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Bayesian probability

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https://www.readbyqxmd.com/read/28637852/testing-the-molecular-clock-using-mechanistic-models-of-fossil-preservation-and-molecular-evolution
#1
Rachel C M Warnock, Ziheng Yang, Philip C J Donoghue
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28633606/exact-bayesian-p-values-for-a-test-of-independence-in-a-2%C3%A2-%C3%A3-%C3%A2-2-contingency-table-with-missing-data
#2
Yan Lin, Stuart R Lipsitz, Debajyoti Sinha, Garrett Fitzmaurice, Steven Lipshultz
Altham (Altham PME. Exact Bayesian analysis of a 2 × 2 contingency table, and Fisher's "exact" significance test. J R Stat Soc B 1969; 31: 261-269) showed that a one-sided p-value from Fisher's exact test of independence in a 2 × 2 contingency table is equal to the posterior probability of negative association in the 2 × 2 contingency table under a Bayesian analysis using an improper prior. We derive an extension of Fisher's exact test p-value in the presence of missing data, assuming the missing data mechanism is ignorable (i...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28630885/bayesian-framework-inspired-no-reference-region-of-interest-quality-measure-for-brain-mri-images
#3
Michael Osadebey, Marius Pedersen, Douglas Arnold, Katrina Wendel-Mitoraj
We describe a postacquisition, attribute-based quality assessment method for brain magnetic resonance imaging (MRI) images. It is based on the application of Bayes theory to the relationship between entropy and image quality attributes. The entropy feature image of a slice is segmented into low- and high-entropy regions. For each entropy region, there are three separate observations of contrast, standard deviation, and sharpness quality attributes. A quality index for a quality attribute is the posterior probability of an entropy region given any corresponding region in a feature image where quality attribute is observed...
April 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28630413/bayesian-inference-of-physiologically-meaningful-parameters-from-body-sway-measurements
#4
A Tietäväinen, M U Gutmann, E Keski-Vakkuri, J Corander, E Hæggström
The control of the human body sway by the central nervous system, muscles, and conscious brain is of interest since body sway carries information about the physiological status of a person. Several models have been proposed to describe body sway in an upright standing position, however, due to the statistical intractability of the more realistic models, no formal parameter inference has previously been conducted and the expressive power of such models for real human subjects remains unknown. Using the latest advances in Bayesian statistical inference for intractable models, we fitted a nonlinear control model to posturographic measurements, and we showed that it can accurately predict the sway characteristics of both simulated and real subjects...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628667/characterization-of-hiv-1-crf90_bf1-and-putative-novel-crfs_bf1-in-central-west-north-and-northeast-brazilian-regions
#5
Mônica Nogueira da Guarda Reis, Gonzalo Bello, Monick Lindenmeyer Guimarães, Mariane Martins Araújo Stefani
The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates...
2017: PloS One
https://www.readbyqxmd.com/read/28624637/developing-a-new-bayesian-risk-index-for-risk-evaluation-of-soil-contamination
#6
M T D Albuquerque, S Gerassis, C Sierra, J Taboada, J E Martín, I M H R Antunes, J R Gallego
Industrial and agricultural activities heavily constrain soil quality. Potentially Toxic Elements (PTEs) are a threat to public health and the environment alike. In this regard, the identification of areas that require remediation is crucial. In the herein research a geochemical dataset (230 samples) comprising 14 elements (Cu, Pb, Zn, Ag, Ni, Mn, Fe, As, Cd, V, Cr, Ti, Al and S) was gathered throughout eight different zones distinguished by their main activity, namely, recreational, agriculture/livestock and heavy industry in the Avilés Estuary (North of Spain)...
June 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28624516/pleistocene-range-shifts-refugia-and-the-origin-of-widespread-species-in-western-palaearctic-water-beetles
#7
David García-Vázquez, David T Bilton, Garth N Foster, I Ribera
Quaternary glacial cycles drove major shifts in both the extent and location of the geographical ranges of many organisms. During glacial maxima, large areas of central and northern Europe were inhospitable to temperate species, and these areas are generally assumed to have been recolonized during interglacials by range expansions from Mediterranean refugia. An alternative is that this recolonization was from non-Mediterranean refugia, in central Europe or western Asia, but data on the origin of widespread central and north European species remain fragmentary, especially for insects...
June 15, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28623726/diagnostic-causal-reasoning-with-verbal-information
#8
Björn Meder, Ralf Mayrhofer
In diagnostic causal reasoning, the goal is to infer the probability of causes from one or multiple observed effects. Typically, studies investigating such tasks provide subjects with precise quantitative information regarding the strength of the relations between causes and effects or sample data from which the relevant quantities can be learned. By contrast, we sought to examine people's inferences when causal information is communicated through qualitative, rather vague verbal expressions (e.g., "X occasionally causes A")...
