bluuebunny/crossref_metadata_2025_split huggingface dataset:
Open-source chemogenomic data-driven algorithms for predicting drug–target interactions
Authors: Hao Ming , Bryant Stephen H , Wang Yanli 
Published: January 2018

AbstractWhile novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug–target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred.
Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers
Authors: Kaur Gurmeet , Subramanian Srikrishna 
Published: January 2018

Abstract

Summary
Cysteine and histidine rich domains (CHORDs), implicated in immunity and disease resistance signaling in plants, and in development and signal transduction in muscles and tumorigenesis in animals, are seen to have a cylindrical three-dimensional structure stabilized by the tetrahedral chelation of two zinc ions. CHORDs are regarded as novel zinc-binding domains and classified independently in Pfam and ECOD. Our sequence and structure analysis reveals that both the zinc-binding sites in CHORD possess a zinc ribbon fold and are likely related to each other by duplication and circular permutation. Interestingly, we also detect an evolutionary relationship between each of the CHORD zinc fingers (ZFs) and the Bruton's tyrosine kinase (Btk)-type ZF of the zinc ribbon fold group. Btk_ZF is found in eukaryotic Tec kinase family proteins that are also implicated in signaling pathways in several lineages of hematopoietic cells involved in mammalian immunity. Our analysis suggests that the unique zinc-stabilized fold seen only in the CHORD and Btk_ZFs likely emerged specifically in eukaryotes to mediate diverse signaling pathways.

Supplementary information
Supplementary data are available at Bioinformatics online.
EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits
Authors: Xu Chao , Fang Jian , Shen Hui , Wang Yu-Ping , Deng Hong-Wen 
Published: January 2018

AbstractMotivationExtreme phenotype sampling (EPS) is a broadly-used design to identify candidate genetic factors contributing to the variation of quantitative traits. By enriching the signals in extreme phenotypic samples, EPS can boost the association power compared to random sampling. Most existing statistical methods for EPS examine the genetic factors individually, despite many quantitative traits have multiple genetic factors underlying their variation. It is desirable to model the joint effects of genetic factors, which may increase the power and identify novel quantitative trait loci under EPS. The joint analysis of genetic data in high-dimensional situations requires specialized techniques, e.g. the least absolute shrinkage and selection operator (LASSO). Although there are extensive research and application related to LASSO, the statistical inference and testing for the sparse model under EPS remain unknown.ResultsWe propose a novel sparse model (EPS-LASSO) with hypothesis test for high-dimensional regression under EPS based on a decorrelated score function. The comprehensive simulation shows EPS-LASSO outperforms existing methods with stable type I error and FDR control. EPS-LASSO can provide a consistent power for both low- and high-dimensional situations compared with the other methods dealing with high-dimensional situations. The power of EPS-LASSO is close to other low-dimensional methods when the causal effect sizes are small and is superior when the effects are large. Applying EPS-LASSO to a transcriptome-wide gene expression study for obesity reveals 10 significant body mass index associated genes. Our results indicate that EPS-LASSO is an effective method for EPS data analysis, which can account for correlated predictors.Availability and implementationThe source code is available at https://github.com/xu1912/EPSLASSO.Supplementary informationSupplementary data are available at Bioinformatics online.
TSAPA: identification of tissue-specific alternative polyadenylation sites in plants
Authors: Ji Guoli , Chen Moliang , Ye Wenbin , Zhu Sheng , Ye Congting , Su Yaru , Peng Haonan , Wu Xiaohui 
Published: January 2018

Abstract

Summary
Alternative polyadenylation (APA) is now emerging as a widespread mechanism modulated tissue-specifically, which highlights the need to define tissue-specific poly(A) sites for profiling APA dynamics across tissues. We have developed an R package called TSAPA based on the machine learning model for identifying tissue-specific poly(A) sites in plants. A feature space including more than 200 features was assembled to specifically characterize poly(A) sites in plants. The classification model in TSAPA can be customized by selecting desirable features or classifiers. TSAPA is also capable of predicting tissue-specific poly(A) sites in unannotated intergenic regions. TSAPA will be a valuable addition to the community for studying dynamics of APA in plants.

Availability and implementation
https://github.com/BMILAB/TSAPA

Supplementary information
Supplementary data are available at Bioinformatics online.
G2S: a web-service for annotating genomic variants on 3D protein structures
Authors: Wang Juexin , Sheridan Robert , Sumer S Onur , Schultz Nikolaus , Xu Dong , Gao Jianjiong 
Published: January 2018

Abstract

Motivation
Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access.

