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https://www.readbyqxmd.com/read/28637310/the-metagenomic-data-life-cycle-standards-and-best-practices
#1
Petra Ten Hoopen, Robert D Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, Guy Cochrane
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing.Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637208/unit-conversions-between-loinc-codes
#2
Ronald G Hauser, Douglas B Quine, Alex Ryder, Sheldon Campbell
Logical Observation Identifiers Names and Codes (LOINC) is the most widely used controlled vocabulary to identify laboratory tests. A given laboratory test can often be reported in more than 1 unit of measure (eg, grams or moles), and LOINC defines unique codes for each unit. Consequently, an identical laboratory test performed by 2 different clinical laboratories may have different LOINC codes. The absence of unit conversions between compatible LOINC codes impedes data aggregation and analysis of laboratory results...
June 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28637128/maximizing-gait-and-balance-behaviors-and-decision-making-processes-of-persons-with-multiple-sclerosis-and-physical-therapists
#3
Elissa Held Bradford, Marcia Finlayson, Andrea White Gorman, Joanne Wagner
PURPOSE: To describe the behavioral decisions used by persons with multiple sclerosis (MS) and physical therapists to maximize gait and balance following outpatient physical therapy. METHODS: A multi-method case series with seven matched pairs (persons with MS-physical therapists). Quota sampling maximized variability among persons with MS (disease steps score range 3-6). Three of the four physical therapists were MS or neurology certified. Persons with MS completed a phone survey, follow-up interview, and standardized questionnaires...
February 7, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28636540/implementation-and-utilization-of-the-molecular-tumor-board-to-guide-precision-medicine
#4
REVIEW
Shuko Harada, Rebecca Arend, Qian Dai, Jessica A Levesque, Thomas S Winokur, Rongjun Guo, Martin J Heslin, Lisle Nabell, L Burt Nabors, Nita A Limdi, Kevin A Roth, Edward E Partridge, Gene P Siegal, Eddy S Yang
BACKGROUND: With rapid advances in genomic medicine, the complexity of delivering precision medicine to oncology patients across a university health system demanded the creation of a Molecular Tumor Board (MTB) for patient selection and assessment of treatment options. The objective of this report is to analyze our progress to date and discuss the importance of the MTB in the implementation of personalized medicine. MATERIALS AND METHODS: Patients were reviewed in the MTB for appropriateness for comprehensive next generation sequencing (NGS) cancer gene set testing based on set criteria that were in place...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636488/workers-exposure-to-bioaerosols-from-three-different-types-of-composting-facilities
#5
Laetitia Bonifait, Geneviève Marchand, Marc Veillette, Hamza M'Bareche, Marie-Eve Dubuis, Carole Pépin, Yves Cloutier, Yves Bernard, Caroline Duchaine
Composting is a natural dynamic biological process used to valorise putrescible organic matter. The composting process can involve vigorous movements of waste material piles, which release high concentrations of bioaerosols into the surrounding environment. There is a lack of knowledge concerning the dispersal of airborne microorganisms emitted by composting plants (CP) as well as the potential occupational exposure of composting workers. The aim of this study was to investigate the workers exposure to bioaerosols during working activities in three different types of composting facilities (domestic, manure, carcass) using two different quantification methods (cultivation and qPCR) for bacteria and moulds concentrations...
June 21, 2017: Journal of Occupational and Environmental Hygiene
https://www.readbyqxmd.com/read/28635539/an-old-challenge-with-new-promises-a-systematic-review-on-comprehensive-geriatric-assessment-in-long-term-care-facilities
#6
Francesco Panza, Vincenzo Solfrizzi, Madia Lozupone, Maria Rosaria Barulli, Francesca D'Urso, Roberta Stallone, Vittorio Dibello, Alessia Noia, Cristina Di Dio, Antonio Daniele, Antonello Bellomo, Davide Seripa, Antonio Greco, Giancarlo Logroscino
Comprehensive geriatric assessment (CGA) is a multidimensional and multidisciplinary diagnostic process focused on determining the clinical profile, pathological risk, residual skills, short- and long-term prognosis, and the personalized therapeutic and care plan of the functionally compromised and frail older subjects. Previous evidence suggested that the effectiveness of CGA programs may be influenced by the settings where the CGA is performed [i.e., hospital, post-hospital discharge/ long-term care facilities (LTCF), or community/home] as well as the specific clinical conditions of older frail individuals...
June 21, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28635382/white-cell-and-platelet-content-affects-the-release-of-bioactive-factors-in-different-blood-derived-scaffolds
#7
S Cabaro, V D'Esposito, R Gasparro, F Borriello, F Granata, G Mosca, F Passaretti, J C Sammartino, F Riccitiello, F Beguinot, P Formisano, G Sammartino
Platelet-derived factors are biomaterials that might accelerate healing process in oral, maxillofacial, and several other applications. Release of specific factors by platelet concentrates is critical to achieving a successful outcome. Here, we have shown that platelet-rich fibrin (PRF) clots were beneficial sources of leukocytes, which may directly affect the release of chemokines and growth factors. When compared with the standard leukocyte-PRF (L-PRF), the experimental low-force modified procedure [defined as advanced-PRF (A-PRF)] entrapped the same content of viable leukocytes, released a similar amount of inflammatory cytokines, but secreted 3-, 1...
