bluuebunny/crossref_metadata_2025_split huggingface dataset:
Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources
Authors: Liu Zhongyang , Guo Feifei , Gu Jiangyong , Wang Yong , Li Yang , Wang Dan , Lu Liang , Li Dong , He Fuchu 
Published: February 2015

Abstract
Motivation: Anatomical Therapeutic Chemical (ATC) classification system, widely applied in almost all drug utilization studies, is currently the most widely recognized classification system for drugs. Currently, new drug entries are added into the system only on users’ requests, which leads to seriously incomplete drug coverage of the system, and bioinformatics prediction is helpful during this process.
Results: Here we propose a novel prediction model of drug-ATC code associations, using logistic regression to integrate multiple heterogeneous data sources including chemical structures, target proteins, gene expression, side-effects and chemical–chemical associations. The model obtains good performance for the prediction not only on ATC codes of unclassified drugs but also on new ATC codes of classified drugs assessed by cross-validation and independent test sets, and its efficacy exceeds previous methods. Further to facilitate the use, the model is developed into a user-friendly web service SPACE ( S imilarity-based P redictor of A TC C od E ), which for each submitted compound, will give candidate ATC codes (ranked according to the decreasing probability_score predicted by the model) together with corresponding supporting evidence. This work not only contributes to knowing drugs’ therapeutic, pharmacological and chemical properties, but also provides clues for drug repositioning and side-effect discovery. In addition, the construction of the prediction model also provides a general framework for similarity-based data integration which is suitable for other drug-related studies such as target, side-effect prediction etc.
Availability and implementation: The web service SPACE is available at http://www.bprc.ac.cn/space
Contact: hefc@nic.bmi.ac.cn or lidong.bprc@foxmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
SPARQL-enabled identifier conversion with Identifiers.org
Authors: Wimalaratne Sarala M. , Bolleman Jerven , Juty Nick , Katayama Toshiaki , Dumontier Michel , Redaschi Nicole , Le Novère Nicolas , Hermjakob Henning , Laibe Camille 
Published: February 2015

Abstract
Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data.
Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data.
Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql .
Contact: sarala@ebi.ac.uk
PolyMarker: A fast polyploid primer design pipeline
Authors: Ramirez-Gonzalez Ricardo H. , Uauy Cristobal , Caccamo Mario 
Published: February 2015

Abstract
Summary: The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local alignments and standard primer design tools to test the viability of the primers. A command line tool and a web interface are available to the community.
Availability and implementation: PolyMarker is available as a ruby BioGem: bio-polyploid-tools. Web interface: http://polymarker.tgac.ac.uk.
Contact: Ricardo.Ramirez-Gonzalez@tgac.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Langston Hughes
Authors: Kutzinski Vera 
Published: February 2015