Results
We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis.

Availability and implementation
The webserver and source codes are freely available at https://g2s.genomenexus.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Analysis of cluster-randomized test-negative designs: cluster-level methods
Authors: Jewell Nicholas P , Dufault Suzanne , Cutcher Zoe , Simmons Cameron P , Anders Katherine L 
Published: January 2018

SUMMARY
Intervention trials of vector control methods often require community level randomization with appropriate inferential methods. For many interventions, the possibility of confounding due to the effects of health-care seeking behavior on disease ascertainment remains a concern. The test-negative design, a variant of the case-control method, was introduced to mitigate this issue in the assessment of the efficacy of influenza vaccination (measured at an individual level) on influenza infection. Here, we introduce a cluster-randomized test-negative design that includes randomization of the intervention at a group level. We propose several methods for estimation and inference regarding the relative risk (RR). The inferential methods considered are based on the randomization distribution induced by permuting intervention assignment across two sets of randomly selected clusters. The motivating example is a current study of the efficacy of randomized releases of Wolbachia-infected Aedes aegypti mosquitoes to reduce the incidence of dengue in Yogyakarta City, Indonesia. Estimation and inference techniques are assessed through a simulation study.
Toward Leveraging Human Connectomic Data in Large Consortia: Generalizability of fMRI-Based Brain Graphs Across Sites, Sessions, and Paradigms
Authors: Cao Hengyi , McEwen Sarah C , Forsyth Jennifer K , Gee Dylan G , Bearden Carrie E , Addington Jean , Goodyear Bradley , Cadenhead Kristin S , Mirzakhanian Heline , Cornblatt Barbara A , Carrión Ricardo E , Mathalon Daniel H , McGlashan Thomas H , Perkins Diana O , Belger Aysenil , Seidman Larry J , Thermenos Heidi , Tsuang Ming T , van Erp Theo G M , Walker Elaine F , Hamann Stephan , Anticevic Alan , Woods Scott W , Cannon Tyrone D 
Published: January 2018

Abstract
While graph theoretical modeling has dramatically advanced our understanding of complex brain systems, the feasibility of aggregating connectomic data in large imaging consortia remains unclear. Here, using a battery of cognitive, emotional and resting fMRI paradigms, we investigated the generalizability of functional connectomic measures across sites and sessions. Our results revealed overall fair to excellent reliability for a majority of measures during both rest and tasks, in particular for those quantifying connectivity strength, network segregation and network integration. Processing schemes such as node definition and global signal regression (GSR) significantly affected resulting reliability, with higher reliability detected for the Power atlas (vs. AAL atlas) and data without GSR. While network diagnostics for default-mode and sensori-motor systems were consistently reliable independently of paradigm, those for higher-order cognitive systems were reliable predominantly when challenged by task. In addition, based on our present sample and after accounting for observed reliability, satisfactory statistical power can be achieved in multisite research with sample size of approximately 250 when the effect size is moderate or larger. Our findings provide empirical evidence for the generalizability of brain functional graphs in large consortia, and encourage the aggregation of connectomic measures using multisite and multisession data.
Investigating the Effectiveness of Current and Modified World Health Organization Guidelines for the Control of Soil-Transmitted Helminth Infections
Authors: Farrell Sam H , Coffeng Luc E , Truscott James E , Werkman Marleen , Toor Jaspreet , de Vlas Sake J , Anderson Roy M 
Published: January 2018

Abstract

Background
Considerable efforts have been made to better understand the effectiveness of large-scale preventive chemotherapy therapy for the control of morbidity caused by infection with soil-transmitted helminths (STHs): Ascaris lumbricoides, Trichuris trichiura, and the 2 hookworm species, Necator americanus and Ancylostoma duodenale. Current World Health Organization (WHO) guidelines for STH control include mass drug administration (MDA) programs based on prevalence measurements, aiming at reducing morbidity in pre–school-aged children (pre-SAC) and school-aged children (SAC) by lowering the prevalence of moderate- to heavy-intensity infections to <1%.

Methods
We project the likely impact of following the current WHO guidelines and assess whether the WHO morbidity goals will be achieved across a range of transmission settings. We also investigate modifications that could be made to the current WHO treatment guidelines, and project their potential impacts in achieving morbidity and transmission control.

