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C Edson Utazi, Emmanuel O Afuecheta, C Christopher Nnanatu
Model-based approaches for the analysis of areal count data are commonplace in spatiotemporal analysis. In Bayesian hierarchical models, a latent process is incorporated in the mean function to account for dependence in space and time. Typically, the latent process is modelled using a conditional autoregressive (CAR) prior. The aim of this paper is to offer an alternative approach to CAR-based priors for modelling the latent process. The proposed approach is based on a spatiotemporal generalization of a latent process Poisson regression model developed in a time series setting...
June 2018: Spatial and Spatio-temporal Epidemiology
Safi U Khan, Ahmad N Lone, Swapna Talluri, Muhammad Z Khan, Muhammad U Khan, Edo Kaluski
AIM: To compare relative efficacy and safety of mechanical compression devices (AutoPulse and LUCAS) with manual compression in patients with cardiac arrest undergoing cardiopulmonary resuscitation (CPR). METHODS: For this Bayesian network meta-analysis, seven randomized controlled trials (RCTs) were selected using PubMed/Medline, EMBASE, and CENTRAL (Inception- 31 October 2017). For all the outcomes, median estimate of odds ratio (OR) from the posterior distribution with corresponding 95% credible interval (Cr I) was calculated...
May 7, 2018: Resuscitation
Eleonora Cella, Elisabetta Riva, Silvia Angeletti, Marta Fogolari, Aletheia Blasi, Vittoria Scolamacchia, Silvia Spoto, Riccardo Bazzardi, Alessia Lai, Caterina Sagnelli, Evangelista Sagnelli, Massimo Ciccozzi
Despite a significantly decrease of acute hepatitis A in the last two decades in Italy, outbreaks mostly occurring in southern Italy were observed. In this study, Bayesian phylogenetic analysis was used to analyze the origin of these epidemics. At this aim, five different datasets of hepatitis A virus sequences were built to perform genotyping by the neighbor-joining method, to estimate the evolutionary rates by using a Bayesian Markov Chain Monte Carlo (MCMC) approach, to investigate the demographic history by independent MCMC runs enforcing both a strict and relaxed clock...
May 8, 2018: Journal of Medical Virology
Zakariya Yahya Algamal, Rahim Alhamzawi, Haithem Taha Mohammad Ali
Gene selection has been proven to be an effective way to improve the results of many classification methods. However, existing gene selection techniques in binary classification regression are sensitive to outliers of the data, heteroskedasticity or other anomalies of the latent response. In this paper, we propose a new Bayesian hierarchical model to overcome these problems in a relatively straightforward way. In particular, we propose a new Bayesian Lasso method that employs a skewed Laplace distribution for the errors and a scaled mixture of uniform distribution for the regression parameters, together with Bayesian MCMC estimation...
April 27, 2018: Computers in Biology and Medicine
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis...
April 27, 2018: Systematic Biology
K V Parag, O G Pybus
Motivation: Inferring the rates of change of a population from a reconstructed phylogeny of genetic sequences is a central problem in macro-evolutionary biology, epidemiology, and many other disciplines. A popular solution involves estimating the parameters of a birth-death process (BDP), which links the shape of the phylogeny to its birth and death rates. Modern BDP estimators rely on random Markov chain Monte Carlo (MCMC) sampling to infer these rates. Such methods, while powerful and scalable, cannot be guaranteed to converge, leading to results that may be hard to replicate or difficult to validate...
April 26, 2018: Bioinformatics
Min Chen, Yanling Ma, Huichao Chen, Jie Dai, Lijuan Dong, Chaojun Yang, Youfang Li, Hongbing Luo, Renzhong Zhang, Xiaomei Jin, Li Yang, Allen Ka Loon Cheung, Manhong Jia, Zhizhong Song
BACKGROUND: Yunnan has the greatest share of reported human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) cases in China. In recent years, HIV prevalence and incidence remained stubbornly high in men who have sex with men (MSM). To follow the dynamics of the HIV-1 epidemic among MSM, HIV-1 genetic characteristics and genetic transmission networks were investigated. METHODS: Blood samples from 190 newly diagnosed HIV-1 cases among MSM were continuously collected at fixed sites from January 2013 to December 2015 in Kunming City, Yunnan Province...
