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https://www.readbyqxmd.com/read/27924018/disgenet-a-comprehensive-platform-integrating-information-on-human-disease-associated-genes-and-variants
#1
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924014/the-string-database-in-2017-quality-controlled-protein-protein-association-networks-made-broadly-accessible
#2
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J Jensen, Christian von Mering
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27920386/does-eutrophication-driven-evolution-change-aquatic-ecosystems
#3
REVIEW
Timothy J Alexander, Pascal Vonlanthen, Ole Seehausen
Eutrophication increases primary production and changes the relative abundance, taxonomic composition and spatial distribution of primary producers within an aquatic ecosystem. The changes in composition and location of resources alter the distribution and flow of energy and biomass throughout the food web. Changes in productivity also alter the physico-chemical environment, which has further effects on the biota. Such ecological changes influence the direction and strength of natural and sexual selection experienced by populations...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27916342/exploring-the-context-for-effective-clinical-governance-in-infection-control
#4
Kate Halton, Lisa Hall, Anne Gardner, Deborough MacBeth, Brett G Mitchell
BACKGROUND: Effective clinical governance is necessary to support improvements in infection control. Historically, the focus has been on ensuring that infection control practice and policy is based on evidence, and that there is use of surveillance and auditing for self-regulation and performance feedback. There has been less exploration of how contextual and organizational factors mediate an infection preventionists (IP's) ability to engage with evidence-based practice and enact good clinical governance...
December 2, 2016: American Journal of Infection Control
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#5
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911955/scholarly-context-adrift-three-out-of-four-uri-references-lead-to-changed-content
#6
Shawn M Jones, Herbert Van de Sompel, Harihar Shankar, Martin Klein, Richard Tobin, Claire Grover
Increasingly, scholarly articles contain URI references to "web at large" resources including project web sites, scholarly wikis, ontologies, online debates, presentations, blogs, and videos. Authors reference such resources to provide essential context for the research they report on. A reader who visits a web at large resource by following a URI reference in an article, some time after its publication, is led to believe that the resource's content is representative of what the author originally referenced...
2016: PloS One
https://www.readbyqxmd.com/read/27907895/mutlbsgenedb-mutated-ligand-binding-site-gene-database
#7
Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao
Mutations at the ligand binding sites (LBSs) can influence protein structure stability, binding affinity with small molecules, and drug resistance in cancer patients. Our recent analysis revealed that ligand binding residues had a significantly higher mutation rate than other parts of the protein. Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo.org/mutLBSgeneDB We collected and curated over 2300 genes (mutLBSgenes) having ∼12 000 somatic mutations at ∼10 000 LBSs across 16 cancer types and selected 744 drug targetable genes (targetable_mutLBSgenes) by incorporating kinases, transcription factors, pharmacological genes, and cancer driver genes...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27907271/adult-attention-deficit-hyperactivity-disorder-diagnosis-management-and-treatment-in-the-dsm-5-era
#8
Joel L Young, David W Goodman
Objective: To increase awareness of adult attention-deficit/hyperactivity disorder (ADHD) in the primary care community and to provide guidance for the management of this condition. Despite its increasing prevalence, adult ADHD largely remains underdiagnosed and inappropriately treated in the United States. The publication of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5), has provided more clear diagnostic criteria for adult ADHD, but a solid framework supporting the transition of ADHD management from pediatric to adult primary care is lacking...
November 17, 2016: Primary Care Companion to CNS Disorders
https://www.readbyqxmd.com/read/27903890/pharos-collating-protein-information-to-shed-light-on-the-druggable-genome
#9
Dac-Trung Nguyen, Stephen Mathias, Cristian Bologa, Soren Brunak, Nicolas Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John Overington, Juhee Patel, Andrew D Rouillard, Stephan Schürer, Timothy Sheils, Anton Simeonov, Larry A Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy Yang, Ajit Jadhav, Tudor I Oprea, Rajarshi Guha
The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903036/cannabis-use-and-its-associated-disorders-clinical-care
#10
Jan Copeland
BACKGROUND: Globally, cannabis is the most widely used and variably regulated illicit drug. The rates of use appeared to be stable in Australia at the time of the 2013 National Drug Strategy Household Survey, but levels of cannabis use disorder are rising and treatment seeking is increasing internationally. OBJECTIVE: This article describes the prevalence of cannabis use, associated disorders (eg harms with early and frequent use), and information on assessment and management...