Born James Langston Hughes in Joplin, Missouri, Langston Hughes (b. 1902–d. 1967) was likely the most influential writer who emerged from the Harlem Renaissance. He was the first one of this group to establish an enduring national and international reputation. Hughes established his national standing as the “Poet Laureate of the Negro Race” with The Weary Blues and the controversial essay “The Negro Artist and the Racial Mountain” in 1926. By the time he graduated from Lincoln University, Pennsylvania, in 1929, he had published a second volume of poems, Fine Clothes to the Jew (1927). Having lived in Mexico for more than a year as a teenager, by 1929 Hughes had also visited West Africa, France (where he spent several months), and Italy. Extended trips to Haiti, Cuba, the Soviet Union, and Spain followed, as did translations of his poems into Spanish, German, French, Russian, and many other languages. Though best known as a poet, Hughes was a prolific and versatile writer working in numerous literary genres as well as in journalism and popular history. Widely celebrated for his blues poetry and, more recently, for his experimental poems from the 1950s and early 1960s, Hispanic American audiences in particular praised Hughes for his verse influenced by international communism. However, this radical verse landed him in serious trouble at home. In the 1940s and 1950s, Hughes became the target of smear campaigns and FBI surveillance. Although Hughes disavowed his political past in his 1953 publicly broadcast testimony before Joseph McCarthy’s infamous Senate subcommittee, a measure of unease about his communist leanings has lingered in Hughes scholarship in the United States, where his radical poetry from the 1930s has traditionally had relatively few admirers—until now. Ironically, the very simplicity that made his writing accessible to and popular with so many different audiences across the world also fueled the belief among many scholars that Hughes’s writing lacked literary complexity. As a result, neither his novels nor his autobiographies have met with abundant critical analysis, much less acclaim. Quite in contrast to Hughes’s short fiction, especially the Simple stories from the 1940s and 1950s, these texts have attracted the critical attention they deserve only since the third quarter of the twentieth century, and especially in the early twenty-first century. Similarly, scholars have neglected Hughes’s plays, his translations of writers such as Federico García Lorca and Jacques Roumain, and his extensive journalism. Since the mid-1990s, however, the landscape of Hughes studies has changed significantly as scholars have increasingly challenged the view of Hughes as a straightforward and even shallow writer. It is changing even more in the twenty-first century.
Switch to Rilpivirine/Emtricitabine/Tenofovir Single-Tablet Regimen of Human Immunodeficiency Virus-1 RNA-Suppressed Patients, Agence Nationale de Recherches sur le SIDA et les Hépatites Virales CO3 Aquitaine Cohort, 2012–2014
Authors: Cazanave Charles , Reigadas Sandrine , Mazubert Cyril , Bellecave Pantxika , Hessamfar Mojgan , Le Marec Fabien , Lazaro Estibaliz , Peytavin Gilles , Bruyand Mathias , Fleury Hervé , Dabis François , Neau Didier 
Published: February 2015

AbstractBackground.  The purpose of this study was to assess the efficacy and tolerability of combined antiretroviral therapy (cART) in human immunodeficiency virus (HIV)-1 virologically suppressed patients who switched to rilpivirine (RPV)/tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC) as a single-tablet regimen (STR).Methods.  A retrospective multicenter cohort study was performed between September 2012 and February 2014 in Bordeaux University Hospital-affiliated clinics. Patients with a plasma HIV viral load (VL) lower than 50 copies/mL and switching to STR were evaluated at baseline, 3, 6, 9, and 12 months from switch time (M3, M6, M9, M12) for VL and other biological parameters. Change from baseline in CD4 cell counts was evaluated at M6 and M12. Virological failure (VF) was defined as 2 consecutive VL &gt;50 copies/mL.Results.  Three hundred four patients were included in the analysis. Single-tablet regimen switch was proposed to 116 patients with adverse events, mostly efavirenz (EFV)-based (n = 59), and to 224 patients for cART simplification. Thirty of 196 patients with available genotype resistance test results displayed virus with ≥1 drug resistance mutation on reverse-transcriptase gene. After 12 months of follow-up, 93.4% (95.5% confidence interval, 89.9–96.2) of patients remained virologically suppressed. There was no significant change in CD4 cell count. During the study period, 5 patients experienced VF, one of them harboring RPV resistance mutation. Clinical cART tolerability improved in 79 patients overall (29.9%) at M6, especially neurological symptoms related to EFV. Fasting serum lipid profiles improved, but a significant estimated glomerular function rate decrease (−11 mL/min/1.73 m2; P &lt; 10−4) was observed.Conclusions.  Overall, virologic suppression was maintained in patients after switching to RPV/TDF/ FTC. This STR strategy was associated with improved tolerability.
Heart failure diagnosis in acute conditions has high agreement with inpatient diagnosis
Authors: Seronde Marie-France , Laribi Said , Collins Sean P. , Deye Nicolas , Logeart Damien , Plaisance Patrick , Cohen-Solal Alain , Mebazaa Alexandre 
Published: February 2015

Objectives
Acute heart failure (AHF) is frequently encountered in the emergency department (ED) or in the cardiac care unit (CCU)/ICU. Discrimination between cardiac and noncardiac cause of dyspnea by clinical means and standard testing is sometimes inadequate. The aim of our study was to assess AHF diagnosis agreement as determined by: (a) the attending physician, (b) the hospital discharge diagnosis, and (c) an adjudication committee.