Results
While the standard guidelines are sufficient at low transmission levels, community-wide treatment (ie, involving pre-SAC, SAC, and adults) is essential if WHO morbidity goals are to be met in moderate- to high-transmission settings. Moreover, removing the recommendation of decreasing the treatment frequency at midline (5–6 years after the start of MDA) further improves the likelihood of achieving morbidity control in SAC.

Conclusions
We meld analyses based on 2 mathematical models of parasite transmission and control by MDA for the dominant STH species, to generate a unified treatment approach applicable across all settings, regardless of which STH infection is most common. We recommend clearly defined changes to the current WHO guidelines.
Between Papacy and Empire: Cardinal Henry Beaufort, the House of Lancaster, and the Hussite Crusades
Authors: Whelan Mark 
Published: January 2018

Abstract
Cardinal Henry Beaufort’s career as papal legate and anti-Hussite crusader was as scandalous as it was brief. Commanded in 1427 by Pope Martin V (1417–31) to spearhead Christendom’s efforts to extirpate the Hussite heresy in Bohemia, Beaufort eventually succeeded in raising a crusading army in England in the summer of 1429 with money from the papacy and the proceeds from taxation levied in the Holy Roman Empire. Beaufort then shocked contemporaries by taking his crusading army not to Bohemia, but instead to France, where it was deployed in support of Lancastrian ambitions. Current scholarship fails to make full sense of Beaufort’s career as anti-Hussite crusader because it has largely viewed it through the prism of Anglo-papal relations. This article will demonstrate that Beaufort’s crusading legation can be far better understood when situated in its contemporary continental context. Framing Beaufort’s career more carefully in the context of papal and imperial politics makes possible a fundamental reassessment of his crusading legation, and highlights hitherto unrecognised factors which pushed him to the fore of the efforts to crush Hussitism. A close study of the responses to Beaufort’s anti-Hussite efforts also points to the hope and concern he generated across Christendom, revealing how historians have underestimated the importance of Beaufort’s legation to the crusading movement in the fifteenth century and the interest which crusading legations could arouse among contemporaries.
The hand-loom weaver and the power loom: a Schumpeterian perspective†
Authors: Allen Robert C 
Published: January 2018

AbstractThe invention of the power loom was a response to the increase in supply of yarn in the 1780s. This led to an expansion of handloom weaving and a rise in earnings in the 1790s, thereby, creating the “golden age”. The high earnings increased the profitability of developing the power loom by raising the value of the labour that it saved. Consequently, less efficient—hence, cheaper to develop—power looms could be brought into commercial use than would have been the case had the golden age not occurred. The power loom, in turn, devalued the old skills, so poverty accompanied progress.
Reported theory use in walking interventions: a literature review and research agenda
Authors: Kadir Mohammad Abdul , Rundle-Thiele Sharyn 
Published: January 2018

SummaryThere is mixed evidence with some suggesting walking can be increased up to the recommended level through interventions based on behaviour change models and others showing partial or no effects [Arbour and Ginis (A randomised controlled trial of the effects of implementation intentions on women’s walking behaviour. Psychol Health, 2009;24:49–65); Merom et al. (Can a motivational intervention overcome an unsupportive environment for walking–findings from the Step-by-Step Study. Ann Behav Med 2009;38:137–46); Ornes and Ransdell (A pilot study examining exercise self-efficacy as a mediator for walking behavior in college-age women. Perceptual Motor Skills, 2010;110:1098–104)]. Taken together, prior studies suggest that ongoing research attention is warranted. Walking behaviour change intervention studies were searched using key search words ‘walking promotion’ and ‘pedometer’ in the PubMed database. Initially, 87 articles were found and 25 walking behaviour change interventions were reviewed to focus attention on reported theory use. Results of the review suggest that interventions that are theoretically underpinned may be no more effective than their counterparts. The Transtheoretical Model (TTM) and Social Cognitive Models were most frequently reported with positive effects noted for TTM use. The review also indicates that using single theory may be better than using multiple theories in a single intervention.
Ethics, effectiveness and population health information interventions: a Canadian analysis
Authors: Greyson Devon , Knight Rod , Shoveller Jean A 
Published: January 2018

