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https://www.readbyqxmd.com/read/28109282/does-a-biomedical-research-centre-affect-patient-care-in-local-hospitals
#1
Catherine A Lichten, Grace Marsden, Alexandra Pollitt, Vasiliki Kiparoglou, Keith M Channon, Jon Sussex
BACKGROUND: Biomedical research can have impacts on patient care at research-active hospitals. We qualitatively evaluated the impact of the Oxford Biomedical Research Centre (Oxford BRC), a university-hospital partnership, on the effectiveness and efficiency of healthcare in local hospitals. Effectiveness and efficiency are conceptualised in terms of impacts perceived by clinicians on the quality, quantity and costs of patient care they deliver. METHODS: First, we reviewed documentation from Oxford BRC and literature on the impact of research activity on patient care...
January 21, 2017: Health Research Policy and Systems
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#2
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28107432/ongoing-speciation-and-gene-flow-between-taxonomically-challenging-trochulus-species-complex-gastropoda-hygromiidae
#3
Małgorzata Proćków, Tomasz Strzała, Elżbieta Kuźnik-Kowalska, Jarosław Proćków, Paweł Mackiewicz
Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy...
2017: PloS One
https://www.readbyqxmd.com/read/28107413/improving-the-conservation-of-mediterranean-chondrichthyans-the-elasmomed-dna-barcode-reference-library
#4
Alessia Cariani, Silvia Messinetti, Alice Ferrari, Marco Arculeo, Juan J Bonello, Leanne Bonnici, Rita Cannas, Pierluigi Carbonara, Alessandro Cau, Charis Charilaou, Najib El Ouamari, Fabio Fiorentino, Maria Cristina Follesa, Germana Garofalo, Daniel Golani, Ilaria Guarniero, Robert Hanner, Farid Hemida, Omar Kada, Sabrina Lo Brutto, Cecilia Mancusi, Gabriel Morey, Patrick J Schembri, Fabrizio Serena, Letizia Sion, Marco Stagioni, Angelo Tursi, Nedo Vrgoc, Dirk Steinke, Fausto Tinti
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles...
2017: PloS One
https://www.readbyqxmd.com/read/28105930/genetic-diversity-among-eight-dendrolimus-species-in-eurasia-lepidoptera-lasiocampidae-inferred-from-mitochondrial-coi-and-coii-and-nuclear-its2-markers
#5
Alexander Kononov, Kirill Ustyantsev, Baode Wang, Victor C Mastro, Victor Fet, Alexander Blinov, Yuri Baranchikov
BACKGROUND: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia. RESULTS: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#6
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28102863/a-taxonomy-of-medical-uncertainties-in-clinical-genome-sequencing
#7
Paul K J Han, Kendall L Umstead, Barbara A Bernhardt, Robert C Green, Steven Joffe, Barbara Koenig, Ian Krantz, Leo B Waterston, Leslie G Biesecker, Barbara B Biesecker
PURPOSE: Clinical next-generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of an unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. METHODS: Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts and themes were extracted in order to expand on a previously published three-dimensional taxonomy of medical uncertainty...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#8
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101893/the-genus-anthopsis-and-its-phylogenetic-position-in-chaetothyriales
#9
Tarek A A Moussa, Bert H G Gerrits van den Ende, Hassan S Al Zahrani, Naif M S Kadasa, Sybren G de Hoog, Somayeh Dolatabadi
The genus Anthopsis was introduced for a black fungus with peculiar, inverted phialides and triangular conidia. The genus accommodates, in addition to the type species Anthopsis deltoidea, which once was reported as a cause of human phaeohyphomycosis, two further taxa: A. catenata and A. microspora. Current taxonomy is mainly based on microscopic structures of phialides. To assess the phylogenetic position of the genus, sequences of the internal transcribed spacer region and partial LSU rDNA were obtained for Anthopsis spp...
January 18, 2017: Mycoses
https://www.readbyqxmd.com/read/28101791/strategies-to-reduce-30-day-readmissions-in-patients-with-cirrhosis
#10
REVIEW
Elliot B Tapper, Michael Volk
PURPOSE OF REVIEW: Approximately, one quarter of patients discharged after a hospitalization for decompensated cirrhosis will be readmitted within 30 days. These readmissions have been associated with increased morbidity and mortality, can be financially harmful to the health system, and may be partially preventable. This review summarizes the literature on readmissions, providing clinicians with tools for risk prediction and a taxonomy for preventative interventions. RECENT FINDINGS: Readmission strategies can be categorized according to complexity (simple versus complex) and specificity (focused versus broad)...
