bluuebunny/crossref_metadata_2025_split huggingface dataset:
MageComet—web application for harmonizing existing large-scale experiment descriptions
Authors: Xue Vincent , Burdett Tony , Lukk Margus , Taylor Julie , Brazma Alvis , Parkinson Helen 
Published: April 2012

Abstract
Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline.
Results: We present MageComet, a web application for biologists and annotators that facilitates the re-annotation of gene expression experiments in MAGE-TAB format. It incorporates data mining, automatic annotation, use of ontologies and data validation to improve the consistency and quality of experimental meta-data from the ArrayExpress Repository.
Availability and implementation: Source and tutorials for MageComet are openly available at goo.gl/8LQPR under the GNU GPL v3 licenses. An implementation can be found at goo.gl/IdCuA
Contact: parkinson@ebi.ac.uk or xue.vin@gmail.com
Electronic cigarettes: achieving a balanced perspective
Authors: Wagener Theodore L. , Siegel Michael , Borrelli Belinda 
Published: April 2012

ABSTRACTConcerns have been raised that the advent of electronic cigarettes (e‐cigarettes) may be harmful to public health, and smokers have been advised by important agencies such as the US Food and Drug Administration not to use them. This paper argues that, while more research is needed on the cost–benefit equation of these products and the appropriate level and type of regulation for them, the harms have tended thus far to be overstated relative to the potential benefits. In particular: concern over repeated inhalation of propylene glycol is not borne out by toxicity studies with this compound; risk of accidental poisoning is no different from many household devices and chemicals available in supermarkets; concern that e‐cigarettes may promote continued smoking by allowing smokers to cope with no‐smoking environments is countered by the observation that most smokers use these products to try to quit and their use appears to enhance quitting motivation; concerns over low nicotine delivery are countered by evidence that the products provide significant craving reduction despite this in some cases; and e‐cigarettes may help reduce toxin exposure to non‐smokers.
Pharmacogenetic markers of CYP2B6 associated with efavirenz plasma concentrations in HIV‐1 infected Thai adults
Authors: Sukasem Chonlaphat , Cressey Tim R. , Prapaithong Pattamawan , Tawon Yardpiroon , Pasomsub Ekawat , Srichunrusami Chutatip , Jantararoungtong Thawinee , Lallement Marc , Chantratita Wasun 
Published: April 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Interindividual variability in efavirenz plasma concentrations is associated with CYP2B6 genetic polymorphisms.• Twenty‐nine different alleles of the CYP2B6 gene are listed. CYP2B6*6, *9, *16, *26, *27 and *28 carriers are reported to be associated with slower efavirenz oral clearance.• The allelic variant 516G>T is associated with diminished activity of CYP2B6 and high efavirenz plasma concentrations are associated with an increase risk of neuropsychological toxicity.WHAT THIS STUDY ADDS• This study identified three SNPs in the CYP2B6 gene which could potentially act as additional independent predictors of efavirenz plasma concentrations beyond that provided by the CYP2B6 c.516G>T polymorphism.• The GAC‐CYP2B6 haplotype (G516T/A785G/C21563T) is associated with higher plasma efavirenz concentrations in HIV‐infected Thai adults.• The CYP2B6 g.18492 T>C polymorphism was significantly associated with lower efavirenz concentrations than those with the homozygous wild‐type.AimsTo investigate the frequency of CYP2B6 polymorphisms and the influence of haplotype structure on plasma efavirenz concentrations in Thai adults with HIV‐1 infection.MethodsGenotyping of nine single nucleotide polymorphisms (SNPs, c.64C>T, c.499C>G, c.516G>T, c.785A>G, c.1375A>G, c.1459C>T, g.3003T>C, g.18492C>T and g.21563C>T) of CYP2B6 were performed using real‐time PCR‐based allelic discrimination on blood samples from 52 HIV‐infected adults who had received an efavirenz‐based regimen. Plasma efavirenz concentrations were measured by high performance liquid chromatography.ResultsThe minor allele frequencies for c.64C>T, c.516G>T, c.785A>G, g.3003C>T, g.18492T>C and g.21563C>T were 0.087, 0.365, 0.413, 0.308 and 0.356, respectively. However, no variant alleles were identified for three SNPs (c.499 C>G, c.1375 A>G and c.1459 C>T). Efavirenz plasma concentrations were significantly associated with c.516G>T (P= 0.0095), c.785A>G (P= 0.0017), g.21563C>T (P= 0.0036) and g.18492C>T (P= 0.0011). The composite CYP2B6 of three SNPs (c.516G ≥ T, c.785A ≥ G and g.21563C ≥ T) genotypes were significantly associated with higher efavirenz concentrations.ConclusionsOur data indicate that the GAC‐CYP2B6 haplotype is associated with higher plasma efavirenz concentrations in HIV‐infected Thai adults.
Use and cost of psychotropic drugs among recipients with autism in a state Medicaid fee‐for‐service programme
Authors: Khanna R. , Jariwala K. , West‐Strum D. 
Published: April 2012

