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variational inference

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https://www.readbyqxmd.com/read/29149838/genetic-variation-in-populations-of-the-earthworm-lumbricus-rubellus-across-contaminated-mine-sites
#1
Craig Anderson, Luis Cunha, Pierfrancesco Sechi, Peter Kille, David Spurgeon
BACKGROUND: Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes...
November 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29146623/variations-in-rotation-of-the-aortic-root-and-membranous-septum-with-implications-for-transcatheter-valve-implantation
#2
Justin T Tretter, Shumpei Mori, Farhood Saremi, Sathish Chikkabyrappa, Kristen Thomas, Fang Bu, Rohit S Loomba, Tarek Alsaied, Diane E Spicer, Robert H Anderson
OBJECTIVE: It is intuitive to suggest that knowledge of the variation in the anatomy of the aortic root may influence the outcomes of transcatheter implantation of the aortic valve (TAVI). We have now assessed such variation. METHODS: We used 26 specimens of normal hearts and 78 CT data sets of adults with a mean age of 64±15 years to measure the dimensions of the membranous septum and to assess any influence played by rotation of the aortic root, inferring the relationship to the atrioventricular conduction axis...
November 16, 2017: Heart: Official Journal of the British Cardiac Society
https://www.readbyqxmd.com/read/29145767/addressing-geographic-confounding-through-spatial-propensity-scores-a-study-of-racial-disparities-in-diabetes
#3
Melanie L Davis, Brian Neelon, Paul J Nietert, Kelly J Hunt, Lane F Burgette, Andrew B Lawson, Leonard E Egede
Motivated by a study exploring differences in glycemic control between non-Hispanic black and non-Hispanic white veterans with type 2 diabetes, we aim to address a type of confounding that arises in spatially referenced observational studies. Specifically, we develop a spatial doubly robust propensity score estimator to reduce bias associated with geographic confounding, which occurs when measured or unmeasured confounding factors vary by geographic location, leading to imbalanced group comparisons. We augment the doubly robust estimator with spatial random effects, which are assigned conditionally autoregressive priors to improve inferences by borrowing information across neighboring geographic regions...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29140912/reliable-testing-battery-for-assessing-physical-qualities-of-elite-academy-rugby-league-players
#4
Nick Dobbin, Richard Hunwicks, Jamie Highton, Craig Twist
Dobbin, N, Hunwicks, R, Highton, J, and Twist, C. Reliable testing battery for assessing physical qualities of elite academy rugby league players. J Strength Cond Res XX(X): 000-000, 2017-This study assessed the interday reliability of a testing battery for the assessment of physical qualities of rugby league players. Fifty players (age 17.1 ± 1.1 years; stature 181.3 ± 6.3 cm; and body mass 89.0 ± 11.6 kg) from 3 Super League academies participated in this study. Tests of countermovement jump performance, 10- and 20-m sprint performance, change of direction, medicine ball throw, and a modified Yo-Yo Intermittent Recovery Test Level 1 (prone Yo-Yo IR1) were completed on 3 separate occasions...
November 14, 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/29138475/the-rises-and-falls-of-opsin-genes-in-59-ray-finned-fish-genomes-and-their-implications-for-environmental-adaptation
#5
Jinn-Jy Lin, Feng-Yu Wang, Wen-Hsiung Li, Tzi-Yuan Wang
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134258/novel-full-length-major-histocompatibility-complex-class-i-allele-discovery-and-haplotype-definition-in-pig-tailed-macaques
#6
Matthew R Semler, Roger W Wiseman, Julie A Karl, Michael E Graham, Samantha M Gieger, David H O'Connor
Pig-tailed macaques (Macaca nemestrina, Mane) are important models for human immunodeficiency virus (HIV) studies. Their infectability with minimally modified HIV makes them a uniquely valuable animal model to mimic human infection with HIV and progression to acquired immunodeficiency syndrome (AIDS). However, variation in the pig-tailed macaque major histocompatibility complex (MHC) and the impact of individual transcripts on the pathogenesis of HIV and other infectious diseases is understudied compared to that of rhesus and cynomolgus macaques...
