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https://www.readbyqxmd.com/read/27911955/scholarly-context-adrift-three-out-of-four-uri-references-lead-to-changed-content
#1
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/27907981/use-of-social-media-in-education-among-medical-students-in-saudi-arabia
#2
Anas Khaleel Alsuraihi, Ahmed Saeed Almaqati, Sultan Adnan Abughanim, Nisreen Abdulrahman Jastaniah
PURPOSE: Social media (SM), a virtual place where people can share, exchange, and communicate their ideas and knowledge, has become the new trend in communication and learning. This study aims to explore Saudi Arabian medical students' usage of SM and to discover the most common resources used in medical education. Furthermore, it aims to illustrate students' belief about the influence of SM on their learning. METHODS: This cross-sectional study administered validated questionnaires to medical students from different universities in Saudi Arabia, via emails, Twitter, Facebook, and short message service...
December 2016: Korean Journal of Medical Education
https://www.readbyqxmd.com/read/27899658/the-big-data-center-from-deposition-to-integration-to-translation
#3
(no author information available yet)
Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27874839/online-access-and-motivation-of-tutors-of-health-professions-higher-education
#4
Federico Monaco, Leopoldo Sarli, Massimo Guasconi, Emanuela Alfieri
The case study of PUNTOZERO as an open web lab for activities, research and support to 5 Master's courses for the health professions is described. A virtual learning environment integrated in a much wider network including social networks and open resources was experimented on for five Master's Courses for the health professions at the University of Parma. A social learning approach might be applied by the engagement of motivated and skilled tutors. This is not only needed for the improvement and integration of the digital and collaborative dimension in higher education, but it aims to introduce issues and biases of emerging e-health and online networking dimensions for future healthcare professionals...
November 22, 2016: Acta Bio-medica: Atenei Parmensis
https://www.readbyqxmd.com/read/27864814/nodegame-real-time-synchronous-online-experiments-in-the-browser
#5
REVIEW
Stefano Balietti
nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform...
November 18, 2016: Behavior Research Methods
https://www.readbyqxmd.com/read/27781083/the-2016-bioinformatics-open-source-conference-bosc
#6
EDITORIAL
Nomi L Harris, Peter J A Cock, Brad Chapman, Christopher J Fields, Karsten Hokamp, Hilmar Lapp, Monica Muñoz-Torres, Heather Wiencko
Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016...
2016: F1000Research
https://www.readbyqxmd.com/read/27775517/sequential-discrete-hashing-for-scalable-cross-modality-similarity-retrieval
#7
Li Liu, Zijia Lin, Ling Shao, Fumin Shen, Guiguang Ding, Jungong Han
With the dramatic development of the Internet, how to exploit large-scale retrieval techniques for multimodal web data has become one of the most popular but challenging problems in computer vision and multimedia. Recently, hashing methods are used for fast nearest neighbor search in large-scale data spaces, by embedding high-dimensional feature descriptors into a similarity-preserving Hamming space with a low dimension. Inspired by this, in this paper, we introduce a novel supervised cross-modality hashing framework which can generate unified binary codes for instances represented in different modalities...
October 19, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27746773/brucella-abortus-strain-2308-wisconsin-genome-importance-of-the-definition-of-reference-strains
#8
Marcela Suárez-Esquivel, Nazareth Ruiz-Villalobos, Amanda Castillo-Zeledón, César Jiménez-Rojas, R Martin Roop Ii, Diego J Comerci, Elías Barquero-Calvo, Carlos Chacón-Díaz, Clayton C Caswell, Kate S Baker, Esteban Chaves-Olarte, Nicholas R Thomson, Edgardo Moreno, Jean J Letesson, Xavier De Bolle, Caterina Guzmán-Verri
Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27706202/pubmedportable-a-framework-for-supporting-the-development-of-text-mining-applications
#9
Kersten Döring, Björn A Grüning, Kiran K Telukunta, Philippe Thomas, Stefan Günther
Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools...
2016: PloS One
https://www.readbyqxmd.com/read/27704592/guidelines-for-use-of-the-approximate-beta-poisson-dose-response-model
#10
Gang Xie, Anne Roiko, Helen Stratton, Charles Lemckert, Peter K Dunn, Kerrie Mengersen
For dose-response analysis in quantitative microbial risk assessment (QMRA), the exact beta-Poisson model is a two-parameter mechanistic dose-response model with parameters α>0 and β>0, which involves the Kummer confluent hypergeometric function. Evaluation of a hypergeometric function is a computational challenge. Denoting PI(d) as the probability of infection at a given mean dose d, the widely used dose-response model PI(d)=1-(1+dβ)-α is an approximate formula for the exact beta-Poisson model. Notwithstanding the required conditions α<β and β>1, issues related to the validity and approximation accuracy of this approximate formula have remained largely ignored in practice, partly because these conditions are too general to provide clear guidance...