2018: PloS One
K H Nicolaides, D Wright, A Syngelaki, A Wright, R Akolekar
OBJECTIVE: To develop fetal and neonatal population weight charts. The rationale for this objective is that while reference ranges of estimated fetal weight (EFW) are representative of the whole population, the traditional approach of deriving birth-weight (BW) charts is misleading because a high proportion of babies born preterm arises from pathological pregnancies. We propose that the reference population for BW charts, as in the case of EFW charts, should be all babies at a given gestational age including those still in utero...
April 26, 2018: Ultrasound in Obstetrics & Gynecology
Cong Xu, Vernon M Chinchilli, Ming Wang
In longitudinal studies, matched designs are often employed to control the potential confounding effects in the field of biomedical research and public health. Because of clinical interest, recurrent time-to-event data are captured during the follow-up. Meanwhile, the terminal event of death is always encountered, which should be taken into account for valid inference because of informative censoring. In some scenarios, a certain large portion of subjects may not have any recurrent events during the study period due to nonsusceptibility to events or censoring; thus, the zero-inflated nature of data should be considered in analysis...
April 22, 2018: Statistics in Medicine
Teguh Hari Sucipto, Tomohiro Kotaki, Kris Cahyo Mulyatno, Siti Churrotin, Amaliah Labiqah, Soegeng Soegijanto, Masanori Kameoka
Dengue virus (DENV) infection is a major health issue in tropical and subtropical areas. Indonesia is one of the biggest dengue endemic countries in the world. In the present study, the phylogenetic analysis of DENV in Bangkalan, Madura Island, Indonesia, was performed in order to obtain a clearer understanding of its dynamics in this country. A total of 359 blood samples from dengue-suspected patients were collected between 2012 and 2014. Serotyping was conducted using a multiplex Reverse Transcriptase-Polymerase Chain Reaction and a phylogenetic analysis of E gene sequences was performed using the Bayesian Markov chain Monte Carlo (MCMC) method...
2018: Journal of Tropical Medicine
David T W Yau, May C M Wong, K F Lam, Colman McGrath
BACKGROUND: Longitudinal invariance is a perquisite for a valid comparison of oral health-related quality of life (OHRQoL) scores over time. Item response theory (IRT) models can assess measurement invariance and allow better estimation of the associations between predictors and latent construct. By extending IRT models, this study aimed to investigate the longitudinal invariance of the two 8-item short forms of the Child Perception Questionnaire (CPQ11-14 ) regression short form (RSF:8) and item-impact short form (ISF:8) and identify factors associated with adolescents' OHRQoL and its change...
April 11, 2018: Health and Quality of Life Outcomes
Yize Zhao, Jian Kang, Qi Long
Ultra-high dimensional variable selection has become increasingly important in analysis of neuroimaging data. For example, in the Autism Brain Imaging Data Exchange (ABIDE) study, neuroscientists are interested in identifying important biomarkers for early detection of the autism spectrum disorder (ASD) using high resolution brain images that include hundreds of thousands voxels. However, most existing methods are not feasible for solving this problem due to their extensive computational costs. In this work, we propose a novel multiresolution variable selection procedure under a Bayesian probit regression framework...
March 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Juliana Merces Hernandez, Luciana Damascena Silva, Edivaldo Costa Sousa Junior, Renato Silva Bandeira, Elmer Abraão Martins Rodrigues, Maria Silvia Souza Lucena, Samya Thalita Picanço Costa, Yvone Benchimol Gabbay
BACKGROUND: Globally, Norovirus (NoV) is considered the most common cause of diarrheal episodes across all age groups. Despite its wide genetic diversity, the GII.4 strain is the most predominant and has been associated with epidemics worldwide. In this study, we characterized sporadic cases of diarrhea from NoV-positive children, during a five-year period (2010-2014). METHODS: A total of 250 NoV-positive samples identified by an enzyme immunoassay (EIA) were subjected to RT-PCR and partial nucleotide sequencing for polymerase and capsid genes...
April 2, 2018: BMC Infectious Diseases
Jing Li, Ting Zhang, Kun Cai, Yongzhogn Jiang, Xuhua Guan, Jianbo Zhan, Wenjing Zou, Zhaohui Yang, Xuesen Xing, Yang Wu, Yi Song, Xuejie Yu, Junqiang Xu
Norovirus (NoV) is a major pathogenic agent of human acute viral gastroenteritis that occurs worldwide. In March 2017, a series of acute NoV-associated gastroenteritis outbreaks occurred in Hubei Province in central China. Here, we sought to better understand the main genotypes and potential evolutionary advantages of circulating NoV strains underlying these outbreaks. During the outbreak, 111 fecal swabs and stool samples were collected from outpatients with acute NoV-associated gastroenteritis in Hubei Province...