November 13, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29134072/genetic-signature-of-last-glacial-maximum-regional-refugia-in-a-circum-antarctic-sea-spider
#7
Anna Soler-Membrives, Katrin Linse, Karen J Miller, Claudia P Arango
The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29134006/cecidonius-pampeanus-gen-et-sp-n-an-overlooked-and-rare-new-gall-inducing-micromoth-associated-with-schinus-in-southern-brazil-lepidoptera-cecidosidae
#8
Gilson R P Moreira, Rodrigo P Eltz, Ramoim B Pase, Gabriela T Silva, Sérgio A L Bordignon, Wolfram Mey, Gislene L Gonçalves
Galls induced by the larval stage of cecidosids (Lepidoptera: Cecidosidae) are complex, multi-trophic systems, still poorly studied. They may be associated with other insect feeding guilds, including inquilines, kleptoparasites, cecidophages, parasitoids, and predators. By causing death of the gall inducer early in life and altering the gall phenotype, inquilines may lead to misidentification of the true gall inducers. Here, we describe through light and scanning electron microscopy Cecidonius pampeanus, a new genus and species of cecidosid moth, from the Pampa biome, south Brazil...
2017: ZooKeys
https://www.readbyqxmd.com/read/29132923/on-the-joint-distribution-of-tree-height-and-tree-length-under-the-coalescent
#9
Ilana M Arbisser, Ethan M Jewett, Noah A Rosenberg
Many statistics that examine genetic variation depend on the underlying shapes of genealogical trees. Under the coalescent model, we investigate the joint distribution of two quantities that describe genealogical tree shape: tree height and tree length. We derive a recursive formula for their exact joint distribution under a demographic model of a constant-sized population. We obtain approximations for the mean and variance of the ratio of tree height to tree length, using them to show that this ratio converges in probability to 0 as the sample size increases...
November 10, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/29132318/bugmat-and-findneighbour-command-line-and-server-applications-for-investigating-bacterial-relatedness
#10
Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W Eyre, Anthony Underwood, Derrick Crook, David H Wyllie
BACKGROUND: Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. Solutions to the problem have application to public health (for example, in the detection of possible disease transmission), and as part of divide-and-conquer strategies selecting groups of similar isolates for computationally intensive methods of phylogenetic inference using (for example) maximal likelihood methods...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29129612/why-lipostatic-set-point-systems-are-unlikely-to-evolve
#11
John R Speakman
OBJECTIVES: Body fatness is widely assumed to be regulated by a lipostatic set-point system, which has evolved in response to trade-offs in the risks of mortality. Increasing fatness makes the risk of starvation lower but increases the risk of predation. Yet other models are available. The aim of this work is to evaluate using mathematical modeling whether set-point systems are more likely to evolve than the alternatives. METHODS: I modeled the trade-off in mortality risks using a simple mathematical model, which generates an optimum level of fatness that is presumed to be the driver for the evolution of a set-point...
October 21, 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29127263/coalescent-processes-with-skewed-offspring-distributions-and-non-equilibrium-demography
#12
Sebastian Matuszewski, Marcel E Hildebrandt, Guillaume Achaz, Jeffrey D Jensen
Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history...
November 10, 2017: Genetics
https://www.readbyqxmd.com/read/29125094/inferring-individual-cow-effects-dairy-system-effects-and-feeding-effects-on-latent-variables-underlying-milk-protein-composition-and-cheese-making-traits-in-dairy-cattle
#13
Christos Dadousis, Claudio Cipolat-Gotet, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
We examined the latent structure of 26 cheese related phenotypes in dairy cattle. Traits related to milk yield and quality (8 traits), milk protein fractions (8 traits), coagulation and curd firmness indicators (CF, 5 traits) and cheese-making phenotypes (cheese yields (%CY) and nutrient recoveries in the curd (REC), 5 traits) were analysed through multivariate factor analysis (MFA) using a varimax rotation. All phenotypes were measured in 1264 Brown Swiss cows. Ten mutual orthogonal, latent variables (factors; Fs) were obtained explaining 74% of the original variability...
