ideal treatment for ami has therefore moved from simply opening the infarct - related artery to include reduction and / or treatment of rpi with the aim to reduce as much lv dysfunction and prevent the untoward end of heart failure . today any comprehensive strategy must not only include establishing reperfusion of the infarct related artery , but also prevent the deleterious effects re - perfusion injury . unfortunately , while the achievement of the first goal is near its peak , the second goal of preventing reperfusion injury has not been as fortunate . this is despite much understanding of the mechanism of injury , which in theory should pave the way for an effective therapy or therapies . several agents have been proposed based on the mechanism of injury and indeed some of these agents have already been tried in experimental and clinical trials . the problem is that when applied to ami in humans , the results are not as impressive . one of the most promising agents for the prevention of rpi in experimental models is sodium nitrite , which has it main mechanism of action on the mitochondrial permeability transport pores ( mptp ) through conversion into nitric oxide ( no ) . the investigators of the niami study used na - nitrite infusion , given intravenously , immediately prior to primary pci for stemi . it is a multi - center , double blind , placebo - controlled randomized trial . the sample size was estimated assuming mean infarct size of 1520 % in stemi patients , based on data from btker et al . they aimed to test at least a 4 point reduction in infarct size for relevance . the primary outcome of the study was reduction in the infarct size which was assessed by echocardiography and cardiac mri at 68 days ( initial infarct size ) and by echocardiography alone at 6 months ( final infarct size ) . the median infarct size was 22 % in the treatment group versus 20 % in placebo group , which did not meet the hypothesis set at 4 % reduction . it is of note that 22 % and 16 % of patients declined cardiac mri in each group respectively . the left ventricular end systolic volume ( lvesv ) was 85 ml in both groups at 68 days , and 75 ml versus 78 ml at 6 months . similarly lv ejection fraction was similar ; 48 % in treatment group versus 45 % in placebo group at 68 days , and 53 % in both groups at 6 months . interestingly there was no significant change in these echocardiographic parameters over the duration of follow up between 68 days and 6 months in both groups . the secondary outcome was reduction in the rise of the plasma levels of biomarkers during the acute phase of stemi . thus , the mean troponin - 1 was slightly lower in the treatment group compared to the placebo group ( 3734 vs 3807 arbitary units ) , while the creatine kinase levels were higher ( 67019 versus 59574 respectively ) . unlike the other negative findings , a very interesting upshot emerged in the pre - specified and post - hoc subgroup analysis . there was a treatment effect favoring nitrites in diabetic patients , which was not seen in non - diabetics . thus there was 4.5 % reduction in infarct size in diabetics , compared to only 0.2 % in non - diabetics . however , the interaction was not statistically significant , perhaps because of the small number of diabetics in the study . type ii statistical error ( only 12 diabetics in the treatment group and 11 in placebo ) . given these post - randomization exclusions or missing data both in the treatment and placebo groups , it is difficult to know how many of these have actually had incomplete biochemical records or cmr studies in the specific subgroups . the naimi study tackles and important problem that arises from both occlusion and reperfusion injury of the myocardium after ami , which eventually lead to lv dysfunction and heart failure . it is a serious attempt to move the bar forward to a more global strategy in the management of ami , a strategy that offers not only effective and timely reperfusion , but also prevents the subsequent reperfusion injury . the investigators used na - nitrites , which showed much promise to prevent reperfusion injury in experimental studies . despite much studied science and understanding of the mechanisms of reperfusion injury , the investigators carefully worked out the sample size assuming 4 points reduction in infarct size . they also evaluated the dose required to achieve optimal plasma level of na - nitrites . however , this remains a blood level that is based on animal models and then translated to the human clinical situation . at these plasma levels , the results were promising in animal models , but disappointing in man . the authors were rightly cautious of the potential side effects of higher doses . in a study by gonzalez et al . longer infusion ( 1 hour ) resulted in higher plasma levels , but with significant haemodynamic changes , sometimes needing saline infusion to maintain blood pressure . the matter is also complicated further by the fact that nitrites , and indeed organic nitrates , appear to have a biphasic effect with more favorable outcomes at smaller doses , and may be none at higher doses . however , given that the drug has shown great promise in animal models , further research into all these questions may be worthwhile . another question is : could direct infusion of the nitrites into the coronary arteries during primary pci result in a better outcome based on better delivery of the agent ? the selection of both treatment and placebo group was obviously rigorous and this is reflected by the high exclusion rates in both the pre - and post - randomization periods . therefore , after all the exclusions , only 229 made it to the final analysis ( 118 in the treatment group and 111 in placebo ) . several studies have shown that all aspects of ami are worse in diabetics than non - diabetics , including the left ventricular dysfunction and remodeling , and subsequently heart failure . therefore , this is group is of special importance , not only in terms of perfusion strategies and antiplatelet therapy , but also for strategies that can limit the reperfusion injury . in the current study , while the results were unimpressive in the whole group , there is evidence in their sub - analysis that diabetic patients may obtain greater benefit than non - diabetics . unfortunately the number of diabetic patients in the study was small , thus may be misleading ( type ii statistical error ) . with the relatively high number of diabetics in the gulf , a modified study is underway in our center to address some of the above questions , especially in diabetic patients , which make nearly half of the stemi patients that we see in the primary pci program . the investigators used a single dose of 70 moles of na - nitrites in 5 ml of water , which is reasonable since multiple doses could dilute the conclusions with the limited number of patients . this dose was calculated based on a previous study to achieve adequate plasma levels in an average 70 kg normal subjects . this , in turn , was suggested by a previous animal model which showed that 5 mol per liter gave an impressive level of prevention of reperfusion injury . another study in healthy individuals showed that this plasma concentration can be achieved by giving an intravenous infusion of 50 mol of na - nitrites over 5 minutes . they used 70 g over the same period of time in the study , thus assuring an adequate dose for the study . the naimi study has tackled one of the most challenging contemporary issues in the management of acute myocardial infarction and used one of the most promising agents currently available to prevent reperfusion injury . nonetheless , it failed to show a significant difference , despite much evidence to support its use from both the science and the experimental models . the first lesson is inevitably is how complex and illusive the issue of prevention of reperfusion injury is today . the second lesson is that there may be vital differences between experimental models and clinical ami in humans that need to be explored further . third , we have learnt how carefully the investigators went about estimating the appropriate dose of na - nitrites in the clinical setting , projecting from data in both experimental models and healthy volunteers . fourth , there is a call to carefully examine the possibility of different doses and / or different routes for the administration of nitrites in stemi patients . fifth , the study highlights how difficult it is to avoid exclusions and missed data which make the task of analysis and conclusions tricky . sixth , and perhaps the most important lesson from the niami study , is that it gives a glimpse of hope to one of the highest risk groups in ami , namely diabetics . it is our intention to set up a research protocol to concentrate on this group that we see frequently in the gulf region . the quest for the optimal strategy to prevent reperfusion injury is intense and is as varied as the mechanisms of injury . it went as far using immunosuppressant agents and catheter cooling as in the chill - mi study , a reminder of the previous experience during cardiac surgery . in conclusion , the niami study tackled an important issue in the management of reperfusion injury after stemi and used one of the most promising agents in experimental models , namely na - nitrites . although the overall result is negative , the study highlighted important issues , especially the promise in diabetic patients .\noutput:\n" }, { "from": "agent", "value": "the naimi trial has recently been published . it assessed one of the most contemporary and challenging issues in the management of acute myocardial infarction ( ami ) , namely prevention of reperfusion injury ( rpi ) after primary pci for st - elevation myocardial infarction ( stemi ) . it investigated the effect of the intravenous administration of na nitrite given immediately prior to primary pci for stemi in 229 patients ( 118 in the treatment group , and 111 in placebo ) . the myocardial infarction ( mi ) size did not differ between the two groups as observed by cardiac mri ( cmr ) with gadolinium enhancement at 68 days or plasma troponin - i and creatine kinase ( ck ) , or by left ventricular ( lv ) volume and ejection fraction ( ef ) as measured by echocardiography at 68 days and again at 6 months . they concluded that iv nitrites did not reduce the infarct size . there was , however , a trend towards benefit in diabetic patients in the post - hoc analysis . the small number of these subjects has probably lead to inconclusive outcome in this subset ." } ]

[ { "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: erlotinib , a small - molecule egfr tyrosine kinase inhibitor , has been approved by the fda for patients with pancreatic cancer and non - small cell lung cancer . skin rash is a well - known side effect related with all egfr blocking agents . it has been suggested that rash could be used as a surrogate marker for response and possibly be associated with prolonged survival . in common with all other egfr inhibitors , skin rash of a highly florid nature is the dose - limiting factor and is usually reversible . there is scant data on acute generalized exanthematous pustulosis ( agep ) with superimposed staphylococcus aureus skin infection caused by erlotinib . treating pancreatic cancer , the fourth leading cause of cancer - related deaths in the united states , the addition of a second cytotoxic agent ( cisplatin or oxaliplatin ) has demonstrated advantage in terms of response rates and progression - free survival , but has not achieved a significant overall survival benefit . a phase iii randomized controlled trial by the national cancer institute of canada clinical trials group ( ncic - ctg ) has shown a statistically significant survival benefit of gemcitabine plus erlotinib compared with gemcitabine alone . based on these data , the fda approved erlotinib to be used with gemcitabine as a first - line treatment for advanced pancreatic cancer . agep is a rare acute reaction that is drug induced in 90 % of the cases and characterized by a widespread , sterile pustular rash . although the term was used for the first time in 1980 by beylot et al . , the disorder is considered to be older than this . initially , it was mistakenly included with pustular psoriasis or classified as a hypersensitivity syndrome to anticonvulsive medications . our patient is a 63 - year - old man with a past medical history of pancreatic adenocarcinoma with liver metastases . less than 1 week after the initiation of tarceva , the patient developed papulopustular acneiform rash on his face ( fig . about 2 days prior to hospital admission , the pustular rash spread to the extremities ( fig . a skin biopsy showed mild mixed inflammatory changes with prominent dermal hemorrhage suggestive of a drug eruption ( fig .3 ) . on the second day of admission , the patient 's symptoms of itching and pain from the erythematous rash improved . on the third and fourth day in the hospitalhis erythematous rash gradually subsided , and the patient was discharged on the seventh hospital day . the patient was followed up by his oncologist and was restarted with gemcitabine which he tolerated without any side effects . in addition , he was then rechallenged with tarceva and , surprisingly , developed another erythematous pustular rash on his face and extensor surfaces plus superimposed methicillin - sensitive s. aureus infection . furthermore , the patient also developed septic arthritis for which he received iv antibiotics and recovered thereafter . agep , a member of the neutrophilic dermatoses was first described by baker and ryan in 1968 