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Fernando Racimo, Jeremy J Berg, Joseph K Pickrell
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred...
January 18, 2018: Genetics
Kan Shao, Andrew J Shapiro
BACKGROUND: Benchmark dose (BMD) modeling is an important step in human health risk assessment and is used as the default approach to identify the point of departure for risk assessment. A probabilistic framework for dose-response assessment has been proposed and advocated by various institutions and organizations; therefore, a reliable tool is needed to provide distributional estimates for BMD and other important quantities in dose-response assessment. OBJECTIVES: We developed an online system for Bayesian BMD (BBMD) estimation and compared results from this software with U...
January 11, 2018: Environmental Health Perspectives
Xiaodan Sun, Yanni Xiao, Zhihang Peng, Ning Wang
Intervention measures among men who have sex with men (MSM) are usually designed to reduce the frequency of high risk behaviors (within-community level), but unfortunately may change the contact network and consequently increase the opportunity for them to have sex with new partners (between-community level). A multi-community periodic model on complex network is proposed to study the two-side effects of interventions on HIV transmission among MSM in China, in which the wanning process of the impacts of interventions are modelled...
January 11, 2018: Scientific Reports
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
Toshihiro Shida, Yuji Endo, Tadashi Shiraishi, Takashi Yoshioka, Kaoru Suzuki, Yuka Kobayashi, Yuki Ono, Toshinori Ito, Tadao Inoue
 We evaluated four representative chemotherapy regimens for unresectable advanced or recurrent KRAS-wild type colorectal cancer: mFOLFOX6, mFOLFOX6+bevacizumab (Bmab), cetuximab (Cmab), or panitumumab (Pmab). We employed a decision analysis method in combination with clinical and economic evidence. The health outcomes of the regimens were analyzed on the basis of overall and progression-free survival. The data were drawn from the literature on randomized controlled clinical trials of the above-mentioned drugs...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
Andrew J Myrick, Thomas C Baker
Gas-chromatography-electroantennographic detection (GC-EAD) is a technique used in the identification of volatile organic compounds (VOCs), such as pheromones and plant host odors, which are physiologically relevant to insects. Although pheromones often elicit large EAD responses, other behaviorally relevant odors may elicit responses that are difficult to discern from noise. Lock-in amplification has long been used to reduce noise in a wide range of applications. Its utility when incorporated with GC-EAD was demonstrated previosuly by chopping (or pulsing) effluent-laden air that flowed over an insect antenna...
January 6, 2018: Journal of Chemical Ecology
Kinley Wangdi, Archie C A Clements, Tai Du, Susana Vaz Nery
BACKGROUND: Dengue remains an important public health problem in Timor-Leste, with several major epidemics occurring over the last 10 years. The aim of this study was to identify dengue clusters at high geographical resolution and to determine the association between local environmental characteristics and the distribution and transmission of the disease. METHODS: Notifications of dengue cases that occurred from January 2005 to December 2013 were obtained from the Ministry of Health, Timor-Leste...
January 4, 2018: Parasites & Vectors
Fernando Antoneli, Fernando M Passos, Luciano R Lopes, Marcelo R S Briones
Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law...
2018: PloS One
Peng Guo, Bo Zhu, Hong Niu, Zezhao Wang, Yonghu Liang, Yan Chen, Lupei Zhang, Hemin Ni, Yong Guo, El Hamidi A Hay, Xue Gao, Huijiang Gao, Xiaolin Wu, Lingyang Xu, Junya Li
BACKGROUND: Running multiple-chain Markov Chain Monte Carlo (MCMC) provides an efficient parallel computing method for complex Bayesian models, although the efficiency of the approach critically depends on the length of the non-parallelizable burn-in period, for which all simulated data are discarded. In practice, this burn-in period is set arbitrarily and often leads to the performance of far more iterations than required. In addition, the accuracy of genomic predictions does not improve after the MCMC reaches equilibrium...
January 3, 2018: BMC Bioinformatics
Theo H E Meuwissen, Ulf G Indahl, Jørgen Ødegård
BACKGROUND: Non-linear Bayesian genomic prediction models such as BayesA/B/C/R involve iteration and mostly Markov chain Monte Carlo (MCMC) algorithms, which are computationally expensive, especially when whole-genome sequence (WGS) data are analyzed. Singular value decomposition (SVD) of the genotype matrix can facilitate genomic prediction in large datasets, and can be used to estimate marker effects and their prediction error variances (PEV) in a computationally efficient manner. Here, we developed, implemented, and evaluated a direct, non-iterative method for the estimation of marker effects for the BayesC genomic prediction model...
December 27, 2017: Genetics, Selection, Evolution: GSE
Nasrin Ghanbari, Eric Clarkson, Matthew Kupinski, Xin Li
A method for optimization of an adaptive Single Photon Emission Computed Tomography (SPECT) system is presented. Adaptive imaging systems can quickly change their hardware configuration in response to data being generated in order to improve image quality for a specific task. In this work we simulate an adaptive SPECT system and propose a method for finding the adaptation that maximizes the performance on a signal estimation task. To start with, a simulated object model containing a spherical signal is imaged with a scout configuration...
