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https://www.readbyqxmd.com/read/28088033/a-bayesian-spatial-random-parameters-tobit-model-for-analyzing-crash-rates-on-roadway-segments
#1
Qiang Zeng, Huiying Wen, Helai Huang, Mohamed Abdel-Aty
This study develops a Bayesian spatial random parameters Tobit model to analyze crash rates on road segments, in which both spatial correlation between adjacent sites and unobserved heterogeneity across observations are accounted for. The crash-rate data for a three-year period on road segments within a road network in Florida, are collected to compare the performance of the proposed model with that of a (fixed parameters) Tobit model and a spatial (fixed parameters) Tobit model in the Bayesian context. Significant spatial effect is found in both spatial models and the results of Deviance Information Criteria (DIC) show that the inclusion of spatial correlation in the Tobit regression considerably improves model fit, which indicates the reasonableness of considering cross-segment spatial correlation...
January 11, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28087736/imputation-of-orofacial-clefting-data-identifies-novel-risk-loci-and-sheds-light-on-the-genetic-background-of-cleft-lip-%C3%A2-cleft-palate-and-cleft-palate-only
#2
Kerstin U Ludwig, Anne C Böhmer, John Bowes, Miloš Nikolić, Nina Ishorst, Niki Wyatt, Nigel L Hammond, Lina Gölz, Frederic Thieme, Sandra Barth, Hannah Schuenke, Johanna Klamt, Malte Spielmann, Khalid Aldhorae, Augusto Rojas-Martinez, Markus M Nöthen, Alvaro Rada-Iglesias, Michael J Dixon, Michael Knapp, Elisabeth Mangold
Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is among the most common human birth defects with multifactorial etiology. Here, we present results from a genome-wide imputation study of nsCL/P in which, after adding replication cohort data, four novel risk loci for nsCL/P are identified (at chromosomal regions 2p21, 14q22, 15q24 and 19p13). On a systematic level, we show that the association signals within this high-density dataset are enriched in functionally-relevant genomic regions that are active in both human neural crest cells (hNCC) and mouse embryonic craniofacial tissue...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#3
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28086992/therapies-for-bruxism-a-systematic-review-and-network-meta-analysis-protocol
#4
Mauro Elias Mesko, Brian Hutton, Jovito Adiel Skupien, Rafael Sarkis-Onofre, David Moher, Tatiana Pereira-Cenci
BACKGROUND: Bruxism is a sleep disorder characterized by grinding and clenching of the teeth that may be related to irreversible tooth injuries. It is a prevalent condition occurring in up to 31% of adults. However, there is no definitive answer as to which of the many currently available treatments (including drug therapy, intramuscular injections, physiotherapy, biofeedback, kinesiotherapy, use of intraoral devices, or psychological therapy) is the best for the clinical management of the different manifestations of bruxism...
January 13, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28086751/quantifying-predictors-for-the-spatial-diffusion-of-avian-influenza-virus-in-china
#5
Lu Lu, Andrew J Leigh Brown, Samantha J Lycett
BACKGROUND: Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the routes of transmission in avian species between geographic regions can be numerous and complex. Using nucleotide sequences from the internal protein coding segments of AIV, we performed a Bayesian phylogeographic study to uncover regional routes of transmission and factors predictive of the rate of viral diffusion within China...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28081278/population-structure-of-annona-crassiflora-an-endemic-plant-species-of-the-brazilian-cerrado
#6
R Gwinner, T A Setotaw, F A Rodrigues, D V C França, F A da Silveira, L A S Pio, M Pasqual
Habitat fragmentation has numerous consequences, particularly to endemic species, and has a negative impact on the genetic diversity of neglected species, leading to genetic drift. Annona crassiflora Mart. is a species that is endemic to Brazil, and its incidence in the Cerrado biome has decreased. The identification and characterization of its remaining diversity is necessary for its conservation. Our aim was to study the population structure of A. crassiflora populations from different Cerrado regions in Minas Gerais State, Brazil (Corinto, Curvelo, Carmo da Mata, Boa Esperança, and Paraguaçu) using inter-simple sequence repeat (ISSR) markers and DNA content...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28081273/assessing-the-impact-of-retreat-mechanisms-in-a-simple-antarctic-ice-sheet-model-using-bayesian-calibration
#7
Kelsey L Ruckert, Gary Shaffer, David Pollard, Yawen Guan, Tony E Wong, Chris E Forest, Klaus Keller
The response of the Antarctic ice sheet (AIS) to changing climate forcings is an important driver of sea-level changes. Anthropogenic climate change may drive a sizeable AIS tipping point response with subsequent increases in coastal flooding risks. Many studies analyzing flood risks use simple models to project the future responses of AIS and its sea-level contributions. These analyses have provided important new insights, but they are often silent on the effects of potentially important processes such as Marine Ice Sheet Instability (MISI) or Marine Ice Cliff Instability (MICI)...