as exanthematic pustular psoriasis . the term pustuloses exanthmatiques aigus gnralises ( peag ) was introduced by the french dermatologist c. beylot in 1980 . this pustular skin eruption , with an incidence of 15 per million / year , has an equal age and gender distribution . it is a self - limiting disease , with the following clinical features : ( 1 ) numerous , small non - follicular , intraepidermal or subcorneal pustules ( 5 mm ) on an erythematous background ; ( 2 ) typical histopathological changes ; ( 3 ) fever ( 38c ) ; ( 4 ) blood neutrophil counts 710 / l , and ( 5 ) an acute evolution with spontaneous resolution of pustules within less than 15 days . the agep validation score of the european severe cutaneous adverse reactions ( euroscar ) study group has been used to establish the diagnosis . a score between 8 and 12 for agep is a definitive diagnosis . in our case , the score was 11 according to the validation score of the euroscar study group ( table 1 ) . the principal differential diagnoses of agep consist of pustular psoriasis , sweet 's syndrome , pustular erythema multiforme , toxic epidermal necrolysis , drug rash with eosinophilia and systemic symptoms , subcorneal pustulosis ( sneddon - wilkinson syndrome ) , pustular vasculitis , and bullous impetigo . i , after drug intake , antigen - presenting cells activate drug - specific t cells by presentation of the drug to mhc class i ( for cd8 + t cells ) and class ii ( for cd4 + t cells ) in the lymph nodes . drugs can be covalently bound to the peptide / mhc complex or in a labile , noncovalent way . this is followed by expansion and migration of t cells into the dermis and epidermis . in phase ii , the infiltrating t cells release extended amounts of cxcl8 , which is a neutrophil - attracting chemokine , resulting in neutrophilic inflammation . in addition to cxcl8 , the t cells also induce interferon , interleukin 4 , and interleukin 5 , and these all provoke eosinophilic and neutrophilic aggregation . phase iii is characterized by the attachment of an increasing number of neutrophils at the site of inflammation to adhesion molecules ( e.g. icam - 1 ) expressed on activated endothelial cells . migration of these polymorphonuclear leukocytes along the increasing cxcl8 gradient through the dermis and the epidermis into the vesicles results in the formation of pustules . moreau et al . proposed that agep is a delayed type of hypersensitivity reaction . another possible mechanism is the production of antigen - antibody complexes induced by an infection or drug that activates the complement system , which in turn leads to neutrophil chemotaxis . the typical histopathology and immunochemistry of agep is characterized by spongiform subcorneal and / or intraepidermal pustules , marked papillary edema ( occasionally with the formation of a subepidermal blister ) , and polymorphous perivascular infiltrates with neutrophils and exocytosis of some eosinophils . in a minority of cases , , agep has been attributed to a variety of causes such as viral infections , chlamydia pneumoniae infection or hypersensitivity to mercury , but the skin reaction is primarily an adverse response to drugs . antibiotics have been implicated as the causative agents in 80 % of the affected individuals . in our case , skin rash is a well - known side effect related with all egfr blocking agents . it has been suggested that rash could be used as a surrogate marker for response and possibly be associated with prolonged survival . erlotinib inhibits egfr tyrosine kinase and leads to growth arrest of keratinocyte and follicular obstruction with subsequent inflammation leading to rash development . microbiologic stains and cultures from most cases of skin rash usually do not show an infectious cause . superimposed secondary bacterial infection has been reported as in our case , where superimposed s. aureus skin infection developed . the case we report here developed a severe papulopustular rash 45 days after initiation of erlotinib , predominantly on the face but then gradually progressing to his bilateral upper extremities , chest , and lower extremities . due to the self - limiting course of agepno therapy is available to prevent lesion extension and a further decline of the patient 's general condition . the causative drug has to be discontinued which we did the first day of admission and antibiotics are not to be given unless there is superinfection of the skin lesions . superimposed s. aureus skin infectionwe believe there is a chronological relationship between starting an efgr inhibitor and the occurrence of superimposed s. aureus skin infection in which pustulosis is usually sterile in most of the cases . we report this case in order to draw attention to and to further gain understanding of the potential adverse effects of erlotinib and to avoid unnecessary investigation and / or administration of expensive medications . this case report also demonstrates that erlotinib ( tarceva ) is becoming universally recognized as a causative agent of agep . these include utilizing the validation score for diagnosis of agep , applying the appropriate treatment methods , as well as mentioning the severe infectious implications . furthermore , this case report demonstrates the potential consequences of rechallenging patients with erlotinib , that is , additional life - threatening infectious complications as well as the unexpected and unique reoccurrence of the rare skin reaction agep .\noutput:\n" }, { "from": "agent", "value": "acute generalized exanthematous pustulosis ( agep ) is a rare acute reaction that is drug induced in 90 % of the cases and characterized by a widespread , sterile pustular rash . erlotinib , a small - molecule egfr tyrosine kinase inhibitor , has been approved by the fda for patients with pancreatic cancer and non - small cell lung cancer . skin rash is a well - known side effect related with all egfr blocking agents . it has been suggested that rash could be used as a surrogate marker for response and possibly be associated with prolonged survival . we report a case of rare presentation of agep involving an adverse effect of erlotinib . the commonly reported adverse effects of erlotinib are mild skin eruptions . however , our case describes the rare presentation of agep induced by erlotinib . the estimated incidence rate of agep is approximately 15 cases per million / year ." } ]

[ { "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: cancer immunotherapy targeting enhancement of anti - tumor t cell reactivity has received significant attention in recent years , mainly due to the favorable clinical responses of immune checkpoint inhibitors , such as anti - ctla4 and anti - pd - 1 antibodies ( 1 ) . anti - pd - 1 antibodies in particular showed significant objective responses in clinical trials for some solid tumors , such as malignant melanoma ( 30 % ) , non - small cell lung cancer ( nsclc ; 20 % ) , renal cell carcinoma ( 17 % ) , and etc ( 2345 ) . to this end , two pd - 1 antibody drugs , nivolumab and pembrolizumab , have received us fda approval for treatment of advanced melanoma , nsclc , and metastatic renal cell carcinoma . also , antibodies against pd - l1 , a ligand for pd - 1 , are being tested in clinical trials for various types of cancers ( 6 ) . thus , therapeutic strategies targeting the pd - 1 / pd - l1 axis have considerable potential to contribute to the treatment of multiple types of tumors . pd - 1 is an inhibitory receptor expressed mainly on activated t cells , b cells and monocytes ( 78 ) . pd - l1 and pd - l2 are best - known ligands for pd - 1 ( 910 ) . both are expressed on hematopoietic cells ( dendritic cells , mast cells , macrophages , t cells and b cells ) , whereas pd - l1 is also expressed on non - hematopoietic cells ( endothelial and epithelial cells ) ( 1112 ) . interestingly , pd - l1 expression is increased on various types of cancer cells , suggesting that this molecule is used for immunoresistance of cancer cells ( 13 ) . biochemically , pd - 1 delivers inhibitory signal through its intracellular cytoplasmic domain , which contains immunoreceptor tyrosine - based switch motif ( itsm ) and immunoreceptor tyrosine - based inhibitory motif ( itim ) . ligation of pd - l1 with pd - 1 induces phosphorylation of itsm and itim and recruits shp - 1 and -2 , which inhibits t cell receptor downstream signaling ( 1415 ) . in murine in vivo studies , pd - 1 deficiency led to the development of autoimmune diseases such as lupus - like syndrome and dilated cardiomyopathy ( 1617 ) . therefore , one can expect that systemic treatment with pd - 1 blocking antibodies in cancer patients will lead to autoimmune side effects . indeed , 10 to 15 % of treated patients developed grade 3 ~ 4 drug - related toxicities , although these toxicities were less severe than those of blocking antibodies against ctla4 , another co - inhibitory receptor on t cells ( 181920 ) . in this study , to utilize pd - 1 blockade in a t - cell specific manner rather than systemically , we tried to inhibit endogenous pd - 1 function in t cells by overexpressing a pd - 1 mutant on t cells that is designed compete with endogenous pd - 1 in a dominant negative manner . the mutant receptor was generated by deleting the cytoplasmic domain of pd - 1 , which we call pd - 1 decoy . t cells expressing pd - 1 decoy showed increased production of ifn - when co - cultured with pd - l1 expressing tumor cells in vitro and showed increased tumor regression in vivo . thus , inhibiting pd - 1 function in tumor - specific t cells will be a beneficial strategy for enhancing t cell - mediated anti - cancer therapy without the systemic toxicity induced by pd - 1 blockade . the mice were maintained in a specific pathogen - free facility at the research institute national cancer center , korea in accordance with the guidelines of the institutional animal care and use committee . phoenix eco and phoenix gp cell lines were provided by garry nolan ( stanford university ) . the cdna of extracellular and trans - membrane portion of mouse pd - 1 ( amino acid 1 - 199 ) was cloned into pmig - w retroviral expression vector ( a gift from yosef refaeli , national jewish medical and research center ) to generate pd - 1 decoy . for pd -1-cd28 chimera , the cdna of the cytoplasmic portion of mouse cd28 ( amino acid 177 ~ 218 ) was linked to the cdna of extracellular and trans - membrane portion of pd - 1 ( amino acid 1 ~ 199 ) by blunt end ligation . pd - 1 decoy and pd -1-cd28 chimera cdnas were inserted in front of the ires - gfp cassette in pmig - w to use gfp as an expression marker . phoenix gp cells were transiently transfected with a vsv - g ( pmd.g ) - coding plasmid and the retroviral plasmids by calcium - phosphate transfection . after 48 hours , the cultured supernatant containing vsv - g pseudotyped retrovirus was harvested . after 3 ~ 5 days , gfp populations were sorted by flow cytometry to generate stable cell lines producing the retrovirus . the supernatants harvested from the stable cell lines were concentrated 10 fold using a 100 kda cut - off centricon ( millipore ) to increase t cell - transduction efficiency . b6 splenocytes were activated with anti - cd3 antibody ( 5 g / ml ) plus anti - cd28 antibody ( 2 g / ml ) for 24 hours . splenocytes from ot - i and pmel - 1 mice were activated with ova257 - 264 peptide ( 1 m ) or hgp100 peptide ( 1 m ) , respectively . the activated t cells were transduced with the concentrated retroviral supernatant plus polybrene ( 6 mg / ml ) by spin infection . after 48 hours , the transduced t cells were rested for 3 days in the presence of recombinant human il - 2 ( 30 u / ml ) without further stimulation . pe - conjugated anti - mouse pd - 1 antibody ( clone : j43 , bd bioscience ) was used to detect pd - 1 decoy , pd -1-cd28 chimera , and endogenous pd - 1 . gfp populations were composed of 60 ~ 70 % of cd8 t cells and 25 ~ 35 % of cd4 t cells before cell sorting . the sorted t cells ( 210 ) were stimulated with indicated amount of anti - cd3 antibody in the presence of irradiated splenocytes ( 210 ) for 48 hours followed by ifn - elisa . retrovirus - tranduced ot - i cells ( serial dilution from 10 to 10 cells ) were cultured with mc38 - ova cells ( 110 ) or e.g7 - ova cells ( 110 ) for 24 hours . the cultured supernatants were harvested and ifn - was measured by elisa . for testing the efficacy of pd -1-cd28 chimera , pmel - 1 cells were transduced and co - cultured with ifn - ( 20 ng / ml ) - treated b16 melanoma cells for 48 hours followed by ifn - elisa . e.g7 cells ( 210 ) were subcutaneously injected into b6 mice on day 0 . after 7 days , the retrovirus - transduced ot - i cells ( 210 ) were adoptively transferred into the tumor - bearing mice via intravenous injection . tumor growth was measured every 3 to 4 days from day 7 until mice were euthanized . the approximate tumor sizes were calculated using the following formula : lengthwidth ( mm ) . the mice were maintained in a specific pathogen - free facility at the research institute national cancer center , korea in accordance with the guidelines of the institutional animal care and use committee . phoenix eco and phoenix gp cell lines were provided by garry nolan ( stanford university ) . the cdna of extracellular and trans - membrane portion of mouse pd - 1 ( amino acid 1 - 199 ) was cloned into pmig - w retroviral expression vector ( a gift from yosef refaeli , national jewish medical and research center ) to generate pd - 1 decoy . for pd -1-cd28 chimera , the cdna of the cytoplasmic portion of mouse cd28 ( amino acid 177 ~ 218 ) was linked to the cdna of extracellular and trans - membrane portion of pd - 1 ( amino acid 1 ~ 199 ) by blunt end ligation . pd - 1 decoy and pd -1-cd28 chimera cdnas were inserted in front of the ires - gfp cassette in pmig - w to use gfp as an expression marker . phoenix gp cells were transiently transfected with a vsv - g ( pmd.g ) - coding plasmid and the retroviral plasmids by calcium - phosphate transfection . after 48 hours , the cultured supernatant containing vsv - g pseudotyped retrovirus was harvested . after 3 ~ 5 days , gfp populations were sorted by flow cytometry to generate stable cell lines producing the retrovirus . the supernatants harvested from the stable cell lines were concentrated 10 fold using a 100 kda cut - off centricon ( millipore ) to increase t cell - transduction efficiency . b6 splenocytes were activated with anti - cd3 antibody ( 5 g / ml ) plus anti - cd28 antibody ( 2 g / ml ) for 24 hours . splenocytes from ot - i and pmel - 1 mice were activated with ova257 - 264 peptide ( 1 m ) or hgp100 peptide ( 1 m ) , respectively . the activated t cells were transduced with the concentrated retroviral supernatant plus polybrene ( 6 mg / ml ) by spin infection . after 48 hours , the transduced t cells were rested for 3 days in the presence of recombinant human il - 2 ( 30 u / ml ) without further stimulation . pe - conjugated anti - mouse pd - 1 antibody ( clone : j43 , bd bioscience ) was used to detect pd - 1 decoy , pd -1-cd28 chimera , and endogenous pd - 1 . gfp populations were composed of 60 ~ 70 % of cd8 t cells and 25 ~ 35 % of cd4 t cells before cell sorting . the sorted t cells ( 210 ) were stimulated with indicated amount of anti - cd3 antibody in the presence of irradiated splenocytes ( 210 ) for 48 hours followed by ifn - elisa . retrovirus - tranduced ot - i cells ( serial dilution from 10 to 10 cells ) were cultured with mc38 - ova cells ( 110 ) or e.g7 - ova cells ( 110 ) for 24 hours . the cultured supernatants were harvested and ifn - was measured by elisa . for testing the efficacy of pd -1-cd28 chimera , pmel - 1 cells were transduced and co - cultured with ifn - ( 20 ng / ml ) - treated b16 melanoma cells for 48 hours followed by ifn - elisa . e.g7 cells ( 210 ) were subcutaneously injected into b6 mice on day 0 . after 7 days , the retrovirus - transduced ot - i cells ( 210 ) were adoptively transferred into the tumor - bearing mice via intravenous injection . tumor growth was measured every 3 to 4 days from day 7 until mice were euthanized . the approximate tumor sizes were calculated using the following formula : lengthwidth ( mm ) . in order to generate a dominant negative mutant of pd - 1 , we designed a deletion mutant of pd - 1 , pd - 1 decoy , which includes the extracellular and transmembrane domain of pd - 1 with its intracellular domain deleted . this design allows pd - 1 decoy to bind the ligand , but prevents it from delivering inhibitory signals inside the cell . therefore , this mutant receptor is expected to compete with endogenous pd - 1 for ligand binding and inhibit endogenous pd - 1 function . to overexpress pd - 1 decoy on t cellsretrovirus - transduced t cells were identified by gfp expression since the retroviral vector contains gfp cdna as a reporter . when activated mouse splenic t cells were transduced with the retrovirus , transduction efficiency was approximately 65 % , as measured by gfp positivity . gfp - positive t cells transduced with a pd - 1 decoy - encoding virus were more strongly stained with anti - pd - 1 antibody than those transduced with empty virus , which ensured overexpression of transduced pd - 1 decoy ( fig . we hypothesized that overexpressed pd - 1 decoy would diminish the co - inhibitory function of endogenous pd - 1 and enhance functional activation of t cells . to test this idea , we sorted gfp - positive t cells via flow cytometry and stimulated them with anti - cd3 in the presence of irradiated splenocytes . when we measured secreted ifn - in the culture supernatant , pd - 1 decoy - expressing t cells produced 2 ~ 3 fold more cytokines than control t cells ( fig . therefore , it is very likely that pd - 1 decoy interrupts binding of endogenous pd - 1 to pd - 1 ligands on splenocytes and inhibits endogenous pd - 1 function . next , we examined whether this functional enhancement of t cells could be applied to the anti - tumor reactivity of tumor - specific t cells . for this purposeova - transfected tumor cell lines and ova - specific tcr - transgenic cd8 t cells ( ot - 1 ) served as target tumors and tumor - specific t cells respectively . ot - it cells transduced with the pd - 1 decoy - encoding retrovirus showed 55 ~ 65 % transduction efficiency ( gfp positivity ) , and the level of pd - 1 decoy expressed in the gfp - positive population was higher than that of endogenous pd - 1 expressed in the empty - vector - transduced control cells ( fig .2 a ) . for ova - expressing tumor cell lines , we chose mc38 - ova , mouse colon cancer cells transfected with ova , and e.g7 , a mouse lymphoma cell line transfected with ova because both cell lines express pd - l1 , a ligand of pd - 1 , on their cell surface ( fig . when pd - 1 decoy - transduced ot - 1 t cells were incubated with these cell lines , they produced a higher amount of ifn - than control ot - 1 t cells ( fig . the degree of enhancement of ifn - production was higher for e.g7 - stimulated t cells than that for mc -38-ova - stimulated t cells , which was correlated with higher pd - l1 expression on e.g7 cells than that on mc -38-ova . hence , pd - 1 decoy improves the reactivity of tumor antigen - specific t cells in response to pd - l1 - expressing tumor cells . in our previous study on ctla4 , another inhibitory receptor on t cell surface , we reported that replacing the inhibitory cytoplasmic domain of ctla4 with the stimulatory cytoplasmic domain of cd28 resulted in conversion of the negative signal of ctla4 to a positive signal ( 21 ) . thus , overexpression of this chimeric receptor on tumor - specific t cells led to enhanced t - cell mediated tumor regression owing to the dominant negative effect on endogenous ctla4 as well as the additional surrogate cd28 costimulatory signal . in this study , we also tested if a similar substitution of the cd28 cytoplasmic domain for the cytoplasmic domain of pd - 1 would further increase t cell reactivity by providing additional costimulation . for this experiment , we generated a pd -1-cd28 chimera that consists of the extracellular and transmembrane domain of pd - 1 and the intracellular cytoplasmic domain of cd28 ( fig . , we used another tumor antigen - specific tcr transgenic ( pmel - 1 ) cd8 t cells which recognize gp100 melanoma antigen . as a target tumor cell line , b16 melanoma cells were used . although b16 cells showed moderate levels of pd - l1 expression on the cell surface , ifn - treatment further enhanced pd - l1 expression ( fig .3 b ) . therefore , we incubated pmel - 1 t cells transduced with pd - 1 decoy or pd -1-cd28 chimera virus with ifn -- treated b16 cells , and measured ifn - production from this co - culture . similar to the results from ot - 1 t cells , pd - 1 decoy - transduced pmel - 1 t cells produced a higher amount of ifn - than control cells . however , it did not further enhance ifn - production from pmel - 1 t cells when compared with pd - 1 decoy ( fig . this observation indicates that this chimera only exerted its dominant negative function without further costimulatory activity . this result is in stark contrast to a previous report that a pd -1-cd28 chimera in humans delivered cd28 signal in a cd28 - null lymphoma cell line ( 22 ) . this discrepancy may be due to slight differences in construct design between the two chimeras . our chimera used the transmembrane domain of pd - 1 molecule and the other used the transmembrane domain of cd28 . thus , the cd28 domain in our construct may not have been able to dimerize to deliver its activation signal . in contrast , the previously published construct can dimerize because it has the transmembrane and cytoplasmic domain of cd28 , which can be linked by disulfide bonds . this dimerization did not seem to affect the binding of this molecule to pd - l1 . nonetheless , our result showed that the inhibition of endogenous pd - 1 signals with pd - 1 decoy alone was sufficient to enhance the functional activity of tumor - specific t cells . finally , we investigated whether pd - 1 decoy - mediated functional enhancement of t cells could increase therapeutic efficacy in vivo using a mouse model of anti - tumor t cell therapy . when ot - 1 t cells were adoptively transferred to subcutaneous e.g7 tumor - bearing mice , tumor growth was significantly reduced . pd - 1 decoy overexpression in ot - 1 t cells greatly potentiated tumor regression in this model , consistently with the results from in vitro functional studies ( fig . this result demonstrates that functional blockade of pd - 1 in adoptively transferred tumor - specific t cells without systemic blockade of pd - 1 may be a good strategy to enhance the efficacy of t cell therapy and to bypass potential side effect of autoimmunity at the same time .\noutput:\n" }, { "from": "agent", "value": "programmed death - 1 ( pd - 1 ) is a strong negative regulator of t lymphocytes in tumor - microenvironment . by engaging pd - 1 ligand ( pd - l1 ) on tumor cells , pd - 1 on t cell surface inhibits anti - tumor reactivity of tumor - infiltrating t cells . systemic blockade of pd - 1 function using blocking antibodies has shown significant therapeutic efficacy in clinical trials . however , approximately 10 to 15 % of treated patients exhibited serious autoimmune responses due to the activation of self - reactive lymphocytes . to achieve selective activation of tumor - specific t cells , we generated t cells expressing a dominant - negative deletion mutant of pd - 1 ( pd - 1 decoy ) via retroviral transduction . pd - 1 decoy increased ifn - secretion of antigen - specific t cells in response to tumor cells expressing the cognate antigen . adoptive transfer of pd - 1 decoy - expressing t cells into tumor - bearing mice potentiated t cell - mediated tumor regression . thus , t cell - specific blockade of pd - 1 could be a useful strategy for enhancing both efficacy and safety of anti - tumor t cell 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: colorectal cancer ( crc ) is the third most commonly diagnosed cancer in males and the second in females ( 10 % and 9.2 % of the total cancer incidence , respectively ) , according to globocan worldwide estimates of cancer incidence for 2012 . there is wide geographical variation in the incidence across the world , and nearly 55 % of cases occur in more developed regions .1 the crc incidence trends in high - income countries have varied over the past 20 years2 ; for instance , rates have recently tended to decline in the united states , whereas high rates have been reported in newly developed countries around the globe , where the risk was once low .3 south korea is one example of a country reporting crc as the cancer with the second highest incidence in both sexes , excluding thyroid cancer overdiagnosed in korea .4 the rates increased continuously from 1999 to 20125 in the korean population and nearly caught up to those in western countries .6 this trend in asian countries may reflect increased risk factors for crc , including obesity , irregular and inadequate dietary habits adapting westernized lifestyle as well as various environmental factors that may potentially affect people physically or psychosocially .2,7 as the world cancer research fund and the american institute for cancer research ( wcrf / aicr ) have reported ,8,9 lifestyle factors that very likely confer an increased risk of crc are physical inactivity , obesity , alcohol consumption , and certain dietary habits or patterns . among the diverse crc risk factors , a combination of extrinsic and intrinsic factors may cause differences between individuals ; extrinsic factors including a diet containing certain nutrients and food compositions , and intrinsic for having different genetic background , which may alter gene expression or may function in carcinogenesis .10,11 in this review , we will discuss the dietary factors vitamin d and calcium , which are linked to each other , rather than reviewing factors well known to reduce crc risk . in the 2012 wcrf / aicr continuous update project report on food , nutrition , physical activity , and the prevention of cancer : a global perspective , the evidence for an effect of vitamin d on decreasing crc risk was classified as limited - suggestive , and calcium was classified as having a probable effect on decreasing crc risk .9 over the course of actively conducting studies to prove that these two dietary factors have real effects , vitamin d has been reported to be a protective agent that induces pro - differentiation , anti - proliferative , and growth - inhibitory effects on carcinogenesis12 ,13 in association with a decrease in crc risk . certain previous meta - analyses demonstrated an inverse association between calcium intake and crc risk .14 in addition to dietary factors , genetic changes , known as mutations , will also be discussed , including a review of diet - associated single nucleotide polymorphisms ( snps ) . the above - described risk factors association with crc and the interaction between dietary and genetic factors will be summarized by reviewing relevant studies . an article search was conducted using the electronic database pubmed to identify studies published between january 2000 and march 2015 . the search keywords were combinations of following terms : vitamin d , calcium , crc , and polymorphism . we selected eligible studies based on several inclusion criteria , as follows : ( 1 ) epidemiological studies including cases and controls as well as cohort studies ; ( 2 ) studies investigating the association between dietary factors / genetic variants and crc including adenoma or polyps ; ( 3 ) studies assessing the gene - diet interaction effect on crc ; and ( 4 ) studies using an or or relative ratio and a 95 % ci to estimate crc risk . we assessed the relevance of the studies using a hierarchical approach based on the title , abstract , and full - text article . a flow chart depicting the literature search and the selection of 21 eligible studieswe excluded experimental studies that aimed to examine the association with colorectal neoplasia risk using non - epidemiological approaches ( n = 5 ) , as well as laboratory studies conducted with animals or cell lines ( n = 273 ) . the articles comprising a meta - analysis ( n = 3 ) or a systematic review ( n = 8 ) also were not included in the current study . we excluded certain studies consisting of randomized clinical trials or survival analyses of risk association between cancer cases and healthy controls ( n = 10 ) . four articles were additionally included by using the same keywords and checking for eligible references to other articles . we assessed the study objectives and risk of bias of each selected article by using the national institute for clinical excellence methodology checklist for case - control study .15 the contents of quality assessment included selection of participants , assessment , confounding factors , and statistical analysis . we summarized previous studies based on dietary factors , vitamin d and calcium and collected relevant findings associated with crc risk . for each eligible study , we extracted the publication year , the study design , the geographical location , the number of study subjects ( cases and controls ) , any diet of interest and related genetic polymorphism , and gene - diet interactions associated with a modified crc risk . we identified a total of 21 case - control studies that investigated the association between crc risk and dietary or genetic factors modified by gene - diet interactions . the majority of the studies were conducted in western countries ( n = 16 ) , such as the united states and european countries , whereas a few studies were performed in non - western countries ( n = 5 , mostly japan ) . all of the studies were designed as case - control studies , including 5 nested case - control studies . according to the study subject recruitment , the studies were population based ( n = 12 ) , clinic based ( n = 8 ) , or family based ( n = 1 ) . the studies examined dietary and genetic factors in association with crc risk and also observed gene - diet interactions , mainly focusing on vitamin d and calcium , which share a biological pathway . we grouped the studies by each dietary factor and summarize the findings from the studies in table 11628 and 2.2936 additional study data that are not mentioned in the tables will be discussed separately . both vitamin d and calcium were determined to be protective agents against crc in many quantitative studies . several studies showed data with a significant or to represent cancer risk and with a significant p - value for the comparison of dietary intake between cases and controls . generally , it is known that high levels of vitamin d or calcium intake are associated a decreased risk of developing crc . atoum and tchoporyan16 found that 75 % of crc patients were vitamin deficient , with a significant decrease in serum 25 - hydroxy - vitamin d ( p 0.05 ) . the same study also reported that vitamin d deficiency was associated with an approximately 19-fold higher risk among jordanian patients compared with controls ( p 0.05 ) . similar to the dietary calcium - related studies listed in table 2 , another study by gong et al. 17 found that patients with sporadic colorectal adenomas had significantly lower calcium intake compared with the control group , with a p - value of 0.02 . takeshige et al. 18 found that calcium intake was associated with a decreased risk of colon cancer ( p = 0.06 ) and rectal cancer ( p = 0.10 ) ( the corresponding data from gong et al. 17 and takeshige et al. 18 are not shown in the tables ) . the effect of genetic factors was determined for several representative gene polymorphisms related to vitamin d , calcium , or both , as follows : vitamin d receptor ( vdr ) , vitamin d 24 - hydroxylase ( cyp24a1 ) , vitamin d 25 - hydroxylase ( cyp2r1 ) , calcium sensing receptor ( casr ) , transient receptor potential cation channel ( trpm7 ) , and cyclin d1 protein ( ccnd1 ) polymorphisms .37,38 the vdr gene polymorphisms were diversely studied with regard to crc development . among the reviewed studies , many examined tru9i , bsmi , apai , taqi , foki , and group - specific component / vitamin d - binding protein ( gc ) . several , such as tru9i and bsmi , were found to be reliably associated with a decreased risk , whereas for others , such as taqi and gc , there was no significant a relationship between the gene polymorphism and crc risk . based on the allele frequency in genotypes , the frequency of certain alleles distinctly increased cancer risk . the difference between the vdr foki ff and ff genotypes was shown in a study by wong et al. 29 boyapati et al. 19 reported that the calcium - colorectal adenoma association varied with the vdr bsmi genotype , indicating that individuals with at least one b allele were at much lower risk , with or = 0.25 ( 0.080.80 ) , p trend = 0.02 ( these data are not shown in the tables ) . however , there have been different results regarding the allelic expression of the same gene ( vdr apai ) in different populations . takeshige et al. 18 determined that vdr apai aa / aa was associated with a decreased risk of rectal cancer reporting or = 0.75 ( 0.560.99 ) in a japanese population , whereas kupfer et al. 20 demonstrated that the vdr apai t allele was associated with an increased crc risk reporting or = 1.15 ( 1.001.33 ) among the population of african americans . two studies listed in table 2 , or those by dong et al. 30 and peters et al. 31 ( 2004 ) , reported significant associations in analyses by cancer anatomic site and diplotype , in which both studies examined the casr gene polymorphism by stratified analyses due to statistical insignificance . for proximal colon , casr ivs3 + 1048tt was associated with an increased risk with or = 1.35 ( 1.011.18 ) and casr ivs6 + 16cc with a decreased reporting or = 0.43 ( 0.190.97 ) .30 by the diplotype analysis conducted with casr , a decreased risk was observed with or = 0.56 ( 0.360.88 ) .31 in combination with dietary and genetic factors , genetic polymorphism can influence the dietary absorption level , which can affect the risk of cancer . atoum and tchoporyan16 found that the absorption of vitamin d among crc patients can be affected by the t allele of vdr taqi . compared with the healthy control group , the case group had a lower level of vitamin d in a comparison based on the frequency of the t allele . vitamin d absorption levels in tt - and tt - genotyped cases were significantly lower than those in controls ( table 1 ) . in contrast , the dietary intake level can modify the effect of genetic polymorphism on the risk of cancer development . for instance , takeshige et al. 18 indicated that vdr foki did not have a significant association with cancer risk but seemed to be associated with a decreased risk of colon cancer , especially among individuals with high intake of vitamin d. in the same study , it was also found that vdr apai aa / aa showed a decreased rectal cancer risk , with or = 0.75 ( 0.560.99 ) , p = 0.04 . among the cases with the same genotype and a high calcium intake , a higher degree of reductionwas detected , with or = 0.53 ( 0.360.79 ) , p = 0.05 ( these data are not shown in the tables ) . in a cohort of singaporean chinese , wong et al. 29 observed the effect of vdr foki only in the lower dietary calcium category , and this effect depended on the f allele in a gene dose - dependent manner ( these data are shown in table 2 ) . this review summarizes the previous epidemiological studies that have investigated the effects of dietary factors and genetic polymorphisms on crc risk . to understand the variety of potential factors that may influence crc risk , the gene - diet interactions among diverse study populations have been examined according to stratification by dietary intake or allele frequency in gene expression . dietary factors are commonly recognized as modifiable factors that can have a profound influence on cancer and tumor behavior .8 therefore , the relationship between dietary factors and crc risk has long attracted a great deal of attention . the effects of vitamin d and calcium on crc risk and its incidence have been extensively studied .9 mounting evidence supports an inverse association of vitamin d with colorectal adenoma or cancer incidence ,3942 and a long - term inadequate vitamin d status might lead to a progressive increase in crc incidence in humans .10 high intake of calcium has also consistently been reported to lower the risk of crc .14,4345 as protective nutrients against crc , vitamin d and calcium are closely related to each other due to the role of vitamin d in maintaining calcium levels . calcium homeostasis is critical for the inhibition of cancerous tumor development , and the active metabolites of vitamin d , 1,25 ( oh ) 2d3 play a mediating role in intestinal calcium absorption to prevent homeostatic disruption .19,30 in addition to preventing carcinogenesis in the colon and rectum , vitamin d and calcium are diversely linked to biological responses , including dna synthesis and inhibition of double - strand breaks caused by endogenous or exogenous factors .10,19 the association between vitamin d and calcium is also well known to account for the physiologic functions and regulation of genes responsible for cell proliferation , differentiation , angiogenesis , and apoptosis .4648 nutrient metabolism - associated gene variants have been studied to investigate their implication in crc .4952 various genes , such as casr , cyp2r1 , cyp27a1 , cyp27b1 , cyp24a1 , vdr , and gc , have been identified to be activated by different forms of vitamin d metabolites .21,53 certain genes , such as vdr and casr , can mediate the interaction between dietary factors and can possibly modify physiologic pathways . vitamin d exerts its effects on calcium metabolism through binding the vdr gene , which regulates the transcription of genes involved in calcium absorption46 and which is involved in the wnt / catenin signaling pathway , a central pathway in crc development .11,32,53 additionally , the promoter region of the casr gene contains a vitamin d response element that may also modify the calcium uptake level .50,54 determination of crc risk is further complicated by interaction with genetic factors in conjunction with environmental stimuli , such as dietary intake . previous studies have demonstrated that gene - diet interactions may influence cancer risk . dietary intake and the polymorphic genotype of different genesinteract with each other , modulating crc risk .12,16,18,19,29,55,56 the interaction between diet and genes may contribute to modulating the risk of crc or adenoma . guerreiro et al. 32 reported that high calcium intake was more markedly associated with lowering crc risk in those carrying the polymorphic allele ( dv / vv ) of the apc gene ( adenomatous polyposis coli ; tumor suppressor gene ) than in those without that allele in the portuguese population . kupfer et al. 20 reported a significant result in african americans , suggesting that there was a significant vdr gene - vitamin d interaction in lowering crc risk . in both studies , dietary intake seemed to modulate the associations that were originally not present in the gene - crc and diet - crc comparisons . the frequency of certain alleles that differentiate genetic expression can alter the absorption level of nutrients in subjects . atoum and tchoporyan16 conducted a study in jordanians and reported an inverse association with crc risk in a gene dose - dependent manner . nutrient absorption may be inhibited based on the frequency of a certain type of allele in both crc patients and controls . in this study , the expression of more t alleles resulted in a lower level of vitamin d absorption , which was linked to a higher crc risk . the findings suggest that the type of allele has its own effects ; therefore , the allele frequency in a gene may modulate the ultimate results , with additive effects of dietary intake . boyapati et al. 19 reported that those with at least one b allele , representing the restriction site , appeared to have a reduced risk of colorectal adenoma under the condition of high vitamin d intake . although many previous epidemiological studies have investigated the association with susceptibility to crc , the results show wide ethnic variation by location or population .49,52,53,5759 most of the studies discussed above were conducted in different populations with diverse ethnic and environmental backgrounds . analyses of the effects of the same polymorphisms on crc association yielded unreliable results , occasionally providing inverse results between different study populations . this may imply that in investigations of crc , all people do not share the same background . to achieve a better understanding of crc in specified populations , environmental differences and genetic variations that exist within groups