Patients and methods
Between 2010 and 2011, consecutive patients arriving for dyspnea in our hospital were prospectively included. A convenience sample of patients was enrolled in this analysis. Patients were admitted through the ED (280 patients) or through CCU/ICU (112 patients) for undifferentiated dyspnea.

Results
Overall, few differences were observed between the initial diagnosis and the hospital discharge diagnosis or the adjudicated diagnosis. Among the 200 patients with an initial diagnosis of AHF, hospital discharge diagnosis confirmed AHF (alone or combined) in 191 (95.5%) patients and the adjudication committee confirmed AHF (alone or combined) in 196 (98%) patients.

Conclusion
Our study showed considerable agreement between different AHF diagnostic standards. An initial AHF diagnosis on the basis of clinical signs and biological parameters utilizing B-type natriuretic peptide testing has high agreement and accuracy with the hospital discharge and adjudicated diagnosis of AHF. The present study also shows that the accuracy of the initial AHF diagnosis allows rapid inclusion in AHF trials. These results, if confirmed in a broader cohort of patients, suggest that the initial ED diagnosis is highly accurate and reliable to guide further inpatient management.
Biliary Atresia Is Associated With Hypertension
Authors: Matloff Robyn G. , Diamond Rebekah , Weinberg Alan , Arnon Ronen , Saland Jeffrey M. 
Published: February 2015

AbstractObjectives:The improved survival of pediatric liver transplant recipients is accompanied by an increase in long‐term comorbidities. A recently highlighted concern, hypertension, is associated with chronic kidney disease (CKD) in this population and can result in other target‐organ damage during childhood. The prevalence of hypertension in pediatric liver transplantation is imprecisely known. In addition, individual etiologies of liver failure may convey different risks of hypertension. We sought to study the effect of liver transplantation on the prevalence of hypertension and CKD in patients with biliary atresia (BA).Methods:We conducted a retrospective chart review of 160 patients with BA followed at the Mount Sinai Medical Center, New York, from 1987 to 2012. Data were accumulated from the initial and subsequent visits at approximately 6 months, 1, 3, 5, 10, and 15 years of age. Hypertension was defined as systolic blood pressure ≥95th percentile for age, sex, height, and/or use of antihypertensive medication. Renal function was examined over time. Data were stratified by liver transplantation status at the time of visit.Results:A high prevalence of hypertension was observed from the initial visit through age 10, independent of transplant status (transplanted: 48% initial visit and 13% after 10 years vs nontransplanted: 55% initial visit and 17% after 10 years [P = ns for transplant status]). Mean estimated glomerular filtration rate (eGFR) was lower among liver transplant patients as compared with nontransplant patients and declined posttransplant. The incidence of CKD was higher among transplant patients.Conclusions:Hypertension is common among children with BA, independent of liver transplant status. Transplant patients had significantly reduced renal function, which continued to decline over time. Hypertension was not associated with reduced eGFR.
Difficulty Achieving Vitamin D Sufficiency With High‐Dose Oral Repletion Therapy in Infants With Cholestasis
Authors: Jensen Melissa , Abu‐El‐Haija Maisam , Bishop Warren , Rahhal Riad M. 
Published: February 2015