2017: PloS One
https://www.readbyqxmd.com/read/28081166/comparison-of-criteria-for-choosing-the-number-of-classes-in-bayesian-finite-mixture-models
#8
Kazem Nasserinejad, Joost van Rosmalen, Wim de Kort, Emmanuel Lesaffre
Identifying the number of classes in Bayesian finite mixture models is a challenging problem. Several criteria have been proposed, such as adaptations of the deviance information criterion, marginal likelihoods, Bayes factors, and reversible jump MCMC techniques. It was recently shown that in overfitted mixture models, the overfitted latent classes will asymptotically become empty under specific conditions for the prior of the class proportions. This result may be used to construct a criterion for finding the true number of latent classes, based on the removal of latent classes that have negligible proportions...
2017: PloS One
https://www.readbyqxmd.com/read/28081134/pain-a-statistical-account
#9
REVIEW
Abby Tabor, Michael A Thacker, G Lorimer Moseley, Konrad P Körding
Perception is seen as a process that utilises partial and noisy information to construct a coherent understanding of the world. Here we argue that the experience of pain is no different; it is based on incomplete, multimodal information, which is used to estimate potential bodily threat. We outline a Bayesian inference model, incorporating the key components of cue combination, causal inference, and temporal integration, which highlights the statistical problems in everyday perception. It is from this platform that we are able to review the pain literature, providing evidence from experimental, acute, and persistent phenomena to demonstrate the advantages of adopting a statistical account in pain...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28081133/the-power-of-malaria-vaccine-trials-using-controlled-human-malaria-infection
#10
Luc E Coffeng, Cornelus C Hermsen, Robert W Sauerwein, Sake J de Vlas
Controlled human malaria infection (CHMI) in healthy human volunteers is an important and powerful tool in clinical malaria vaccine development. However, power calculations are essential to obtain meaningful estimates of protective efficacy, while minimizing the risk of adverse events. To optimize power calculations for CHMI-based malaria vaccine trials, we developed a novel non-linear statistical model for parasite kinetics as measured by qPCR, using data from mosquito-based CHMI experiments in 57 individuals...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28080966/active-interoceptive-inference-and-the-emotional-brain
#11
REVIEW
Anil K Seth, Karl J Friston
We review a recent shift in conceptions of interoception and its relationship to hierarchical inference in the brain. The notion of interoceptive inference means that bodily states are regulated by autonomic reflexes that are enslaved by descending predictions from deep generative models of our internal and external milieu. This re-conceptualization illuminates several issues in cognitive and clinical neuroscience with implications for experiences of selfhood and emotion. We first contextualize interoception in terms of active (Bayesian) inference in the brain, highlighting its enactivist (embodied) aspects...
November 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28080124/statistical-learning-of-parts-and-wholes-a-neural-network-approach
#12
David C Plaut, Anna K Vande Velde
Statistical learning is often considered to be a means of discovering the units of perception, such as words and objects, and representing them as explicit "chunks." However, entities are not undifferentiated wholes but often contain parts that contribute systematically to their meanings. Studies of incidental auditory or visual statistical learning suggest that, as participants learn about wholes they become insensitive to parts embedded within them, but this seems difficult to reconcile with a broad range of findings in which parts and wholes work together to contribute to behavior...
January 12, 2017: Journal of Experimental Psychology. General
https://www.readbyqxmd.com/read/28079510/a-comparison-of-discontinuation-rates-of-tofacitinib-and-biologic-disease-modifying-antirheumatic-drugs-in-rheumatoid-arthritis-a-systematic-review-and-bayesian-network-meta-analysis
#13
Sun-Kyeong Park, Min-Young Lee, Eun-Jin Jang, Hye-Lin Kim, Dong-Mun Ha, Eui-Kyung Lee
OBJECTIVES: The purpose of this study was to compare the discontinuation rates of tofacitinib and biologics (tumour necrosis factor inhibitors (TNFi), abatacept, rituximab, and tocilizumab) in rheumatoid arthritis (RA) patients considering inadequate responses (IRs) to previous treatment(s). METHODS: Randomised controlled trials of tofacitinib and biologics - reporting at least one total discontinuation, discontinuation due to lack of efficacy (LOE), and discontinuation due to adverse events (AEs) - were identified through systematic review...
