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https://www.readbyqxmd.com/read/28100788/genomic-infectious-disease-epidemiology-in-partially-sampled-and-ongoing-outbreaks
#1
Xavier Didelot, Christophe Fraser, Jennifer Gardy, Caroline Colijn
Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100590/inferring-individual-inbreeding-and-demographic-history-from-segments-of-identity-by-descent-in-ficedula-flycatcher-genome-sequences
#2
Marty Kardos, Anna Qvarnström, Hans Ellegren
Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287 Ficedula flycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28100171/genome-wide-standing-variation-facilitates-long-term-response-to-bidirectional-selection-for-antibody-response-in-chickens
#3
Mette Lillie, Zheya Sheng, Christa F Honaker, Ben J Dorshorst, Christopher M Ashwell, Paul B Siegel, Örjan Carlborg
BACKGROUND: Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. RESULTS: We observed wide genome involvement in response to this selection regime...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100168/effects-of-pleistocene-sea-level-fluctuations-on-mangrove-population-dynamics-a-lesson-from-sonneratia-alba
#4
Yuchen Yang, Jianfang Li, Shuhuan Yang, Xinnian Li, Lu Fang, Cairong Zhong, Norman C Duke, Renchao Zhou, Suhua Shi
BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation. RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods...
January 18, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28099330/clarifying-the-debate-on-population-based-screening-for-breast-cancer-with-mammography-a-systematic-review-of-randomized-controlled-trials-on-mammography-with-bayesian-meta-analysis-and-causal-model
#5
Tony Hsiu-Hsi Chen, Amy Ming-Fang Yen, Jean Ching-Yuan Fann, Paula Gordon, Sam Li-Sheng Chen, Sherry Yueh-Hsia Chiu, Chen-Yang Hsu, King-Jen Chang, Won-Chul Lee, Khay Guan Yeoh, Hiroshi Saito, Supannee Promthet, Chisato Hamashima, Alimin Maidin, Fredie Robinson, Li-Zhong Zhao
BACKGROUND: The recent controversy about using mammography to screen for breast cancer based on randomized controlled trials over 3 decades in Western countries has not only eclipsed the paradigm of evidence-based medicine, but also puts health decision-makers in countries where breast cancer screening is still being considered in a dilemma to adopt or abandon such a well-established screening modality. METHODS: We reanalyzed the empirical data from the Health Insurance Plan trial in 1963 to the UK age trial in 1991 and their follow-up data published until 2015...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28097663/the-evolution-of-male-nuptial-colour-in-a-sexually-dimorphic-group-of-fishes-percidae-etheostomatinae
#6
P J Ciccotto, T C Mendelson
To test hypotheses explaining variation in elaborate male colouration across closely related species groups, ancestral-state reconstructions and tests of phylogenetic signal and correlated evolution were used to examine the evolution of male body and fin colouration in a group of sexually dichromatic stream fishes known as darters (Percidae: Etheostomatinae). The presence or absence of red-orange and blue-green male colour traits were scored across six body regions in 99 darter species using a recently estimated amplified fragment length polymorphism (AFLP) phylogeny for comparative analyses...
January 18, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28097076/a-critical-issue-in-model-based-inference-for-studying-trait-based-community-assembly-and-a-solution
#7
Cajo J F Ter Braak, Pedro Peres-Neto, Stéphane Dray
Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two p-values (the pmax test)...
2017: PeerJ
https://www.readbyqxmd.com/read/28095480/inference-of-candidate-germline-mutator-loci-in-humans-from-genome-wide-haplotype-data
#8
Cathal Seoighe, Aylwyn Scally
The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles...