AbstractBackground  There has been a significant increase in the prevalence of autism in the USA in the past few decades. The purpose of this study was to provide recent estimates of psychotropic drug use and costs among individuals with autism enrolled in Medicaid programme.Method  A cross‐sectional analysis of 2007 Mississippi (MS) Medicaid fee‐for‐service (FFS) programme administrative‐claims data was performed. Study sample included recipients (<65 years) who had a medical services claim with a diagnosis of autism in 2007. Psychotropic drug patterns of use and costs were studied. Factors predicting the use of psychotropic drugs were identified using logistic regression analyses. Average number and cost of psychotropic drug claims per recipient were reported. Costs were reported from the perspective of MS Medicaid.Results  In 2007, there were 1330 recipients with a diagnosis of autism in MS Medicaid FFS programme. Among these recipients, 66.32% had a claim for psychotropic drug during the year. Roughly 39% of recipients with autism had a claim for antipsychotics, 31.58% for stimulants, 19.55% for antidepressants, 19.40% for other psychotropics and 14.81% for anxiolytics/hypnotics/sedatives. Results from regression analyses highlighted variation in psychotropic drug use by demographic and co‐morbid factors. There were a total of 12 618 claims for psychotropic drugs filled by recipients with autism in 2007, at an average of 14 (±12) claims per recipient. The total cost of these claims paid for by MS Medicaid FFS programme was ∼$2 million. Antipsychotics accounted for more than half (∼58%) of the total costs, and had the highest average cost per claim ($291 ± 205).Conclusions  The results of this study indicate a high use of psychotropic drugs among individuals with autism enrolled in a state Medicaid programme. There is an urgent need to study the risk–benefit profile of these drugs in this growing population. Psychotropic drug use was found to vary by demographic and co‐morbid factors. Among the different classes of psychotropic drugs, antipsychotics were the most commonly used and had the highest cost per claim.
Neuropathology of the hippocampus in FTLD‐Tau with Pick bodies: a study of the BrainNet Europe Consortium
Authors: Kovacs G. G. , Rozemuller A. J. M. , van Swieten J. C. , Gelpi E. , Majtenyi K. , Al‐Sarraj S. , Troakes C. , Bódi I. , King A. , Hortobágyi T. , Esiri M. M. , Ansorge O. , Giaccone G. , Ferrer I. , Arzberger T. , Bogdanovic N. , Nilsson T. , Leisser I. , Alafuzoff I. , Ironside J. W. , Kretzschmar H. , Budka H. 
Published: April 2012

G. G. Kovacs, A. J. M. Rozemuller, J. C. van Swieten, E. Gelpi, K. Majtenyi, S. Al‐Sarraj, C. Troakes, I. Bódi, A. King, T. Hortobágyi, M. M. Esiri, O. Ansorge, G. Giaccone, I. Ferrer, T. Arzberger, N. Bogdanovic, T. Nilsson, I. Leisser, I. Alafuzoff, J. W. Ironside, H. Kretzschmar and H. Budka (2013) Neuropathology and Applied Neurobiology39, 166–178Neuropathology of the hippocampus in FTLD‐Tau with Pick bodies: a study of the BrainNet Europe ConsortiumAims: Frontotemporal lobar degeneration with Pick bodies (Pick's disease) is characterized by the presence of tau immunoreactive spherical structures in the cytoplasm of neurones. In view of confusion about the molecular pathology of Pick's disease, we aimed to evaluate the spectrum of tau pathology and concomitant neurodegeneration‐associated protein depositions in the characteristically affected hippocampus. Methods: We evaluated immunoreactivity (IR) for tau (AT8, 3R, 4R), α‐synuclein, TDP43, p62, and ubiquitin in the hippocampus, entorhinal and temporal cortex in 66 archival cases diagnosed neuropathologically as Pick's disease. Results: Mean age at death was 68.2 years (range 49–96). Fifty‐two (79%) brains showed 3R immunoreactive spherical inclusions in the granule cells of the dentate gyrus. These typical cases presented mainly with the behavioural variant of frontotemporal dementia, followed by progressive aphasia, mixed syndromes or early memory disturbance. α‐Synuclein IR was seen only in occasional spherical tau‐positive inclusions, TDP‐43 IR was absent, and 4R IR was present only as neurofibrillary tangles in pyramidal neurones. Aβ IR was observed in 16 cases; however, the overall level of Alzheimer's disease‐related alterations was mainly low or intermediate (n = 3). Furthermore, we identified six cases with unclassifiable tauopathy. Conclusions: (i) Pick's disease may occur also in elderly patients and is characterized by a relatively uniform pathology with 3R tau inclusions particularly in the granule cells of dentate gyrus; (ii) even minor deviation from these morphological criteria suggests a different disorder; and (iii) immunohistological revision of archival cases expands the spectrum of tauopathies that require further classification.
Isoflurane causes neocortical but not hippocampal‐dependent memory impairment in mice
Authors: FIDALGO A. R. , CIBELLI M. , WHITE J. P. M. , NAGY I. , WAN Y. , MA D. 
Published: April 2012