December 2016: Australian Family Physician
https://www.readbyqxmd.com/read/27902504/a-password-protected-web-site-for-mothers-expressing-milk-for-their-preterm-infants
#11
MaryAnn Blatz, Donna Dowling, Patricia W Underwood, Amy Bieda, Gregory Graham
BACKGROUND: Research has demonstrated that breast milk significantly decreases morbidities that impact length of stay for preterm infants, but there is a need to test interventions to improve breastfeeding outcomes. Since many Americans are using technologies such as the Intranet and smartphones to find health information and manage health, a Web site was developed for mothers who provide breast milk for their preterm hospitalized infants. PURPOSE: This study examined the efficacy of a Web site for mothers to educate them about breast milk expression and assist them in monitoring their breast milk supply...
November 29, 2016: Advances in Neonatal Care: Official Journal of the National Association of Neonatal Nurses
https://www.readbyqxmd.com/read/27902453/environmental-and-occupational-exposure-to-cadmium-in-iran-a-systematic-review
#12
Leila Tavakkoli, Narges Khanjani
INTRODUCTION: Cadmium (Cd) is one of the heavy metals that have negative effects on human health. In Iran, there is no policy to regularly measure Cd in the general population. However, some studies have been performed on special groups and in different cities of Iran. This paper has reviewed these studies and human contamination levels in Iran. METHOD AND MATERIALS: All accessible electronic information resources such as Scientific Information Database (SID), Magiran, IranMedex, PubMed, Web of Knowledge, Google Scholar and Science Direct were searched, with relevant phrases and their Persian translations...
December 1, 2016: Reviews on Environmental Health
https://www.readbyqxmd.com/read/27900930/availability-of-pulmonary-rehabilitation-in-primary-care-for-patients-with-copd-a-cross-sectional-study-in-sweden
#13
Mats Arne, Margareta Emtner, Karin Lisspers, Karin Wadell, Björn Ställberg
BACKGROUND: Pulmonary rehabilitation (PR) is an important, evidence-based component for the management of individuals with chronic obstructive pulmonary disease (COPD). In daily practice, the majority of COPD patients are treated in primary care. However, information about the availability of PR in primary care in Sweden is lacking. The aim was to investigate the availability of rehabilitation resources in primary care settings for patients with COPD in Sweden. METHODS: A cross-sectional descriptive design was applied, using web-based questionnaires sent to all primary care centres in four regions, comprising more than half of the 9...
2016: European Clinical Respiratory Journal
https://www.readbyqxmd.com/read/27900461/microbial-food-web-drivers-in-tropical-reservoirs
#14
Carolina Davila Domingues, Lucia Helena Sampaio da Silva, Luciana Machado Rangel, Leonardo de Magalhães, Adriana de Melo Rocha, Lúcia Meirelles Lobão, Rafael Paiva, Fábio Roland, Hugo Sarmento
Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM)...
November 29, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27899692/jenkins-ci-an-open-source-continuous-integration-system-as-a-scientific-data-and-image-processing-platform
#15
Ioannis K Moutsatsos, Imtiaz Hossain, Claudia Agarinis, Fred Harbinski, Yann Abraham, Luc Dobler, Xian Zhang, Christopher J Wilson, Jeremy L Jenkins, Nicholas Holway, John Tallarico, Christian N Parker
High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS)...
November 29, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27899673/diseasemeth-version-2-0-a-major-expansion-and-update-of-the-human-disease-methylation-database
#16
Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu, Yan Zhang
The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease-gene associations from 216 201 to 679 602...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899668/cyanobase-%C3%A2-a-large-scale-update-on-its-20th-anniversary
#17
Takatomo Fujisawa, Rei Narikawa, Shin-Ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai, Yasukazu Nakamura
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899649/protein-ontology-pro-enhancing-and-scaling-up-the-representation-of-protein-entities
#18
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#19
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899630/european-nucleotide-archive-in-2016
#20
Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra Ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA...
November 29, 2016: Nucleic Acids Research
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