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https://www.readbyqxmd.com/read/28482868/the-epidemiology-of-drowning-in-low-and-middle-income-countries-a-systematic-review
#1
Matthew D Tyler, David B Richards, Casper Reske-Nielsen, Omeed Saghafi, Erica A Morse, Robert Carey, Gabrielle A Jacquet
BACKGROUND: According to the World Health Organization, drowning is the 3rd leading cause of unintentional injury-related deaths worldwide, accounting for 370,000 annual deaths and 7% of all injury-related deaths. Low- and middle-income countries are the most affected, accounting for 91% of unintentional drowning deaths. METHODS: The authors performed a systematic review of literature indexed in EMBASE, PubMed, Web of Science, Cochrane Library, and Traumatology journals formerly indexed in PubMed in January 2014 and again in September 2016...
May 8, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28453688/edlib-a-c-c%C3%A2-library-for-fast-exact-sequence-alignment-using-edit-distance
#2
Martin Šošic, Mile Šikic
Summary: We present Edlib, an open-source C/C ++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be easily adopted as a building block for future bioinformatics tools. Availability and Implementation: Source code, installation instructions and test data are freely available for download at https://github...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453677/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#3
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453415/connecting-the-libraries-and-athletics-through-instruction-and-outreach
#4
Lara Sapp, K T L Vaughan
This column describes the approaches taken by librarians and staff at James Madison University (JMU) Libraries & Educational Technologies (LET) to extend library support to university athletics. The model resembles that used for outreach to academic programs and was first adapted to the semi-clinical, nonacademic Strength & Conditioning Department, then to JMU Athletics as a whole. Librarians offered targeted instructional sessions, orientations, and asynchronous learning modules embedded in the learning management system...
April 2017: Medical Reference Services Quarterly
https://www.readbyqxmd.com/read/28405750/efficacy-and-safety-of-scarpa-fascia-preservation-during-abdominoplasty-a-systematic-review-and-meta-analysis
#5
Xiangyang Xiao, Limin Ye
INTRODUCTION: Scarpa fascia preservation might be a promising approach to reduce seroma and other complications after abdominoplasty. However, the results remained controversial. We conducted a systematic review and meta-analysis to evaluate the efficacy and safety of scarpa fascia preservation in patients with abdominoplasty. METHODS: PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases were systematically searched. Randomized controlled trials and clinical controlled trials assessing the effect of scarpa fascia preservation versus control (without scarpa fascia) during abdominoplasty were included...
January 27, 2017: Aesthetic Plastic Surgery
https://www.readbyqxmd.com/read/28377684/data-day-to-day-building-a-community-of-expertise-to-address-data-skills-gaps-in-an-academic-medical-center
#6
Alisa Surkis, Fred Willie Zametkin LaPolla, Nicole Contaxis, Kevin B Read
BACKGROUND: The New York University Health Sciences Library data services team had developed educational material for research data management and data visualization and had been offering classes at the request of departments, research groups, and training programs, but many members of the medical center were unaware of these library data services. There were also indications of data skills gaps in these subject areas and other data-related topics. CASE PRESENTATION: The data services team enlisted instructors from across the medical center with data expertise to teach in a series of classes hosted by the library...
April 2017: Journal of the Medical Library Association: JMLA
https://www.readbyqxmd.com/read/28377683/interinstitutional-collaboration-for-end-user-bioinformatics-training-cytoscape-as-a-case-study
#7
Marci D Brandenburg, Rolando Garcia-Milian
BACKGROUND: This case study describes the value of and need for interinstitutional collaboration to train biomedical researchers in data visualization, using Cytoscape network analysis software as an example. To provide training on Cytoscape software to Yale University biomedical researchers, a collaboration was formed between the Yale Harvey Cushing/John Hay Whitney Medical Library's (CWML's) biomedical sciences research support librarian and the University of Michigan (U-M) Taubman Health Sciences Library's bioinformationist, who has expertise in Cytoscape software...