BackgroundThe aim of this study is to investigate the effect of general anaesthesia induced by isoflurane with buprenorphine on hippocampus‐dependent and neocortex‐dependent memory, respectively, in mice, and in addition, to compare the effects of such anaesthesia on these memory processes with the effects induced by lipopolysaccharide (LPS) administration on the same memory processes.MethodsTo assess hippocampus‐dependent memory, isoflurane (for 15 min) after buprenorphine injection, or LPS 100 μg/kg (intraperitoneally) was administered 24 h before or after fear conditioning. The effect of these treatments on hippocampus‐dependent memory was assessed using contextual fear‐conditioning tasks at day 4. To assess neocortex‐dependent memory, isoflurane anaesthesia or LPS was given 72 h after contextual fear conditioning. Neocortex‐dependent memory assessment was performed at day 32.ResultsUnlike LPS injection, isoflurane with buprenorphine‐induced anaesthesia does not impair freezing responses in hippocampus‐dependent fear‐conditioning memory tasks. On anterograde amnesia assessment: 49.67 ± 6.87% for the anaesthesia group and 54.5 ± 4.12% for the control group. On retrograde amnesia assessment: 47.16 ± 8.71% for the anaesthesia group and 54.5 ± 4.12% for control group; P > 0.05. Thus, neither isoflurane nor buprenorphine impair hippocampus‐dependent memory. However, on the neocortex‐dependent memory task, both isoflurane‐induced anaesthesia and LPS‐induced inflammation result in reduced freezing responses: 62.13 ± 5.80% for the anaesthesia group, 74.63 ± 5.69% for the LPS group, and 81.75 ± 3.26% for the control group; P < 0.05 compared with control group.ConclusionGeneral anaesthesia induced by isoflurane with buprenorphine may result in impairment of neocortex‐dependent memory in mouse. However, general anaesthesia so induced does not impair hippocampus‐dependent memory in mouse in our experimental conditions.
Influence of multicomponent apheresis on donors’ haematological and coagulation parameters, iron storage and platelet function
Authors: Macher S. , Sipurzynski‐Budraβ S. , Rosskopf K. , Semmelrock M. , Prüller F. , Griesbacher A. , Lanzer G. , Schallmoser K. 
Published: April 2012

Background and Objectives  Multicomponent collection (MCC) enables production and processing of various blood components during one apheresis session. In this prospective crossover study, the effects of donating platelets (PLTs) and packed red blood cells (PRBCs) on donor’s blood cell count, coagulation, PLT function and iron state were analysed.Materials and Methods  Forty‐eight MCCs were performed using two different cell separators (Fenwal Amicus®, CaridianBCT Trima Accel®). Two units of platelet concentrates and one unit of PRBCs were collected during each session. Full blood cell count and iron status were obtained on day 0 before and after apheresis, day 2, day 14 and day 42. PLT function was analysed by aggregometry and rotation thromboelastometry in parallel with coagulation tests before and after MCC and at day 2.Results  Multicomponent collection was well tolerated without adverse side effects. Blood cell count and iron parameters declined and most of them (haemoglobin, haematocrit, transferrin, transferrin saturation and ferritin) were significantly below baseline values until at least day 42 after donation. Absent iron stores were seen in 31·3% of the donors. In contrast, PLTs significantly exceeded pre‐donation values after 14 days and remained significantly increased for 42 days. After 2 days, coagulation parameters were only slightly (P > 0·05) altered, whereas PLT function was significantly reduced.Conclusion  Multicomponent collection is an obviously safe procedure; however, the significant long‐term impact on the donor’s blood count and iron store, as well as impaired PLT function, has to be considered in regard to donor safety.
Safety of micafungin in prospective and retrospective clinical trials
Authors: Ullmann Andrew J. , Klaas Wibke 
Published: April 2012

