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https://www.readbyqxmd.com/read/28767674/versatile-ion-s5xl-sequencer-for-targeted-next-generation-sequencing-of-solid-tumors-in-a-clinical-laboratory
#1
Meenakshi Mehrotra, Dzifa Yawa Duose, Rajesh R Singh, Bedia A Barkoh, Jawad Manekia, Michael A Harmon, Keyur P Patel, Mark J Routbort, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
BACKGROUND: Next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory. METHODS: Eighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study...
2017: PloS One
https://www.readbyqxmd.com/read/28761942/necrotising-ulcerative-gingivitis-a-literature-review
#2
James Dufty, Nikolaos Gkranias, Nikos Donos
PURPOSE: The literature surrounding necrotising ulcerative gingivitis (NUG) is extensive, yet the rare nature of this disease means that there is a lack of good quality research available. This paper aims to scrutinise the literature and provide an up-to-date summary of the available information. MATERIALS AND METHODS: A literature search was performed electronically using the Cochrane Library, Ovid Medline, Embase, PubMed Clinical Queries and Google Scholar. Keyword searches were carried out, utilising MeSH terms and free text...
July 31, 2017: Oral Health & Preventive Dentistry
https://www.readbyqxmd.com/read/28757791/multimedia-field-test-thinking-about-exposures-there-s-an-app-for-that
#3
Matthew M Carper
Anxiety Coach is a smartphone application ("app") for iOS devices that is billed as a self-help program for anxiety in youth and adults. The app is currently available in the iTunes store for a one-time fee of $4.99. Anxiety Coach is organized around three related content areas: (a) self-monitoring of anxiety symptoms, (b) learning about anxiety and its treatment, and (c) guiding users through the development of a fear hierarchy and completion of exposure tasks. Although the app includes psychoeducation about anxiety as well as information regarding specific skills individuals can use to cope with anxiety (e...
February 2017: Cognitive and Behavioral Practice
https://www.readbyqxmd.com/read/28742975/tumor-imaging-instruction-and-assessment-at-chiropractic-colleges-in-north-america-a-pilot-study-with-implications-for-national-board-of-chiropractic-examiners-content
#4
Kathleen L Linaker, Sarah A Arpin, Charles P Fischer, Michael Sackett, Lesley Georger
OBJECTIVE: This pilot study tested a survey instrument pertaining to the instruction and assessment of tumor imaging in chiropractic training programs. The secondary purpose was to gather data regarding credentials of lead instructors, textbook and resource use, and tumors taught and assessed. METHODS: An electronic survey was distributed to lead tumor imaging instructors at all chiropractic colleges in the United States and Canada. A focus group of tumor imaging instructors was conducted to clarify ambiguous data...
July 25, 2017: Journal of Chiropractic Education
https://www.readbyqxmd.com/read/28714821/leaving-the-lecture-behind-putting-pubmed-instruction-into-the-hands-of-the-students
#5
Rose L Turner, Andrea M Ketchum, Melissa A Ratajeski, Charles B Wessel
This column describes the development of a one-shot PubMed instruction class for medical students at a health sciences library. Background information on the objective is presented and discussed in the context of educational practice literature. The new course design centers on a guided group method of instruction in order to integrate more active learning. Surveyed students reported that the method was an effective way to learn how to search PubMed and that they preferred it to a traditional lecture. Pros and cons of the method are offered for other health sciences libraries interested in presenting PubMed instruction in a similar manner...
July 2017: Medical Reference Services Quarterly
https://www.readbyqxmd.com/read/28672765/discovery-and-annotation-of-plant-endogenous-target-mimicry-sequences-from-public-transcriptome-libraries-a-case-study-of-prunus-persica
#6
Gökhan Karakülah
Novel transcript discovery through RNA sequencing has substantially improved our understanding of the transcriptome dynamics of biological systems. Endogenous target mimicry (eTM) transcripts, a novel class of regulatory molecules, bind to their target microRNAs (miRNAs) by base pairing and block their biological activity. The objective of this study was to provide a computational analysis framework for the prediction of putative eTM sequences in plants, and as an example, to discover previously un-annotated eTMs in Prunus persica (peach) transcriptome...
June 28, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28670209/surveying-hospital-nurses-to-discover-educational-needs-and-preferences
#7
J Michael Lindsay, Sandy Oelschlegel, Martha Earl
OBJECTIVE: The author investigated the educational needs of nurses in an American Nurses Credentialing Center Magnet hospital to determine topics of interest, instruction time and delivery preferences, and interest in a research information skills certificate provided by the library. METHODS: A 9-question survey was distributed to 1,500 nursing staff of the hospital through email. RESULTS: Surveys were completed by 865 respondents, which represented a response rate of 58%...
July 2017: Journal of the Medical Library Association: JMLA
https://www.readbyqxmd.com/read/28650949/efficacy-and-safety-of-tranexamic-acid-in-orthopedic-fracture-surgery-a-meta-analysis-and-systematic-literature-review
#8
Kamil Amer, Saqib Rehman, Christopher Haydel
BACKGROUND: Tranexamic acid (TXA) is an anti-fibrinolytic drug that has been shown to be effective in reducing blood loss and the need for transfusions after several orthopedic surgeries. However, the effectiveness of TXA use in orthopedic fracture surgeries still remains unclear. The purpose of this meta-analysis was to review existing literature with interest in the effectiveness and safety of TXA treatment in reducing total blood loss and transfusion rates for patients who underwent surgery for fracture repairs...
June 12, 2017: Journal of Orthopaedic Trauma
https://www.readbyqxmd.com/read/28631297/an-augmented-reality-tool-for-learning-spatial-anatomy-on-mobile-devices
#9
Nishant Jain, Patricia Youngblood, Matthew Hasel, Sakti Srivastava
Augmented Realty (AR) offers a novel method of blending virtual and real anatomy for intuitive spatial learning. Our first aim in the study was to create a prototype AR tool for mobile devices. Our second aim was to complete a technical evaluation of our prototype AR tool focused on measuring the system's ability to accurately render digital content in the real world. We imported Computed Tomography (CT) data derived virtual surface models into a 3D Unity engine environment and implemented an AR algorithm to display these on mobile devices...
June 20, 2017: Clinical Anatomy
https://www.readbyqxmd.com/read/28629816/tinospora-species-an-overview-of-their-modulating-effects-on-the-immune-system
#10
REVIEW
Md Areeful Haque, Ibrahim Jantan, Syed Nasir Abbas Bukhari
ETHNOPHARMACOLOGICAL RELEVANCE: Studies on the effects of natural immunomodulators to heal various diseases related to the immune system have been a growing interest in recent years. Amongst the medicinal plants, Tinospora species (family; Menispermaceae) have been one of the widely investigated plants for their modulating effects on the immune system due to their wide use in ethnomedicine to treat various ailments related to immune-related diseases. However, their ethnopharmacological uses are mainly with limited or without scientific basis...
June 16, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28482868/the-epidemiology-of-drowning-in-low-and-middle-income-countries-a-systematic-review
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
April 2017: Journal of Clinical Pharmacy and Therapeutics
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