November 10, 2017: Journal of Dairy Research
https://www.readbyqxmd.com/read/29124465/the-origin-of-wild-populations-of-toxicodendron-succedaneum-on-mainland-japan-revealed-by-genetic-variation-in-chloroplast-and-nuclear-dna
#14
Yuichiro Hiraoka, Ichiro Tamaki, Atsushi Watanabe
Toxicodendron succedaneum: (L.) Kuntze is a tree cultivated for the production of sumac wax, which is extracted from the mesocarp. There are several hypotheses regarding the origin of T. succedaneum on mainland Japan. In this study, the geographical distribution of genetic variation in 13 wild populations on Honshu, Shikoku, Kyushu, and Ryukyu Islands, Japan was investigated and compared with that of individuals from continental Asia. Seven chloroplast DNA haplotypes of T. succedaneum were observed in Japan and could be divided into three lineages based on relatedness between haplotypes...
November 9, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/29121389/analyzing-community-weighted-trait-means-across-environmental-gradients-should-phylogeny-stay-or-should-it-go
#15
Leandro D S Duarte, Vanderlei Julio Debastiani, Marcos Bergmann Carlucci, José Alexandre Felizola Diniz-Filho
Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community-weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect those analyses...
November 9, 2017: Ecology
https://www.readbyqxmd.com/read/29120516/carbon-cycle-confidence-and-uncertainty-exploring-variation-among-soil-biogeochemical-models
#16
William R Wieder, Melannie D Hartman, Benjamin Sulman, Ying-Ping Wang, Charles D Koven, Gordon B Bonan
Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs...
November 9, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29119932/relevance-of-cyp2c9-function-in-valproate-therapy
#17
Katalin Monostory, Andrea Nagy, Katalin Toth, Tamas Budi, Adam Kiss, Mate Deri, Gabor Csukly
Genetic polymorphisms of drug metabolizing enzymes can substantially modify the pharmacokinetics of a drug and eventually its efficacy or toxicity; however, inferring a patient's drug metabolizing capacity merely from his or her genotype can lead to false prediction. Non-genetic host factors (age, sex, disease states) and environmental factors (nutrition, co-medication) can transiently alter the enzyme expression and activities resulting in genotype-phenotype mismatch. Although valproic acid is a well-tolerated anticonvulsant, pediatric patients are particularly vulnerable to valproate injury that can be partly attributed to the age-related differences in metabolic pathways...
November 9, 2017: Current Neuropharmacology
https://www.readbyqxmd.com/read/29118739/resolving-species-level-changes-in-a-representative-soil-bacterial-community-using-microfluidic-quantitative-pcr
#18
Hannah Kleyer, Robin Tecon, Dani Or
Rapid advances in genome sequencing technologies enable determination of relative bacterial abundances and community composition, yet, changes at the species level remain difficult to detect despite importance for certain ecological inferences. We present a method for extraction and direct quantification of species composition of a predefined multispecies bacterial community using microfluidic-based quantitative real-time PCR (qPCR). We employ a nested PCR approach based on universal 16S rRNA gene pre-amplification followed by detection and quantification of absolute abundance of bacterial species using microfluidic array of parallel singleplex qPCR reactions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29117751/phenotypic-and-mtdna-variation-in-philippine-kappaphycus-cottonii-gigartinales-rhodophyta
#19
Richard V Dumilag, William George M Gallardo, Christian Philip C Garcia, YeaEun You, Alyssa Keren G Chaves, Lance Agahan
Members of the carrageenan-producing seaweeds of the genus Kappapphycus have a complicated taxonomic history particularly with regard to species identification. Many taxonomic challenges in this group have been currently addressed with the use of mtDNA sequences. The phylogenetic status and genetic diversity of one of the lesser known species, Kappaphycus cottonii, have repeatedly come into question. This study explored the genetic variation in Philippine K. cottonii using the mtDNA COI-5P gene and cox2-3 spacer sequences...
November 9, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29117116/seasonal-variation-in-essential-oil-compositions-and-antioxidant-properties-of-acorus-calamus-l-accessions
#20
Archana Parki, Pinky Chaubey, Om Prakash, Ravendra Kumar, Anil K Pant
Background:Acorus calamus (Sweet flag) is a known herbal drug commonly used in traditional medicine. Our aim was to perform seasonal and altitudinal phytochemical screening to assess the antioxidant activity of the essential oils in the rhizome and leaves of A. calamus from three different altitudes. Methods: Phytochemical screening was performed using GC/MS analysis and in vitro antioxidant assay was done by different methods. Results: The essential oils mainly contained α-asarone, β-asarone (35.3-90.6%), and Z-isoelemicin (1...
November 8, 2017: Medicines (Basel, Switzerland)
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