September 2017: IEEE Transactions on Radiation and Plasma Medical Sciences
David B Dahl, Ryan Day, Jerry W Tsai
We propose a random partition distribution indexed by pairwise similarity information such that partitions compatible with the similarities are given more probability. The use of pairwise similarities, in the form of distances, is common in some clustering algorithms (e.g., hierarchical clustering), but we show how to use this type of information to define a prior partition distribution for flexible Bayesian modeling. A defining feature of the distribution is that it allocates probability among partitions within a given number of subsets, but it does not shift probability among sets of partitions with different numbers of subsets...
2017: Journal of the American Statistical Association
Takumi Motoya, Koo Nagasawa, Yuki Matsushima, Noriko Nagata, Akihide Ryo, Tsuyoshi Sekizuka, Akifumi Yamashita, Makoto Kuroda, Yukio Morita, Yoshiyuki Suzuki, Nobuya Sasaki, Kazuhiko Katayama, Hirokazu Kimura
Human norovirus (HuNoV) is a leading cause of viral gastroenteritis worldwide, of which GII.4 is the most predominant genotype. Unlike other genotypes, GII.4 has created various variants that escaped from previously acquired immunity of the host and caused repeated epidemics. However, the molecular evolutionary differences among all GII.4 variants, including recently discovered strains, have not been elucidated. Thus, we conducted a series of bioinformatic analyses using numerous, globally collected, full-length GII...
2017: Frontiers in Microbiology
Jakub Dotlačil
Cognitive architectures have often been applied to data from individual experiments. In this paper, I develop an ACT-R reader that can model a much larger set of data, eye-tracking corpus data. It is shown that the resulting model has a good fit to the data for the considered low-level processes. Unlike previous related works (most prominently, Engelmann, Vasishth, Engbert & Kliegl, ), the model achieves the fit by estimating free parameters of ACT-R using Bayesian estimation and Markov-Chain Monte Carlo (MCMC) techniques, rather than by relying on the mix of manual selection + default values...
December 18, 2017: Topics in Cognitive Science
Vu Dinh, Aaron E Darling, Frederick A Matsen Iv
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a posterior distribution on trees, have become a popular if computationally expensive means of doing phylogenetics. Modern data collection technologies are quickly adding new sequences to already substantial databases. With all current techniques for Bayesian phylogenetics, computation must start anew each time a sequence becomes available, making it costly to maintain an up-to-date estimate of a phylogenetic posterior...
December 13, 2017: Systematic Biology
Qiao-Guo Tan, Weitao Zhou, Wen-Xiong Wang
Metal contamination is a major problem in many estuaries. Toxicokinetic models are the useful tools for predicting metal accumulation in estuarine organisms and managing the associated ecological risks. However, obtaining toxicokinetic parameter values with sufficient predictive power is challenging for the dynamic estuarine waters. In this study, we determined the toxicokinetics of multiple metals in the oyster Crassostrea hongkongensis in a dynamic estuary polluted by metals using a 48-day transplant experiment...
December 13, 2017: Environmental Science & Technology
Wentao Fan, Yuliang Xu, Pu Zhang, Peng Chen, Yiran Zhu, Ziqiang Cheng, Xiaona Zhao, Yongxia Liu, Jianzhu Liu
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages...
November 14, 2017: Oncotarget
Linsong Dong, Ming Fang, Zhiyong Wang
MixP is an implementation that uses the Pareto principle to perform genomic prediction. This study was designed to develop two new computing strategies: one strategy for nonMCMC-based MixP (FMixP), and the other one for MCMC-based MixP (MMixP). The difference is that MMixP can estimate variances of SNP effects and the probability that a SNP has a large variance, but FMixP cannot. Simulated data from an international workshop and real data on large yellow croaker were used as the materials for the study. Four Bayesian methods, BayesA, BayesCπ, MMixP and FMixP, were used to compare the predictive results...
December 8, 2017: Scientific Reports
Oyetunji E Ogundijo, Xiaodong Wang
BACKGROUND: Samples of molecular sequence data of a locus obtained from random individuals in a population are often related by an unknown genealogy. More importantly, population genetics parameters, for instance, the scaled population mutation rate Θ=4N e μ for diploids or Θ=2N e μ for haploids (where N e is the effective population size and μ is the mutation rate per site per generation), which explains some of the evolutionary history and past qualities of the population that the samples are obtained from, is of significant interest...
December 8, 2017: BMC Bioinformatics
Marjolein F Q Kluytmans-van den Bergh, Suzan P van Mens, Manon R Haverkate, Martin C J Bootsma, Jan A J W Kluytmans, Marc J M Bonten
BACKGROUND Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are emerging worldwide. Contact precautions are recommended for known ESBL-E carriers to control the spread of ESBL-E within hospitals. OBJECTIVE This study quantified the acquisition of ESBL-E rectal carriage among patients in Dutch hospitals, given the application of contact precautions. METHODS Data were used from 2 cluster-randomized studies on isolation strategies for ESBL-E: (1) the SoM study, performed in 14 Dutch hospitals from 2011 through 2014 and (2) the R-GNOSIS study, for which data were limited to those collected in a Dutch hospital in 2014...
December 7, 2017: Infection Control and Hospital Epidemiology
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