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https://www.readbyqxmd.com/read/28102789/implications-for-research-and-practice-of-the-biographic-approach-for-storytelling
#1
Beverley Ewens, Joyce Hendricks, Deb Sundin
Background Intensive care unit survivors face many physical and psychological difficulties during their recovery following discharge from hospital. These difficulties can significantly affect their quality of life. Healthcare providers and survivors' families often do not understand what recovery means in this population, which may affect the support provided. Aim To consider the potential of the biographical method in helping to create stories that illustrate recovery in intensive care survivors and other populations...
January 23, 2017: Nurse Researcher
https://www.readbyqxmd.com/read/28096351/uncovering-hidden-variation-in-polyploid-wheat
#2
Ksenia V Krasileva, Hans A Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H Ramirez-Gonzalez, Xiaodong Wang, Philippa Borrill, Christine Fosker, Sarah Ayling, Andrew L Phillips, Cristobal Uauy, Jorge Dubcovsky
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#3
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28086786/widespread-introgression-in-deep-sea-hydrothermal-vent-mussels
#4
Corinna Breusing, Robert C Vrijenhoek, Thorsten B H Reusch
BACKGROUND: The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28079282/troubling-issues-at-the-frontier-of-animal-tracking-for-conservation-and-management
#5
Steven J Cooke, Vivian M Nguyen, Steven T Kessel, Nigel E Hussey, Nathan Young, Adam T Ford
Developments in electronic tagging and tracking, including biotelemetry and biologging, have provided unprecedented insight into the ecology of wild animals (Cooke et al. 2004) and revealed hidden movement patterns, habitat associations, animal-environment interactions, and mortality rates for even the most cryptic of species (Hussey et al. 2015; Kays et al. 2015). Natural history, ecology (including movement ecology), conservation, and resource management have all benefitted from the application of this technology...
January 12, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28078496/theoretical-and-empirical-comparisons-of-methods-to-estimate-the-size-of-hard-to-reach-populations-a-systematic-review
#6
REVIEW
Paul Wesson, Arthur Reingold, Willi McFarland
Worldwide, the HIV epidemic is concentrated among hidden populations (i.e., female sex workers, men who have sex with men, and people who inject drugs). To understand the true scope and scale of the HIV epidemic, estimates of the sizes of these populations are needed. Various methods are available to enumerate hidden populations, but the degree of agreement between these methods has not been formally evaluated. We systematically reviewed the peer-reviewed literature to assess the extent to which different population size estimation methods provide the same estimate of a target population...
January 11, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/28068925/effectiveness-of-a-serological-tool-to-predict-malaria-transmission-intensity-in-an-elimination-setting
#7
Rajika Lasanthi Dewasurendra, Janaka Nandana Dias, Nuno Sepulveda, Geethika Sharmini Abayaweera Gunawardena, Naduviladath Chandrasekharan, Chris Drakeley, Nadira Dharshani Karunaweera
BACKGROUND: Sri Lanka achieved the WHO certificate as a malaria free country in September 2016, thus monitoring of malaria transmission using sensitive and effective tools is an important need. Use of age-specific antibody prevalence as a serological tool to predict transmission intensity is proven to be a cost effective and reliable method under elimination settings. This paper discusses the correlation of four anti-malarial antibodies against vivax and falciparum malaria with the declining transmission intensities in two previously high malaria endemic districts i...
January 9, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28052496/species-interactions-and-the-effects-of-climate-variability-on-a-wetland-amphibian-metacommunity
#8
Courtney L Davis, David A W Miller, Susan C Walls, William J Barichivich, Jeffrey W Riley, Mary E Brown
Disentangling the role that multiple interacting factors have on species responses to shifting climate poses a significant challenge. However, our ability to do so is of utmost importance to predict the effects of climate change on species distributions. We examined how populations of three species of wetland-breeding amphibians, which varied in life history requirements, responded to a six-year period of extremely variable precipitation. This interval was punctuated by both extensive drought and heavy precipitation and flooding, providing a natural experiment to measure community responses to environmental perturbations...
January 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28046021/the-effect-of-parasite-infection-on-stable-isotope-turnover-rates-of-%C3%AE-15n-%C3%AE-13c-and-%C3%AE-34s-in-multiple-tissues-of-eurasian-perch-perca-fluviatilis
#9
Elizabeth Yohannes, Claudia Grimm, Karl-Otto Rothhaupt, Jasminca Behrmann-Godel
Stable isotope analysis of commercially and ecologically important fish can improve understanding of life-history and trophic ecology. However, accurate interpretation of stable isotope values requires knowledge of tissue-specific isotopic turnover that will help to describe differences in the isotopic composition of tissues and diet. We performed a diet-switch experiment using captive-reared parasite-free Eurasian perch (Perca fluviatilis) and wild caught specimens of the same species, infected with the pike tapeworm Triaenophorus nodulosus living in host liver tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28045893/a-hidden-markov-model-approach-for-simultaneously-estimating-local-ancestry-and-admixture-time-using-next-generation-sequence-data-in-samples-of-arbitrary-ploidy
#10
Russell Corbett-Detig, Rasmus Nielsen
Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28039028/genome-wide-association-studies-in-maize-praise-and-stargaze
#11
REVIEW
Yingjie Xiao, Haijun Liu, Liuji Wu, Marilyn Warburton, Jianbing Yan
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to technical advances in next-generation sequencing (NGS) applications. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review aims to summarize current GWAS efforts in maize functional genomics, and discuss future prospects in the omics era. The general goal of a GWAS analysis is to link genotypic variantions to corresponding differences in phenotype using the most appropriate statistical model in a given population...
