bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAESTROweb: a web server for structure-based protein stability prediction
Authors: Laimer Josef , Hiebl-Flach Julia , Lengauer Daniel , Lackner Peter 
Published: February 2016

Abstract
Summary: The prediction of change in stability upon point mutations in proteins has many applications in protein analysis and engineering. We recently adjoined a new structure-based method called MAESTRO, which is distributed as command line program. We now provide access to the most important features of MAESTRO by an easy to use web service. MAESTROweb allows the prediction of change in stability for user-defined mutations, provides a scan functionality for the most (de)stabilizing n-point mutations for a maximum of n = 5, creates mutation sensitivity profiles and evaluates potential disulfide bonds. MAESTROweb operates on monomers, multimers and biological assemblies as defined by PDB.
Availability and implementation: MAESTROweb is freely available for non-commercial use at https://biwww.che.sbg.ac.at/maestro/web.
Contact: peter.lackner@sbg.ac.at
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions
Authors: Niu Zhen , Chasman Deborah , Eisfeld Amie J. , Kawaoka Yoshihiro , Roy Sushmita 
Published: February 2016

Abstract
Motivation: Identifying the shared and pathogen-specific components of host transcriptional regulatory programs is important for understanding the principles of regulation of immune response. Recent efforts in systems biology studies of infectious diseases have resulted in a large collection of datasets measuring host transcriptional response to various pathogens. Computational methods to identify and compare gene expression modules across different infections offer a powerful way to identify strain-specific and shared components of the regulatory program. An important challenge is to identify statistically robust gene expression modules as well as to reliably detect genes that change their module memberships between infections.
Results: We present MULCCH (MULti-task spectral Consensus Clustering for Hierarchically related tasks), a consensus extension of a multi-task clustering algorithm to infer high-confidence strain-specific host response modules under infections from multiple virus strains. On simulated data, MULCCH more accurately identifies genes exhibiting pathogen-specific patterns compared to non-consensus and nonmulti-task clustering approaches. Application of MULCCH to mammalian transcriptional response to a panel of influenza viruses showed that our method identifies clusters with greater coherence compared to non-consensus methods. Further, MULCCH derived clusters are enriched for several immune system-related processes and regulators. In summary, MULCCH provides a reliable module-based approach to identify molecular pathways and gene sets characterizing commonality and specificity of host response to viruses of different pathogenicities.
Availability and implementation: The source code is available at https://bitbucket.org/roygroup/mulcch
Contact: sroy@biostat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EpimiRBase: a comprehensive database of microRNA-epilepsy associations
Authors: Mooney Catherine , Becker Brett A. , Raoof Rana , Henshall David C. 
Published: February 2016

Abstract
Summary: MicroRNAs are short non-coding RNA which function to fine-tune protein levels in all cells. This is achieved mainly by sequence-specific binding to 3′ untranslated regions of target mRNA. The result is post-transcriptional interference in gene expression which reduces protein levels either by promoting destabilisation of mRNA or translational repression. Research published since 2010 shows that microRNAs are important regulators of gene expression in epilepsy. A series of microRNA profiling studies in rodent and human tissue has revealed that epilepsy is associated with wide ranging changes to microRNA levels in the brain. These are thought to influence processes including cell death, inflammation and re-wiring of neuronal networks. MicroRNAs have also been identified in the blood after injury to the brain and therefore may serve as biomarkers of epilepsy. EpimiRBase is a manually curated database for researchers interested in the role of microRNAs in epilepsy. The fully searchable database includes information on up- and down-regulated microRNAs in the brain and blood, as well as functional studies, and covers both rodent models and human epilepsy.
Availability and implementation: EpimiRBase is available at http://www.epimirbase.eu
Contact: catherinemooney@rcsi.ie
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts
Authors: Cavalcante Raymond G. , Patil Snehal , Weymouth Terry E. , Bendinskas Kestutis G. , Karnovsky Alla , Sartor Maureen A. 
Published: February 2016

Abstract
Motivation: Capabilities in the field of metabolomics have grown tremendously in recent years. Many existing resources contain the chemical properties and classifications of commonly identified metabolites. However, the annotation of small molecules (both endogenous and synthetic) to meaningful biological pathways and concepts still lags behind the analytical capabilities and the chemistry-based annotations. Furthermore, no tools are available to visually explore relationships and networks among functionally related groups of metabolites (biomedical concepts). Such a tool would provide the ability to establish testable hypotheses regarding links among metabolic pathways, cellular processes, phenotypes and diseases.
Results: Here we present ConceptMetab, an interactive web-based tool for mapping and exploring the relationships among 16 069 biologically defined metabolite sets developed from Gene Ontology, KEGG and Medical Subject Headings, using both KEGG and PubChem compound identifiers, and based on statistical tests for association. We demonstrate the utility of ConceptMetab with multiple scenarios, showing it can be used to identify known and potentially novel relationships among metabolic pathways, cellular processes, phenotypes and diseases, and provides an intuitive interface for linking compounds to their molecular functions and higher level biological effects.
Availability and implementation: http://conceptmetab.med.umich.edu
Contacts: akarnovsky@umich.edu or sartorma@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MuCor: mutation aggregation and correlation
Authors: Kroll Karl W. , Eisfeld Ann-Katherin , Lozanski Gerard , Bloomfield Clara D. , Byrd John C. , Blachly James S. 
Published: February 2016