SummaryManaging fungal diseases remains a major challenge for clinicians despite the improved armamentarium of antifungal agents. This review identified 19 publications reporting safety data on micafungin. Two of these publications were spin off publications, the remaining 17 (15 prospective, two retrospective) were included in the main assessment. Major adverse events reported which occurred in more than 2% in the study populations were infusion‐related, gastro‐intestinal and hepatic (LFT parameters elevations). Micafungin demonstrated significantly less renal events compared with liposomal amphotericin B and less hepatic events compared with voriconazole. Compared with fluconazole no significant treatment‐related adverse events were found except one trial reporting significantly less somnolence but more chills. Micafungin has a similar favourable safety profile in comparison with other echinocandins or fluconazole.
Pneumocystis jirovecii: a peculiar fungus posing particular problems for therapy and prophylaxis
Authors: Hof H. 
Published: April 2012

SummaryPneumocystis spp. are peculiar fungi, because they lack ergosterol in their cytoplasmic membrane. Furthermore, they go through various sexual and non‐sexual stages in a living host; the cysts, which are able to survive in the environment, are the infectious agents. The various species are more or less specific for a mammalian host. Pneumocystis jirovecii is pathogenic for humans. Transient colonisation of children and adults with this fungus occurs frequently. As a typical opportunist it can induce an overt disease in immunocompromised patients only. In particular those patients with an impaired cell‐mediated immune system, namely AIDS patients or transplant recipients taking immunosuppressive agents, are affected. The leading clinical feature is a bilateral interstitial pneumonia characterised by progressive dyspnoea, tachypnoea and non‐productive cough. Finally, the interstitial pneumonia will lead to hampered gas exchange resulting in a marked decrease in paO2 and consequently to a rather low haemoglobin saturation. Pneumocystsis spp. do not grow on artificial media. Diagnosis is made by demonstration of fungal cells on microscopy preferentially by immunofluorescence staining or by the highly sensitive PCR method. A standardisation of the molecular methods is still lacking, since different DNA sequences are amplified in each case. Quantification by real‐time PCR can help to differentiate between infection and mere colonisation. Among the common antifungals only the echinocandins are active at least against the cyst forms. The principal therapeutic agents remain, however, antibacterial and anti‐parasitic agents, such as cotrimoxazole, clindamycin, primaquine, pentamidine and atovaquone. In addition, an improvement of the immunosuppression is warranted. Prophylaxis is indicated in those individuals with a prolonged cell‐mediated immunodeficiency.
Distribution of PDIA3 transcript and protein in rat testis and sperm cells
Authors: Zhao XJ , Tang RZ , Wang ML , Guo WL , Liu J , Li L , Xing WJ 
Published: April 2012

ContentsProtein disulphide isomerase family A3 (PDIA3) has an activity of thioredoxin, widely expressed in multiple tissues and involved in multiple cellular processes. It was recently found in human and mouse sperm cells and could affect sperm–egg fusion. Therefore, the present investigation aims to identify PDIA3 mRNA and protein in rat testis and sperm cells. Rat PDIA3 cDNA was cloned by RT‐PCR. The cRNA riboprobe was transcribed from PDIA3 cDNA and was used to display PDIA3 mRNA location in rat testes by in situ hybridization. PDIA3 protein distribution was also observed in testis and sperm cells by immunohistochemistry and immunocytochemistry, respectively. The rat PDIA3 transcript and protein were localized in the cells from spermatocytes to the spermatozoa phases of rat testes, mostly in the pachytene spermatocytes. PDIA3 protein was also observed on the intact sperm membrane including the tail. The rat PDIA3 gene is transcribed and translated through the whole spermatogenesis process, and the PDIA3 protein is spread all over the sperm cell membrane. The results provide some primary information about PDIA3 in testis and sperm for further study on PDIA3 function in rat spermatogenesis and sperm–egg fusion.
Narrow‐band imaging on screening of esophageal lesions using an ultrathin transnasal endoscopy
Authors: Kawai Takashi , Takagi Yu , Yamamoto Kei , Hayama Yasutaka , Fukuzawa Mari , Yagi Kenji , Fukuzawa Masakatsu , Kataoka Mikinori , Kawakami Kohei , Itoi Takao , Moriyasu Fuminori , Matsubayashi Jun , Nagao Toshitaka 
Published: April 2012