December 27, 2016: Molecular Plant
https://www.readbyqxmd.com/read/28033717/active-community-based-case-finding-for-tuberculosis-with-limited-resources
#12
Bindu Karki, Guenter Kittel, Ignatius Bolokon, Trevor Duke
Papua New Guinea is one of the 14 highest-burden countries for tuberculosis (TB) infection, but few community-based studies exist. We evaluated a low-cost method of active community case finding in Kabwum and Wasu in Morobe Province, Papua New Guinea. Over 3 months we visited 26 villages and screened adults and children for symptoms and signs of TB. Sputum samples were examined using smear microscopy. A total of 1700 people had chronic symptoms, of which 267 were suspicious for TB on further examination. Sputum from 230 symptomatic adults yielded 97 samples that were positive for acid-fast bacilli...
December 1, 2016: Asia-Pacific Journal of Public Health
https://www.readbyqxmd.com/read/28028941/the-computer-program-structure-for-assigning-individuals-to-populations-easy-to-use-but-easier-to-misuse
#13
Jinliang Wang
The computer program Structure implements a Bayesian method, based on a population genetics model, to assign individuals to their source populations using genetic marker data. It is widely applied in the fields of ecology, evolutionary biology, human genetics and conservation biology for detecting hidden genetic structures, inferring the most likely number of populations (K), assigning individuals to source populations, and estimating admixture and migration rates. Recently, several simulation studies repeatedly concluded that the program yields erroneous inferences when samples from different populations are highly unbalanced in size...
December 27, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28026036/the-re-emerging-arboviral-threat-hidden-enemies-the-emergence-of-obscure-arboviral-diseases-and-the-potential-use-of-wolbachia-in-their-control
#14
Heverton Leandro Carneiro Dutra, Eric Pearce Caragata, Luciano Andrade Moreira
Mayaro, Oropouche, and O'Nyong-Nyong share many traits with more prominent arboviruses, like dengue and yellow fever, chikungunya, and Zika. These include severe clinical symptoms, multiple animal hosts, and widespread vector species living in close proximity to human habitats, all of which constitute significant risk factors for more frequent outbreaks in the future, greatly increasing the potential of these hidden enemies to follow Zika and become the next wave of global arboviral threats. Critically, the current dearth of knowledge on these arboviruses might impede the success of future control efforts, including the potential application of Wolbachia pipientis...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28025204/novel-probabilistic-models-of-spatial-genetic-ancestry-with-applications-to-stratification-correction-in-genome-wide-association-studies
#15
Anand Bhaskar, Adel Javanmard, Thomas A Courtade, David Tse
MOTIVATION: Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure...
December 25, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28017411/less-hidden-celiac-disease-but-increased-gluten-avoidance-without-a-diagnosis-in-the-united-states-findings-from-the-national-health-and-nutrition-examination-surveys-from-2009-to%C3%A2-2014
#16
Rok Seon Choung, Aynur Unalp-Arida, Constance E Ruhl, Tricia L Brantner, James E Everhart, Joseph A Murray
OBJECTIVE: To investigate the trends in the prevalence of diagnosed celiac disease (CD), undiagnosed CD, and people without celiac disease avoiding gluten (PWAG) in the civilian noninstitutionalized US population from 2009 to 2014. PATIENTS AND METHODS: We studied the occurrence of CD and PWAG in the 2009 to 2014 National Health and Nutrition Examination Surveys. The serum of all participants aged 6 years or older from the National Health and Nutrition Examination Surveys from 2009 to 2014 was tested for CD serology at Mayo Clinic...
December 5, 2016: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/28004838/genome-wide-analysis-of-long-term-evolutionary-domestication-in-drosophila-melanogaster
#17
Mark A Phillips, Anthony D Long, Zachary S Greenspan, Lee F Greer, Molly K Burke, Bryant Villeponteau, Kennedy C Matsagas, Cristina L Rizza, Laurence D Mueller, Michael R Rose
Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28002465/inference-of-functionally-relevant-n-acetyltransferase-residues-based-on-statistical-correlations
#18
Andrew F Neuwald, Stephen F Altschul
Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27984553/prevalence-and-predictors-of-human-immunodeficiency-virus-and-selected-sexually-transmitted-infections-among-people-who-inject-drugs-in-dar-es-salaam-tanzania-a-new-focus-to-get-to-zero
#19
Elia John Mmbaga, Kåre Moen, Neema Makyao, Melkizedeck Leshabari
BACKGROUND: Previous studies in Tanzania indicated that human immunodeficiency virus (HIV) prevalence among people who inject drugs (PWIDs) could be as high as 40%. We aim to provide data on the prevalence of HIV and sexually transmitted infection among PWIDs to inform national plans to get to zero. MATERIALS AND METHODS: Respondent-driven sampling was used to collect drug use, and sexual practices data among PWIDs aged 15 years and older. Blood samples were examined for HIV, herpes simplex virus type 2, syphilis, and hepatitis B...
December 14, 2016: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/27979909/distinct-cellular-states-determine-calcium-signaling%C3%A2-response
#20
Jason Yao, Anna Pilko, Roy Wollman
The heterogeneity in mammalian cells signaling response is largely a result of pre-existing cell-to-cell variability. It is unknown whether cell-to-cell variability rises from biochemical stochastic fluctuations or distinct cellular states. Here, we utilize calcium response to adenosine trisphosphate as a model for investigating the structure of heterogeneity within a population of cells and analyze whether distinct cellular response states coexist. We use a functional definition of cellular state that is based on a mechanistic dynamical systems model of calcium signaling...
December 15, 2016: Molecular Systems Biology
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