June 14, 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28622788/a-questionnaire-study-of-associations-between-potential-risk-factors-and-salmonella-status-in-swedish-dairy-herds
#9
Estelle C C Ågren, Jenny Frössling, Helene Wahlström, Ulf Emanuelson, Susanna Sternberg Lewerin
In this study associations between potential risk factors and salmonella status in Swedish dairy herds were investigated. A case-control study design was used, including existing as well as new cases. Herds were assigned a salmonella status on the basis of antibody analysis of bulk milk samples. Information on potential risk factors was collected from registry data and from farmers via a questionnaire. Univariable and multivariable logistic regression analyses were used to investigate associations between salmonella status and potential risk factors...
August 1, 2017: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/28622399/comparative-longterm-mortality-trends-in-cancer-vs-ischemic-heart-disease-in-puerto-rico
#10
David Torres, Luis R Pericchi, Hernando Mattei, Juan C Zevallos
OBJECTIVE: Although contemporary mortality data are important for health assessment and planning purposes, their availability lag several years. Statistical projection techniques can be employed to obtain current estimates. This study aimed to assess annual trends of mortality in Puerto Rico due to cancer and Ischemic Heart Disease (IHD), and to predict shorterm and longterm cancer and IHD mortality figures. METHODS: Age-adjusted mortality per 100,000 population projections with a 50% interval probability were calculated utilizing a Bayesian statistical approach of Age-Period-Cohort dynamic model...
June 2017: Puerto Rico Health Sciences Journal
https://www.readbyqxmd.com/read/28617228/prediction-models-for-drug-induced-hepatotoxicity-by-using-weighted-molecular-fingerprints
#11
Eunyoung Kim, Hojung Nam
BACKGROUND: Drug-induced liver injury (DILI) is a critical issue in drug development because DILI causes failures in clinical trials and the withdrawal of approved drugs from the market. There have been many attempts to predict the risk of DILI based on in vivo and in silico identification of hepatotoxic compounds. In the current study, we propose the in silico prediction model predicting DILI using weighted molecular fingerprints. RESULTS: In this study, we used 881 bits of molecular fingerprint and used as features describing presence or absence of each substructure of compounds...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28614414/species-specific-variation-in-nesting-and-postfledging-resource-selection-for-two-forest-breeding-migrant-songbirds
#12
Julianna M A Jenkins, Frank R Thompson, John Faaborg
Habitat selection is a fundamental component of community ecology, population ecology, and evolutionary biology and can be especially important to species with complex annual habitat requirements, such as migratory birds. Resource preferences on the breeding grounds may change during the postfledging period for migrant songbirds, however, the degree to which selection changes, timing of change, and whether all or only a few species alter their resource use is unclear. We compared resource selection for nest sites and resource selection by postfledging juvenile ovenbirds (Seiurus aurocapilla) and Acadian flycatchers (Empidonax virescens) followed with radio telemetry in Missouri mature forest fragments from 2012-2015...
2017: PloS One
https://www.readbyqxmd.com/read/28611440/declaration-of-local-chemical-eradication-of-the-argentine-ant-bayesian-estimation-with-a-multinomial-mixture-model
#13
Yoshiko Sakamoto, Naoki H Kumagai, Koichi Goka
Determining the success of eradication of an invasive species requires a way to decide when its risk of reoccurrence has become acceptably low. In Japan, the area populated by the Argentine ant, Linepithema humile (Mayr), is expanding, and eradication via chemical treatment is ongoing at various locations. One such program in Tokyo was apparently successful, because the ant population decreased to undetectable levels within a short time. However, construction of a population model for management purposes was difficult because the probability of detecting ants decreases rapidly as the population collapses...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28609437/shifting-brucellosis-risk-in-livestock-coincides-with-spreading-seroprevalence-in-elk
#14
Angela Brennan, Paul C Cross, Katie Portacci, Brandon M Scurlock, William H Edwards
Tracking and preventing the spillover of disease from wildlife to livestock can be difficult when rare outbreaks occur across large landscapes. In these cases, broad scale ecological studies could help identify risk factors and patterns of risk to inform management and reduce incidence of disease. Between 2002 and 2014, 21 livestock herds in the Greater Yellowstone Area (GYA) were affected by brucellosis, a bacterial disease caused by Brucella abortus, while no affected herds were detected between 1990 and 2001...