AbstractBackground and Aim:  Ultrathin transnasal endoscopy, used extensively in Japan, is considered to have inferior image quality and suction performance, and questionable diagnostic performance. So the aim of the present study was to compare the diagnostic performance of white light (WL) examination and non‐magnified narrow‐band imaging (NBI) examination in screening for esophageal disorders with ultrathin transnasal endoscopy.Methods:  A prospective case study of 105 consecutive patients screened for upper gastrointestinal disorders at a single clinic in Tokyo Medical University Hospital. All subjects were diagnosed using WL, NBI and Lugol‐staining examinations. Areas ≥ 5 mm clearly not a Lugol‐staining lesion were defined as esophageal disorders and the rates of detection of the two examination methods (WL vs NBI) were compared.Results:  For WL examination, the sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy (concordance rate) for esophageal disorders were 19.6%, 98.1%, 90.9%, 55.4%, and 59.2%, respectively, versus 60.8% 96.2%, 93.9%, 71.4%, and 78.6% for NBI.Conclusion:  A useful level of diagnostic performance for esophageal disorders can be achieved with non‐magnified narrow‐band NBI ultrathin transnasal endoscopy.
Multiple‐antibiotic‐resistant Helicobacter pylori infection eradicated with a tailor‐made quadruple therapy
Authors: Nakajima Shigemi , Inoue Hisayuki , Inoue Tetsuya , Maruoka Yuri 
Published: April 2012

AbstractIn 2008, a 44‐year‐old woman with mild epigastralgia diagnosed as having Helicobacter pylori‐positive chronic gastritis without peptic ulcer underwent eradication therapy with lansoprazole (LPZ), amoxicillin (AMPC) and clarithromycin (CAM) for 7 days, but it failed, so treatment with rabeprazole, AMPC, and metronidazole (MNZ) for another 7 days was given, but it also failed. She was then prescribed a modified, 14‐day sequential therapy of LPZ and AMPC with an increased dose of CAM followed by MNZ supplement, but the infection was still not eradicated. The H. pylori was cultured and examined for antibiotic susceptibility with the agar dilution method and was found to be resistant to CAM, MNZ, and levofloxacin, and non‐sensitive to AMPC, namely multiple‐antibiotic‐resistant, although sensitive to minocycline. The CYP2C19 genotype of the patient was an extensive metabolizer (G681A: G/A, G636A: G/G). In 2010, she gave informed consent for a 14‐day, tailor‐made, modified classical (or modified high‐dose PPI + AMPC) quadruple therapy comprising 30 mg LPZ, 500 mg AMPC and 500 mg bismuth subnitrate, qid, and 100 mg minocycline, bid. Two months later, her urea breath test was negative. Histology and bacterial culture were still negative 1 year after the therapy. She did not have any adverse events during or after the novel therapy, nor did she feel any further epigastralgia.
Hemopexin is upregulated in rat intestinal mucosa injured by indomethacin
Authors: Takagi Tomohisa , Naito Yuji , Okada Hitomi , Takaoka Megumi , Oya‐Ito Tomoko , Yamada Shinya , Hirai Yasuko , Mizushima Katsura , Yoshida Naohisa , Kamada Kazuhiro , Katada Kazuhiro , Uchiyama Kazuhiko , Ishikawa Takeshi , Handa Osamu , Yagi Nobuaki , Konishi Hideyuki , Kokura Satoshi , Ichikawa Hiroshi , Yoshikawa Toshikazu 
Published: April 2012

AbstractBackground and Aims:  Recent advancements in capsule endoscopy and double‐balloon endoscopy have revealed that non‐steroidal anti‐inflammatory drugs (NSAIDs), such as indomethacin, can induce small intestinal mucosal damage. However, the precise pathogenesis and therapeutic strategy have not been fully revealed. The aim of the present study was to determine the upregulated proteins in the small intestine exposed to indomethacin.Methods:  Indomethacin (10 mg/kg) was administered subcutaneously to male Wistar rats to induce small intestinal damage and the severity of the intestinal injury was evaluated by measuring the area of visible ulcerative lesions. The intestinal mucosal tissue samples were collected and then analyzed by two‐dimensional gel electrophoresis, with matrix‐assisted laser desorption/ionization time‐of‐flight spectrometer peptide mass fingerprinting being used to determine the differentially expressed proteins between normal and injured intestinal mucosa.Results:  Among several protein spots showing differential expression, one, hemopexin (HPX), was identified as upregulated in indomethacin‐induced injured intestinal mucosa using the MASCOT search engine.Conclusion:  HPX was identified as upregulated protein in the small intestine exposed to indomethacin. HPX may be responsible for the development of the intestinal inflammation induced by NSAIDs.