of individuals must be considered . this current study represented the lack of studies related diet - gene interaction in asian countries , compared to western countries . this suggests the necessity of further researches on asian populations that may different from western countries and their culture . in conclusion , this review demonstrates that dietary consumption of vitamin d and calcium may decrease the risk of crc or adenoma . the findings suggest that gene - diet interactions may possibly alter the associations among dietary intake , genetic polymorphisms , and crc risk . however , the observations regarding effect modification are still controversial , which may be partly due to different exposures for each individual or population . further studies conducted with different target populations are actively needed to investigate the implications of gene - diet interactions for crc . identification of modifiable risk factors in various locations may help to effectively and broadly reduce the disease burden from an epidemiological or public health point of view . dietary factors are commonly recognized as modifiable factors that can have a profound influence on cancer and tumor behavior .8 therefore , the relationship between dietary factors and crc risk has long attracted a great deal of attention . the effects of vitamin d and calcium on crc risk and its incidence have been extensively studied .9 mounting evidence supports an inverse association of vitamin d with colorectal adenoma or cancer incidence ,3942 and a long - term inadequate vitamin d status might lead to a progressive increase in crc incidence in humans .10 high intake of calcium has also consistently been reported to lower the risk of crc .14,4345 as protective nutrients against crc , vitamin d and calcium are closely related to each other due to the role of vitamin d in maintaining calcium levels . calcium homeostasis is critical for the inhibition of cancerous tumor development , and the active metabolites of vitamin d , 1,25 ( oh ) 2d3 play a mediating role in intestinal calcium absorption to prevent homeostatic disruption .19,30 in addition to preventing carcinogenesis in the colon and rectum , vitamin d and calcium are diversely linked to biological responses , including dna synthesis and inhibition of double - strand breaks caused by endogenous or exogenous factors .10,19 the association between vitamin d and calcium is also well known to account for the physiologic functions and regulation of genes responsible for cell proliferation , differentiation , angiogenesis , and apoptosis .4648 nutrient metabolism - associated gene variants have been studied to investigate their implication in crc .4952 various genes , such as casr , cyp2r1 , cyp27a1 , cyp27b1 , cyp24a1 , vdr , and gc , have been identified to be activated by different forms of vitamin d metabolites .21,53 certain genes , such as vdr and casr , can mediate the interaction between dietary factors and can possibly modify physiologic pathways . vitamin d exerts its effects on calcium metabolism through binding the vdr gene , which regulates the transcription of genes involved in calcium absorption46 and which is involved in the wnt / catenin signaling pathway , a central pathway in crc development .11,32,53 additionally , the promoter region of the casr gene contains a vitamin d response element that may also modify the calcium uptake level .50,54 determination of crc risk is further complicated by interaction with genetic factors in conjunction with environmental stimuli , such as dietary intake . previous studies have demonstrated that gene - diet interactions may influence cancer risk . dietary intake and the polymorphic genotype of different genesinteract with each other , modulating crc risk .12,16,18,19,29,55,56 the interaction between diet and genes may contribute to modulating the risk of crc or adenoma . guerreiro et al. 32 reported that high calcium intake was more markedly associated with lowering crc risk in those carrying the polymorphic allele ( dv / vv ) of the apc gene ( adenomatous polyposis coli ; tumor suppressor gene ) than in those without that allele in the portuguese population . kupfer et al. 20 reported a significant result in african americans , suggesting that there was a significant vdr gene - vitamin d interaction in lowering crc risk . in both studies , dietary intake seemed to modulate the associations that were originally not present in the gene - crc and diet - crc comparisons . the frequency of certain alleles that differentiate genetic expression can alter the absorption level of nutrients in subjects . atoum and tchoporyan16 conducted a study in jordanians and reported an inverse association with crc risk in a gene dose - dependent manner . nutrient absorption may be inhibited based on the frequency of a certain type of allele in both crc patients and controls . in this study , the expression of more t alleles resulted in a lower level of vitamin d absorption , which was linked to a higher crc risk . the findings suggest that the type of allele has its own effects ; therefore , the allele frequency in a gene may modulate the ultimate results , with additive effects of dietary intake . boyapati et al. 19 reported that those with at least one b allele , representing the restriction site , appeared to have a reduced risk of colorectal adenoma under the condition of high vitamin d intake . although many previous epidemiological studies have investigated the association with susceptibility to crc , the results show wide ethnic variation by location or population .49,52,53,5759 most of the studies discussed above were conducted in different populations with diverse ethnic and environmental backgrounds . analyses of the effects of the same polymorphisms on crc association yielded unreliable results , occasionally providing inverse results between different study populations . this may imply that in investigations of crc , all people do not share the same background . to achieve a better understanding of crc in specified populations , environmental differences and genetic variations that exist within groups of individuals must be considered . this current study represented the lack of studies related diet - gene interaction in asian countries , compared to western countries . this suggests the necessity of further researches on asian populations that may different from western countries and their culture . in conclusion , this review demonstrates that dietary consumption of vitamin d and calcium may decrease the risk of crc or adenoma . the findings suggest that gene - diet interactions may possibly alter the associations among dietary intake , genetic polymorphisms , and crc risk . however , the observations regarding effect modification are still controversial , which may be partly due to different exposures for each individual or population . further studies conducted with different target populations are actively needed to investigate the implications of gene - diet interactions for crc . identification of modifiable risk factors in various locations may help to effectively and broadly reduce the disease burden from an epidemiological or public health point of view .\noutput:\n" }, { "from": "agent", "value": "the incidence trends of colorectal cancer have varied over time , and there is wide geographical variation across the world . regarding colorectal cancer , diverse modifiable environmental or intrinsic risk factors have been investigated . this review summarizes the effects of both dietary intake of vitamin d and calcium in particular and diet - associated genetic factors on colorectal cancer risk . we searched the electronic database pubmed for articles published between january 2000 and march 2015 . we reviewed case - control studies that included dietary factors , genetic polymorphisms , and gene - diet interactions in association with colorectal cancer risk . overall , 21 studies were selected as eligible studies . these studies demonstrated that dietary consumption of vitamin d and calcium may decrease the risk of colorectal cancer or adenoma . colorectal carcinogenesis was discussed in conjunction with dietary factors and mediating genetic factors . the epidemiological findings suggested that the gene - diet interactions may possibly alter the associations between dietary intake , genetic polymorphisms , and the risk of colorectal cancer . however , the reported effects of the same potential factors on colorectal cancer risk were inconsistent , depending on the study population and geographical location . this finding may imply the necessity of considering the environmental differences and genetic variations existing between individuals or specified populations . therefore , further studies are required to investigate modifiable risk factors in diverse locations to derive useful implications for colorectal neoplasia ." } ]

[ { "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 meaning of synthetic , as defined in a dictionary , is combination , composition , putting together , opposite of analysis ; building up of separate elements especially of conception or propositions or facts , into a connected whole . combined with biology , it became synthetic biology meaning engineering complex living systems through novel assemblies of biological molecules . although useful engineering system based on t4 , t7 , , or other viruses has been introduced , the technology is mostly fully developed in the filamentous phages ( figure 1 ) . phages are viruses that infect bacterial cells , and many commercial vectors for recombinant dna studies are from phages . phage display is a practical example of how we can make synthetic viruses for different purposes . using standard recombinant dna technology , interested foreign peptides ( or proteins ) expressioncan be realized by incorporation of corresponding coding sequences onto each replicable viral coat dna ( figure 2 ) . piii minor coat protein engineering ( type 3 ) is relatively well known for insertion of foreign peptides . foreign peptides displayed on all five piii subunits are constrained to lie very close to each other , but their attachment to the virion surface is probably quite flexible . for these reasons , it is likely that such displayed peptides can form multivalent interactions with immobilized selectors or cellular receptors . phage display has been developed for use as information mining tools , in which the diversity of the amino acid libraries presented by the phage gives the binding information between the peptide and its target . recently , the synthetic phage displaying fab in piii region was utilized as in phage display and expanded its capacity of expressing peptide sizes and their selectivity and sensitivity . taken together , phage display was used to identify the peptides mimicking many functional peptides including chemokines or chemokine receptors , which was then utilized for studying or targeting the role of chemokines and receptors ( also see table 1 ) . lee group mostly utilized pviii engineering for tissue engineering purposes but also did piii engineering for making multifunctional synthetic phages on sensing or capturing purposes ( table 1 ) . the landscape peptide presentation on the major coat protein of the filamentous phage has been utilized to template inorganic crystals for energy and memory storage devices and make stimulus responsive materials . the phage has also been exploited for medical applications , such as targeted drug , gene , imaging agent delivery , and a tissue engineering scaffold material . presented a cell signaling rgd motif on pviii proteins for a tissue engineering scaffold application . the approach which is used to display a foreign peptide on every copy of pviii protein demonstrated how other functionally designed groups can be presented on the phage filament with quantitative analyses on the characteristics of the inserts and their constrained sequences expressed on a phage particle . other minor coat proteins , pvi , pvii , or pix , have been used in phagemid format , which will have mosaic display of inserted foreign peptides . fusion proteins were expressed on pvii and piv from the phagemid as procoats with ompa and pelb leaders . since these proteins are likely to interact with one another in the phage capsid , the method may be useful to engineer antibodies or intergrins which are dimeric proteins . this technology was later extended to construct a large , human single - chain fv ( scfv ) antibody library on pix . a mosaic display using type 88 or 33 systems overcomes two potential disadvantages of pviii major coat modification ( type 8 ) and piii minor coat modification . to minimize recombination between the recombinant and wild type pviii genes , the sequence of the recombinant pviii gene is designed to be very different from the wild type pviii gene , while encoding the same amino acid sequences . similarly , type 33 system has two piii genes of one full length and one truncated ( amino acids 198408 ) . the former expresses a functional piii , while the second gene produces a fusion protein . tissue engineering scaffolding materials are ultimately designed to imitate the extracellular matrix ( ecm ) , a fibrous protein network that houses the cells in vivo . this network provides cells with physical support and guidance through a specific topographical and chemical presentation of various adhesive sites and growth factors . therefore , in order to control cellular behaviors such as adhesion , proliferation , and differentiation within the man - made scaffolds , their surface functionalization with bioactive molecules is highly