bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Authors: Arnold Christian , Bhat Pooja , Zaugg Judith B. 
Published: March 2016

Abstract
Motivation: The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding.
Results: We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments.
Availability and implementation: SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/.
Contact: judith.zaugg@embl.de
Supplementary information: Supplementary data are available at Bioinformatics online.
BLESS 2: accurate, memory-efficient and fast error correction method
Authors: Heo Yun , Ramachandran Anand , Hwu Wen-Mei , Ma Jian , Chen Deming 
Published: March 2016

Abstract
Summary: The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes.
Availability and implementation: Freely available at https://sourceforge.net/projects/bless-ec
Contact: dchen@illinois.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data
Authors: Wang Sufang , Gribskov Michael , Hazbun Tony R. , Pascuzzi Pete E. 
Published: March 2016

Abstract
Summary: The NCI-60 human tumor cell line panel is an invaluable resource for cancer researchers, providing drug sensitivity, molecular and phenotypic data for a range of cancer types. CellMiner is a web resource that provides tools for the acquisition and analysis of quality-controlled NCI-60 data. CellMiner supports queries of up to 150 drugs or genes, but the output is an Excel file for each drug or gene. This output format makes it difficult for researchers to explore the data from large queries. CellMiner Companion is a web application that facilitates the exploration and visualization of output from CellMiner, further increasing the accessibility of NCI-60 data.
Availability and Implementation: The web application is freely accessible at https://pul-bioinformatics.shinyapps.io/CellMinerCompanion. The R source code can be downloaded at https://github.com/pepascuzzi/CellMinerCompanion.git.
Contact: ppascuzz@purdue.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-scale prediction of moonlighting proteins using diverse protein association information
Authors: Khan Ishita K. , Kihara Daisuke 
Published: March 2016

Abstract
Motivation: Moonlighting proteins (MPs) show multiple cellular functions within a single polypeptide chain. To understand the overall landscape of their functional diversity, it is important to establish a computational method that can identify MPs on a genome scale. Previously, we have systematically characterized MPs using functional and omics-scale information. In this work, we develop a computational prediction model for automatic identification of MPs using a diverse range of protein association information.
Results: We incorporated a diverse range of protein association information to extract characteristic features of MPs, which range from gene ontology (GO), protein–protein interactions, gene expression, phylogenetic profiles, genetic interactions and network-based graph properties to protein structural properties, i.e. intrinsically disordered regions in the protein chain. Then, we used machine learning classifiers using the broad feature space for predicting MPs. Because many known MPs lack some proteomic features, we developed an imputation technique to fill such missing features. Results on the control dataset show that MPs can be predicted with over 98% accuracy when GO terms are available. Furthermore, using only the omics-based features the method can still identify MPs with over 75% accuracy. Last, we applied the method on three genomes: Saccharomyces cerevisiae, Caenorhabditis elegans and Homo sapiens, and found that about 2–10% of proteins in the genomes are potential MPs.
Availability and Implementation: Code available at http://kiharalab.org/MPprediction
Contact: dkihara@purdue.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated eligibility screening and monitoring for genotype-driven precision oncology trials
Authors: Eubank Michael H , Hyman David M , Kanakamedala Amritha D , Gardos Stuart M , Wills Jonathan M , Stetson Peter D 
Published: March 2016

Abstract
The Information Systems Department at Memorial Sloan Kettering Cancer Center developed the DARWIN Cohort Management System (DCMS). The DCMS identifies and tracks cohorts of patients based on genotypic and clinical data. It assists researchers and treating physicians in enrolling patients to genotype-matched IRB-approved clinical trials. The DCMS sends automated, actionable, and secure email notifications to users with information about eligible or enrolled patients before their upcoming appointments. The system also captures investigators input via annotations on patient eligibility and preferences on future status updates. As of August 2015, the DCMS is tracking 159,893 patients on both clinical operations and research cohorts. 134 research cohorts have been established and track 64,473 patients. 51,192 of these have had one or more genomic tests including MSK-IMPACT, comprising the pool eligible for genotype-matched studies. This paper describes the design and evolution of this Informatics solution.
Therapeutic potential of RQ-00311651, a novel T-type Ca2+ channel blocker, in distinct rodent models for neuropathic and visceral pain
Authors: Sekiguchi Fumiko , Kawara Yuma , Tsubota Maho , Kawakami Eri , Ozaki Tomoka , Kawaishi Yudai , Tomita Shiori , Kanaoka Daiki , Yoshida Shigeru , Ohkubo Tsuyako , Kawabata Atsufumi 
Published: March 2016