January 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28095427/mobile-phones-and-mental-well-being-initial-evidence-suggesting-the-importance-of-staying-connected-to-family-in-rural-remote-communities-in-uganda
#9
Amber L Pearson, Elizabeth Mack, Judith Namanya
Due to the ubiquity of mobile phones around the globe, studies are beginning to analyze their influence on health. Prior work from developed countries highlights negative mental health outcomes related to overuse of mobile phones. However, there is little work on mental health impacts of mobile phone use or ownership in developing countries. This is an important gap to address because there are likely variations in mental health impacts of mobile phones between developing and developed countries, due to cultural nuances to phone use and distinct variations in financial models for obtaining mobile phone access in developing countries...
2017: PloS One
https://www.readbyqxmd.com/read/28095423/influences-of-host-community-characteristics-on-borrelia-burgdorferi-infection-prevalence-in-blacklegged-ticks
#10
Holly B Vuong, Grace S Chiu, Peter E Smouse, Dina M Fonseca, Dustin Brisson, Peter J Morin, Richard S Ostfeld
Lyme disease is a major vector-borne bacterial disease in the USA. The disease is caused by Borrelia burgdorferi, and transmitted among hosts and humans, primarily by blacklegged ticks (Ixodes scapularis). The ~25 B. burgdorferi genotypes, based on genotypic variation of their outer surface protein C (ospC), can be phenotypically separated as strains that primarily cause human diseases-human invasive strains (HIS)-or those that rarely do. Additionally, the genotypes are non-randomly associated with host species...
2017: PloS One
https://www.readbyqxmd.com/read/28095193/semisupervised-multilabel-multi-instance-learning-for-structured-data
#11
Hossein Soleimani, David J Miller
Many classification tasks require both labeling objects and determining label associations for parts of each object. Example applications include labeling segments of images or determining relevant parts of a text document when the training labels are available only at the image or document level. This task is usually referred to as multi-instance (MI) learning, where the learner typically receives a collection of labeled (or sometimes unlabeled) bags, each containing several segments (instances). We propose a semisupervised MI learning method for multilabel classification...
January 17, 2017: Neural Computation
https://www.readbyqxmd.com/read/28093294/strehler-mildvan-correlation-is-a-degenerate-manifold-of-gompertz-fit
#12
Andrei E Tarkhov, Leonid I Menshikov, Peter O Fedichev
Gompertz empirical law of mortality is often used in practical research to parametrize survival fraction as a function of age with the help of just two quantities: the Initial Mortality Rate (IMR) and the Gompertz exponent, inversely proportional to the Mortality Rate Doubling Time (MRDT). The IMR is often found to be inversely related to the Gompertz exponent, which is the dependence commonly referred to as Strehler-Mildvan (SM) correlation. In this paper, we address fundamental uncertainties of the Gompertz parameters inference from experimental Kaplan-Meier plots and show, that a least squares fit often leads to an ill-defined non-linear optimization problem, which is extremely sensitive to sampling errors and the smallest systematic demographic variations...
January 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28090753/inferring-infection-hazard-in-wildlife-populations-by-linking-data-across-individual-and-population-scales
#13
Kim M Pepin, Shannon L Kay, Ben D Golas, Susan S Shriner, Amy T Gilbert, Ryan S Miller, Andrea L Graham, Steven Riley, Paul C Cross, Michael D Samuel, Mevin B Hooten, Jennifer A Hoeting, James O Lloyd-Smith, Colleen T Webb, Michael G Buhnerkempe
Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed...
January 16, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28081571/robust-inference-from-conditional-logistic-regression-applied-to-movement-and-habitat-selection-analysis
#14
Marie-Caroline Prima, Thierry Duchesne, Daniel Fortin
Conditional logistic regression (CLR) is widely used to analyze habitat selection and movement of animals when resource availability changes over space and time. Observations used for these analyses are typically autocorrelated, which biases model-based variance estimation of CLR parameters. This bias can be corrected using generalized estimating equations (GEE), an approach that requires partitioning the data into independent clusters. Here we establish the link between clustering rules in GEE and their effectiveness to remove statistical biases in variance estimation of CLR parameters...