Abstract
Motivation: There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many types of reports. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls.
Availability and implementation: Source code is freely available at https://github.com/blachlylab/mucor and a Docker image is available at https://hub.docker.com/r/blachlylab/mucor/
Contact: james.blachly@osumc.edu
Supplementary data: Supplementary data are available at Bioinformatics online.
PAA: an R/bioconductor package for biomarker discovery with protein microarrays
Authors: Turewicz Michael , Ahrens Maike , May Caroline , Marcus Katrin , Eisenacher Martin 
Published: February 2016

Abstract
Summary: The R/Bioconductor package Protein Array Analyzer (PAA) facilitates a flexible analysis of protein microarrays for biomarker discovery (esp., ProtoArrays). It provides a complete data analysis workflow including preprocessing and quality control, uni- and multivariate feature selection as well as several different plots and results tables to outline and evaluate the analysis results. As a main feature, PAA’s multivariate feature selection methods are based on recursive feature elimination (e.g. SVM-recursive feature elimination, SVM-RFE) with stability ensuring strategies such as ensemble feature selection. This enables PAA to detect stable and reliable biomarker candidate panels.
Availability and implementation: PAA is freely available (BSD 3-clause license) from http://www.bioconductor.org/packages/PAA/.
Contact: michael.turewicz@rub.de or martin.eisenacher@rub.de
Optimization of alignment-based methods for taxonomic binning of metagenomics reads
Authors: Jaillard Magali , Tournoud Maud , Meynier Faustine , Veyrieras Jean-Baptiste 
Published: February 2016

Abstract
Motivation: Alignment-based taxonomic binning for metagenome characterization proceeds in two steps: reads mapping against a reference database (RDB) and taxonomic assignment according to the best hits. Beyond the sequencing technology and the completeness of the RDB, selecting the optimal configuration of the workflow, in particular the mapper parameters and the best hit selection threshold, to get the highest binning performance remains quite empirical.
Results: We developed a statistical framework to perform such optimization at a minimal computational cost. Using an optimization experimental design and simulated datasets for three sequencing technologies, we built accurate prediction models for five performance indicators and then derived the parameter configuration providing the optimal performance. Whatever the mapper and the dataset, we observed that the optimal configuration yielded better performance than the default configuration and that the best hit selection threshold had a large impact on performance. Finally, on a reference dataset from the Human Microbiome Project, we confirmed that the optimized configuration increased the performance compared with the default configuration.
Availability and implementation: Not applicable.
Contact: magali.dancette@biomerieux.com
Supplementary information: Supplementary data are available at Bioinformatics online.
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications
Authors: Cui Ya , Chen Xiaowei , Luo Huaxia , Fan Zhen , Luo Jianjun , He Shunmin , Yue Haiyan , Zhang Peng , Chen Runsheng 
Published: February 2016

Abstract
Summary: We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions.
Availability and implementation: BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/.
Contact: rschen@ibp.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
ASDB: a resource for probing protein functions with small molecules
Authors: Liu Zhihong , Ding Peng , Yan Xin , Zheng Minghao , Zhou Huihao , Xu Yuehua , Du Yunfei , Gu Qiong , Xu Jun 
Published: February 2016

Abstract
Summary: Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets.
Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/with the major web browsers.
Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
MOCCASIN: converting MATLAB ODE models to SBML
Authors: Gómez Harold F. , Hucka Michael , Keating Sarah M. , Nudelman German , Iber Dagmar , Sealfon Stuart C. 
Published: February 2016

Abstract
Summary: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging—especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format.
Availability and implementation: MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin.
Contact: mhucka@caltech.edu
Supplementary information: More information is available at https://github.com/sbmlteam/moccasin.
Managing research and surveillance projects in real-time with a novel open-source
e
Management tool designed for under-resourced countries
Authors: Steiner Andreas , Hella Jerry , Grüninger Servan , Mhalu Grace , Mhimbira Francis , Cercamondi Colin I , Doulla Basra , Maire Nicolas , Fenner Lukas 
Published: February 2016

