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https://www.readbyqxmd.com/read/29134141/metabarcoding-analysis-of-the-stomach-contents-of-the-antarctic-toothfish-dissostichus-mawsoni-collected-in-the-antarctic-ocean
#1
Tae-Ho Yoon, Hye-Eun Kang, Soo Rin Lee, Jae-Bong Lee, Gun Wook Baeck, Hyun Park, Hyun-Woo Kim
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species...
2017: PeerJ
https://www.readbyqxmd.com/read/29112054/lower-extremity-stiffness-considerations-for-testing-performance-enhancement-and-injury-risk
#2
Jon Brazier, Sean Maloney, Chris Bishop, Paul J Read, Anthony N Turner
Brazier, J, Maloney, S, Bishop, C, Read, PJ, and Turner, AN. Lower extremity stiffness: considerations for testing, performance enhancement, and injury risk. J Strength Cond Res XX(X): 000-000, 2017-Force-deformation characteristics of the lower limb have been associated with athletic performance and may modulate the risk of injury. Despite these known associations, measurements of lower extremity stiffness are not commonly administered by strength and conditioning coaches. This review provides an overview of the available literature pertaining to the effects of lower extremity stiffness on physical performance and injury risk...
November 1, 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/29111872/views-of-clinical-trial-participants-on-the-readability-and-their-understanding-of-informed-consent-documents
#3
Rita Sommers, Cornelius Werendly Van Staden, Francois Steffens
BACKGROUND: One of the ethical imperatives for a valid consent process in clinical medication trials is that the process be guided by and recorded in an informed consent document (ICD). Concerns have been expressed, however, about readability and participant understanding of ICDs, which are often 10-20 pages long. Objective measures of readability and understanding have been used to support these concerns in several articles, but surprisingly the voice of trial participants on ICDs has not been heard in previous studies...
November 7, 2017: AJOB Empirical Bioethics
https://www.readbyqxmd.com/read/29105646/randomness-in-quantum-mechanics-philosophy-physics-and-technology
#4
Manabendra Nath Bera, Antonio Acín, Marek Kuś, Morgan W Mitchell, Maciej Lewenstein
This progress report covers recent developments in the area of quantum randomness, which is an extraordinarily interdisciplinary area that belongs not only to physics, but also to philosophy, mathematics, computer science, and technology. For this reason the article contains three parts that will be essentially devoted to different aspects of quantum randomness, and even directed, although not restricted, to various audiences: a philosophical part, a physical part, and a technological part. For these reasons the article is written on an elementary level, combining simple and non-technical descriptions with a concise review of more advanced results...
December 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/29104850/psd-microscopy-a-new-technique-for-adaptive-local-scanning-of-microscale-objects
#5
Mehdi Rahimi, Yantao Shen
A position-sensitive detector/device (PSD) is a sensor that is capable of tracking the location of a laser beam on its surface. PSDs are used in many scientific instruments and technical applications including but not limited to atomic force microscopy, human eye movement monitoring, mirrors or machine tool alignment, vibration analysis, beam position control and so on. This work intends to propose a new application using the PSD. That is a new microscopy system called scanning PSD microscopy. The working mechanism is about putting an object on the surface of the PSD and fast scanning its area with a laser beam...
2017: Robotics and Biomimetics
https://www.readbyqxmd.com/read/29083982/stop-the-spam-conference-ethics-and-decoding-the-subtext-in-post-truth-science-what-would-denis-diderot-say
#6
Vural Özdemir, Collet Dandara, Nezih Hekim, Kean Birch, Simon Springer, Tanja Kunej, Laszlo Endrenyi
Science and its practice always had a subtext, subject to influence by scientists', funders', and other innovation actors' values and assumptions. The recent emergence of post-truth, authoritarian and populist penchants, in both developed and developing countries, has further blurred the already fluid boundaries between material scientific facts and their social construction/shaping by scientific subtext, human values, powers, and hegemony. While there are certain checks, balances, and oversight mechanisms for publication ethics, other pillars of science communication, most notably, scientific conferences and their governance, are ill prepared for post-truth science...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29079861/impact-of-dna-extraction-sample-dilution-and-reagent-contamination-on-16s-rrna-gene-sequencing-of-human-feces
#7
Eliana P Velásquez-Mejía, Jacobo de la Cuesta-Zuluaga, Juan S Escobar
Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing...
