bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis
Authors: Itzel Timo , Scholz Peter , Maass Thorsten , Krupp Markus , Marquardt Jens U. , Strand Susanne , Becker Diana , Staib Frank , Binder Harald , Roessler Stephanie , Wang Xin Wei , Thorgeirsson Snorri , Müller Martina , Galle Peter R. , Teufel Andreas 
Published: September 2014

Abstract
Motivation : Co-regulated genes are not identified in traditional microarray analyses, but may theoretically be closely functionally linked [guilt-by-association (GBA), guilt-by-profiling]. Thus, bioinformatics procedures for guilt-by-profiling/association analysis have yet to be applied to large-scale cancer biology.
We analyzed 2158 full cancer transcriptomes from 163 diverse cancer entities in regard of their similarity of gene expression, using Pearson’s correlation coefficient (CC). Subsequently, 428 highly co-regulated genes (|CC| ≥ 0.8) were clustered unsupervised to obtain small co-regulated networks. A major subnetwork containing 61 closely co-regulated genes showed highly significant enrichment of cancer bio-functions. All genes except kinesin family member 18B (KIF18B) and cell division cycle associated 3 (CDCA3) were of confirmed relevance for tumor biology. Therefore, we independently analyzed their differential regulation in multiple tumors and found severe deregulation in liver, breast, lung, ovarian and kidney cancers, thus proving our GBA hypothesis. Overexpression of KIF18B and CDCA3 in hepatoma cells and subsequent microarray analysis revealed significant deregulation of central cell cycle regulatory genes. Consistently, RT-PCR and proliferation assay confirmed the role of both genes in cell cycle progression.
Finally, the prognostic significance of the identified KIF18B- and CDCA3-dependent predictors ( P = 0.01, P = 0.04) was demonstrated in three independent HCC cohorts and several other tumors.
In summary, we proved the efficacy of large-scale guilt-by-profiling/association strategies in oncology. We identified two novel oncogenes and functionally characterized them. The strong prognostic importance of downstream predictors for HCC and many other tumors indicates the clinical relevance of our findings.
Contact : andreas.teufel@ukr.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The Ensembl REST API: Ensembl Data for Any Language
Authors: Yates Andrew , Beal Kathryn , Keenan Stephen , McLaren William , Pignatelli Miguel , Ritchie Graham R. S. , Ruffier Magali , Taylor Kieron , Vullo Alessandro , Flicek Paul 
Published: September 2014

Abstract
Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language.
Availability and implementation: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest .
Contact: ayates@ebi.ac.uk or flicek@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Clinical Practice Guideline for the Management of Chronic Kidney Disease in Patients Infected With HIV: 2014 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Lucas Gregory M. , Ross Michael J. , Stock Peter G. , Shlipak Michael G. , Wyatt Christina M. , Gupta Samir K. , Atta Mohamed G. , Wools-Kaloustian Kara K. , Pham Paul A. , Bruggeman Leslie A. , Lennox Jeffrey L. , Ray Patricio E. , Kalayjian Robert C. 
Published: September 2014

AbstractIt is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.
Hadronic gamma-rays from RX J1713.7−3946?
Authors: Gabici S. , Aharonian F. A. 
Published: September 2014

Abstract
RX J1713.7−3946 is a key object to check the supernova remnant paradigm of the origin of Galactic cosmic rays. While the origin of its gamma-ray emission (hadronic versus leptonic) is still debated, the hard spectrum at GeV energies reported by the Fermi collaboration is generally interpreted as a strong argument in favour of a leptonic scenario. On the contrary, we show that hadronic interactions can naturally explain the gamma-ray spectrum if gas clumps are present in the supernova remnant shell. The absence of thermal X-rays from the remnant fits well within this scenario.
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli
Authors: Clarke Justin E. , Kime Louise , Romero A. David , McDowall Kenneth J. 
Published: September 2014

