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Bayesian modeling

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https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#1
J L Zhang, Y P Li, G H Huang, B W Baetz, J Liu
In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making...
March 6, 2017: Water Research
https://www.readbyqxmd.com/read/28340274/regularized-quantile-regression-applied-to-genome-enabled-prediction-of-quantitative-traits
#2
M Nascimento, F F E Silva, M D V de Resende, C D Cruz, A C C Nascimento, J M S Viana, C F Azevedo, L M A Barroso
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28339547/effectiveness-of-the-strengthening-families-programme-10-14-in-poland-cluster-randomized-controlled-trial
#3
David R Foxcroft, Howard Callen, Emma L Davies, Katarzyna Okulicz-Kozaryn
: The Strengthening Families Programme for youth aged 10-14 and parents/carers (SFP10-14) is a family-based prevention intervention with positive results in trials in the United States. We assessed the effectiveness of SFP10-14 for preventing substance misuse in Poland. : Cluster randomized controlled trial with 20 communities (511 families; 614 young people) were allocated to SFP10-14 or a control arms. Primary outcomes were alcohol, smoking and other drug use. Secondary outcomes included parenting practices, parent-child relations, and child problem behaviour...
October 24, 2016: European Journal of Public Health
https://www.readbyqxmd.com/read/28338966/a-comparison-of-sensitivity-specificity-imputation-direct-imputation-and-fully-bayesian-analysis-to-adjust-for-exposure-misclassification-when-validation-data-are-unavailable
#4
Marine Corbin, Stephen Haslett, Neil Pearce, Milena Maule, Sander Greenland
Purpose: Measurement error is an important source of bias in epidemiological studies. We illustrate three approaches to sensitivity analysis for the effect of measurement error: imputation of the 'true' exposure based on specifying the sensitivity and specificity of the measured exposure (SS); direct imputation (DI) using a regression model for the predictive values; and adjustment based on a fully Bayesian analysis. Methods: We deliberately misclassify smoking status in data from a case-control study of lung cancer...
March 14, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28338643/geographical-correlations-between-indoor-radon-concentration-and-risks-of-lung-cancer-non-hodgkin-s-lymphoma-and-leukemia-during-1999-2008-in-korea
#5
Mina Ha, Seung-Sik Hwang, Sungchan Kang, No-Wook Park, Byung-Uck Chang, Yongjae Kim
Indoor radon is the second most important risk factor for lung cancer and may also be a risk factor for hematopoietic cancers, particularly in children and adolescents. The present study measured indoor radon concentration nationwide at 5553 points during 1989-2009 and spatially interpolated using lognormal kriging. The incidences of lung cancer, non-Hodgkin's lymphoma (NHL), and leukemia, stratified by sex and five-year age groups in each of the 234 administrative regions in the country during 1999-2008, were obtained from the National Cancer Registry and used to calculate the standardized incidence ratios...
March 24, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28337862/bayesian-sensitivity-analysis-of-a-1d-vascular-model-with-gaussian-process-emulators
#6
A Melis, R H Clayton, A Marzo
One-dimensional models of the cardiovascular system can capture the physics of pulse waves, but involve many parameters. Since these may vary among individuals, patient-specific models are difficult to construct. Sensitivity analysis can be used to rank model parameters by their effect on outputs, and to quantify how uncertainty in parameters influences output uncertainty. This type of analysis is often conducted with a Monte Carlo method, where large numbers of model runs are used to assess input-output relations...