June 21, 2017: Platelets
https://www.readbyqxmd.com/read/28635128/development-of-a-classification-model-for-non-alcoholic-steatohepatitis-nash-using-confocal-raman-micro-spectroscopy
#8
Jie Yan, Yang Yu, Jeon Woong Kang, Zhi Yang Tam, Shuoyu Xu, Eliza Li Shan Fong, Surya Pratap Singh, Ziwei Song, Lisa Tucker-Kellogg, Peter T C So, Hanry Yu
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disorder in developed countries [1]. A subset of individuals with NAFLD progress to non-alcoholic steatohepatitis (NASH), an advanced form of NAFLD which predisposes individuals to cirrhosis, liver failure and hepatocellular carcinoma. The current gold standard for NASH diagnosis and staging is based on histological evaluation, which is largely semi-quantitative and subjective. To address the need for an automated and objective approach to NASH detection, we combined Raman micro-spectroscopy and machine learning techniques to develop a classification model based on a well-established NASH mouse model, using spectrum pre-processing, biochemical component analysis (BCA) and logistic regression...
June 21, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28634868/occurrence-removal-and-health-risk-assessment-of-phthalate-esters-in-the-process-streams-of-two-different-wastewater-treatment-plants-in-lagos-and-ogun-states-nigeria
#9
O O Olujimi, O A Aroyeun, T F Akinhanmi, T A Arowolo
Phthalate esters (PEs) are one of the environmentally active organic pollutants capable of causing endocrine disruption. The levels of PE congeners were determined in the influent and effluent from Covenant Oxidation Pond (COP) and Ikeja Wastewater Treatment Plant (IWWTP). Standard methods were adopted for determining the physical and chemical parameters of the water samples. The water samples for PE congener's determination were collected, acidified and stored at 4 °C prior to liquid-liquid extraction and analysis by gas chromatograph...
July 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28634487/dynamic-inertia-weight-binary-bat-algorithm-with-neighborhood-search
#10
Xingwang Huang, Xuewen Zeng, Rui Han
Binary bat algorithm (BBA) is a binary version of the bat algorithm (BA). It has been proven that BBA is competitive compared to other binary heuristic algorithms. Since the update processes of velocity in the algorithm are consistent with BA, in some cases, this algorithm also faces the premature convergence problem. This paper proposes an improved binary bat algorithm (IBBA) to solve this problem. To evaluate the performance of IBBA, standard benchmark functions and zero-one knapsack problems have been employed...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28634467/brain-network-activation-technology-does-not-assist-with-concussion-diagnosis-and-return-to-play-in-football-athletes
#11
Steven P Broglio, Richelle Williams, Andrew Lapointe, Ashley Rettmann, Brandon Moore, Sean K Meehan, James T Eckner
BACKGROUND: Concussion diagnosis and management remains a largely subjective process. This investigation sought to evaluate the utility of a novel neuroelectric measure for concussion diagnosis and return to play decision-making. HYPOTHESIS: Brain Network Activation (BNA) scores obtained within 72-h of injury will be lower than the athlete's preseason evaluation and that of a matched control athlete; and the BNA will demonstrate ongoing declines at the return to play and post-season time points, while standard measures will have returned to pre-injury and control athlete levels...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28634427/leveraging-food-and-drug-administration-adverse-event-reports-for-the-automated-monitoring-of-electronic-health-records-in-a-pediatric-hospital
#12
Huaxiu Tang, Imre Solti, Eric Kirkendall, Haijun Zhai, Todd Lingren, Jaroslaw Meller, Yizhao Ni
The objective of this study was to determine whether the Food and Drug Administration's Adverse Event Reporting System (FAERS) data set could serve as the basis of automated electronic health record (EHR) monitoring for the adverse drug reaction (ADR) subset of adverse drug events. We retrospectively collected EHR entries for 71 909 pediatric inpatient visits at Cincinnati Children's Hospital Medical Center. Natural language processing (NLP) techniques were used to identify positive diseases/disorders and signs/symptoms (DDSSs) from the patients' clinical narratives...