Abstract
Escherichia coli endoribonuclease E has a major influence on gene expression. It is essential for the maturation of ribosomal and transfer RNA as well as the rapid degradation of messenger RNA. The latter ensures that translation closely follows programming at the level of transcription. Recently, one of the hallmarks of RNase E, i.e. its ability to bind via a 5′-monophosphorylated end, was shown to be unnecessary for the initial cleavage of some polycistronic tRNA precursors. Here we show using RNA-seq analyses of ribonuclease-deficient strains in vivo and a 5′-sensor mutant of RNase E in vitro that, contrary to current models, 5′-monophosphate-independent, ‘direct entry’ cleavage is a major pathway for degrading and processing RNA. Moreover, we present further evidence that direct entry is facilitated by RNase E binding simultaneously to multiple unpaired regions. These simple requirements may maximize the rate of degradation and processing by permitting multiple sites to be surveyed directly without being constrained by 5′-end tethering. Cleavage was detected at a multitude of sites previously undescribed for RNase E, including ones that regulate the activity and specificity of ribosomes. A potentially broad role for RNase G, an RNase E paralogue, in the trimming of 5′-monophosphorylated ends was also revealed.
Anatomy-Based Eligibility Measure for Robotic-Assisted Bypass Surgery
Authors: Escoto Abelardo , Trejos Ana Luisa , Patel Rajni V. , Goela Aashish , Kiaii Bob 
Published: September 2014

Objective Robotic-assisted endoscopic single-vessel small thoracotomy allows clinicians to perform coronary artery bypass grafting surgery in a minimally invasive manner using the da Vinci Surgical System. Not all patients are suitable for this technique, and the lack of an appropriate method for patient eligibility avoids completion of the procedure robotically. The objective of this study was to develop a patient eligibility method based on the anatomy of the chest of the patient. Methods Preoperative computed tomography thorax scans of 110 patients were analyzed. Two-dimensional measurements taken on the axial images were used with the goal of finding a relation between the anatomy of the patient and the completion of the procedure robotically. Results Patients with a distance from the left anterior descending coronary artery to the anterior chest wall of smaller than 15 mm have a 20% probability of requiring conversion of the procedure to open surgery. This probability increases if the chest of the patient is very elliptical, having an anterior-posterior dimension of less than 45% of the transverse dimension. Conclusions The smaller the distance is from the left anterior descending artery to the anterior chest wall, the lower the chances are of completing the procedure robotically.
Robotically Assisted, Completely Endoscopic Transmyocardial Revascularization is Feasible
Authors: Brunsting Louis A. , Snyder Averel B. , Espinal Eric A. , Srivastava Sudhir P. 
Published: September 2014

Objective The purpose of this study was to assess the feasibility of an endoscopic, optical-fiber-based, laser delivery system (LDS) developed to perform sole-therapy transmyocardial revascularization (TMR) in a totally endoscopic, robotically assisted operation. Methods Forty-two patients were enrolled in a multicenter, prospective, single-arm clinical trial conducted at four US centers between 2005 and 2007. Transmyocardial revascularization was performed completely endoscopically with robotic assistance, introducing the Holmium:Yttrium aluminum garnet (YAG) LDS via a 5-mm port. Completion of the operation endoscopically defined procedural success. Clinical data were recorded before, during, and at least 30 days after the procedure. Results All patients had Canadian Cardiovascular Score angina class IV at baseline. The mean ejection fraction was 49% (range [R], 28–71), the mean age was 59.1 years (R, 36–80), 71% (30/42) were men, 86% (36/42) underwent previous coronary artery bypass grafting surgery, and 76% (32/42) underwent prior coronary stenting. Procedural success was accomplished in 93% (39/42). For the procedural successes, the mean number of TMR channels was 32 (R, 16–50), the median operative time was 88 minutes (R, 48–250 minutes), and the median length of stay postoperatively was 2.5 days (R, 1–10). There was no operative or 30-day mortality, and no patient received any transfusion. At 30 days, freedom from major adverse cardiac events was 95% (two patients had transient congestive heart failure). At the median 6-month follow-up (single-center data, n = 12), the mean (SD) Canadian Cardiovascular Score angina score was 1.3 (0.05) ( P < 0.001 vs baseline). Conclusions Robotically assisted TMR can be performed using an endoscopic, optical-fiber-based LDS, with high procedural success, avoidance of early adverse clinical events, and potential for successful angina relief.
Robotic Coronary Artery Bypass Grafting Decreases 30-Day Complication Rate, Length of Stay, and Acute Care Facility Discharge Rate Compared with Conventional Surgery
Authors: Leyvi Galina , Forest Stephen J. , Srinivas Vankeepuram S. , Greenberg Mark , Wang Nan , Mais Alec , Snyder Max J. , DeRose Joseph J. 
Published: September 2014