Abstract
T-type Ca2+ channels (T channels), particularly Cav3.2 among the 3 isoforms, play a role in neuropathic and visceral pain. We thus characterized the effects of RQ-00311651 (RQ), a novel T-channel blocker, in HEK293 cells transfected with human Cav3.1 or Cav3.2 by electrophysiological and fluorescent Ca2+ signaling assays, and also evaluated the antiallodynic/antihyperalgesic activity of RQ in somatic, visceral, and neuropathic pain models in rodents. RQ-00311651 strongly suppressed T currents when tested at holding potentials of −65 ∼ −60 mV, but not −80 mV, in the Cav3.1- or Cav3.2-expressing cells. RQ-00311651 also inhibited high K+-induced Ca2+ signaling in those cells. In mice, RQ, administered intraperitoneally (i.p.) at 5 to 20 mg/kg or orally at 20 to 40 mg/kg, significantly suppressed the somatic hyperalgesia and visceral pain-like nociceptive behavior/referred hyperalgesia caused by intraplantar and intracolonic administration of NaHS or Na2S, H2S donors, respectively, which involve the enhanced activity of Cav3.2 channels. RQ-00311651, given i.p. at 5 to 20 mg/kg, exhibited antiallodynic or antihyperalgesic activity in rats with spinal nerve injury–induced neuropathy or in rats and mice with paclitaxel-induced neuropathy. Oral and i.p. RQ at 10 to 20 mg/kg also suppressed the visceral nociceptive behavior and/or referred hyperalgesia accompanying cerulein-induced acute pancreatitis and cyclophosphamide-induced cystitis in mice. The analgesic and antihyperalgesic/antiallodynic doses of oral and i.p. RQ did not significantly affect the locomotor activity and motor coordination. Together, RQ is considered a state-dependent blocker of Cav3.1/Cav3.2 T channels and may serve as an orally available analgesic for treatment of neuropathic and inflammatory pain including distinct visceral pain with minimum central side effects.
The effect of local vs remote experimental pain on motor learning and sensorimotor integration using a complex typing task
Authors: Dancey Erin , Murphy Bernadette A. , Andrew Danielle , Yielder Paul 
Published: March 2016

Abstract
Recent work demonstrated that capsaicin-induced acute pain improved motor learning performance; however, baseline accuracy was very high, making it impossible to discern the impact of acute pain on motor learning and retention. In addition, the effects of the spatial location of capsaicin application were not explored. Two experiments were conducted to determine the interactive effects of acute pain vs control (experiment 1) and local vs remote acute pain (experiment 2) on motor learning and sensorimotor processing. For both experiments, somatosensory evoked potential (SEP) amplitudes and motor learning acquisition and retention (accuracy and response time) data were collected at baseline, after application, and after motor learning. Experiment 1: N11 (P < 0.05), N13 (P < 0.05), and N30 (P < 0.05) SEP peak amplitudes increased after motor learning in both groups, whereas the N20 SEP peak increased in the control group (P < 0.05). At baseline, the intervention group outperformed the control group in accuracy (P < 0.001). Response time improved after motor learning (P < 0.001) and at retention (P < 0.001). Experiment 2: The P25 SEP peak decreased in the local group after application of capsaicin cream (P < 0.01), whereas the N30 SEP peaks increased after motor learning in both groups (P < 0.05). Accuracy improved in the local group at retention (P < 0.005), and response time improved after motor learning (P < 0.005) and at retention (P < 0.001). This study suggests that acute pain may increase focal attention to the body part used in motor learning, contributing to our understanding of how the location of pain impacts somatosensory processing and the associated motor learning.
Prognosis of patients with syncope seen in the emergency room department: an evaluation of four different risk scores recommended by the European Society of Cardiology guidelines
Authors: Barón-Esquivias Gonzalo , Fernández-Cisnal Agustín , Arce-León Álvaro , Toro Rocio , Cantero-Pérez Eva , Parejo-Matos Juan , Romero-Rodriguez Nieves , Montero Emilio , Martinez Angel 
Published: March 2016

Aim
To apply, analyze, and evaluate the four syncope risk scores recommended by the 2009 European guidelines and the different parameters that they use to predict death, syncope recurrence, and hospital readmission in the population seen in the emergency room department (ERD) for syncope.