2017: PloS One
https://www.readbyqxmd.com/read/28606562/the-efficacy-and-safety-of-3-types-of-interventions-for-stroke-prevention-in-patients-with-cardiovascular-and-cerebrovascular-diseases-a-network-meta-analysis
#15
Qian Sun, Shumei Chang, Songtao Lu, Yajing Zhang, Yajun Chang
PURPOSE: The goal of this study was to compare the relative efficacy and safety of different types of interventions for stroke prevention in patients with cardiovascular and cerebrovascular diseases. METHODS: This network meta-analysis (NMA) was conducted with a random effects model of Bayesian framework using Stata version 12.0. Odds ratios (ORs) and their credible intervals (CrIs) were applied for the efficacy and safety evaluation of various medical interventions, including aspirin, dipyridamole, ticlopidine, warfarin, and apixaban...
June 10, 2017: Clinical Therapeutics
https://www.readbyqxmd.com/read/28606348/about-ganoderma-boninense-in-oil-palm-plantations-of-sumatra-and-peninsular-malaysia-ancient-population-expansion-extensive-gene-flow-and-large-scale-dispersion-ability
#16
Maxime Mercière, Romain Boulord, Catherine Carasco-Lacombe, Christophe Klopp, Yang-Ping Lee, Joon-Sheong Tan, Sharifah S R Syed Alwee, Alba Zaremski, Hubert De Franqueville, Frédéric Breton, Létizia Camus-Kulandaivelu
Wood rot fungi form one of the main classes of phytopathogenic fungus. The group includes many species, but has remained poorly studied. Many species belonging to the Ganoderma genus are well known for causing decay in a wide range of tree species around the world. Ganoderma boninense, causal agent of oil palm basal stem rot, is responsible for considerable yield losses in Southeast Asian oil palm plantations. In a large-scale sampling operation, 357 sporophores were collected from oil palm plantations spread over peninsular Malaysia and Sumatra and genotyped using 11 SSR markers...
June 2017: Fungal Biology
https://www.readbyqxmd.com/read/28597236/bayesian-analysis-of-the-piecewise-diffusion-decision-model
#17
William R Holmes, Jennifer S Trueblood
Most past research on sequential sampling models of decision-making have assumed a time homogeneous process (i.e., parameters such as drift rates and boundaries are constant and do not change during the deliberation process). This has largely been due to the theoretical difficulty in testing and fitting more complex models. In recent years, the development of simulation-based modeling approaches matched with Bayesian fitting methodologies has opened the possibility of developing more complex models such as those with time-varying properties...
June 8, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28595376/deisom-a-hierarchical-bayesian-model-for-identifying-differentially-expressed-isoforms-using-biological-replicates
#18
Hao Peng, Yifan Yang, Shandian Zhe, Jian Wang, Michael Gribskov, Yuan Alan Qi
Motivation: High-throughput mRNA sequencing (RNA-Seq) is a powerful tool for quantifying gene expression. Identification of transcript isoforms that are differentially expressed in different conditions, such as in patients and healthy subjects, can provide insights into the molecular basis of diseases. Current transcript quantification approaches, however, do not take advantage of the shared information in the biological replicates, potentially decreasing sensitivity and accuracy. Results: We present a novel hierarchical Bayesian model called DEIsoM (Differentially Expressed Isoform detection from Multiple biological replicates) for identifying DE (Differentially Expressed) isoforms from multiple biological replicates representing two conditions, e...
June 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28595349/prenatal-exposure-to-antimalarials-decreases-the-risk-of-cardiac-but-not-non-cardiac-neonatal-lupus-a-single-centre-cohort-study
#19
Julie Barsalou, Edgar Jaeggi, Carl A Laskin, Patrick Brown, Simon Y Tian, Robert M Hamilton, Earl D Silverman
Objective: . Recent studies have suggested that prenatal exposure to HCQ reduces the risk of cardiac neonatal lupus. The aim of this study is to assess if maternal intake of antimalarials (AMs) throughout pregnancy lowered the risk of cardiac and non-cardiac neonatal lupus. Methods: . Consecutive children seen between 1 January 1984 to 1 October 2013 born to women with a CTD and positive anti-Ro and/or anti-La antibodies were eligible for this single-centre retrospective cohort study...
June 8, 2017: Rheumatology
https://www.readbyqxmd.com/read/28593078/non-chemical-risk-assessment-for-lifting-and-low-back-pain-based-on-bayesian-threshold-models
#20
Sudha P Pandalai, Matthew W Wheeler, Ming-Lun Lu
BACKGROUND: Self-reported low back pain (LBP) has been evaluated in relation to material handling lifting tasks, but little research has focused on relating quantifiable stressors to LBP at the individual level. The National Institute for Occupational Safety and Health (NIOSH) Composite Lifting Index (CLI) has been used to quantify stressors for lifting tasks. A chemical exposure can be readily used as an exposure metric or stressor for chemical risk assessment (RA). Defining and quantifying lifting nonchemical stressors and related adverse responses is more difficult...
June 2017: Safety and Health At Work
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