Objective The objective of this study was to compare the short-term outcomes of robotic with conventional on-pump coronary artery bypass grafting (CABG). Methods The study population included 2091 consecutive patients who underwent either conventional or robotic CABG from January 2007 to March 2012. Preoperative, intraoperative, and 30-day postoperative variables were collected for each group. To compare the incidence of rapid recovery between conventional and robotic CABG, the surrogate variables of early discharge and discharge to home (vs rehabilitation or acute care facility) were evaluated. A multivariate logistic regression analysis was used. Results One hundred fifty robotic and 1619 conventional CABG cases were analyzed. Multivariate logistic regression analysis demonstrated that robotic surgery was astrongpredictoroflower30-day complications [odds ratio (OR), 0.24; P =0.005], short length of stay (OR, 3.31; P < 0.001), and decreased need for an acute care facility (OR, 0.55; P = 0.032). In the presence of complications (New York State Complication Composite), the robotic technique was not associated with a change in discharge status. Conclusions In this retrospective review, robotic CABG was associated with a lower 30-day complication rate, a shorter length of stay, and a lower incidence of acute care facility discharge than conventional on-pump CABG. It may suggest a more rapid recovery to preoperative status after robotic surgery; however, only a randomized prospective study could confirm the advantages of a robotic approach.
Mini-invasive Aortic Surgery: Personal Experience
Authors: Spinelli Francesco , Stilo Francesco , La Spada Michele , Benedetto Filippo , De Caridi Giovanni , Barillà David , Giardina Massimiliano , David Antonio 
Published: September 2014

Objective In this study, we retrospectively evaluated our experience in minilaparotomy (MINI) and compared the results with conventional open repair (OPEN). Methods From January 2005 to December 2012, we surgically treated 234 consecutive patients with elective infrarenal abdominal aortic aneurysms, 195 men and 39 women, with a mean age of 74 years. Inclusion criteria for MINI were not ruptured abdominal aortic aneurysm, increased surgical risk, anatomical limits for endovascular repair, no previous surgical invasion of the abdominal cavity, and no requirement for concomitant abdominal surgical invasion. Surgical treatment was OPEN in 113 patients (48.3%) and MINI through an 8- to 14-cm incision in 121 patients (51.7%). Epidural anesthesia has been added in 26.5% and in 19.3% of the MINI and OPEN patients, respectively. Mortality, complications, aortic clamping time, operative time, need for postoperative morphine therapy, time to solid diet, and length of hospital stay were registered. Results The MINI has been performed in all patients selected, with 72 aortoaortic grafts and 49 aortobisiliac grafts. Early mortality was 1.6% versus 3.5% ( P > 0.5); 1-, 3-, and 5-year mortality were 7% versus 9%, 19% versus 22%, and 29% versus 34% ( P > 0.5); complications were 12.2% versus 26.6% ( P > 0.05); mean (SD) clamping time was 48 (12) versus 44 (14) minutes ( P > 0.5); mean (SD) operative time was 218.72 (41.95) versus 191.44 (21.73) minutes ( P > 0.025); mean (SD) estimated intraoperative blood loss was 425.64 (85.95) versus 385.30 (72.41) mL ( P > 0.1); mean (SD) morphine consumption in the group given epidural and the group not given epidural was 0 (2) and 2 (2) mg intravenously (IV) versus 2 (4) ( P < 0.5) and 4 (3) mg IV ( P > 0.1); mean (SD) ambulation was 2.1 (0.6) versus 4.1 (2.7) ( P < 0.5); mean (SD) time to solid diet was 2.1 (0.4) versus 3.5 (1.6) ( P < 0.5); and mean (SD) length of hospital stay was 4.9 (1.64) versus 7.35 (1.95) days ( P > 0.05), in the MINI and OPEN groups, respectively. Postoperative hernia at 3 years was 18% versus 23% in the MINI and OPEN groups ( P < 0.5), respectively. Conclusions The MINI gives the patients a significantly shorter period of recovery with the quality and safety of the OPEN. This experience suggested extending the indication to all surgical candidates without local limitations.
mInDel: an efficient pipeline for high-throughput InDel marker discovery
Authors: Lv Yuanda , Liu Yuhe , Zhang Xiaolin , Zhao Han 
Published: September 2014