March 24, 2017: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/28337122/cerebrospinal-fluid-cortisol-mediates-brain-derived-neurotrophic-factor-relationships-to-mortality-after-severe-tbi-a-prospective-cohort-study
#7
Miranda J Munoz, Raj G Kumar, Byung-Mo Oh, Yvette P Conley, Zhensheng Wang, Michelle D Failla, Amy K Wagner
Distinct regulatory signaling mechanisms exist between cortisol and brain derived neurotrophic factor (BDNF) that may influence secondary injury cascades associated with traumatic brain injury (TBI) and predict outcome. We investigated concurrent CSF BDNF and cortisol relationships in 117 patients sampled days 0-6 after severe TBI while accounting for BDNF genetics and age. We also determined associations between CSF BDNF and cortisol with 6-month mortality. BDNF variants, rs6265 and rs7124442, were used to create a gene risk score (GRS) in reference to previously published hypothesized risk for mortality in "younger patients" (<48 years) and hypothesized BDNF production/secretion capacity with these variants...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28336478/an-extended-protocol-for-usability-validation-of-medical-devices-research-design-and-reference-model
#8
Martin Schmettow, Raphaela Schnittker, Jan Maarten Schraagen
This paper proposes and demonstrates an extended protocol for usability validation testing of medical devices. A review of currently used methods for the usability evaluation of medical devices revealed two main shortcomings. Firstly, the lack of methods to closely trace the interaction sequences and derive performance measures. Secondly, a prevailing focus on cross-sectional validation studies, ignoring the issues of learnability and training. The U.S. Federal Drug and Food Administration's recent proposal for a validation testing protocol for medical devices is then extended to address these shortcomings: (1) a novel process measure 'normative path deviations' is introduced that is useful for both quantitative and qualitative usability studies and (2) a longitudinal, completely within-subject study design is presented that assesses learnability, training effects and allows analysis of diversity of users...
March 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28335713/erratum-to-an-integrative-bayesian-dirichlet-multinomial-regression-model-for-the-analysis-of-taxonomic-abundances-in-microbiome-data
#9
W Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A Shelburne, Marina Vannucci
No abstract text is available yet for this article.
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#10
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334312/efficient-inference-for-genetic-association-studies-with-multiple-outcomes
#11
Helene Ruffieux, Anthony C Davison, Jorg Hager, Irina Irincheeva
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single clinical outcome on many genetic variants one by one, but there is an increasing demand for joint analysis of many molecular outcomes and genetic variants in order to unravel functional interactions. Unfortunately, most existing approaches to joint modeling are either too simplistic to be powerful or are impracticable for computational reasons...
March 16, 2017: Biostatistics
https://www.readbyqxmd.com/read/28334230/guided-bayesian-imputation-to-adjust-for-confounding-when-combining-heterogeneous-data-sources-in-comparative-effectiveness-research
#12
Joseph Antonelli, Corwin Zigler, Francesca Dominici
In comparative effectiveness research, we are often interested in the estimation of an average causal effect from large observational data (the main study). Often this data does not measure all the necessary confounders. In many occasions, an extensive set of additional covariates is measured for a smaller and non-representative population (the validation study). In this setting, standard approaches for missing data imputation might not be adequate due to the large number of missing covariates in the main data relative to the smaller sample size of the validation data...
March 3, 2017: Biostatistics
https://www.readbyqxmd.com/read/28334223/is-bamm-flawed-theoretical-and-practical-concerns-in-the-analysis-of-multi-rate-diversification-models
#13
Daniel L Rabosky, Jonathan S Mitchell, Jonathan Chang
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical framework that uses reversible jump MCMC to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore and coauthors (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (1) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (2) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (3) diversification rate estimates from BAMM are unreliable...
February 21, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334179/bayesian-distributed-lag-interaction-models-to-identify-perinatal-windows-of-vulnerability-in-children-s-health
#14
Ander Wilson, Yueh-Hsiu Mathilda Chiu, Hsiao-Hsien Leon Hsu, Robert O Wright, Rosalind J Wright, Brent A Coull
Epidemiological research supports an association between maternal exposure to air pollution during pregnancy and adverse children's health outcomes. Advances in exposure assessment and statistics allow for estimation of both critical windows of vulnerability and exposure effect heterogeneity. Simultaneous estimation of windows of vulnerability and effect heterogeneity can be accomplished by fitting a distributed lag model (DLM) stratified by subgroup. However, this can provide an incomplete picture of how effects vary across subgroups because it does not allow for subgroups to have the same window but different within-window effects or to have different windows but the same within-window effect...
