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https://www.readbyqxmd.com/read/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#1
Dominik Kopczynski, Harald Barsnes, Pål R Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends
Summary: The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334108/fast-admixture-analysis-and-population-tree-estimation-for-snp-and-ngs-data
#2
Yu Jade Cheng, Thomas Mailund, Rasmus Nielsen
Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components. We introduce a new optimization algorithm for the classical STRUCTURE model in a maximum likelihood framework. Using analyses of real data we show that the new method finds solutions with higher likelihoods than the state-of-the-art method inthe same computational time. The optimization algorithm is also applicable to models based on genotype likelihoods, that can account for the uncertainty in genotype-calling associated with Next Generation Sequencing (NGS) data...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333216/buddysuite-command-line-toolkits-for-manipulating-sequences-alignments-and-phylogenetic-trees
#3
Stephen R Bond, Karl E Keat, Sofia N Barreira, Andreas D Baxevanis
The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28288034/the-current-use-of-social-media-in-undergraduate-nursing-education-a-review-of-the-literature
#4
Jennifer Gunberg Ross, Shannon Marie Myers
Social media, including blogs, Twitter, wikis, Facebook, YouTube, and Ning, provides an opportunity for nurse educators to engage undergraduate nursing students who are members of the millennial generation in active learning while enhancing knowledge and fostering communication. Despite the rise of social media usage in undergraduate nursing education, there is a significant deficiency of empirical evidence supporting the efficacy and outcomes of these teaching strategies. This article provides an overview of social media use in undergraduate nursing education and a review of the existing research related to social media use in prelicensure nursing education...
March 11, 2017: Computers, Informatics, Nursing: CIN
https://www.readbyqxmd.com/read/28257959/the-immune-microenvironment-genome-wide-copy-number-aberrations-and-survival-in-mesothelioma
#5
Bibhusal Thapa, Adriana Salcedo, Xihui Lin, Marzena Walkiewicz, Carmel Murone, Malaka Ameratunga, Khashyar Asadi, Siddhartha Deb, Stephen Arthur Barnett, Simon Knight, Paul Mitchell, D Neil Watkins, Paul C Boutros, Thomas John
INTRODUCTION: Results of recent clinical studies of immune checkpoint inhibitors in malignant pleural mesothelioma (MPM) have dampened initial enthusiasm. However, the immune environment and targets of these treatments such as program cell death protein 1 (PD-1) and its ligand PD-L1 have not been well characterised in MPM. Using a large cohort of patients, we investigated PD-L1 expression, immune infiltrates and genome-wide copy number status and correlated them to clinicopathological features...
February 28, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28225466/the-use-of-social-media-in-graduate-medical-education-a-systematic-review
#6
Madeline Sterling, Peggy Leung, Drew Wright, Tara F Bishop
PURPOSE: Despite the growing presence of social media in graduate medical education (GME), few studies have attempted to characterize their effect on residents and their training. The authors conducted a systematic review of the peer-reviewed literature to understand the effect of social media on resident (1) education, (2) recruitment, and (3) professionalism. METHOD: The authors identified English-language peer-reviewed articles published through November 2015 using Medline, Embase, Cochrane, PubMed, Scopus, and ERIC...
February 21, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28186027/expanding-the-reach-of-continuing-educational-offerings-through-a-web-based-virtual-network-the-experience-of-inspirenet
#7
Noreen C Frisch, Pat Atherton, Elizabeth M Borycki, Grace Mickelson, Agnes Black, Helen Novak Lauscher, Jennifer Cordeiro
Virtual platforms using webinars, e-posters, e-newsletters, wikis and blogs connect people who have common interests in new ways. When those individuals are healthcare providers, a professional network that operates on a virtual platform can support their needs for learning, professional development and information currency. The practice of e-learning for continuing professional development is emerging , particularly in nursing where shift work shift inhibits their ability to attend conferences and classes...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28157142/using-wikis-to-build-nursing-concept-maps-promoting-group-interactive-learning
#8
Lilly Mathew
No abstract text is available yet for this article.
February 2017: Computers, Informatics, Nursing: CIN
https://www.readbyqxmd.com/read/28131145/preferred-methods-of-learning-for-nursing-students-in-an-on-line-degree-program
#9
Debra Hampton, Patricia F Pearce, Debra K Moser
Investigators have demonstrated that on-line courses result in effective learning outcomes, but limited information has been published related to preferred teaching strategies. Delivery of on-line courses requires various teaching methods to facilitate interaction between students, content, and technology. The purposes of this study were to understand student teaching/learning preferences in on-line courses to include (a) differences in preferred teaching/learning methods for on-line nursing students across generations and (b) which teaching strategies students found to be most engaging and effective...
January 2017: Journal of Professional Nursing: Official Journal of the American Association of Colleges of Nursing
https://www.readbyqxmd.com/read/28092529/sub-category-classifiers-for-multiple-instance-learning-and-its-application-to-retinal-nerve-fiber-layer-visibility-classification
#10
Siyamalan Manivannan, Caroline Cobb, Stephen Burgess, Emanuele Trucco
We propose a novel multiple instance learning method to assess the visibility (visible/not visible) of the retinal nerve fiber layer (RNFL) in fundus camera images. Using only image-level labels, our approach learns to classify the images as well as to localize the RNFL visible regions. We transform the original feature space to a discriminative subspace, and learn a region-level classifier in that subspace. We propose a margin-based loss function to jointly learn this subspace and the region-level classifier...
January 16, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#11
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28025202/calypso-a-user-friendly-web-server-for-mining-and-visualizing-microbiome-environment-interactions
#12
Martha Zakrzewski, Carla Proietti, Jonathan J Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause
Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page...
December 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27998935/cymer-cytometry-analysis-using-knime-docker-and-r
#13
B Muchmore, M E Alarcon-Riquelme
Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed...
December 20, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27993772/p3bsseq-parallel-processing-pipeline-software-for-automatic-analysis-of-bisulfite-sequencing-data
#14
Phuc-Loi Luu, Daniela Gerovska, Mikel Arrospide-Elgarresta, Sugoi Retegi-Carrión, Hans R Schöler, Marcos J Araúzo-Bravo
MOTIVATION: Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. RESULTS: We developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards...
October 6, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27922118/mining-visualizing-and-comparing-multidimensional-biomolecular-data-using-the-genomics-data-miner-gmine-web-server
#15
Carla Proietti, Martha Zakrzewski, Thomas S Watkins, Bernard Berger, Shihab Hasan, Champa N Ratnatunga, Marie-Jo Brion, Peter D Crompton, John J Miles, Denise L Doolan, Lutz Krause
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27911955/scholarly-context-adrift-three-out-of-four-uri-references-lead-to-changed-content
#16
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
#17
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
#18
(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...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27874839/online-access-and-motivation-of-tutors-of-health-professions-higher-education
#19
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
#20
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
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