Abstract
Objective A software tool is developed to facilitate data entry and to monitor research projects in under-resourced countries in real-time.
Methods The e Management tool “odk_planner” is written in the scripting languages PHP and Python. The odk_planner is lightweight and uses minimal internet resources. It was designed to be used with the open source software Open Data Kit (ODK). The users can easily configure odk_planner to meet their needs, and the online interface displays data collected from ODK forms in a graphically informative way. The odk_planner also allows users to upload pictures and laboratory results and sends text messages automatically. User-defined access rights protect data and privacy.
Results We present examples from four field applications in Tanzania successfully using the e Management tool: 1) clinical trial; 2) longitudinal Tuberculosis (TB) Cohort Study with a complex visit schedule, where it was used to graphically display missing case report forms, upload digitalized X-rays, and send text message reminders to patients; 3) intervention study to improve TB case detection, carried out at pharmacies: a tablet-based electronic referral system monitored referred patients, and sent automated messages to remind pharmacy clients to visit a TB Clinic; and 4) TB retreatment case monitoring designed to improve drug resistance surveillance: clinicians at four public TB clinics and lab technicians at the TB reference laboratory used a smartphone-based application that tracked sputum samples, and collected clinical and laboratory data.
Conclusions The user friendly, open source odk_planner is a simple, but multi-functional, Web-based e Management tool with add-ons that helps researchers conduct studies in under-resourced countries.
Triclosan Exposure is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish
Authors: Gaulke Christopher A. , Barton Carrie L. , Proffitt Sarah , Tanguay Robert L. , Sharpton Thomas J. 
Published: February 2016

AbstractGrowing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genusPseudomonasappeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome’s interaction with environmental chemicals.
Women managing women
Authors: Hurst Jane , Leberman Sarah , Edwards Margot 
Published: February 2016

Purpose– The purpose of this paper is to examine the intersections between the way women’s careers develop, the hierarchical relationships between women and the resulting implications for gender equity in the workplace.Design/methodology/approach– While a considerable body of research exists on gender in the workplace, the intersection between the way in which women ' s careers develop and the influence hierarchical relationships between women in the workplace have on that career development are under-researched. This paper examines existing relevant research, discusses the implications of these intersecting areas and raises areas for future academic research, as well as the development of organizational practice.Findings– The nature of the hierarchical relationships between women in the workplace is an important but under-researched factor when considering the career development of women. Delving into the experiences of women managers and employees, both good and bad, enables a deeper understanding of the role these relationships play in shaping the careers of women. From this, personal and organizational strategies can be developed that enhance workplace relationships and the career development of women.Originality/value– This paper encourages academics and practitioners to critically consider the connections between hierarchical workplace relationships and career development as part of organizational practice and further gender equity research.
Supervisor support and work engagement of hotel employees in Malaysia
Authors: Ling Suan Choo , Mohd Nasurdin Aizzat 
Published: February 2016

Purpose
– This study aims to examine the impact of supervisor support and to assess the moderating role of gender on employee work engagement in the context of the Malaysian hospitality industry.

Design/methodology/approach
– Data were collected from a sample of 438 customer-contact employees in Malaysian upscale hotels and tested using the partial least squares technique.

Findings
– The findings indicated that supervisor support positively influences work engagement and that this positive relationship was stronger for male employees than female employees.

Research limitations/implications
– The results highlight that supervisor support plays a critical role in fostering greater employee work engagement. In addition, different approaches need to be utilized by supervisors in supporting their male and female subordinates.

Originality/value
– This study extends the existing literature by examining the role of gender in moderating the relationship between supervisor support and work engagement, especially within the context of a developing country (i.e. Malaysia), using structural equation modelling.
Beyond sex
Authors: Cheung Ho Kwan , Lindsey Alex , King Eden , Hebl Michelle R 
Published: February 2016

Purpose– Influence tactics are prevalent in the workplace and are linked to crucial outcomes such as career success and helping behaviours. The authors argue that sex role identity affects women’s choice of influence tactics in the workplace, but they only receive positive performance ratings when their behaviours are congruent with gender role expectation. Furthermore, the authors hypothesize that these relationships may be moderated by occupational continuance commitment. Results suggest that femininity is negatively related to the use of influence tactics overall, and this relationship is moderated by occupational continuance commitment.Design/methodology/approach– In all, 657 women working in the construction industry were surveyed for their continuance occupational commitment and sex role identity and 465 supervisors whose responses are linked with the subordinates are surveyed for the women’s influence tactics and performance ratings.Findings– Results suggested that femininity was negatively related to the use of influence tactics overall, and this relationship was moderated by occupational continuance commitment. Results also showed that women’s use of influence tactics was only positively received in terms of performance ratings when the influence tactic was congruent with gender role expectations.Research limitations/implications– The results of this current study suggest that not all women are equally likely to use influence tactics and not all tactics result in positive perceptions of performance. Feminine women in general refrain from using influence tactics unless they are driven to stay in a given occupation, but they only receive positive results when their behaviours are congruent with society’s gender role expectations.Originality/value– Past research has mostly focused on broad differences between males and females, and this study has shown that there are more nuanced differences that can more accurately describe the effects of gender disposition (i.e. sex role identity) on influence tactics. It also emphasizes the importance of occupational commitment as a boundary condition, which influences women to step out of their gender roles even though they may be penalized with lower performance ratings.