February 27, 2017: Biostatistics
https://www.readbyqxmd.com/read/28334079/how-do-cold-adapted-plants-respond-to-climatic-cycles-interglacial-expansion-explains-current-distribution-and-genomic-diversity-in-primula-farinosa-l
#15
Spyros Theodoridis, Christophe Randin, Peter Szövényi, Florian C Boucher, Theofania S Patsiou, Elena Conti
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model...
December 21, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28334051/dissecting-the-relationships-of-igg-subclasses-and-complements-in-membranous-lupus-nephritis-and-idiopathic-membranous-nephropathy
#16
Woong Na, Kijong Yi, Young Soo Song, Moon Hyang Park
Membranous lupus nephritis (MLN) and idiopathic membranous nephropathy (IMN) are kidney diseases with similar morphology, but distinct etiologies, both producing glomeruli with immune deposits. Immunoglobulins and complements, the main components of the deposits, can be detected by immunofluorescence (IF) microscopy. Previous researches characterized the immune deposits only individually, but not the interactions between them. To study these relationships we analyzed an IF profile of IgG subclasses and complements (IgG1, IgG2, IgG3, IgG4, C3, C1q, and C4) in 53 and 95 cases of biopsy-confirmed MLNs and IMNs, respectively, mainly using information theory and Bayesian networks...
2017: PloS One
https://www.readbyqxmd.com/read/28333230/bayesian-analysis-of-evolutionary-divergence-with-genomic-data-under-diverse-demographic-models
#17
Yujin Chung, Jody Hey
We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation with Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333053/evaluation-of-the-information-content-of-long-term-wastewater-characteristics-data-in-relation-to-activated-sludge-model-parameters
#18
Jamal Alikhani, Imre Takacs, Ahmed Al-Omari, Sudhir Murthy, Arash Massoudieh
A parameter estimation framework was used to evaluate the ability of observed data from a full-scale nitrification-denitrification bioreactor to reduce the uncertainty associated with the bio-kinetic and stoichiometric parameters of an activated sludge model (ASM). Samples collected over a period of 150 days from the effluent as well as from the reactor tanks were used. A hybrid genetic algorithm and Bayesian inference were used to perform deterministic and parameter estimations, respectively. The main goal was to assess the ability of the data to obtain reliable parameter estimates for a modified version of the ASM...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28331847/learning-parsimonious-classification-rules-from-gene-expression-data-using-bayesian-networks-with-local-structure
#19
Jonathan Lyle Lustgarten, Jeya Balaji Balasubramanian, Shyam Visweswaran, Vanathi Gopalakrishnan
The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilities to summarize the observed data. We extend a Bayesian Rule Learning (BRL-GSS) algorithm, previously shown to be a significantly better predictor than other classical approaches in this domain. It searches a space of Bayesian networks using a decision tree representation of its parameters with global constraints, and infers a set of IF-THEN rules...
March 2017: Data (Basel)
https://www.readbyqxmd.com/read/28331603/low-leopard-populations-in-protected-areas-of-maputaland-a-consequence-of-poaching-habitat-condition-abundance-of-prey-and-a-top-predator
#20
Tharmalingam Ramesh, Riddhika Kalle, Havard Rosenlund, Colleen T Downs
Identifying the primary causes affecting population densities and distribution of flagship species are necessary in developing sustainable management strategies for large carnivore conservation. We modeled drivers of spatial density of the common leopard (Panthera pardus) using a spatially explicit capture-recapture-Bayesian approach to understand their population dynamics in the Maputaland Conservation Unit, South Africa. We camera-trapped leopards in four protected areas (PAs) of varying sizes and disturbance levels covering 198 camera stations...
March 2017: Ecology and Evolution
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