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https://www.readbyqxmd.com/read/28107052/trait-evolution-in-adaptive-radiations-modeling-and-measuring-interspecific-competition-on-phylogenies
#1
Magnus Clarke, Gavin H Thomas, Robert P Freckleton
The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106916/a-bayesian-analysis-of-quantal-bioassay-experiments-incorporating-historical-controls-via-bayes-factors
#2
Luis G León Novelo, Andrew Womack, Hongxiao Zhu, Xiaowei Wu
This paper addresses model-based Bayesian inference in the analysis of data arising from bioassay experiments. In such experiments, increasing doses of a chemical substance are given to treatment groups (usually rats or mice) for a fixed period of time (usually 2 years). The goal of such an experiment is to determine whether an increased dosage of the chemical is associated with increased probability of an adverse effect (usually presence of adenoma or carcinoma). The data consists of dosage, survival time, and the occurrence of the adverse event for each unit in the study...
January 20, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28106417/chaos-and-regularity-in-the-doubly-magic-nucleus-208-pb
#3
B Dietz, A Heusler, K H Maier, A Richter, B A Brown
High-resolution experiments have recently lead to a complete identification (energy, spin, and parity) of 151 nuclear levels up to an excitation energy of E_{x}=6.20  MeV in ^{208}Pb [Heusler et al., Phys. Rev. C 93, 054321 (2016)PRVCAN2469-998510.1103/PhysRevC.93.054321]. We present a thorough study of the fluctuation properties in the energy spectra of the unprecedented set of nuclear bound states. In a first approach, we group states with the same spin and parity into 14 subspectra, analyze standard statistical measures for short- and long-range correlations, i...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28105911/integrating-gene-set-analysis-and-nonlinear-predictive-modeling-of-disease-phenotypes-using-a-bayesian-multitask-formulation
#4
Mehmet Gönen
BACKGROUND: Identifying molecular signatures of disease phenotypes is studied using two mainstream approaches: (i) Predictive modeling methods such as linear classification and regression algorithms are used to find signatures predictive of phenotypes from genomic data, which may not be robust due to limited sample size or highly correlated nature of genomic data. (ii) Gene set analysis methods are used to find gene sets on which phenotypes are linearly dependent by bringing prior biological knowledge into the analysis, which may not capture more complex nonlinear dependencies...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#5
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103522/perceived-emotional-social-support-in-bereaved-spouses-mediates-the-relationship-between-anxiety-and-depression
#6
Nicholas C Jacobson, Kayla A Lord, Michelle G Newman
BACKGROUND: Prior research has shown that anxiety symptoms predict later depression symptoms following bereavement. Nevertheless, no research has investigated mechanisms of the temporal relationship between anxiety and later depressive symptoms or examined the impact of depressive symptoms on later anxiety symptoms following bereavement. METHODS: The current study examined perceived emotional social support as a possible mediator between anxiety and depressive symptoms in a bereaved sample of older adults (N =250)...
January 5, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28103192/audio-visual-speaker-diarization-based-on-spatiotemporal-bayesian-fusion
#7
Israel Gebru, Sileye Ba, Xiaofei Li, Radu Horaud
Speaker diarization consists of assigning speech signals to people engaged in a dialogue. An audio-visual spatiotemporal diarization model is proposed. The model is well suited for challenging scenarios that consist of several participants engaged in multi-party interaction while they move around and turn their heads towards the other participants rather than facing the cameras and the microphones. Multiple-person visual tracking is combined with multiple speech-source localization in order to tackle the speech-to-person association problem...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28101887/abiraterone-or-enzalutamide-in-advanced-castration-resistant-prostate-cancer-an-indirect-comparison
#8
Akhil Chopra, Mina Georgieva, Gilberto Lopes, Chong Ming Yeo, Benjamin Haaland
BACKGROUND: To perform a comparative effectiveness analyses between enzalutamide and abiraterone acetate in both the pre-docetaxel and post-docetaxel settings based on published phase III randomized trials. METHODS: The primary measure of efficacy was the posterior probability that enzalutamide outperforms abiraterone acetate (AA) with prednisone in terms of overall survival (OS) on average. Indirect meta-estimates were generated from four randomized studies in the context of a Bayesian hierarchical model with study-specific efficacy estimates meta-analyzed on the log scale...
January 19, 2017: Prostate
https://www.readbyqxmd.com/read/28099997/on-joint-estimation-of-gaussian-graphical-models-for-spatial-and-temporal-data
#9
Zhixiang Lin, Tao Wang, Can Yang, Hongyu Zhao
In this article, we first propose a Bayesian neighborhood selection method to estimate Gaussian Graphical Models (GGMs). We show the graph selection consistency of this method in the sense that the posterior probability of the true model converges to one. When there are multiple groups of data available, instead of estimating the networks independently for each group, joint estimation of the networks may utilize the shared information among groups and lead to improved estimation for each individual network...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099991/bayescat-bayesian-co-estimation-of-alignment-and-tree
#10
Heejung Shim, Bret Larget
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the alignment is ignored, resulting, possibly, in overstated certainty in phylogeny estimates. We develop a joint model for co-estimating phylogeny and sequence alignment which improves estimates from the traditional approach by accounting for uncertainty in the alignment in phylogenetic inferences...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099442/a-whole-genome-dartseq-and-snp-analysis-for-genetic-diversity-assessment-in-durum-wheat-from-central-fertile-crescent
#11
Faheem Shehzad Baloch, Ahmad Alsaleh, Muhammad Qasim Shahid, Vahdettin Çiftçi, Luis E Sáenz de Miera, Muhammad Aasim, Muhammad Azhar Nadeem, Husnu Aktaş, Hakan Özkan, Rüştü Hatipoğlu
Until now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers' small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis...