March 28, 2018: Virus Research
Paulino Pérez-Rodríguez, Rocío Acosta-Pech, Sergio Pérez-Elizalde, Ciro Velasco Cruz, Javier Suárez Espinosa, José Crossa
Genomic selection (GS) has become a tool for selecting candidates in plant and animal breeding programs. In the case of quantitative traits, it is common to assume that the distribution of the response variable can be approximated by a normal distribution. However, it is known that the selection process leads to skewed distributions. There is vast statistical literature on skewed distributions, but the skew normal distribution is of particular interest in this research. This distribution includes a third parameter that drives the skewness, so that it generalizes the normal distribution...
March 27, 2018: G3: Genes—Genomes—Genetics
Quan Wang, Hang-Xing Li, Kun-Miao Wang, Xiao Wang, Zhe Xue, Lei Jia, Lin Du, Qi-Hua Zhao
Mixed azide and zwitterionic pyridiniums built Co(II) coordination polymer and its temperature-dependent magnetic properties are represented. We use Markov chain Monte Carlo (MCMC) method to fit the data, and find the following results: (1) there are strong correlations between the model parameters; (2) the data above the 28 K temperature are well fitted by the magnetism model.
March 26, 2018: Chemistry, An Asian Journal
Adrian Quintero, Emmanuel Lesaffre
Hierarchical models are extensively used in pharmacokinetics and longitudinal studies. When the estimation is performed from a Bayesian approach, model comparison is often based on the deviance information criterion (DIC). In hierarchical models with latent variables, there are several versions of this statistic: the conditional DIC (cDIC) that incorporates the latent variables in the focus of the analysis and the marginalized DIC (mDIC) that integrates them out. Regardless of the asymptotic and coherency difficulties of cDIC, this alternative is usually used in Markov chain Monte Carlo (MCMC) methods for hierarchical models because of practical convenience...
March 26, 2018: Statistics in Medicine
Forrest D Freund, William A Freyman, Carl J Rothfels
PREMISE OF THE STUDY: Inferring the evolution of characters in Isoëtes has been problematic, as these plants are morphologically conservative and yet highly variable and homoplasious within that conserved base morphology. However, molecular phylogenies have given us a valuable tool for testing hypotheses of character evolution within the genus, such as the hypothesis of ongoing morphological reductions. METHODS: We examined the reduction in lobe number on the underground trunk, or corm, by combining the most recent molecular phylogeny with morphological descriptions gathered from the literature and observations of living specimens...
March 24, 2018: American Journal of Botany
Marcello Mezzasalma, Mirko Di Febbraro, Fabio Maria Guarino, Gaetano Odierna, Danilo Russo
In this work, we performed a biogeographic analysis with Bayesian binary MCMC (BBM) statistical dispersal-vicariance analysis (S-DIVA) and species distribution models (SDM) on three phylogenetically closely related Mediterranean whipsnakes (Hierophis gemonensis, H. carbonarius, H. viridiflavus), to investigate the pathways of their geographical diversification and locate putative refugial areas in the last glacial maximum (LGM). Our analysis suggests that the diversification processes between the studied species overall followed an east-west route, from eastern Greece to the Iberian Peninsula and continental France, highlighting a significant role of dispersal and vicariance processes at both inter- and intraspecific levels...
February 1, 2018: Zoology: Analysis of Complex Systems, ZACS
Rhiannon K Owen, Nicola J Cooper, Terence J Quinn, Rosalind Lees, Alex J Sutton
OBJECTIVE: Network meta-analyses have extensively been used to compare the effectiveness of multiple interventions for healthcare policy and decision-making. However, methods for evaluating the performance of multiple diagnostic tests are less established. In a decision-making context, we are often interested in comparing and ranking the performance of multiple diagnostic tests, at varying levels of test thresholds, in one simultaneous analysis. STUDY DESIGN AND SETTING: Motivated by an example of cognitive impairment diagnosis following stroke, we synthesized data from 13 studies assessing the efficiency of two diagnostic tests: Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA), at two test thresholds: MMSE <25/30 and <27/30, and MoCA <22/30 and <26/30...
March 13, 2018: Journal of Clinical Epidemiology
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