April 2017: Journal of the Medical Library Association: JMLA
https://www.readbyqxmd.com/read/28290711/visualising-a-rare-and-complex-case-of-advanced-hilar-cholangiocarcinoma
#8
Jia Qu, Albert Fung, Paul Kelly, Gordon Tait, Paul D Greig, Anne Agur, Ian D McGilvray, Jodie Jenkinson
The Toronto Video Atlas of Liver, Pancreas, Biliary, and Transplant Surgery (TVASurg) is a free online library of three-dimensional (3D) animation-enhanced surgical videos, designed to instruct surgical fellows in hepato-pancreato-biliary (HPB) and transplant procedures. The video 'Klatskin tumours: Extended left hepatectomy with complex portal vein reconstruction and in situ cold perfusion of the liver', which is available to watch at http://TVASurg.ca , is a unique and valuable visual resource for surgeons in training to assist them in learning this rare procedure...
January 2017: Journal of Visual Communication in Medicine
https://www.readbyqxmd.com/read/28182018/genome-wide-base-resolution-mapping-of-dna-methylation-in-single-cells-using-single-cell-bisulfite-sequencing-scbs-seq
#9
Stephen J Clark, Sébastien A Smallwood, Heather J Lee, Felix Krueger, Wolf Reik, Gavin Kelsey
DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28177134/the-influence-of-combination-use-of-cyp450-inducers-on-the-pharmacokinetics-of-voriconazole-a-systematic-review
#10
REVIEW
T-Y Li, W Liu, K Chen, S-Y Liang, F Liu
WHAT IS KNOWN AND OBJECTIVES: Voriconazole is a triazole antifungal agent and is extensively metabolized via cytochrome P450 (CYP450); therefore, special precautions need to be taken when co-administered with a known CYP450 inducer, which may lead to treatment failure. The influence of some CYP450 inducers on the pharmacokinetics of voriconazole has been described in previous studies, but a systematic review was lacking. In this study, we carried out a systematic review to assess the influence of CYP450 inducers on the pharmacokinetic (PK) parameters of voriconazole...
February 8, 2017: Journal of Clinical Pharmacy and Therapeutics
https://www.readbyqxmd.com/read/28128045/the-new-frontier-of-public-health-education
#11
David Birnbaum, Kathryn Gretsinger, Ursula Ellis
Purpose The aim of this paper is to describe the experience and educational benefits of a course that has several unique educational design features. Design/methodology/approach This includes narrative description of faculty and student experience from participants in a flipped-instructional-design inter-professional education course. Findings "Improving Public Health - An Interprofessional Approach to Designing and Implementing Effective Interventions" is an undergraduate public health course open to students regardless of background...
February 6, 2017: Leadership in Health Services
https://www.readbyqxmd.com/read/28125523/machine-learning-based-classification-of-38-years-of-spine-related-literature-into-100-research-topics
#12
David C Sing, Lionel N Metz, Stefan Dudli
STUDY DESIGN: Retrospective review. OBJECTIVE: To identify the top 100 spine research topics. SUMMARY OF BACKGROUND DATA: Recent advances in "machine learning," or computers learning without explicit instructions, have yielded broad technological advances. Topic modeling algorithms can be applied to large volumes of text to discover quantifiable themes and trends. METHODS: Abstracts were extracted from the National Library of Medicine PubMed database from five prominent peer-reviewed spine journals (European Spine Journal [ESJ], The Spine Journal [SpineJ], Spine, Journal of Spinal Disorders and Techniques [JSDT], Journal of Neurosurgery: Spine [JNS])...
June 1, 2017: Spine
https://www.readbyqxmd.com/read/28112636/designing-an-interactive-web-based-tutorial-for-health-sciences-students-a-collaborative-library-project
#13
Sharon Leslie
This column describes the creation of an online interactive tutorial for health sciences students in a general library at a large, urban university. The project was a collaborative effort among the health sciences subject librarian, the library's web programmer, an assessment and user services librarian, and an instructional support specialist. The column details the initial exploration, design, web programming, student usability study, and subsequent upgrades to the tutorial. Implementation of the tutorial is discussed as well as sampled student input...
