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https://www.readbyqxmd.com/read/29474523/progressive-approach-for-snp-calling-and-haplotype-assembly-using-single-molecular-sequencing-data
#1
Fei Guo, Dan Wang, Lusheng Wang
Motivation: Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. The new technologies can provide Single Molecular Sequencing (SMS) data that cover about 90% of positions over chromosomes. However, the SMS data has a higher error rate comparing to 1% error rate for short reads. Thus, it becomes very difficult for SNP calling and haplotype assembly using SMS reads. Most existing technologies do not work properly for the SMS data...
February 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29469598/supporting-ethics-educators-in-canadian-occupational-therapy-and-physical-therapy-programs-a-national-interprofessional-knowledge-exchange-project
#2
Anne Hudon, Émilie Blackburn, Maude Laliberté, Kadija Perreault, Barbara Mazer, Debbie Ehrmann Feldman, Bryn Williams-Jones, Matthew Hunt
Ethics education is the cornerstone of professional practice, fostering knowledge and respect for core ethical values among healthcare professionals. Ethics is also a subject well-suited for interprofessional education and collaboration. However, there are few initiatives to gather experiences and share resources among ethics educators in rehabilitation. We thus undertook a knowledge exchange project to: 1) share knowledge about ethics training across Canadian occupational and physical therapy programs, and 2) build a community of educators dedicated to improving ethics education...
February 22, 2018: Journal of Interprofessional Care
https://www.readbyqxmd.com/read/29454060/aop-db-a-database-resource-for-the-exploration-of-adverse-outcome-pathways-through-integrated-association-networks
#3
Maureen E Pittman, Stephen W Edwards, Cataia Ives, Holly M Mortensen
The Adverse Outcome Pathway (AOP) framework describes the progression of a toxicity pathway from molecular perturbation to population-level outcome in a series of measurable, mechanistic responses. The controlled, computer-readable vocabulary that defines an AOP has the ability to, automatically and on a large scale, integrate AOP knowledge with publically available sources of biological high-throughput data and its derived associations. To support the discovery and development of putative (existing) and potential AOPs, we introduce the AOP-DB, an exploratory database resource that aggregates association relationships between genes and their related chemicals, diseases, pathways, species orthology information, ontologies, and gene interactions...
February 14, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29447297/development-of-a-decision-aid-for-cardiopulmonary-resuscitation-and-invasive-mechanical-ventilation-in-the-intensive-care-unit-employing-user-centered-design-and-a-wiki-platform-for-rapid-prototyping
#4
Ariane Plaisance, Holly O Witteman, Annie LeBlanc, Jennifer Kryworuchko, Daren Keith Heyland, Mark H Ebell, Louisa Blair, Diane Tapp, Audrey Dupuis, Carole-Anne Lavoie-Bérard, Carrie Anna McGinn, France Légaré, Patrick Michel Archambault
BACKGROUND: Upon admission to an intensive care unit (ICU), all patients should discuss their goals of care and express their wishes concerning life-sustaining interventions (e.g., cardiopulmonary resuscitation (CPR)). Without such discussions, interventions that prolong life at the cost of decreasing its quality may be used without appropriate guidance from patients. OBJECTIVES: To adapt an existing decision aid about CPR to create a wiki-based decision aid individually adapted to each patient's risk factors; and to document the use of a wiki platform for this purpose...
2018: PloS One
https://www.readbyqxmd.com/read/29394970/remission-rate-of-acute-lymphoblastic-leukemia-all-in-adolescents-and-young-adults-aya
#5
Anita Vallacha, Ghulam Haider, Wiky Raja, Dinesh Kumar
OBJECTIVE: To determine the remission rate in adolescent and young adult (AYA) patients with acute lymphoblastic leukemia (ALL). STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Department of Oncology, Jinnah Postgraduate Medical Centre (JPMC), Karachi from January, 2016 to March, 2017. METHODOLOGY: Adolescent and young adult (AYA) patients aged 15-39 years, newly diagnosed with acute lymphoblastic leukemia from January, 2016 to March, 2017...
February 2018: Journal of the College of Physicians and Surgeons—Pakistan: JCPSP
https://www.readbyqxmd.com/read/29280050/niftypet-a-high-throughput-software-platform-for-high-quantitative-accuracy-and-precision-pet-imaging-and-analysis
#6
Pawel J Markiewicz, Matthias J Ehrhardt, Kjell Erlandsson, Philip J Noonan, Anna Barnes, Jonathan M Schott, David Atkinson, Simon R Arridge, Brian F Hutton, Sebastien Ourselin
We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis...
December 26, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/29233408/structured-academic-discussions-through-an-online-education-specific-platform-to-improve-pharm-d-students-learning-outcomes
#7
Srikanth Kolluru, James T Varughese
OBJECTIVE: To facilitate active academic discussions using an online, education-centered platform and reinforce concepts, in order to improve overall course outcomes. MATERIALS AND METHODS: A third year integrated pharmacotherapy course was enrolled on an online searchable platform, Piazza®, to facilitate academic discussions. Students could ask, answer, and explore content, and build on submitted answers in wiki style in collaboration. Instructor posted learning objectives, endorsed student responses with correct answers and led follow-up discussions...