ABSTRACTObjectives:Oral high‐dose repletion vitamin D therapy, also known as stoss therapy, can be effective in the treatment of nutritional vitamin D deficiency rickets in infants and young children without liver disease and in patients with cystic fibrosis. There is no literature about this approach in infants with new‐onset cholestasis.Methods:This was a retrospective chart review of infants with cholestasis from March 2010 to March 2012 at a pediatric tertiary care center. Four cases satisfied the inclusion criteria, and were described in detail.Results:All of the patients received oral high‐dose repletion therapy with ergocalciferol (vitamin D2) 300,000 IU daily for 2 to 3 days. Follow‐up vitamin D levels approximately 4 weeks later showed failure to achieve sufficiency levels (>20 ng/dL) in any patient.Conclusions:Unlike infants without liver disease, use of oral high‐dose repletion therapy may not be adequate as treatment of vitamin D deficiency in the setting of cholestasis.
Baseline Analysis of a Young α‐1‐Antitrypsin Deficiency Liver Disease Cohort Reveals Frequent Portal Hypertension
Authors: Teckman Jeffrey H. , Rosenthal Philip , Abel Robert , Bass Lee M. , Michail Sonia , Murray Karen F. , Rudnick David A. , Thomas Daniel W. , Spino Cathie , Arnon Ronen , Hertel Paula M. , Heubi James , Kamath Binita M. , Karnsakul Wikrom , Loomes Kathleen M. , Magee John C. , Molleston Jean P. , Romero Rene , Shneider Benjamin L. , Sherker Averell H. , Sokol Ronald J. ,   Childhood Liver Disease Research Network (ChiLDReN)
Published: February 2015

ABSTRACTObjectives:α‐1‐Antitrypsin (A1AT) deficiency is a common genetic disease with an unpredictable and highly variable course. The Childhood Liver Disease Research and Education Network is a National Institutes of Health, multicenter, longitudinal consortium studying pediatric liver diseases, with the objective of prospectively defining natural history and identifying disease modifiers.Methods:Longitudinal, cohort study of A1AT patients' birth through 25 years diagnosed as having liver disease, type PIZZ or PISZ. Medical history, physical examination, laboratory, imaging, and standardized survey tool data were collected during the provision of standard of care.Results:In the present report of the cohort at baseline, 269 subjects were enrolled between November 2008 and October 2012 (208 with their native livers and 61 postliver transplant). Subjects with mild disease (native livers and no portal hypertension [PHT]) compared to severe disease (with PHT or postliver transplant) were not different in age at presentation. A total of 57% of subjects with mild disease and 76% with severe disease were jaundiced at presentation (P = 0.0024). A total of 29% of subjects with native livers had PHT, but age at diagnosis and growth were not different between the no‐PHT and PHT groups (P > 0.05). Subjects with native livers and PHT were more likely to have elevated bilirubin, ALT, AST, INR, and GGTP than the no‐PHT group (P << 0.001), but overlap was large. Chemistries alone could not identify PHT.Conclusions:Many subjects with A1AT presenting with elevated liver tests and jaundice improve spontaneously. Subjects with PHT have few symptoms and normal growth. Longitudinal cohort follow‐up will identify genetic and environmental disease modifiers.
Occult Blood and Perianal Examination
Authors: Moran Christopher J. , Kaplan Jess L. , Winter Harland S. , Masiakos Peter T. 
Published: February 2015

ABSTRACTObjectives:Pediatric inflammatory bowel disease (IBD) often presents insidiously and standard blood tests are normal in 20% of patients. We hypothesize that fecal occult blood testing (FOBT) and the perianal examination in addition to blood tests provide important information during the screening process for IBD. The aim of the present study was to measure the diagnostic value of adding FOBT and perianal examination to standard screening laboratories in evaluating children and adolescents for IBD.Methods:The medical records of consecutive patients undergoing ileocolonoscopy for IBD were reviewed. Laboratory test results, FOBT, and perianal examination before the decision to perform the ileocolonoscopy were recorded. Standard limits of laboratory tests were used. Multivariate logistic regression was performed on a discovery cohort and applied to an independent validation cohort.Results:The discovery cohort included 335 patients (85 IBD and 250 non‐IBD). A total of 61.2% had FOBT and perianal examination performed before the decision to perform the ileocolonoscopy. A total of 119 patients had complete blood testing, FOBT, and perianal examination available for full analysis. The sensitivity of the laboratory testing was 80.5% for IBD, and the sensitivity of FOBT with perianal examination was 66.9%. The combined sensitivity of laboratory testing and FOBT with perianal examination was, however, 97.6%. The most predictive model included C‐reactive protein, platelet counts, and FOBT with perianal examination and was superior to the laboratory value‐only model (P < 0.001) that was validated in a separate cohort.Conclusions:Perianal examination and FOBT improve sensitivity in screening children for IBD.
Fungal arthritis secondary to Colletotrichum gloeosporioides
Authors: Cho Jonathan C. , Sharma Rajendra S. , Sutton Deanna A. , Wiederhold Nathan P. , Sanders Carmita , Wickes Brian L. , Estrada Sandy J. 
Published: February 2015