desirable . furthermore the control over density of such bioactive groups and their geometric patterning has been shown important in biomaterials ' ability to modulate such behaviors . majority of current fabrication methods rely on chemical processing to functionalize biomaterials . with this method the final density of bioactive groups presented on the surfaceis ultimately dictated by the bulk solution concentration . the local binding properties of the material surface , such as charge or availability of reactive groups or receptors , dictate the final spacing of the bioactive groups . most techniques that allow for a very precise micro - and nanoscale chemical patterning of a substrate are lithography based ( i.e. , dip - pen lithography ) and are hard to replicate in large scale or in three - dimensional scaffold materials . recently developed nanofabrication techniques , such as peptide self - assembly , electrospinning , and polymer phase - separation , come closer to mimicking the natural ecm topographically ; however , the controlled presentation of single or multiple functional groups is still lacking . their nanoscale size and inherent monodispersity of their shape and surface chemistry are better than what can be achieved with most synthetic nanoparticles to date . both genetic and chemical pathways have been used to modify either single or multiple virus capsid proteins with functional groups . moreover novel binding ligands can be found through evolutionary phage display screening methods . such functionalized virus particles have been demonstrated to selectively bind both inorganic and organic particles . additionally the templation of virus particles has been utilized for electronic and magnetic materials , as well as a variety of medical applications . it has a defined long - rod shape at 880 nm long and 6.7 nm in diameter , with precisely positioned major and minor capsid proteins . these coat proteins can be genetically engineered to express short peptide groups . m13 has been previously genetically engineered phage to display cell - adhesive peptides such as rgd and ikvav on every copy of its pviii protein . furthermore such modified filamentous phage for construction of aligned two - and three - dimensional materials that are able to support and control the polarization of cells such as fibroblasts and neural progenitor cells was demonstrated . chimeric displays of binding groups on m13 phage have been demonstrated previously for drug delivery , elisa , and electronic applications . additional engineering of the m13 phage to express biotin - like hpq motifs on their capsid proteins will allow for a functional expansion of potential scaffold interactions with the cells , as it will be able to present a variety of immobilized avidin conjugated growth factors and cytokines . unique biochemical and structural features of genetically engineered phage can be also used in the context of tissue engineering in order to control cellular growth or differentiation ( figure 3 , ) . merzlyak et al . , for example , have explored the use of genetically modified m13 phage as a novel building block for neural cell engineering materials to make functional biomaterials for tissue regeneration by chemical cue control . this was accomplished by engineering the phage to display specific cell signaling motifs and then assembling the viral particles into a macroscopic scaffolding material . many peptide expression systems have previously been demonstrated on the various capsid proteins of the phage through creation of peptide libraries . however , as a biological particle for peptide display , phages possess the inherent limitation of having to be successfully expressed and assembled within the e. coli bacteria host , which restricts the type and number of peptides that can be displayed . they developed a novel cloning approach for display of an integrin - binding rgd motif on every copy of the pviii major coat protein . the researchers constructed the phage using a partial library , in which an engineered octamer insert for pviii included a constrained rgd group that was surrounded by flanking degenerate residues . this allowed for expression of inserts that retained the desired function of the rgd motif and yet were biologically compatible with e. coli during the intricate phage replication process . after construction of engineered phage that stably displayed either rgd - or ikvav - peptide groups on every copy of the pviii protein , they constructed aligned two - and three - dimensional scaffolding materials containing phage and tested their applicability for tissue engineering . biocompatibility of the synthetic phage materials was tested by growing nih - 3t3 fibroblast and neural progenitor cells on phage films and in phage containing media . both cell types showed normal morphology and proliferation when in direct contact with phage materials . neural progenitor cells either retained their progenitor state or differentiated towards the neural cell phenotype depending on media conditions . it was then demonstrated that three - dimensional phage materials could support proliferation and differentiation of neural progenitor cells . both rgd - and ikvav - phage matrices facilitated colony formation of neural progenitor cells , which sustained a viability of over 85 % during the seven - day observation period . in comparison to rge and wild type phage controls , rgd and ikvav phage resulted in enhanced binding and spreading of neural progenitor cells with high specificity . finally , by simple extrusion or spinning of phage solution , the researchers constructed aligned three - dimensional phage fiber matrices with embedded neural progenitor cells . the resulting phage fibers encouraged neural cell differentiation and directed cell growth parallel to the long axis of the fibers . . showed mechanical shearing of phage solution on a glass substrate which resulted in two - dimensional directionally oriented films . these oriented films were shown to direct the alignment and morphology of fibroblasts , osteoblasts , and neural cells . studies on chemical cue and physical cue provided by synthetic phages were performed with the rgd - and dgea - peptides engineering phage films and fibers . yoo et al . demonstrated the early osteogenic differentiation of mouse preosteoblasts by using collagen - derived dgea - peptide on nanofibrous phage tissue matrices . they constructed major coat engineered with dgea , dgda - , or egea - peptides . by genetic engineering of phages , they could construct nanofiber - like shaped phages having 2700 copies of the target peptides from the inserted genes with 2 and 2.7 nm spacing laterally and axially , respectively . by constructing the phage - based tissue matrix systems , they could investigate the specific effect of biochemical cues , which can be tuned precisely at a single amino acid level with little change in other physical and chemical properties . they characterized the chemical cue or physical cue effects of dgea - and of rgd - peptides on the synthetic m13 phage backbone by applying mc3t3 preosteoblast cells on fabricated phage 2d film and 3d fibers . the cells are spread very well throughout the samples on the dgea - phage matrices . cells on dgda , egea , or rge - phages , which are different in one single amino acid from dgea - or rgd - phages , showed that the responses are dgea peptide - specific , in which synthetic phage - based chemical cues can be controlled by genetic engineering . competition assay with corresponding peptide with the engineered phage confirmed that the peptide specific chemical cues were controlled by synthetic phage . the dgea - peptide specific outgrown morphology of preosteoblasts forms on the 2d cultures phage matrices , which were also observed in 3d cultures . in addition , the dgea - specific morphological responses of preosteoblast cells are linked with early osteogenic differentiation by dgea - peptides . the self - assembly capabilities of phage with patterning techniques can enhance the phages ' specific biochemical and physical cues . yoo et al . developed a facile patterning method of patterning genetically engineered m13 bacteriophage by employing microcontact printing methods to provide human fibroblast cells with specific biochemical and physical cues . they demonstrated that nanofibrous structures , along with the biochemical signals presented by the phage microstructures , are critical to guide cellular growth and morphologies . the enhanced cellular morphological responses to rgd - phage topology rather than to rgd - peptide itself show that phage nanofibrous structure contributes in controlling physical cues . especially rod - like viruses such as m13 and tmv can control their physical cues and mechanical cues even only by their concentration . lin et al . reported the formation of diverse patterns which resulted from drying a solution of rod - like tmv particles in a glass capillary tube . the concentration of tmv , the salt concentration in aqueous solution , and the surface properties of the capillary tube interior were used as three key factors to govern such combined self - assembly behavior . the formation of hierarchical structures which can be again used for guiding directional cellular growth was determined by the preferred orientation of tmv at the air - liquid interface as well as the pinning - depinning process . by controlling the key factors , they could generate the surface roughness together with patterned structure , which was then used for rat aortic smooth muscle cell ( smc ) culture for the direct orientation of cells . they could finally generate either stress - induced smc alignment or 2d patterns by utilizing the tmv patterns . the physiological cellular environments present a variety of cell signaling motives simultaneously including adhesive sites , growth factor , and other cytokine molecules to influence the cellular behavior . similarly engineering materials incorporating several signaling motivessimultaneously have shown this synergy to be more effective than single motives alone . jeffrey hubbell 's group demonstrated that the incorporation of several functional peptide groups derived from the laminin into a fibrin matrix at the same time resulted in a synergistic effect on cell differentiation . the cell neurites were extended further in the peptide combination matrix then predicted by just an additive effect from each peptide 's contribution . immobilization of growth factor molecules to the matrix surface , instead of their untethered encapsulation within it , can decrease the uncontrolled release of these molecules , as well as their internalization and metabolization by the cells , and therefore provide the cells with a more directed and sustained signal , further influencing their behavior . yoo et al . developed a facile growth factor immobilization system by utilizing multiple functionalized m13 synthetic phage based matrices . the immobilized growth factor by m13 synthetic phage , together with phage 's nanostructure itself , can give simplified cellular environment which actually consists of signaling motifs , growth factors , and topological structure effects . multiple signalling and therapeutic peptide motifs can be simultaneously displayed on the piii , pviii , and pix protein coats of m13 phages through genetic modification . they constructed his - pro - gln ( hpq ) peptide either on pviii or on piii phage coat proteins . the hpq motif allows binding to streptavidin - conjugated molecules , so that streptavidin - conjugated growth factor can be immobilized without any size limitation decorating on m13 phage coat protein . this facile growth factor immobilization approach by synthetic phage may be useful for studying biochemical cues in cell biology and also creating tissue engineering materials . through the hpq sites , they were able to immobilize streptavidin - conjugated fgfb and ngf onto phage matrices . they also modified rgd peptide , which is well known to promote cell adhesion and well distribution of cells , on major coat proteins . they demonstrated that the growth factors immobilized on the multifunctionalized m13 phage matrices with hpq - and rgd - peptides were functional and could direct cell growth towards desired cellular morphologies by rgd peptide and towards cellular fate , fgfb for proliferation and ngf for differentiation ( figure 3 ) . with the phage particle modular with an hpq motif , a variety of factors can be immobilized on the phage matrix , correspondingly influencing different cell behaviors or even different cell types . for example , egf factor can be immobilized on the phage to induce differentiation of the progenitor cells to the neuronal phenotype . similarly a bone morphogenic protein ( bmp ) and insulin growth factor ( igf ) can be immobilized to assist in the differentiation of osteoblast cells . furthermore vascular endothelial growth factor ( vegf ) can be immobilized on the matrix to enhance endothelial cell adhesion for vascular tissue engineering . several excellent recent reviews describe the function of many biologically relevant short peptide groups , growth factors , and cytokines . additionally as vascular cells are aligned in their native environment the alignment capabilities of the phage matricesif needed even further functionalization of the phage can be accomplished by various chemical conjugation schemes , which have recently been employed in modifying other virus particles . after the design and engineering of the individual phage macromolecules , their various ratios can be mixed into a homogenous solution at different concentrations