Methods and results
A total of 323 patients aged older than 14 years [mean age 59 (32–75) years] and seen in ERD for syncope over a 2-month period were included in the study; 50.7% were women. Patients were evaluated using the four risk scores and were followed up for at least 2 years. In all, 275 patients (85.2%) were discharged directly from ERD after evaluation. During 28±5 months of follow-up, 8% died, 18.3% presented a further syncopal episode, and 18.6% were readmitted to hospital. Only two of the four risk scores were useful in risk discrimination, but no statistically significant differences were detected between predicted risk and observed risk. Multivariate analysis indicated relationships between age and death, a history of cardiovascular disease and syncope recurrence, and between presyncopal palpitations and hospital readmission.

Conclusion
Although a large number of events occur after syncope, the risk scores recommended by guidelines overestimate risk, but there were no statistically significant differences between observed and predicted risk.
Bortezomib, Dexamethasone, Mitoxantrone, and Vinorelbine (BDMV): An Active Reinduction Regimen for Children With Relapsed Acute Lymphoblastic Leukemia and Asparaginase Intolerance
Authors: Yeo Kee K. , Gaynon Paul S. , Fu Cecilia H. , Wayne Alan S. , Sun Weili 
Published: March 2016

Background:
Children with relapsed acute lymphoblastic leukemia (ALL) typically receive vincristine-prednisone-l-asparaginase-doxorubicin reinduction chemotherapy similar to contemporary induction regimens. However, up to 20% of patients are unable to receive vincristine-prednisone-l-asparaginase-doxorubicin secondary to asparaginase intolerance. We report our experience with a promising reinduction regimen for children with relapsed ALL who are unable to receive asparaginase.

Patients and Methods:
This is a single institution, retrospective review of the safety and activity of bortezomib, dexamethasone, mitoxantrone, and vinorelbine (BDMV) in patients with relapsed ALL. Complete remission and adverse events after reinduction were study endpoints. Patients treated with BDMV between 2012 and 2015 were identified. Response and adverse events (AEs) were assessed by review of medical records. Standard response criteria were used and AEs were graded based on NCI CTCAEv4.0.

Results:
Seven of 10 patients achieved complete remission after 1 cycle of BDMV, with 4 achieving minimal residual disease negativity. The most common ≥grade 3 nonhematological toxicities were infection (91%), gastrointestinal (45%), metabolic (45%), and cardiovascular (9%).

Conclusions:
BDMV is an active reinduction regimen for children with relapsed ALL who cannot receive asparaginase. The toxicity profile is as expected for this patient population. Further prospective clinical trials are warranted to evaluate the safety and efficacy of BDMV.
The Pransky interview: Aldo Zini, President and CEO of Aethon, Inc.
Authors: Pransky Joanne 
Published: March 2016

Purpose
– The following paper is a “Q
&
A interview” conducted by Joanne Pransky of Industrial Robot Journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry engineer-turned successful business leader, regarding the commercialization and challenges of bringing technological inventions to market while overseeing a company. This paper aims to discuss these issues.

Design/methodology/approach
– The interviewee is Aldo Zini, President and CEO of Aethon, Inc., a robotics and software company that has developed an innovative automated platform to improve internal supply logistics. In this interview, Zini shares some of the technical and business details that have led up to the latest version of Aethon’s core product, the TUG, a mobile autonomous robot with more than 450 installs worldwide.

Findings
– Zini received a BS in Industrial Engineering from the University of Pittsburgh and a master’s in Public Management (Health Systems IT) from Carnegie Mellon University. While obtaining his BS degree, Zini did an internship in hospital consulting and became immediately interested in healthcare automation as a way to solve hospital inefficiencies. Zini went on to become the Vice President of Sales and Marketing for Automated Healthcare, which developed the first robotic medication dispensing system for hospitals (ROBOT-Rx) and was acquired by McKesson for $67 million. Before joining and investing in Aethon, Zini was Senior Vice President of sales and marketing for TechRx, one of the largest providers of software solutions to the pharmacy industry, which was sold to NDC Corporation for over $200 million.

Originality/value
– Zini has been leading the technology revolution in hospital automation for more than 25 years. His contributions to technology-driven companies have led to acquisitions worth more than a quarter of a billion dollars. Zini owns several patents in medication-dispensing technology, and is credited with the development of key methodologies in quantifying the value proposition for several technology platforms deployed in hundreds of hospitals across the country.
Ranking of finance journals: a stochastic dominance analysis
Authors: Kao Erin H. , Hsu Chuan-Hao , Lu Yunlin , Fung Hung-Gay 
Published: March 2016

Purpose
– Prior studies in citation-based journal rankings tend to be static to compare across journals. One journal may be judged better in citations than other journals at some points in time but not at the others. The assumption that the citation distribution is normally distributed and that the citation observations are independent and identically distributed (i.i.d.) may not be appropriate. The paper aims to discuss these issues.