2017: PloS One
https://www.readbyqxmd.com/read/28077880/interleukin-2-receptor-%C3%AE-proximal-promoter-hypomethylation-is-associated-with-multiple-sclerosis
#15
J Field, A Fox, M A Jordan, A G Baxter, T Spelman, M Gresle, H Butzkueven, T J Kilpatrick, J P Rubio
Genetic studies have demonstrated association between single-nucleotide polymorphisms within the IL2RA (interleukin-2 receptor α-subunit) gene and risk of developing multiple sclerosis (MS); however, these variants do not have obvious functional consequences. DNA methylation is a source of genetic variation that could impact on autoimmune disease risk. We investigated DNA methylation of the IL2RA promoter in genomic DNA obtained from peripheral blood mononuclear cells and neural tissue using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry...
January 12, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28077077/estimating-genomic-diversity-and-population-differentiation-an-empirical-comparison-of-microsatellite-and-snp-variation-in-arabidopsis-halleri
#16
Martin C Fischer, Christian Rellstab, Marianne Leuzinger, Marie Roumet, Felix Gugerli, Kentaro K Shimizu, Rolf Holderegger, Alex Widmer
BACKGROUND: Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28076391/assessing-sexual-dicromatism-the-importance-of-proper-parameterization-in-tetrachromatic-visual-models
#17
Pierre-Paul Bitton, Kevyn Janisse, Stéphanie M Doucet
Perceptual models of animal vision have greatly contributed to our understanding of animal-animal and plant-animal communication. The receptor-noise model of color contrasts has been central to this research as it quantifies the difference between two colors for any visual system of interest. However, if the properties of the visual system are unknown, assumptions regarding parameter values must be made, generally with unknown consequences. In this study, we conduct a sensitivity analysis of the receptor-noise model using avian visual system parameters to systematically investigate the influence of variation in light environment, photoreceptor sensitivities, photoreceptor densities, and light transmission properties of the ocular media and the oil droplets...
2017: PloS One
https://www.readbyqxmd.com/read/28070995/haplotype-of-platelet-receptor-p2ry12-gene-is-associated-with-residual-clopidogrel-on-treatment-platelet-reactivity
#18
Xiao-Yan Nie, Jun-Lei Li, Yong Zhang, Yang Xu, Xue-Li Yang, Yu Fu, Guang-Kai Liang, Yun Lu, Jian Liu, Lu-Wen Shi
OBJECTIVE: To investigate a possible association between common variations of the P2RY12 and the residual clopidogrel on-treatment platelet reactivity after adjusting for the influence of CYP2C19 tested by thromboelastography (TEG). METHODS: One hundred and eighty patients with acute coronary syndrome (ACS) treated with clopidogrel and aspirin were included and platelet function was assessed by TEG. Five selected P2RY12 single nucleotide polymorphisms (SNPs; rs6798347, rs6787801, rs6801273, rs6785930, and rs2046934), which cover the common variations in the P2RY12 gene and its regulatory regions, and three CYP2C19 SNPs ((*)2,(*)3,(*)17) were genotyped and possible haplotypes were analyzed...
2017: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/28062755/evolutionary-conservation-and-divergence-of-gene-coexpression-networks-in-gossypium-cotton-seeds
#19
Guanjing Hu, Ran Hovav, Corrinne E Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T Page, Joshua A Udall, Jonathan F Wendel
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28060715/probabilistic-low-rank-multitask-learning
#20
Yu Kong, Ming Shao, Kang Li, Yun Fu
In this paper, we consider the problem of learning multiple related tasks simultaneously with the goal of improving the generalization performance of individual tasks. The key challenge is to effectively exploit the shared information across multiple tasks as well as preserve the discriminative information for each individual task. To address this, we propose a novel probabilistic model for multitask learning (MTL) that can automatically balance between low-rank and sparsity constraints. The former assumes a low-rank structure of the underlying predictive hypothesis space to explicitly capture the relationship of different tasks and the latter learns the incoherent sparse patterns private to each task...
January 4, 2017: IEEE Transactions on Neural Networks and Learning Systems
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