to further explore how molecular concentration gradients can influence cellular behavior in vitro models . after such systematic analysis the design parameters that work best can be incorporated into a final mix solution to be tested on the in vivo systems . as the phage material we discussed is ultimately designed for in vivo applications , synthetic phage based future works will explore both in vitro and in vivo immunogenic responses to the phage matrices . we hypothesize that the phage matrix as a foreign protein mass will be recognized as anon - self material , via the complement system . in the immune privileged environment of the central nervous system , microglia , specialized immune cells of the brain , will likely mediate the immune response . previous studies have seen no inflammation related damage at the phage targeted tissue site . however , if the greater concentration of the phage activate the microglia , their recruitment to the site of injury may actually facilitate nerve tissue regeneration by clearance of cellular and ecm debris of the glial scar and expression of the growth factors and the native extra cellular proteins , such as laminin . to explore a similar mechanism of actionthere is currently a phase ii clinical trial study to test the efficacy of injecting macrophage cells to the site of spinal injury on stimulating regeneration . in vitro immunogenic studieswill be conducted to assess the potential of phage materials to induce an immunogenic inflammation reaction . testing the inflammation reaction of nptfe material , a panel measuring the level of immuno stimulating or inhibiting cytokines can be performed on the supernatant from the macrophage cells grown on the phage substrates . tissue culture polystyrene can serve as a negative control , and macrophages stimulated by lipopolysaccharides as a positive control . if very high levels of immunostimulating molecules such as il - 1 or tnf - are noted , phage may be modified to express compliment inhibiting peptides . , in vivo studies can be performed by injecting phage solution into spinal cord area of rat animal subjects . following the injection the behavior of the animalsafter the sacrifice of animal subjects injection site can be evaluated with histological studies to evaluate for tissue inflammation and fibrosis . a previous study that targeted engineered phage solution to a - amyloid plaques in the brain did not see any adverse tissue reactions with histological analysis . control of mechanical and degradation properties of the biomaterials is important for tissue engineering applications . in an optimal engineering scenario the material that is intended to replace or repair a tissue will remain at the site of injury until it is remodeled by the cells and replaced by the naturally produced ecm . previous work with hydrogels has demonstrated that both the concentration of the polymer macromolecule units and the degree of their crosslinking can be used to tune the mechanical properties and the rate of degradation of these materials . lee group encapsulated the phage materials in an agarose gel to keep them stable in the media solution over the course of experiment . a future project that can further improve upon the phage scaffolds is to increase their stability in aqueous media environments . preliminary work conducted in our lab on crosslinking chemically biotinylated phage with streptavidin shows a much improved stability of the phage fibers , which remain in solution for over a week without degradation . drug delivery and tissue engineering materials are often very closely related in both function and architecture . in fact there is one perspective in the scientific community that tissue engineering scaffolds are just a delivery system of cells into the body . additionally the lines between the two areas get blurred when controlled growth factor or cytokine release is incorporated into the matrix to influence either the contained or the surrounding cells . by the streptavidin crosslinking methods described above small therapeutic drug molecules may be incorporated into the matrix . furthermore the link to the phage can be engineered to be dependent on enzymatic cleavage so that the delivered molecules are released only when they are sequestered by the cell activity . therapeutic genetic material can be incorporated into the phage dna and carried within the phage capsule for specific delivery to the cells via receptor uptake . as the m13 phages are nonlytic , they will be continuously produced by the bacteria without causing bacterial wall rupture or the resulting debris . by designing the peptide expression on the phage capsidthey can be more locally targeted to cell receptors ( i.e. , via rgd or other ligands ) . phage display technology has allowed for identification of novel homing peptides that target unknown cell surface proteins . the targeting peptides can be incorporated into bacteriophage coat proteins through the genetic engineering techniques described previously . these include peptides ( rgd , glioma - binding peptide ) , her2 receptor targeting antibody , growth factors ( egf , fgf2 ) , and the penton base of adenovirus . similar to drug delivery , nucleic acid materials are now being incorporated in the scaffolding materials for delivery to the cells . furthermore it has been shown that dna materials that are tethered to the matrix , rather than just encapsulated are more effectively transferred to the cell . phage particles engineered as described above to contain the genetic load for cell delivery as well as specific cell targeting peptides can be cross - linked with streptavidin units to produce stable tissue engineering scaffolds . as these scaffolds get taken up and degraded by cell endocytosis , the phage could release their gene cargo and further induce cell behavior . thanks to phage display technology , we could find various useful peptide information which can be developed further for imaging and diagnosis of certain diseases , such as cancer . for the therapeutic application , antibody phage display has been developed and being tested for clinical approval . another application study of utilizing m13 synthetic phage properties by adopting different useful virus parts was also introduced . constructed hybrid phage with two genes from phage and nucleus integrating gene from aav , called inverted terminal repeats . therefore , the rgd peptide induced internalization of the phage through integrin mediated endocytosis process and the inverted terminal repeats ( itr ) led to improved transgene expression , which is linked to functioning of delivered gene , in the cytoplasm . topical delivery by applying these therapeutic synthetic phage materials onto localized disease areas with specific integrating functions might reduce the risk of the side effects and enhance the efficiency of the drug delivery . in this paper , we have majorly explored the use of m13 bacteriophage ( phage ) as a novel building block together with providing specific functions for tissue engineering materials . prior to using it as a biomimetic tissue engineering scaffold material , an incredible diversity of peptide expression has previously been demonstrated on the various capsid proteins of the phage through creation of peptide libraries . a novel cloning approach to display an integrin binding rgd motif on every copy of pviii was introduced to decorate the phage , the major coat protein of m13 phage . did this by using a partial library method , where an engineered octamer is inserted for the pviii including a constrained rgd group surrounded by a degenerate residue library . this allowed the expression of full inserts that retained the desired rgd motif yet were favorably compatible with all the protein interactions inherent in phage replication process within e. coli . furthermore they systematically analyzed the allowed amino acid sequence space for pviii inserts by making constrained libraries with chemically variable residues ( positive , negative , and hydrophobic ) . this approach can be useful for engineering phage particles with a very dense uniform display of short signal peptide motifs that may be beneficial for tissue engineering materials . after demonstrating the phage as an able filament particle to form aligned scaffolds that are both conducive and instructive to cell growth , further phage design improvements by making it multifunctional can be made . the phage was engineered to incorporate an adhesive peptide motive rgd on pviii and a constrained biotin - like hpq motif on piii protein . there are limits in the ability of the phage to display a multivalency of protein molecules based on the size and sequence of the insert , and it can not be altered via genetic means to present functional carbohydrate molecules . by exploiting the binding affinity of biotin - streptavidin bond , with an engineered biotin - like hpq groupany growth factor , cytokine , or an otherwise therapeutic molecule conjugated to an avidin will be able to bind to our engineered hpq phage and further functionalize the matrix . in summary , we have introduced the utilization of genetically engineered m13 bacteriophage ( synthetic phage ) as a functional building block for tissue engineering matrices that can guide adhesion , polarization , and alignment behavior of cells . we have also presented a number of avenues that can be used to expand this area of research further to immune / chemokine study and use phage for highly functional and useful biomaterials to the potential application area of diagnosis and therapy .\noutput:\n" }, { "from": "agent", "value": "controlling structural organization and signaling motif display is of great importance to design the functional tissue regenerating materials . synthetic phage , genetically engineered m13 bacteriophage has been recently introduced as novel tissue regeneration materials to display a high density of cell - signaling peptides on their major coat proteins for tissue regeneration purposes . structural advantages of their long - rod shape and monodispersity can be taken together to construct nanofibrous scaffolds which support cell proliferation and differentiation as well as direct orientation of their growth in two or three dimensions . this review demonstrated how functional synthetic phage is designed and subsequently utilized for tissue regeneration that offers potential cell 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: ganglion cell tumors ( gct ) are divided into two sub - types : gangliocytoma and ganglioglioma . although association with scoliosis and von recklinghausen 's disease were previously reported in the literature , no gangliocytoma cases concomitant with neuroendocrine tumor of lung have been published . in this report , we aim to present a gangliocytoma case at cervicomedullary junction in a patient with neuroendocrine tumor of lung and discuss diagnosis and treatment options with literature . the patient underwent 2 surgeries previously 6 and 3 year ago due to neuroendocrine tumor of lung and had received octreotide therapy . cervical magnetic resonance ( mr ) imaging revealed a 4514 mm sized mass lesion mixed with cystic and solid components , calcification foci extending from medulla oblongata to c2 level , with edema or infiltration areas extending to c6 level , and the mass was heterogeneous on t1 - weighted mr imaging , hyperintense on t2 - weighted mr imaging and solid components showed intense contrast - enhancing following injection of gadolinium ( gd ) ( fig . after midline myelotomy , a stiff - structured gray tumor with unclear boundaries was encountered . operation was terminated upon detection of increase in temporary somatosensory evoked potential latencies and decrease in motor evoked potential amplitudes during the operation . postoperative neurological examination was intact . on microscopic examination , intense inflammation , lots of ganglion cells with focal calcification that stained positively with s100 and synaptophysin . the patient had no neurologic deficits at 3 - month follow - up and radiographic progression was not detected . ganglioglioma accounts for 0.47.6 % of pediatric central nervous system ( cns ) neoplasms and 1.3 % of those in adults8 ) . they are slowly growing benign tumors and malignant transformation may be seen in less than 10 % 16 ) . generally , they are located in the supratentorial region and most commonly involve temporal lobe . gangliocytoma are 0.1 % to 0.5 % of all cns tumors and children and young adults constitute 60 % of all patients5 ) . intracranial location is usually seen in temporal lobe , frontoparietal region and floor of 3rd ventricle , gangliocytoma involving cerebellum is described as lhermitte - duclos disease5 ) . , nine cases for spinal cord and only one case cervicomedullary junction gangliocytomas were reported in the literature1234567111315 ) . . they may present with neurological symptoms ranging from pain , as in our case , radiculopathy , paraparesis and paraplegia . although there are no significant radiological imaging features , they are usually hypointense on t1 - weighted mr imaging and hyperintense on t2 - weighted mr imaging and are enhancing lesions at different rates15 ) . astrocytoma , brain stem gliomas , ependymomas and metastases should be considered in differential diagnosis . ganglioglioma consist of dysplastic neurons and neoplastic glial cells , whereas gangliocytoma have dysplastic neural cells and normal glial cells212 ) . the glial populations are reactive for gfap , s - 100 protein , and vimentin , but the neurons are for synaptophysin and chromogranin a91014 ) . primary treatment of gct is surgical excision and they are considered resistant to other adjuvant therapies , as they are well - differentiated slow - growing tumors . however , malignant transformations have been reported in the literature5 ) . radiological follow - up is done for patients who underwent total excision , but adjuvant therapy remains controversial in patients who underwent subtotal excision . total resection is difficult in reported cervical - junction gcts . as published in the literature , jacob et al5 ) . reported no clinical and radiographic progression in a partially resected case in 3 - year follow - up . in our case , because of pre - existing neuroendocrine tumor of lung , metastases were considered in the first line and operation has been decided although there were no neurological deficits . although association with scoliosis and von recklinghausen 's disease were previously reported in the literature , no gct cases concomitant with neuroendocrine tumor of lung have been published . with increasingly reported gcts in recent years , they should be kept in mind in the differential diagnosis of intramedullary tumors especially in children and young adults . surgical excision is the primary treatment , but difficulty in total surgical tumor resection is the most important problem .