2017: PloS One
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
#12
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/28099086/maximal-heart-rate-declines-linearly-with-age-independent-of-cardiorespiratory-fitness-levels
#13
Cemal Ozemek, Mitchell H Whaley, W Holmes Finch, Leonard A Kaminsky
There have been many conflicting observations between the linear or curvilinear decline in maximal heart rate (HRmax) with age. The aim of this study was to determine if linear or curvilinear equations would better describe the decline in HRmax with age in individuals of differing cardiorespiratory fitness (CRF) levels. Treadmill cardiopulmonary exercise test (CPX) results from participants (1510 men and 1134 women; 18-76 years) free of overt cardiovascular disease were retrospectively examined using cross-sectional and longitudinal study designs...
January 18, 2017: European Journal of Sport Science
https://www.readbyqxmd.com/read/28098392/bayesian-nonparametric-clustering-in-phylogenetics-modeling-antigenic-evolution-in-influenza
#14
Gabriela B Cybis, Janet S Sinsheimer, Trevor Bedford, Andrew Rambaut, Philippe Lemey, Marc A Suchard
Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods...
January 18, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28097071/the-fishing-and-natural-mortality-of-large-piscivorous-bull-trout-and-rainbow-trout-in-kootenay-lake-british-columbia-2008-2013
#15
Joseph L Thorley, Greg F Andrusak
BACKGROUND: Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout. METHODS: Between 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake...
2017: PeerJ
https://www.readbyqxmd.com/read/28097068/hepatic-fibrosis-and-factors-associated-with-liver-stiffness-in-hiv-mono-infected-individuals
#16
Mihály Sulyok, Tamás Ferenci, Mihály Makara, Gábor Horváth, János Szlávik, Zsófia Rupnik, Luca Kormos, Zsuzsanna Gerlei, Zita Sulyok, István Vályi-Nagy
BACKGROUND: Liver disease has become an important cause of morbidity and mortality even in those HIV-infected individuals who are devoid of hepatitis virus co-infection. The aim of this study was to evaluate the degree of hepatic fibrosis and the role of associated factors using liver stiffness measurement in HIV mono-infected patients without significant alcohol intake. METHODS: We performed a cross-sectional study of 101 HIV mono-infected patients recruited prospectively from March 1, 2014 to October 30, 2014 at the Center for HIV, St István and St László Hospital, Budapest, Hungary...
2017: PeerJ
https://www.readbyqxmd.com/read/28096158/vancomycin-area-under-the-curve-estimation-in-obese-adults-the-peak-improves-precision-and-lowers-bias
#17
Manjunath P Pai, Joseph Hong, Lynne Krop
Vancomycin area under the curve (AUC) estimates may be skewed in obese adults due to weight-dependent pharmacokinetic parameters. We demonstrate that peak and trough measurements reduce bias and improve the precision of vancomycin AUC estimates in obese adults (n=75) and validate this in an independent cohort (n=31). The precision and mean %bias of Bayesian vancomycin AUC estimates are comparable between covariate-dependent (R(2)=0.774, 3.55%) and covariate-independent (R(2)=0.804, 3.28%) models when peaks and troughs are measured but not when restricted to trough only measurements (R(2),= 0...
January 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28095597/recollection-bias-and-its-underpinnings-lessons-from-terrorism-risk-assessments
#18
W Kip Viscusi, Richard J Zeckhauser
Recollection bias is the phenomenon whereby people who observe a highly unexpected event hold current risk beliefs about a similar event that are no higher than their recollection of their prior beliefs. This article replicates and extends the authors' previous study of recollection bias in relation to individuals' perceptions of the risks of terrorism attacks. Over 60% of respondents in a national U.S. sample of over 900 adults believe that the current risk of a future terrorist attack by either an airplane or in a public setting is no higher than they recall having believed, respectively, before the 9/11 attack and before the Boston Marathon bombing...
January 17, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28095591/a-critical-discussion-and-practical-recommendations-on-some-issues-relevant-to-the-nonprobabilistic-treatment-of-uncertainty-in-engineering-risk-assessment
#19
Nicola Pedroni, Enrico Zio, Alberto Pasanisi, Mathieu Couplet
Models for the assessment of the risk of complex engineering systems are affected by uncertainties due to the randomness of several phenomena involved and the incomplete knowledge about some of the characteristics of the system. The objective of this article is to provide operative guidelines to handle some conceptual and technical issues related to the treatment of uncertainty in risk assessment for engineering practice. In particular, the following issues are addressed: (1) quantitative modeling and representation of uncertainty coherently with the information available on the system of interest; (2) propagation of the uncertainty from the input(s) to the output(s) of the system model; (3) (Bayesian) updating as new information on the system becomes available; and (4) modeling and representation of dependences among the input variables and parameters of the system model...
January 17, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28095423/influences-of-host-community-characteristics-on-borrelia-burgdorferi-infection-prevalence-in-blacklegged-ticks
#20
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
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