Introduction:

Colletotrichum spp. are common plant‐pathogenic fungi that usually occur as asymptomatic endophytes on aerial organs of host plants. Of the many Colletotrichum spp. described, only four have been associated with infections in humans, one of these being Colletotrichum gloeosporioides.

Case presentation:
Infections cited in humans due to Colletotrichum spp. typically involve the eye (keratitis/keratomycosis/endophthalmitis) or are subcutaneous in nature and secondary to trauma. We report a clinical case of septic arthritis caused by Colletotrichum gloeosporioides in an immunocompetent 55‐year‐old male. DNA sequencing was performed for identification of the organism. Antifungal susceptibility testing was performed according to the Clinical and Laboratory Standards Institute M38‐A2 standard for broth microdilution testing against filamentous fungi.

Conclusion:
To the best of our knowledge, this is the first case of a Colletotrichum sp., specifically Colletotrichum gloeosporioides, causing septic arthritis in humans. This report highlights the successful treatment of a case of septic arthritis due to Colletotrichum gloeosporioides with voriconazole.
Efficiency, productivity and Islamic banks: an application of DEA and Malmquist index
Authors: Abbas Muhammad , Hammad Rayan S , Elshahat Mohamed Fathy , Azid Toseef 
Published: February 2015

Purpose
– This paper aims to compute the Malmquist Index of Islamic and conventional banks to compare their performance in the sample period of 2005-2009. Islamic banks have been showing tremendous growth throughout the world in recent past. Their progress is exceptional in Islamic countries on account of patronization for religious reasons. There existed vacuum in research of their productivity change over the years.

Design/methodology/approach
– This study tries to apply the Malmquist Index. The Malmquist Total Factor Productivity Index has been further divided into Efficiency Change Index, Technological Change Index, Pure Efficiency Change Index and Scale Efficiency Change Index to obtain an insight about the reasons for the change in productivity.

Findings
– Results indicate that the productivity of Islamic banks decreased in 2007 but it increased in 2008 to 2009. Islamic banks had higher productivity growth from 2005 to 2006, but they experienced lower growth in subsequent years as compared to their conventional counterparts.

Research limitations/implications
– Data were not available before 2005 in Pakistan.

Practical implications
– This study is helpful for the investors and bankers for formulating the future policy.

Social implications
– This study also provides a guideline for establishing the ethical financial institutions.

Originality/value
– This is an original attempt.
Dialogue between the formal and the informal sector in open innovations at the grassroots’ level
Authors: Saxena Stuti 
Published: February 2015

Purpose– Whereas a lot of emphasis has been placed on the open innovations (Chesbrough, 2003, von Hippel, 2005) and their implications in the formal sector, this paper purports to fill the literature gap in identifying the process of dialogue between the formal and the informal sector with reference to the open innovations, emanating at the grassroots’ level, for effecting inclusive and a sustainable development. This causality is being sought to be achieved through initiation, accessibility, building-the-bridges and finding unique solutions to the problems through mutual dialogue and reciprocity. Thus, this interplay of interaction shall facilitate the shaping up of sustainable and inclusive development through the open innovations. It may be pertinent to note here that the present paper shall specifically limit its scope to the conceptualization for such a dialogue to eventually happen in due course of time.Design/methodology/approach– Theoretical build-up.Findings– For harnessing the potential of the innovations at the grassroots, it is important that bridges be built between the informal and the formal spaces.Originality/value– Hitherto, the notion of inclusive and sustainable development was not studied in the research with respect to the open innovations at the grassroots (informal sector). The paper is attempt at filling this gap.