AbstractBackgroundNext-Generation Sequencing (NGS) technologies have emerged as a powerful tool to reveal nucleotide polymorphisms in a high-throughput and cost-effective manner. However, it remains a daunting task to proficiently analyze the enormous volume of data generated from NGS and to identify length polymorphisms for molecular marker discovery. The development of insertion-deletion polymorphism (InDel) markers is in particular computationally intensive, calling for integrated high performance methods to identify InDels with high sensitivity and specificity, which would directly benefit areas from genomic studies to molecular breeding.ResultsWe present here a NGS-based tool for InDel marker discovery (mInDel), a high-performance computing pipeline for the development of InDel markers between any two genotypes. The mInDel pipeline proficiently develops InDel markers by comparing shared region size using sliding alignments between assembled contigs or reference genomes. mInDel has successfully designed thousands of InDel markers from maize NGS data locally and genome-wide. The program needs less than 2 hours to run when using 20 threads on a high-performance computing server to implement 40G data.ConclusionsmInDel is an efficient, integrated pipeline for a high-throughput design of InDel markers between genotypes. It will be particularly applicable to the crop species which require a sufficient amount of DNA markers for molecular breeding selection. mInDel is freely available for downloading atwww.github.com/lyd0527/mInDelwebsite.
Genome-Wide Mapping In A House Mouse Hybrid Zone Reveals Hybrid Sterility Loci And Dobzhansky-Muller Interactions
Authors: Turner Leslie M. , Harr Bettina 
Published: September 2014

ABSTRACTMapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone betweenM. musculus musculusandM. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.
A virtual instrument for quantitative assessment of pitting corrosion
Authors: Ramos I.R. , Valdez S.B. , Zlatev K.R. , Schorr W.M , Carrillo B.M. , Stoytcheva M.S. , Garcia I.R. , Martinez M.M. 
Published: September 2014

Purpose– The purpose of this investigation was to develop a digital instrument for the quantitative evaluation of pitting corrosion in metals.Design/methodology/approach– This investigation comprised two central parts: research, testing and monitoring of the formation of pitting by conventional methods and applying American Society for Testing and Materials (ASTM) Standards, and the development of a virtual instrument based on the LabVIEW 2010 platform.Findings– The methodology used was suitable for the analysis of pitting on carbon steel and aluminum alloy UNS A96061, used in the aerospace industry.Practical implications– This technique allows pits to be to localized, measured and quantified on metallic surfaces, for corrosion evaluation in atmospheric and industrial environments.Originality/value– This combination of conventional and digital methods can assist in corrosion control of pitting in industrial equipment.
Corrosion protection of stainless steel by a self-assembled organosilane bilayer
Authors: Wang Hairen , Li Minya , Qu June , Cao Zhiyong , Chen Geng , Zhou Yang 
Published: September 2014