2017: Biomedical Informatics Insights
https://www.readbyqxmd.com/read/28634329/long-days-enhance-recognition-memory-and-increase-insulin-like-growth-factor-2-in-the-hippocampus
#13
Adriano Dellapolla, Ian Kloehn, Harshida Pancholi, Ben Callif, David Wertz, Kayla E Rohr, Matthew M Hurley, Kimberly M Baker, Samer Hattar, Marieke R Gilmartin, Jennifer A Evans
Light improves cognitive function in humans; however, the neurobiological mechanisms underlying positive effects of light remain unclear. One obstacle is that most rodent models have employed lighting conditions that cause cognitive deficits rather than improvements. Here we have developed a mouse model where light improves cognitive function, which provides insight into mechanisms underlying positive effects of light. To increase light exposure without eliminating daily rhythms, we exposed mice to either a standard photoperiod or a long day photoperiod...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28633862/ultrasound-assisted-methods-for-enhanced-extraction-of-phycobiliproteins-from-marine-macro-algae-gelidium-pusillum-rhodophyta
#14
Rochak Mittal, Hrishikesh A Tavanandi, Vaibhav A Mantri, K S M S Raghavarao
Extraction of phycobiliproteins (R-phycoerythrin, R-PE and R-phycocyanin, R-PC) from macro-algae is difficult due to the presence of large polysaccharides (agar, cellulose etc.) present in the cell wall which offer major hindrance for cell disruption. The present study is aimed at developing most suitable methodology for the primary extraction of R-PE and R-PC from marine macro-algae, Gelidium pusillum(Stackhouse) Le Jolis. Such extraction of phycobiliproteins by using ultrasonication and other conventional methods such as maceration, maceration in presence of liquid nitrogen, homogenization, and freezing and thawing (alone and in combinations) is reported for the first time...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633848/novel-synthesis-of-nanocomposite-for-the-extraction-of-sildenafil-citrate-viagra-from-water-and-urine-samples-process-screening-and-optimization
#15
Arash Asfaram, Mehrorang Ghaedi, Mihir Kumar Purkait
A sensitive analytical method is investigated to concentrate and determine trace level of Sildenafil Citrate (SLC) present in water and urine samples. The method is based on a sample treatment using dispersive solid-phase micro-extraction (DSPME) with laboratory-made Mn@ CuS/ZnS nanocomposite loaded on activated carbon (Mn@ CuS/ZnS-NCs-AC) as a sorbent for the target analyte. The efficiency was enhanced by ultrasound-assisted (UA) with dispersive nanocomposite solid-phase micro-extraction (UA-DNSPME). Four significant variables affecting SLC recovery like; pH, eluent volume, sonication time and adsorbent mass were selected by the Plackett-Burman design (PBD) experiments...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633097/results-of-the-first-international-hiv-1-coreceptor-proficiency-panel-test
#16
Eva Heger, Rolf Kaiser, Elena Knops, Maria Neumann-Fraune, Eugen Schuelter, Alejandro Pironti, Thomas Lengauer, Hauke Walter, Saleta Sierra
BACKGROUND: Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories. OBJECTIVES: We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne. STUDY DESIGN: 12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne...
June 10, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28632819/enzyme-development-for-human-islet-isolation-five-decades-of-progress-or-stagnation
#17
Daniel Brandhorst, Heide Brandhorst, Paul R V Johnson
In comparison to procedures used for the separation of individual cell types from other organs, the process of human pancreatic islet isolation aims to digest the pancreatic exocrine matrix completely without dispersing the individual cells within the endocrine cell cluster. This objective is unique within the field of tissue separation, and outlines the challenge of islet isolation to balance two opposing priorities. Although significant progress has been made in the characterization and production of enzyme blends for islet isolation, there are still numerous areas which require improvement...
2017: Review of Diabetic Studies: RDS
https://www.readbyqxmd.com/read/28632332/microscale-disruption-of-microorganisms-for-parallelized-process-development
#18
REVIEW
Cornelia Walther, Astrid Dürauer
Escherichia coli, Saccharomyces cerevisiae, and Pichia pastoris are the standard platforms for biopharmaceutical production with 40% of all between 2010 to 2014 approved protein drugs produced in those microbial hosts. Typically, products overexpressed E. coli and S. cerevisiae remain in the cytosol or are secreted into the periplasm. Consequently, efficient cell disruption is essential for high product recovery during microbial production. Process development platforms at microscale are essential to shorten time to market...
June 20, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28632303/audition-specific-temporal-processing-deficits-associated-with-language-function-in-children-with-autism-spectrum-disorder
#19
Jennifer H Foss-Feig, Kimberly B Schauder, Alexandra P Key, Mark T Wallace, Wendy L Stone
Sensory processing alterations are highly prevalent in autism spectrum disorder (ASD). Neurobiologically-based theories of ASD propose that abnormalities in the processing of temporal aspects of sensory input could underlie core symptoms of ASD. For example, rapid auditory temporal processing is critical for speech perception, and language difficulties are central to the social communication deficits defining the disorder. This study assessed visual and auditory temporal processing abilities and tested their relation to core ASD symptoms...
June 20, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28632282/consort-extension-for-chinese-herbal-medicine-formulas-2017-recommendations-explanation-and-elaboration
#20
Chung-Wah Cheng, Tai-Xiang Wu, Hong-Cai Shang, You-Ping Li, Douglas G Altman, David Moher, Zhao-Xiang Bian
Chinese herbal medicine (CHM) formulas are the major components of traditional Chinese medicine (TCM) interventions. The general reporting quality of randomized controlled trials (RCTs) of CHM formulas is disappointing, although CONSORT (Consolidated Standards of Reporting Trials) Statement extensions for herbal medicinal interventions and acupuncture interventions are available. A group of TCM clinical experts, methodologists, epidemiologists, and editors has developed this CONSORT Extension for CHM Formulas (CONSORT-CHM Formulas 2017) through a comprehensive process, including publication of the draft version, solicitation of comments, revision, and finalization...
June 27, 2017: Annals of Internal Medicine
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