October 5, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/27694206/the-global-genome-biodiversity-network-ggbn-data-standard-specification
#11
G Droege, K Barker, O Seberg, J Coddington, E Benson, W G Berendsohn, B Bunk, C Butler, E M Cawsey, J Deck, M Döring, P Flemons, B Gemeinholzer, A Güntsch, T Hollowell, P Kelbert, I Kostadinov, R Kottmann, R T Lawlor, C Lyal, J Mackenzie-Dodds, C Meyer, D Mulcahy, S Y Nussbeck, É O'Tuama, T Orrell, G Petersen, T Robertson, C Söhngen, J Whitacre, J Wieczorek, P Yilmaz, H Zetzsche, Y Zhang, X Zhou
Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27663493/biospark-scalable-analysis-of-large-numerical-datasets-from-biological-simulations-and-experiments-using-hadoop-and-spark
#12
Max Klein, Rati Sharma, Chris H Bohrer, Cameron M Avelis, Elijah Roberts
: Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. AVAILABILITY AND IMPLEMENTATION: Source code is licensed under the Apache 2...
September 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27651835/xmetdb-an-open-access-database-for-xenobiotic-metabolism
#13
Ola Spjuth, Patrik Rydberg, Egon L Willighagen, Chris T Evelo, Nina Jeliazkova
Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly available information: which enzyme metabolizes a compound, but neither experimental conditions nor the atoms that undergo metabolization are captured. We present XMetDB, an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27649595/evaluating-the-impact-of-wikis-on-student-learning-outcomes-an-integrative-review
#14
Nina M Trocky, Kathleen M Buckley
Although wikis appear to have been reported as effective tools for educators, uncertainty exists as to their effectiveness in achieving student learning outcomes. The aim of this integrative review was to examine the current evidence on the impact of wikis on student learning in courses requiring collaborative or co-developed assignments or activities. The authors searched several electronic databases for relevant articles and used R. Whittemore and K. Knafl's (2005) integrative review method to analyze and synthesize the evidence...
September 2016: Journal of Professional Nursing: Official Journal of the American Association of Colleges of Nursing
https://www.readbyqxmd.com/read/27554092/training-and-evaluation-corpora-for-the-extraction-of-causal-relationships-encoded-in-biological-expression-language-bel
#15
Juliane Fluck, Sumit Madan, Sam Ansari, Alpha T Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel Peitsch
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training and testing biological relationship extraction systems that we prepared for the BioCreative V BEL track. BEL was designed to capture relationships not only between proteins or chemicals, but also complex events such as biological processes or disease states. A BEL nanopub is the smallest unit of information and represents a biological relationship with its provenance...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27553026/a-randomized-controlled-trial-comparing-in-person-and-wiki-inspired-nominal-group-techniques-for-engaging-stakeholders-in-chronic-kidney-disease-research-prioritization
#16
Meghan J Elliott, Sharon E Straus, Neesh Pannu, Sofia B Ahmed, Andreas Laupacis, George C Chong, David R Hillier, Kate T Huffman, Andrew C Lei, Berlene V Villanueva, Donna M Young, Helen Tam-Tham, Maoliosa Donald, Erin Lillie, Braden J Manns, Brenda R Hemmelgarn
BACKGROUND: Few studies have evaluated stakeholder engagement in chronic kidney disease (CKD) research prioritization. In this two-arm, parallel group randomized controlled trial, we sought to compare an in-person nominal group technique (NGT) approach with an online wiki-inspired alternative to determining the top 10 CKD research priorities, and to evaluate stakeholder engagement and satisfaction with each process. METHODS: Eligible participants included adults ≥18 years with access to a computer and Internet, high health literacy, and from one of the following stakeholder groups: patients with CKD not on dialysis, their caregivers, health care providers who care for patients with CKD, or CKD-related health policymakers...
2016: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/27522083/sdeap-a-splice-graph-based-differential-transcript-expression-analysis-tool-for-population-data
#17
Ei-Wen Yang, Tao Jiang
MOTIVATION: Differential transcript expression (DTE) analysis without predefined conditions is critical to biological studies. For example, it can be used to discover biomarkers to classify cancer samples into previously unknown subtypes such that better diagnosis and therapy methods can be developed for the subtypes. Although several DTE tools for population data, i.e. data without known biological conditions, have been published, these tools either assume binary conditions in the input population or require the number of conditions as a part of the input...
December 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27519173/isoexpresso-a-web-based-platform-for-isoform-level-expression-analysis-in-human-cancer
#18
In Seok Yang, Hyeonju Son, Sora Kim, Sangwoo Kim
BACKGROUND: Alternative splicing events that result in the production of multiple gene isoforms reveals important molecular mechanisms. Gene isoforms are often differentially expressed across organs and tissues, developmental stages, and disease conditions. Specifically, recent studies show that aberrant regulation of alternative splicing frequently occurs in cancer to affect tumor cell transformation and growth. While analysis of isoform expression is important for discovering tumor-specific isoform signatures and interpreting relevant genomic mutations, there is currently no web-based, easy-to-use, and publicly available platform for this purpose...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27505434/chromosome-territory-modeller-and-viewer
#19
Magdalena A Tkacz, Kornel Chromiński, Dominika Idziak-Helmcke, Ewa Robaszkiewicz, Robert Hasterok
This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters...
2016: PloS One
https://www.readbyqxmd.com/read/27499839/shedding-light-on-the-dark-side-of-phylogenetic-comparative-methods
#20
Natalie Cooper, Gavin H Thomas, Richard G FitzJohn
Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods.Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them...
June 2016: Methods in Ecology and Evolution
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