January 2017: Medical Reference Services Quarterly
https://www.readbyqxmd.com/read/28057678/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#14
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27919935/secondary-prevention-lifestyle-interventions-initiated-within-90-days-after-tia-or-minor-stroke-a-systematic-review-and-meta-analysis-of-rehabilitation-programmes
#15
Neil Heron, Frank Kee, Christopher Cardwell, Mark A Tully, Michael Donnelly, Margaret E Cupples
BACKGROUND: Strokes are often preceded by a transient ischaemic attack (TIA) or 'minor' stroke. The immediate period after a TIA/minor stroke is a crucial time to initiate secondary prevention. However, the optimal approach to prevention, including non-pharmacological measures, after TIA is not clear. AIM: To systematically review evidence about the effectiveness of delivering secondary prevention, with lifestyle interventions, in comprehensive rehabilitation programmes, initiated within 90 days of a TIA/minor stroke...
January 2017: British Journal of General Practice: the Journal of the Royal College of General Practitioners
https://www.readbyqxmd.com/read/27803273/preparation-of-an-8-kb-mate-pair-library-for-illumina-sequencing
#16
Elaine Mardis, W Richard McCombie
The "mate-pair" approach for dual end sequencing uses long library fragments (1000-10,000 bp) that are circularized by ligation to the ends of a single, common DNA adaptor of known sequence. Once the ends are mated to the adaptor, a final library of fragments that retain the adaptor and only the ends of the original, circularized piece of DNA can be obtained. This protocol provides instructions for preparing an 8-kb paired-end library suitable for sequencing on the Illumina instrument. These are large-insert libraries, and the initial shearing will use various parameters and different instruments to achieve the desired high-size fraction...
November 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27797782/imagej-matlab-a-bidirectional-framework-for-scientific-image-analysis-interoperability
#17
Mark C Hiner, Curtis T Rueden, Kevin W Eliceiri
Summary: ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining a standard for translation between matrix and image data structures, researchers are empowered to select the best tool for their image-analysis tasks. Availability and Implementation: Freely available extension to ImageJ2 ( http://imagej.net/Downloads ). Installation and use instructions available at http://imagej.net/MATLAB_Scripting...
February 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27685099/separation-and-parallel-sequencing-of-the-genomes-and-transcriptomes-of-single-cells-using-g-t-seq
#18
Iain C Macaulay, Mabel J Teng, Wilfried Haerty, Parveen Kumar, Chris P Ponting, Thierry Voet
Parallel sequencing of a single cell's genome and transcriptome provides a powerful tool for dissecting genetic variation and its relationship with gene expression. Here we present a detailed protocol for G&T-seq, a method for separation and parallel sequencing of genomic DNA and full-length polyA(+) mRNA from single cells. We provide step-by-step instructions for the isolation and lysis of single cells; the physical separation of polyA(+) mRNA from genomic DNA using a modified oligo-dT bead capture and the respective whole-transcriptome and whole-genome amplifications; and library preparation and sequence analyses of these amplification products...
November 2016: Nature Protocols
https://www.readbyqxmd.com/read/27649594/the-keys-to-success-in-doctoral-studies-a-preimmersion-course
#19
Deborah Salani, Laura Dean Albuja, Khitam Azaiza
This article will review an innovative on-line preimmersion course for a hybrid doctor of nursing practice (DNP) program and a traditional face-to-face doctor of philosophy nursing program. The doctoral candidates include both postbaccalaureate and postmaster's students. The authors of the preimmersion course developed and initiated the course in order to address various issues that have surfaced in discussions between students and faculty. Examples of common themes identified include writing skills, statistics, life-work-school balance, and navigating instructional technology...
September 2016: Journal of Professional Nursing: Official Journal of the American Association of Colleges of Nursing
https://www.readbyqxmd.com/read/27594429/introducing-a-virtual-reality-experience-in-anatomic-pathology-education
#20
Emilio Madrigal, Shyam Prajapati, Juan C Hernandez-Prera
OBJECTIVES: A proper examination of surgical specimens is fundamental in anatomic pathology (AP) education. However, the resources available to residents may not always be suitable for efficient skill acquisition. We propose a method to enhance AP education by introducing high-definition videos featuring methods for appropriate specimen handling, viewable on two-dimensional (2D) and stereoscopic three-dimensional (3D) platforms. METHODS: A stereo camera system recorded the gross processing of commonly encountered specimens...
October 2016: American Journal of Clinical Pathology
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