March 2017: Currents in Pharmacy Teaching & Learning
https://www.readbyqxmd.com/read/29196478/efficacy-of-hypnotherapy-compared-to-cognitive-behavioural-therapy-for-mild-to-moderate-depression-study-protocol-of-a-randomised-controlled-rater-blind-trial-wiki-d
#8
Kristina Fuhr, Cornelie Schweizer, Christoph Meisner, Anil Batra
INTRODUCTION: Despite a substantial number of studies providing evidence for the efficacy of psychological treatment for mild-to-moderate depression, maximally only 50% of participants respond to treatment, even when using gold-standard treatments such as cognitive-behavioural therapy (CBT) and interpersonal therapy. New approaches such as the 'third wave' psychotherapies have provided promising results; however, studies concerning the comparison with evidence-based treatments are lacking...
December 1, 2017: BMJ Open
https://www.readbyqxmd.com/read/29186298/simulate-simulating-complex-landscapes-of-transposable-elements-of-populations
#9
Robert Kofler
Motivation: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. Results: To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions...
November 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29178606/empowering-students-with-the-hidden-curriculum
#10
Hilary Neve, Tracey Collett
BACKGROUND: The hidden curriculum (HC) refers to unscripted, ad hoc learning that occurs outside the formal, taught curriculum and can have a powerful influence on the professional development of students. While this learning may be positive, it may conflict with that taught in the formal curriculum. Medical schools take a range of steps to address these negative effects; however, the existence and nature of the concept tends to be hidden from students. METHODS: Since 2007, our medical school has incorporated into its small group programme an educational activity exploring the concept of the hidden curriculum...
November 27, 2017: Clinical Teacher
https://www.readbyqxmd.com/read/29149304/tobacco-content-in-video-games-categorization-of-tobacco-typologies-and-gamer-recall
#11
Susan R Forsyth, Ruth E Malone
Introduction: Tobacco content has been identified in popular video games played by adolescents. To date, there are no established instruments for categorizing tobacco content. We describe development and demonstrate the use of an instrument to categorize types of tobacco content. Methods: Interviews were conducted with 61 participants: 20 adolescents (mean age 17.7), and 41 adults (mean age 23.9), who discussed favorite games and recalled tobacco content. All games mentioned were examined for tobacco content by watching movies of game play on YouTube, examining individual game Wiki sites, and reviewing content descriptors provided by the Entertainment Software Rating Board (ESRB), Common Sense Media and the Internet Movie Database (IMDb)...
November 15, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/29126402/using-social-media-to-support-small-group-learning
#12
Duncan Cole, Emma Rengasamy, Shafqat Batchelor, Charles Pope, Stephen Riley, Anne Marie Cunningham
BACKGROUND: Medical curricula are increasingly using small group learning and less didactic lecture-based teaching. This creates new challenges and opportunities in how students are best supported with information technology. We explored how university-supported and external social media could support collaborative small group working on our new undergraduate medical curriculum. METHODS: We made available a curation platform (Scoop.it) and a wiki within our virtual learning environment as part of year 1 Case-Based Learning, and did not discourage the use of other tools such as Facebook...
November 10, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/29118973/the-2017-bioinformatics-open-source-conference-bosc
#13
EDITORIAL
Nomi L Harris, Peter J A Cock, Brad Chapman, Christopher J Fields, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres, Bastian Greshake Tzovaras, Heather Wiencko
The Bioinformatics Open Source Conference (BOSC) is a 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. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data...
2017: F1000Research
https://www.readbyqxmd.com/read/29074455/evanescence-wave-based-technology-for-the-rapid-and-sensitive-quantification-of-biological-analytes
#14
Manfred Schawaller, Claudio Rhyner, Max Wiki, Gerald Quapil, Torsten Zuberbier, Cezmi A Akdis, Reto Crameri
No abstract text is available yet for this article.
October 23, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29042212/morfpred-plus-computational-identification-of-morfs-in-protein-sequences-using-physicochemical-properties-and-hmm-profiles
#15
Ronesh Sharma, Maitsetseg Bayarjargal, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma
MOTIVATION: Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. METHOD: In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences...
October 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29036693/icg-a-wiki-driven-knowledgebase-of-internal-control-genes-for-rt-qpcr-normalization
#16
Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang, Wanzhu Zuo, Yang Zhang, Wenming Zhao, Yiming Bao, Jingfa Xiao, Songnian Hu, Lili Hao, Zhang Zhang
Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#17
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29029599/liverwiki-a-wiki-based-database-for-human-liver
#18
Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu
BACKGROUND: Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort...
October 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29028899/phandango-an-interactive-viewer-for-bacterial-population-genomics
#19
James Hadfield, Nicholas J Croucher, Richard J Goater, Khalil Abudahab, David M Aanensen, Simon R Harris
Summary: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29025823/standing-collaboration-a-study-protocol-for-developing-clinical-standards
#20
Louise K Wiles, Peter D Hibbert, Jacqueline H Stephens, Enrico Coiera, Johanna Westbrook, Jeffrey Braithwaite, Ric O Day, Ken M Hillman, William B Runciman
INTRODUCTION: Despite widespread availability of clinical practice guidelines (CPGs), considerable gaps continue between the care that is recommended ('appropriate care') and the care provided. Problems with current CPGs are commonly cited as barriers to providing 'appropriate care'.Our study aims to develop and test an alternative method to keep CPGs accessible and up to date. This method aims to mitigate existing problems by using a single process to develop clinical standards (embodied in clinical indicators) collaboratively with researchers, healthcare professionals, patients and consumers...
October 11, 2017: BMJ Open
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