October 27, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29078748/whole-genome-assembly-of-babesia-ovata-and-comparative-genomics-between-closely-related-pathogens
#8
Junya Yamagishi, Masahito Asada, Hassan Hakimi, Takeshi Q Tanaka, Chihiro Sugimoto, Shin-Ichiro Kawazu
BACKGROUND: Babesia ovata, belonging to the phylum Apicomplexa, is an infectious parasite of bovids. It is not associated with the manifestation of severe symptoms, in contrast to other types of bovine babesiosis caused by B. bovis and B. bigemina; however, upon co-infection with Theileria orientalis, it occasionally induces exacerbated symptoms. Asymptomatic chronic infection in bovines is usually observed only for B. ovata. Comparative genomic analysis could potentially reveal factors involved in these distinguishing characteristics; however, the genomic and molecular basis of these phenotypes remains elusive, especially in B...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29076946/mapping-the-informed-consent-process-for-left-ventricular-assist-devices
#9
Savitri E Fedson, Kelly K MacKenzie, Estevan D Delgado, Mackenzie N Abraham, Jerry D Estep, Jennifer S Blumenthal-Barby, Courtenay R Bruce
Ethical, practical, and medical challenges affect decisions about left ventricular assist device (LVAD) implantation. The informed consent document (IC-Doc) is integral to the decision-making process and structures informed consent conversations. The objective of this study was to analyze IC-Docs to identify the information patients and their families receive about LVAD implantation to create a model IC-Doc. We requested IC-Doc for LVAD implantation from LVAD programs in the United States. We analyzed them in three areas: medical and technical content, patient knowledge gaps, and syntax...
October 23, 2017: ASAIO Journal: a Peer-reviewed Journal of the American Society for Artificial Internal Organs
https://www.readbyqxmd.com/read/29062542/understanding-plain-english-summaries-a-comparison-of-two-approaches-to-improve-the-quality-of-plain-english-summaries-in-research-reports
#10
Emma Kirkpatrick, Wendy Gaisford, Elaine Williams, Elizabeth Brindley, Doreen Tembo, David Wright
PLAIN ENGLISH SUMMARY: There is a need for the authors of research reports to be able to communicate their work clearly and effectively to readers who are not familiar with the research area. The National Institute for Health Research (NIHR), along with a number of other funding bodies and journals, require researchers to write short lay summaries, often termed plain English summaries (PESs), to make research accessible to the general public. Because many researchers write using technical, specialised language, particularly in scientific reports, writing PESs can be challenging...
2017: Res Involv Engagem
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#11
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29043423/preliminary-report-from-the-world-health-organisation-chest-radiography-in-epidemiological-studies-project
#12
REVIEW
Nasreen Mahomed, Nicholas Fancourt, John de Campo, Margaret de Campo, Aliu Akano, Thomas Cherian, Olivia G Cohen, David Greenberg, Stephen Lacey, Neera Kohli, Henrique M Lederman, Shabir A Madhi, Veronica Manduku, Eric D McCollum, Kate Park, Jose Luis Ribo-Aristizabal, Naor Bar-Zeev, Katherine L O'Brien, Kim Mulholland
Childhood pneumonia is among the leading infectious causes of mortality in children younger than 5 years of age globally. Streptococcus pneumoniae (pneumococcus) is the leading infectious cause of childhood bacterial pneumonia. The diagnosis of childhood pneumonia remains a critical epidemiological task for monitoring vaccine and treatment program effectiveness. The chest radiograph remains the most readily available and common imaging modality to assess childhood pneumonia. In 1997, the World Health Organization Radiology Working Group was established to provide a consensus method for the standardized definition for the interpretation of pediatric frontal chest radiographs, for use in bacterial vaccine efficacy trials in children...
October 2017: Pediatric Radiology
https://www.readbyqxmd.com/read/29037517/comparative-studies-of-different-types-of-osteosynthesis-on-the-human-corpse-preparation-in-bilateral-antero-lateral-flail-chest
#13
Sina Grupp, Veronika Fürst, Thomas Buder, Alexander Fichte, Sebastian Krinner, Roman T Carbon, Friedrich F Hennig, Andreas Langenbach, Stefan Schulz-Drost
INTRODUCTION: Bilateral flail chest injuries are challenging in treatment and comparatively often require an operative stabilization of the anterior chest wall to re-establish normal physiological conditions of the chest wall in shape and statics. Various procedures have been described which are technically sophisticated for the surgeon. Consequently there is an increasing interest in potentials of operative care and their effectiveness on the anterolateral chest wall. MATERIALS AND METHODS: 12 Human cadavers were prepared and the natural Sternum Position (NP) was marked...