\noutput:\n" }, { "from": "agent", "value": "ganglion cell tumors ( gct ) are divided into two subtypes : gangliocytoma and ganglioglioma . intramedullary gangliocytomas are extremely rare . a 20 - year - old male patient with pain of neck , who also had a previously known neuroendocrine tumor of lung , was operated for mass found in the cervicomedullary junction with a presumptive diagnosis of metastases . only partial resection could be performed . pathological diagnosis had been reported as gangliocytoma . only ten cases of intramedullary gangliocytoma have been reported in the literature . although association with scoliosis and von recklinghausen 's disease were previously reported in the literature , no gangliocytoma case concomitant with endocrine tumor of lung have been published . pathological study is the most important diagnostic method for gangliocytomas . surgical excision is the primary treatment , but difficulty in total surgical tumor resection is the most important problem ." } ]

[ { "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: almost 55 years after its introduction , fluorescein angiography ( fa ) is still a helpful test in most retinal diseases , including diabetic retinopathy ( dr ) .1 traditional angiograms explore 3050 of the retina at once ; however , visualization of peripheral retina is fundamental in order to assess nonperfused areas , vascular leakage , microvascular abnormalities , and neovascularizations ( nvs ) .2 hence , the evaluation of the peripheral retina is crucial for screening , diagnosis , monitoring , treatment , and prognosis of dr. 3 in order to extend the field of view and , thus , to obtain wide - field ( 30 and 200 ) and ultra - wide - field ( 200 ) fundus photography and ultra - wide - field fluorescein angiography ( uwfa ) , 3 different strategies have been applied in the past years , namely 1 ) photomontage of traditional angiograms ( eg , 7 standard field [ 7sf ] and 2 field protocols exploring 75 and 45 , respectively ) ; 42 ) additional lens applied to a standard fundus camera or confocal selective laser ophthalmoscope ( cslo ) extending the field of view ( eg , staurenghi lens 5 and spectralis ultra - wide - field lens 6 ) ; 3 ) dedicate instrumentation ( eg , pomerantzeff camera ,7 panoret ,8 and retcam 9 ) . unfortunately , all these instruments did not break into clinical practice due to several drawbacks , including need of mydriasis , technical skill by photographer , patient cooperation , limited resolution , need of clear media , and contact lens . commercialized for the first time in the year 2000 , optos ultra - wide - field camera ( optos , plc , scotland ) is a cslo device with a panoramic ellipsoid mirror , which allows the imaging of 82 % of the retina ( 200 ) in a single image with no need of mydriasis or contact lens . compared to conventional digital acquisition systems , optos showed a 2-fold increase of field of view .10 furthermore , uwfa through optos system visualizes a significantly wider total retinal surface compared to heidelberg spectralis ultra - wide - field lens .6 almost 15 years from its introduction , optos uwfa proved to be a useful tool in several retinal diseases , including dr . the aim of this narrative review was to provide an overview of the role of the most recent technique of uwfa in dr . a pubmed engine search was carried out using the term diabetic retinopathy paired withultra wide field fluorescein angiography , ultra - wide field fluorescein angiography , ultra wide - field fluorescein angiography , ultra - wide - field fluorescein angiography , ultrawide field fluorescein angiography , ultra widefield fluorescein angiography , and ultrawide angiography . all studies published in english up to july 2016 irrespective of their publication status were reviewed , and relevant publications were included in this review . in 2008 , friberg et al10 were the first to report the feasibility of uwfa in 30 eyes of 30 patients affected by dr . compared to standard systems , they observed that uwfa allowed to image a greater area of both retinal surface ( 8.71.6 vs 3.40.76 disc diameter [ dd ] , p 0.001 ) and retinal ischemia ( 16.915 vs 3.44.26 sectors , p 0.05 ) , albeit with a reduction in image quality . in a retrospective case series including 218 eyes of 118 dr patients , wessel et al2 compared uwfa to a simulated 7sf . uwfa disclosed 3.2 times more total retinal surface , 3.9 times more nonperfusion , 1.9 times more nv , and 3.8 times more laser panretinal photocoagulation ( prp ) - treated area . notably , uwfa revealed retinal pathology in 10 % of the eye judged normal with 7sf . the study by wessel et al2 implies that uwfa may change the degree of dr by revealing more retinal pathology and it may even lead to the diagnosis of dr in patients judged normal using standard angiograms . since capillary nonperfusion upregulates pro - angiogenic and pro - inflammatory factors ( eg , vascular endothelial growth factor [ vegf ] , insulin growth factor , angiopoietin 1 and 2 , fibroblast growth factor 2 , tumor necrosis factor , interleukin 1 [ il - 1 ] , il - 8 , monocyte chemoattractant protein 1 ) thought a hypoxia - induced mechanism , it has been postulated that peripheral ischemia can lead to nv and diabetic macular edema ( dme ) .11,12 in a retrospective case series by oliver and schwartz13 involving 218 eyes of 118 patients , peripheral nonperfusion was significantly linked to both anterior and posterior nv , conversely no significant association with dme was found . in the same study , the authors described a novel angiographic features of dr , termed peripheral vessel leakage ( pvl ) , that is the late leakage from retinal vessels seen as hyperfluorescence extending beyond vessel wall occurring in the setting of active retinopathy . pvl has been linked to peripheral nonperfusion and nv , but not to dme . however , the association between dme and peripheral ischemia was supported by other studies where capillary nonperfusion was assessed through a quantitative approach , generating a percentage of ischemia over the total retina area called ischemic index ( isi ) . to estimate isi , pixels contained in nonperfused areas are calculated and divided by the number of pixels of the whole retina surface . since optos relies on a parabolic mirror and converts a 3 dimensional image to a 2 dimensional image , it induces peripheral distortion , and this has an impact on isi calculation ; in order to minimize this phenomenon and calculate the precise area of nonperfusion , tan et al14 proposed a corrected isi expressed in mm based on stereographic projection software , which strongly correlated with the uncorrected index . wessel et al15 retrospectively reviewed 122 eyes of 70 nave patients and found a positive correlation between isi and dme . interestingly , peripheral ischemia turned out to be an independent risk factor for dme development . in a retrospective case series involving 148 eyes of 76 patients , patel et al16 found recalcitrant dme to be worse in patients with higher dr severity and isi . correlation among capillary nonperfusion , pvl , macular leakage , and epiretinal nvs is shown in figure 1 . sim et al17 retrospectively investigated the relationship between peripheral and diabetic macular ischemia ( dmi ) quantified by means of isi and foveal avascular zone area , respectively . they found a positive correlation between these 2 variables , indicating how both the conditions share a common pathogenesis , that is , capillary nonperfusion . in a retrospective casecontrol study , kim et al18 observed that peripheral nonperfusion , together with nv and pvl , had higher incidence in eyes with recurrent post - vitrectomy diabetic vitreous hemorrhage ( pvdvh ) compared to non - pvdvh ones . once again , such difference was not appreciated with 7sf . moreover , peripheral ischemia turned out to be associated with dr severity and predominantly peripheral lesions , defined as 50 % of a specific dr lesions outside the 7sf . although uwfa has been extensively studied as a diagnostic tool , it may also have a role in dr treatment . since prp has been associated with several side effects ( ie , visual acuity reduction , visual field constriction , dme onset / worsening , choroidal detachment , angle - closure glaucoma , and decrease in color vision ) , reddy et al19 reported 2 cases of trp with nv regression and no prp - related side effects , and this observation was further corroborated by a prospective study by muqit et al. 20 in a pilot randomized study comparing trp , minimally traumatic ( mt ) prp and standard intensity ( si ) prp , muqit et al21 demonstrated that trp was as effective as si - prp in inducing nv regression , but with higher reduction in cmt . uwfa is a fascinating tool extremely useful in the diagnosis , staging , management , and therapy of dr . the ability of uwfa to show more retinal pathology even in eyes judged normal with 7sf is stimulating . since most of the present knowledge comes from clinical trials based on 7sf protocol , those results need to be reconsidered in view of uwfa revolution , as simple transposition of prior information could be misleading . at the state of the art , most of the studies involving uwfa in dr lacks high quality features , including being prospective , randomized , with large sample , and long - term follow - up . the diabetic retinopathy clinical research network ( drcrnet ) protocol aa is currently investigating whether evaluation of retinal far periphery on uwfa improves the ability to assess dr and predicts rates of dr worsening over time compared to 7sf . the possibility to precisely quantifythe peripheral ischemia ( ie , isi ) is extremely appealing especially for research purposes . isi has already been correlated with pvl , dme , dmi , and dr severity ; however , little is known about the variation of isi after intravitreal ( iv ) injections . mir et al22 reported a reduction of retinal non - perfusion in patients with retinal vein occlusion undergoing ranibizumab iv injections . however , these observations are based on qualitative assessment ; moreover , so far , such evaluation has not been performed in eyes with dr . the impact of anti - vegf agents and steroids on peripheral ischemia in dr has to be still determined . in a pilot study23this group of authors showed how dexamethasone sustained release implant reduces capillary nonperfusion in dr . despite the small sample size , this study opens a new field in retinal imaging and evaluation of the effect of iv drugs on 1 ) severity and progression of dr and 2 ) peripheral retinal vessels and their correlation to macular status . quantitative assessment of retinal ischemia could also be useful in the clinical setting , for example , to further classify patients with severe nonproliferative dr based on the risk of developing nv given a certain isi score . acquired in different steered positions , it is now possible to evaluate almost the entire retinal vascular up to the ora serrata , as proposed by singer et al. 24 it seems that single image can underestimate the real peripheral ischemia , especially in case of dr. 25 algorithms to correct the image distortion created by uwfa are very useful in order to rectify isi values .26 although really fascinating , the role of trp needs to be clarified in large , prospective , randomized trial with long follow - up against prp . several interesting observations have been pointed out by recent studies ; however , further high - quality trials are warranted in order to confirm the prior investigations and to translate them into the everyday clinical practice .\noutput:\n" }, { "from": "agent", "value": "fluorescein angiography ( fa ) is a useful examination in patients suffering from diabetic retinopathy ( dr ) . traditional angiograms explore 3050 of the retina at once ; however , visualization of peripheral retina is fundamental in order to assess nonperfused areas , vascular leakage , microvascular abnormalities , and neovascularizations . in order to expand the field of view , wide - field and ultra - wide - field imaging has been developed allowing to image up to 200 of retinal surface in one single shot . the aim of this narrative review was to provide an overview of the role of the most recent technique of ultra - wide - field fluorescein angiography in dr ." } ]