January 2017: Current Gastroenterology Reports
https://www.readbyqxmd.com/read/28101333/behaviour-change-interventions-to-influence-antimicrobial-prescribing-a-cross-sectional-analysis-of-reports-from-uk-state-of-the-art-scientific-conferences
#11
T M Rawson, L S P Moore, A M Tivey, A Tsao, M Gilchrist, E Charani, A H Holmes
BACKGROUND: To improve the quality of antimicrobial stewardship (AMS) interventions the application of behavioural sciences supported by multidisciplinary collaboration has been recommended. We analysed major UK scientific research conferences to investigate AMS behaviour change intervention reporting. METHODS: Leading UK 2015 scientific conference abstracts for 30 clinical specialties were identified and interrogated. All AMS and/or antimicrobial resistance(AMR) abstracts were identified using validated search criteria...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28100927/resolution-of-morphology-based-taxonomic-delusions-acrocordiella-basiseptospora-blogiascospora-clypeosphaeria-hymenopleella-lepteutypa-pseudapiospora-requienella-seiridium-and-strickeria
#12
W M Jaklitsch, A Gardiennet, H Voglmayr
Fresh material, type studies and molecular phylogeny were used to clarify phylogenetic relationships of the nine genera Acrocordiella, Blogiascospora, Clypeosphaeria, Hymenopleella, Lepteutypa, Pseudapiospora, Requienella, Seiridium and Strickeria. At first sight, some of these genera do not seem to have much in common, but all were found to belong to the Xylariales, based on their generic types. Thus, the most peculiar finding is the phylogenetic affinity of the genera Acrocordiella, Requienella and Strickeria, which had been classified in the Dothideomycetes or Eurotiomycetes, to the Xylariales...
December 2016: Persoonia
https://www.readbyqxmd.com/read/28100792/evolutionary-history-of-the-asian-horned-frogs-megophryinae-integrative-approaches-to-timetree-dating-in-the-absence-of-a-fossil-record
#13
Stephen Mahony, Nicole M Foley, S D Biju, Emma C Teeling
Molecular dating studies typically need fossils to calibrate the analyses. Unfortunately, the fossil record is extremely poor or presently non-existent for many species groups, rendering such dating analysis difficult. One such group is the Asian horned frogs (Megophryinae). Sampling all generic nomina, we combined a novel ∼5kb dataset composed of four nuclear and three mitochondrial gene fragments to produce a robust phylogeny, with an extensive external morphological study to produce a working taxonomy for the group...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100017/subspecies-delineation-amid-phenotypic-geographic-and-genetic-discordance-in-a-songbird
#14
Jennifer Walsh, Irby J Lovette, Virginia Winder, Chris S Elphick, Brian J Olsen, W Gregory Shriver, Adrienne I Kovach
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28098550/determination-of-elizabethkingia-diversity-by-maldi-tof-mass-spectrometry-and-whole-genome-sequencing
#15
Helle Brander Eriksen, Heidi Gumpert, Cecilie Haase Faurholt, Henrik Westh
In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in silico DNA-DNA hybridization of 35 Elizabethkingia strains indicated that the species taxonomy should be further explored.
February 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28098255/annual-time-series-analysis-of-aqueous-edna-reveals-ecologically-relevant-dynamics-of-lake-ecosystem-biodiversity
#16
Iliana Bista, Gary R Carvalho, Kerry Walsh, Mathew Seymour, Mehrdad Hajibabaei, Delphine Lallias, Martin Christmas, Simon Creer
The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae)...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097452/toward-the-optimal-strategy-for-sustained-weight-loss-in-overweight-cancer-survivors-a-systematic-review-of-the-literature
#17
REVIEW
Meeke Hoedjes, Maartje M van Stralen, Sheena Tjon A Joe, Matti Rookus, Flora van Leeuwen, Susan Michie, Jacob C Seidell, Ellen Kampman
PURPOSE: To gain more insight into the optimal strategy to achieve weight loss and weight loss maintenance in overweight and obese cancer survivors after completion of initial treatment, this systematic review aimed to provide an overview of the literature on intervention effects on weight, to describe intervention components used in effective interventions, to identify and synthesize behaviour change techniques (BCTs) and to assess the frequency with which these BCTs were used in effective interventions...
January 18, 2017: Journal of Cancer Survivorship: Research and Practice
https://www.readbyqxmd.com/read/28089840/biogeography-and-diversification-dynamics-of-the-african-woodpeckers
#18
Jérôme Fuchs, Jean-Marc Pons, Rauri C K Bowie
The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/ Mesopicos/ Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times...
January 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28087527/floc-formation-reduces-the-ph-stress-experienced-by-microorganisms-living-in-alkaline-environments
#19
C J Charles, S P Rout, K A Patel, S Akbar, A P Laws, B R Jackson, S A Boxall, P N Humphreys
: The survival of microorganisms within a cementitious geological disposal facility for radioactive wastes is heavily dependent on their ability to survive the calcium dominated, hyper-alkaline conditions resulting from the dissolution of the cementitious materials. The present study shows that the formation of flocs, composed of a complex mixture of extracellular polymeric substances (EPS), provides protection against alkaline pH values up to pH 13.0. The flocs were dominated by Alishewanella and Dietzia sp, producing a mannose rich carbohydrate fraction incorporating extracellular DNA, resulting in Ca(2+) sequestration...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28087059/fatigue-in-parkinson-s-disease
#20
REVIEW
Karen Herlofson, Benzi M Kluger
Fatigue is one of the most common nonmotor symptoms in Parkinson's disease and may affect a wide range of everyday activities, cause disability and reduce quality of life. It occurs at every stage of PD, and once present will often persist and may worsen over time. Lack of a consensus of definition and classification, and a range of different self-reporting scales has so far made the study of fatigue challenging. We review a unifying taxonomy for defining fatigue in clinical and research contexts as well as case definition criteria for PD-related fatigue...
December 29, 2016: Journal of the Neurological Sciences
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