Purpose– The purpose of this paper is to construct a self-assembled double layer of organosilane on the surface of stainless steel and to investigate its corrosion inhibitive capability.Design/methodology/approach– A monolayer of 3-glycidoxypropyltrimethoxysilane (GPTMS) was grafted onto an oxidized AISI 430SS (AISI 430 stainless steel) surface substrate from dry toluene solution. The hydrolysis of 1H,1H,2H,2H-perfluorodecyltriethoxysilane (PFDS) molecules was used to anchor a second organic layer from mixed water-ethanol solution. The adsorption behavior and corrosion inhibition properties of the monolayer and also the bilayer were investigated by potentiodynamic polarization, scanning electron microscope (SEM), Fourier transformed infrared spectroscopy (FTIR) and contact angle measurements.Findings– The GPTMS/PFDS bilayer was successfully deposited onto the oxidized AISI 430SS surface. The optimal assembling time for the filming of the first GPTMS monolayer is 6 hours. Suitable values of pH and temperature of the PFDS self-assembly solution were pivotal to the successful deposition of the second layer. Compared to the GPTMS monolayer, the GPTMS/PFDS bilayer exhibited a significant enhancement of the corrosion inhibition performance of AISI 430SS in NaCl solution.Research limitations/implications– The contact angle value measured on the bilayer-modified surface was somewhat lower than the reported value of a complete fluorinated surface. However, further optimization of the assembling condition is needed to obtain more orderly and denser films.Originality/value– This paper provides useful information regarding the preparation of an organosilane bilayer on the surface of stainless steel and its corrosion inhibition properties in NaCl solution. It illustrates potential application prospects of GPTMS/PFDS bilayers for surface treatment of stainless steel.
Electropolymerization of poly(aniline-co-p-toluidine) on copper and its application as a corrosion inhibitor
Authors: Rashid Mohd , Sabir Suhail , Waware Umesh , A. Rahim Afidah 
Published: September 2014

Purpose
– This paper aims to compare the inhibitive effects of polyaniline (PAni), poly(p-toluidine) and poly(aniline-co-p-toluidine) in hydrochloric acid (HCl) solution.

Design/methodology/approach
– The electrochemical deposition of PAni, poly(p-toluidine) and poly(aniline-co-p-toluidine) on pure copper metal was studied potentiodynamically. The copolymer deposited was characterized by Fourier transform infrared (FTIR) spectroscopy, ultraviolet (UV)-visible spectroscopy and scanning electron microscopy (SEM). The corrosion inhibition studies on copper electrode were performed using electrochemical methods, viz, open circuit potential (OCP) measurements, potentiodynamic polarization scans and electrochemical impedance spectroscopy (EIS) tests, conducted in 0.1 M HCl solution.

Finding
– The results of the study reveal that the copolymer of poly(aniline-co-p-toluidine) at the optimum concentration of 1 × 10−3 M has better corrosion inhibition efficiency as compared to PAni and poly(p-toluidine).

Research limitations/implications
– The conducting polymers are difficult to deposit on the metal surface because of their high dissolution tendency before the electropolymerization potential of the monomer is achieved.

Practical implications
– From an environmental viewpoint, poly(aniline-co-p-toluidine) is a toxic and hazardous conducting polymer.

Originality/value
– The paper demonstrates that poly(aniline-co-p-toluidine) showed better dispersion in different organic solvents and had higher corrosion inhibition efficiency than PAni.
Tyranny of distance: the challenges of coordinating a multinational consortium
Authors: Forro Denise 
Published: September 2014

Purpose
– This study aims to evaluate and report on the challenges faced by a multinational academic library consortium with a heterogeneous membership and widely varying collection resources.

Design/methodology/approach
– The author uses a case study approach based on direct experience obtained with coordinating the word of such a consortium, from its nascent stages to its fully functional present-day form.

Findings
– Coordinating the work of an academic library consortium that spans the globe presents challenges such as an inability to set a meeting time – and place – that is agreeable to all and copyright laws that vary from one country to the next. Cataloging practices may affect the system’s ability to select an appropriate supplier based on reported journal holdings, but this problem is easily solved by a careful review of local practices and the system’s search algorithms.

Originality/value
– This article is of interest to anyone involved in a library consortium, regardless of its geographic boundaries.