January 5, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/28079030/neuromusculoskeletal-model-self-calibration-for-on-line-sequential-bayesian-moment-estimation
#14
Diana Ruiz Bueno, Luis Montano
OBJECTIVE: Neuromusculoskeletal models involve many subject-specific physiological parameters that need to be adjusted to adequately represent muscle properties. Traditionally, neuromusculoskeletal models have been calibrated with a forward-inverse dynamic optimization which is time-consuming and unfeasible for rehabilitation therapy. Non self-calibration algorithms have been applied to these models. To the best of our knowledge, the algorithm proposed in this work is the first on-line calibration algorithm for muscle models that allows a generic model to be adjusted to different subjects in a few steps...
January 12, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28077933/bayespop-probabilistic-population-projections
#15
Hana Ševčíková, Adrian E Raftery
We describe bayesPop, an R package for producing probabilistic population projections for all countries. This uses probabilistic projections of total fertility and life expectancy generated by Bayesian hierarchical models. It produces a sample from the joint posterior predictive distribution of future age- and sex-specific population counts, fertility rates and mortality rates, as well as future numbers of births and deaths. It provides graphical ways of summarizing this information, including trajectory plots and various kinds of probabilistic population pyramids...
December 2016: Journal of Statistical Software
https://www.readbyqxmd.com/read/28077895/applying-naive-bayesian-networks-to-disease-prediction-a-systematic-review
#16
Mostafa Langarizadeh, Fateme Moghbeli
INTRODUCTION: Naive Bayesian networks (NBNs) are one of the most effective and simplest Bayesian networks for prediction. OBJECTIVE: This paper aims to review published evidence about the application of NBNs in predicting disease and it tries to show NBNs as the fundamental algorithm for the best performance in comparison with other algorithms. METHODS: PubMed was electronically checked for articles published between 2005 and 2015. For characterizing eligible articles, a comprehensive electronic searching method was conducted...
October 2016: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/28077778/uncertain-tree-discriminating-among-competing-approaches-to-the-phylogenetic-analysis-of-phenotype-data
#17
Mark N Puttick, Joseph E O'Reilly, Alastair R Tanner, James F Fleming, James Clark, Lucy Holloway, Jesus Lozano-Fernandez, Luke A Parry, James E Tarver, Davide Pisani, Philip C J Donoghue
Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28077441/predicting-ifn-%C3%AE-responses-after-bcg-vaccination-in-humans-from-macaques-a-proof-of-concept-study-of-immunostimulation-immunodynamic-modelling-methods
#18
Sophie J Rhodes, Charlotte Sarfas, Gwenan M Knight, Andrew White, Ansar A Pathan, Helen McShane, Thomas G Evans, Helen Fletcher, Sally Sharpe, Richard G White
INTRODUCTION: Macaques play a central role in human tuberculosis(TB) vaccine development. Immune and challenge responses differ across macaque and human subpopulations. We determined which macaque subpopulations best predicted immune responses in different human subpopulations, using novel immunostimulation/immunodynamic modelling methods in a proof of concept study. METHODS: Data on IFN-γ secreting CD4+ T cells over time after recent BCG vaccination were available for 55 humans and 81 macaques...
January 11, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28076696/proton-pump-inhibitors-for-preventing-non-steroidal-anti-inflammatory-drug-induced-gastrointestinal-toxicity-a-systematic-review
#19
Man Yang, Min He, Miao Zhao, Bing Zou, Jun Liu, Ling-Min Luo, Qiu-Lan Li, Jun-Hui He, Ping-Guang Lei
OBJECTIVE: Proton pump inhibitors (PPIs) are recommended for preventing gastrointestinal lesions induced by non-steroidal anti-inflammatory drug (NSAID). We performed this study (1) to evaluate the effectiveness and safety of PPIs, (2) to explore the association between effectiveness and potential influential factors, and (3) to investigate the comparative effect of different PPIs. METHODS: MEDLINE, EMBASE, and the Cochrane Library were searched to identify randomized controlled trials comparing different classes of PPIs, or comparing PPIs with placebo, H2 receptor antagonists or misoprostol in NSAIDs users...
January 11, 2017: Current Medical Research and Opinion
https://www.readbyqxmd.com/read/28076674/trajectories-of-perinatal-depressive-and-anxiety-symptoms-in-a-community-cohort
#20
Hamideh Bayrampour, Lianne Tomfohr, Suzanne Tough
OBJECTIVE: The evidence on trajectories of perinatal depression is mostly based on studies composed of women at high risk for poor mental health. Research on maternal anxiety trajectories is also scarce. Using a large community cohort, the All Our Babies study, in Alberta, Canada, we examined trajectories of perinatal depressive and anxiety symptoms and compared characteristics of women across trajectories. METHODS: Anxiety and depressive symptoms were measured at the second and third trimesters and at 4 and 12 months postpartum among 1,445 women recruited between May 2008 and December 2010...
November 2016: Journal of Clinical Psychiatry
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