Design/methodology/approach
– This study uses a stochastic dominance (SD) analysis, which overcomes the dynamic nature of changes in citation over time. The SD method proposed by Linton, Maasoumi, and Whang (hereafter LMW, 2005) does not require the data to be i.i.d. We use the LMW method to compare the relative ranking of 23 finance journals using citations for all articles from them during 1990-2010.

Findings
– The study indicates that the citation distribution changes over time. Thus a SD analysis is a better approach for a comparison of journal ranking. The findings unambiguously place JF, JFE, RFS, JFQA, and JFI in the top five spots of the finance journal ranking. The “near-top” journals, such as JBF, JCF, and FM, are not clear cut in the SD analysis.

Research limitations/implications
– The results confirm that ranking for the lower ranked journals may change over time especially, but the top three journals appear to be robust across methods and over time.

Originality/value
– The results of SD analysis provides more convincing evidence on finance journal ranking and could be useful to rank academic institutions, faculty research quality, and help the authors to decide what to read and which journals are influential.
Developmental and behavioural effects of the endophytic Fusarium moniliforme Fe14 towards Meloidogyne graminicola in rice
Authors: Le H.T.T. , Padgham J.L. , Hagemann M.H. , Sikora R.A. , Schouten A. 
Published: March 2016

AbstractThe root‐knot nematode, Meloidogyne graminicola, is an important pest of rice in many rice production areas worldwide. The endophyte Fusarium moniliforme strain Fe14, isolated from a disinfected root of rice, has previously shown potential antagonistic activity against M. graminicola. This study shows the effects of Fe14 on M. graminicola behaviour, infection, development and reproduction. The endophyte Fe14 colonisation significantly reduced M. graminicola penetration into rice roots by 55% and increased the male to female ratio nine times. The endophyte also delayed juvenile development into female inside the rice root. These results suggest a suboptimal performance of the giant cell and a cumulative effect of the endophyte on the long‐term root‐knot nematode population development. In split‐root assays, the application of Fe14 at the inducer side significantly reduced nematode invasion at the responder side by 38% and 60% in two independent trials. This result suggests a systemic effect of the endophyte on rice plants. The root exudates from Fe14‐treated plants were either less attractive or had repellent effect on nematode movement. The results, when compared to what was described for other endophytic Fusarium against other nematode species, may indicate a basal response mechanism initiated in the plant by endophytic Fusarium spp. The present study may give leads for unravelling the molecular mechanisms responsible for the induced systemic defence responses in plants.
Creating a critical mass eliminates the effects of stereotype threat on women's mathematical performance
Authors: Pennington Charlotte R. , Heim Derek 
Published: March 2016

BackgroundWomen in mathematical domains may become attuned to situational cues that signal a discredited social identity, contributing to their lower achievement and underrepresentation.AimThis study examined whether heightened in‐group representation alleviates the effects of stereotype threat on women's mathematical performance. It further investigated whether single‐sex testing environments and stereotype threat influenced participants to believe that their ability was fixed (fixed mindset) rather than a trait that could be developed (growth mindset).Sample and methodOne hundred and forty‐four female participants were assigned randomly to a self‐as‐target or group‐as‐target stereotype threat condition or to a control condition. They completed a modular arithmetic maths test and a mindset questionnaire either alone or in same‐sex groups of 3–5 individuals.ResultsParticipants solved fewer mathematical problems under self‐as‐target and group‐as‐target stereotype threat when they were tested alone, but these performance deficits were eliminated when they were tested in single‐sex groups. Participants reported a weaker growth mindset when they were tested under stereotype threat and in single‐sex groups. Moreover, evidence of inconsistent mediation indicated that single‐sex testing environments negatively predicted mindset but positively predicted mathematical performance.ConclusionsThese findings suggest that single‐sex testing environments may represent a practical intervention to alleviate stereotype threat effects but may have a paradoxical effect on mindset.
Processing Conversational Implicatures: Alternatives and Counterfactual Reasoning
Authors: van Tiel Bob , Schaeken Walter 
Published: March 2016

AbstractIn a series of experiments, Bott and Noveck (2004) found that the computation of scalar inferences, a variety of conversational implicature, caused a delay in response times. In order to determine what aspect of the inferential process that underlies scalar inferences caused this delay, we extended their paradigm to three other kinds of inferences: free choice inferences, conditional perfection, and exhaustivity in “it”‐clefts. In contrast to scalar inferences, the computation of these three kinds of inferences facilitated response times. Following a suggestion made by Chemla and Bott (2014), we propose that the time it takes to compute a conversational implicature depends on the structural characteristics of the required alternatives.