October 9, 2017: Injury
https://www.readbyqxmd.com/read/29036413/smooth-quantile-normalization
#14
Stephanie C Hicks, Kwame Okrah, Joseph N Paulson, John Quackenbush, Rafael A Irizarry, Héctor Corrada Bravo
Between-sample normalization is a critical step in genomic data analysis to remove systematic bias and unwanted technical variation in high-throughput data. Global normalization methods are based on the assumption that observed variability in global properties is due to technical reasons and are unrelated to the biology of interest. For example, some methods correct for differences in sequencing read counts by scaling features to have similar median values across samples, but these fail to reduce other forms of unwanted technical variation...
July 10, 2017: Biostatistics
https://www.readbyqxmd.com/read/29031156/hiv-misdiagnosis-a-root-cause-analysis-leading-to-improvements-in-hiv-diagnosis-and-patient-care
#15
Raynell Lang, Carmen Charlton, Brenda Beckthold, Kiana Kadivar, Stephanie Lavoie, Debbie Caswell, Paul N Levett, Greg B Horsman, John Kim, M John Gill
BACKGROUND: Standard diagnostic testing for HIV infection has traditionally relied on a high sensitivity HIV antibody screening test using an enzyme-linked immunosorbent assay (ELISA) followed by a high specificity antibody confirmatory test such as a Western Blot. Recently several of the screening assays have been enhanced with an ability to identify p24 antigen thereby narrowing the diagnostic window. OBJECTIVES: To explore the implications of enhanced HIV screening methods that may be leading to HIV misdiagnoses...
October 9, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/29028869/mg-rast-version-4-lessons-learned-from-a-decade-of-low-budget-ultra-high-throughput-metagenome-analysis
#16
Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama, Travis Harrison, Tobias Paczian, William L Trimble, Andreas Wilke
As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline...
September 26, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28992517/application-of-next-generation-sequencing-toward-sensitive-detection-of-enteric-viruses-isolated-from-celery-samples-as-an-example-of-produce
#17
Zhihui Yang, Mark Mammel, Efstathia Papafragkou, Kaoru Hida, Christopher A Elkins, Michael Kulka
Next generation sequencing (NGS) holds promise as a single application for both detection and sequence identification of foodborne viruses; however, technical challenges remain due to anticipated low quantities of virus in contaminated food. In this study, with a focus on data analysis using several bioinformatics tools, we applied NGS toward amplification-independent detection and identification of norovirus at low copy (<10(3) copies) or within multiple strains from produce. Celery samples were inoculated with human norovirus (stool suspension) either as a single norovirus strain, a mixture of strains (GII...
August 3, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28991994/technical-note-validation-of-an-automated-system-for-monitoring-and-restricting-water-intake-in-group-housed-beef-steers
#18
K Allwardt, C Ahlberg, A Broocks, K Bruno, A Taylor, S Place, C Richards, C Krehbiel, M Calvo-Lorenzo, U DeSilva, D VanOverbeke, R Mateescu, C Goad, M M Rolf
The Insentec Roughage Intake Control (RIC) system has been validated for the collection of water intake; however, this system has not been validated for water restriction. The objective of this validation was to evaluate the agreement between direct observations and automated intakes collected by the RIC system under both ad libitum and restricted water conditions. A total of 239 crossbred steers were used in a 3-d validation trial, which assessed intake values generated by the RIC electronic intake monitoring system for both ad libitum water intake ( = 122; BASE) and restricted water intake ( = 117; RES)...
September 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28990683/the-effect-of-unit-depth-and-probe-load-on-the-reliability-of-muscle-shear-wave-elastography-variables-affecting-reliability-of-swe
#19
Abdulrahman M Alfuraih, Philip O'Connor, Elizabeth Hensor, Ai Lyn Tan, Paul Emery, Richard J Wakefield
PURPOSE: There is currently no standardized method for muscle shear wave elastography (SWE). The objective of this study was to investigate the effect of unit of measurement, depth, and probe load on the reliability of muscle SWE. METHODS: The vastus lateralis, biceps femoris, biceps brachii, and abductor digiti minimi muscles were scanned on 20 healthy participants. The SWE readings were measured in shear wave velocity (m/s) and Young's modulus (kPa). Three acquisitions of varying depths were acquired from vastus lateralis...
October 9, 2017: Journal of Clinical Ultrasound: JCU
https://www.readbyqxmd.com/read/28986563/impact-of-sequencing-depth-and-read-length-on-single-cell-rna-sequencing-data-of-t-cells
#20
Simone Rizzetto, Auda A Eltahla, Peijie Lin, Rowena Bull, Andrew R Lloyd, Joshua W K Ho, Vanessa Venturi, Fabio Luciani
Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses...
October 6, 2017: Scientific Reports
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