Summary
Population health information interventions (PHIIs) use information in efforts to promote health. PHIIs may push information to a target audience (communication), pull information from the public (surveillance), or combine both in a bidirectional intervention. Although PHIIs have often been framed as non-invasive and ethically innocuous, in reality they may be intrusive into people’s lives, affecting not only their health but their senses of security, respect, and self-determination. Ethical acceptability of PHIIs may have impacts on intervention effectiveness, potentially giving rise to unintended consequences. This article examines push, pull, and bidirectional PHIIs using empirical data from an ethnographic study of young mothers in Greater Vancouver, Canada. Data were collected from October 2013 to December 2014 via naturalistic observation and individual interviews with 37 young mothers ages 16-22. Transcribed interviews and field notes were analyzed using inductive qualitative thematic analysis. Both push and pull interventions were experienced as non-neutral by the target population, and implementation factors on a structural and individual scale affected intervention ethics and effectiveness. Based on our findings, we suggest that careful ethical consideration be applied to use of PHIIs as health promotion tools. Advancing the ‘ethics of PHIIs’ will benefit from empirical data that is informed by information and computer science theory and methods. Information technologies, digital health promotion services, and integrated surveillance programs reflect important areas for investigation in terms of their effects and ethics. Health promotion researchers, practitioners, and ethicists should explore these across contexts and populations.
UK consumer perceptions of a novel till-receipt ‘traffic-light’ nutrition system
Authors: Cole Matthew , Peek Hayden , Cowen Daniel 
Published: January 2018

AbstractFront-of-pack (FoP) traffic light nutrition labelling has been widely proposed as a tool to improve public health nutrition. Current evidence suggests that whilst consumers generally find them to be useful and an important source of information about a particular food or ingredient, this may have limited value in isolation when considering a person’s overall nutritional intake. This study sought to examine UK consumers’ use of existing FoP traffic light food labelling and ascertain public perception of a novel ‘till-receipt’ summary providing nutritional information about consumers entire shopping purchases. In total, 237 respondents completed an online questionnaire between May and June 2016. Almost two-thirds were female (n = 152, 64.1%) and the largest proportion of responses were received from those aged 25–32 years (n = 53, 22.4%) and 41–50 years (n = 53, 22.4%). About 83.5% of respondents suggested that they currently use traffic light information to inform their food purchases and ‘health’ was reported as the most important factor influencing food choice (42.2%; n = 100). Notably, 54.4% of respondents indicated that the novel till-receipt system could provide a solution to the potential limitations of existing FoP labelling and could help inform healthier food purchases. Our findings strengthen the existing evidence base to suggest that traffic light information is a useful tool to aid consumer food purchases. Moreover, our outcomes propose that consumers may benefit from a new receipt-based traffic light system which provides a more holistic summary of their entire food purchases.
Billfishes in a changing world
Authors: Kerstetter David W , Schratwieser Jason 
Published: January 2018

Abstract
The 6th International Billfish Symposium (IBS) was held in September 2016 at the headquarters of the International Game Fish Association in Dania Beach, Florida (USA). In addition to providing a venue for presenting new research on istiophorid and xiphiid billfishes, the IBS’s objective was to highlight known uncertainties about the biology and fisheries of these species, particularly at the level of regional fisheries management organizations, such as the International Commission for the Conservation of Atlantic Tunas (ICCAT). The 6th IBS was attended by 60 participants from seven countries, contributing a total of 34 oral and five poster presentations. One of the other goals of the IBS was to collectively develop a plan for future IBS events. The next IBS is tentatively scheduled for 2021. We summarize here the main outcomes of the 6th IBS and preface the articles presented at the symposium that are included in this article theme set.
Admitting a Coarse Embedding is Not Preserved Under Group Extensions
Authors: Arzhantseva Goulnara , Tessera Romain 
Published: January 2018

AbstractWe construct a finitely generated group which is an extension of two finitely generated groups coarsely embeddable into Hilbert space but which itself does not coarsely embed into Hilbert space. Our construction also provides a new infinite monster group: the first example of a finitely generated group that does not coarsely embed into Hilbert space and yet does not contain a weakly embedded expander.
Doppelgängers: Bijections of Plane Partitions
Authors: Hamaker Zachary , Patrias Rebecca , Pechenik Oliver , Williams Nathan 
Published: January 2018

AbstractWe say two posets are doppelgängers if they have the same number of P-partitions of each height k. We give a uniform framework for bijective proofs that posets are doppelgängers by synthesizing K-theoretic Schubert calculus techniques of H. Thomas and A. Yong with M. Haiman’s rectification bijection and an observation of R. Proctor. Geometrically, these bijections reflect the rational equivalence of certain subvarieties of minuscule flag manifolds. As a special case, we provide the 1st bijective proof of a 1983 theorem of R. Proctor—that plane partitions of height k in a rectangle are equinumerous with plane partitions of height k in a shifted trapezoid.