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https://www.readbyqxmd.com/read/28346824/weighted-pseudolikelihood-for-snp-set-analysis-with-multiple-secondary-outcomes-in-case-control-genetic-association-studies
#1
Tamar Sofer, Elizabeth D Schifano, David C Christiani, Xihong Lin
We propose a weighted pseudolikelihood method for analyzing the association of a SNP set, example, SNPs in a gene or a genetic pathway or network, with multiple secondary phenotypes in case-control genetic association studies. To boost analysis power, we assume that the SNP-specific effects are shared across all secondary phenotypes using a scaled mean model. We estimate regression parameters using Inverse Probability Weighted (IPW) estimating equations obtained from the weighted pseudolikelihood, which accounts for case-control sampling to prevent potential ascertainment bias...
March 27, 2017: Biometrics
https://www.readbyqxmd.com/read/28346484/a-neighborhood-wide-association-study-nwas-example-of-prostate-cancer-aggressiveness
#2
Shannon M Lynch, Nandita Mitra, Michelle Ross, Craig Newcomb, Karl Dailey, Tara Jackson, Charnita M Zeigler-Johnson, Harold Riethman, Charles C Branas, Timothy R Rebbeck
PURPOSE: Cancer results from complex interactions of multiple variables at the biologic, individual, and social levels. Compared to other levels, social effects that occur geospatially in neighborhoods are not as well-studied, and empiric methods to assess these effects are limited. We propose a novel Neighborhood-Wide Association Study(NWAS), analogous to genome-wide association studies(GWAS), that utilizes high-dimensional computing approaches from biology to comprehensively and empirically identify neighborhood factors associated with disease...
2017: PloS One
https://www.readbyqxmd.com/read/28345905/metatox-web-application-for-predicting-structure-and-toxicity-of-xenobiotics-metabolites
#3
Anastasia V Rudik, Vladislav M Bezhentsev, Alexander V Dmitriev, Dmitry S Druzhilovskiy, Alexey A Lagunin, Dmitry A Filimonov, Vladimir V Poroikov
A new freely available web-application MetaTox (http://www.way2drug.com/mg) for prediction of xenobiotic's metabolism and calculation toxicity of metabolites based on the structural formula of chemicals has been developed. MetaTox predicts metabolites, which are formed by nine classes of reactions (aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation). The calculation of probability for generated metabolites is based on analyses of "structure-biotransformation reactions" and "structure-modified atoms" relationships using a Bayesian approach...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345775/quantification-of-the-position-and-depth-of-the-flexor-hallucis-longus-groove-in-euarchontans-with-implications-for-the-evolution-of-primate-positional-behavior
#4
Gabriel S Yapuncich, Erik R Seiffert, Doug M Boyer
OBJECTIVE: On the talus, the position and depth of the groove for the flexor hallucis longus tendon have been used to infer phylogenetic affinities and positional behaviors of fossil primates. This study quantifies aspects of the flexor hallucis longus groove (FHLG) to test if: (1) a lateral FHLG is a derived strepsirrhine feature, (2) a lateral FHLG reflects inverted and abducted foot postures, and (3) a deeper FHLG indicates a larger muscle. METHODS: We used linear measurements of microCT-generated models from a sample of euarchontans (n = 378 specimens, 125 species) to quantify FHLG position and depth...
March 27, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28344825/identification-of-filamin-a-and-b-as-potential-biomarkers-for-prostate-cancer
#5
Niven R Narain, Anne R Diers, Arleide Lee, Socheata Lao, Joyce Y Chan, Sally Schofield, Joe Andreazi, Rakibou Ouro-Djobo, Joaquin J Jimenez, Tracey Friss, Nikunj Tanna, Aditee Dalvi, Sihe Wang, Dustin Bunch, Yezhou Sun, Wenfang Wu, Khampaseuth Thapa, Stephane Gesta, Leonardo O Rodrigues, Viatcheslav R Akmaev, Vivek K Vishnudas, Rangaprasad Sarangarajan
AIM: A novel strategy for prostate cancer (PrCa) biomarker discovery is described. MATERIALS & METHODS: In vitro perturbation biology, proteomics and Bayesian causal analysis identified biomarkers that were validated in in vitro models and clinical specimens. RESULTS: Filamin-B (FLNB) and Keratin-19 were identified as biomarkers. Filamin-A (FLNA) was found to be causally linked to FLNB. Characterization of the biomarkers in a panel of cells revealed differential mRNA expression and regulation...
March 2017: Future Science OA
https://www.readbyqxmd.com/read/28343169/a-bayesian-semiparametric-factor-analysis-model-for-subtype-identification
#6
Jiehuan Sun, Joshua L Warren, Hongyu Zhao
Disease subtype identification (clustering) is an important problem in biomedical research. Gene expression profiles are commonly utilized to infer disease subtypes, which often lead to biologically meaningful insights into disease. Despite many successes, existing clustering methods may not perform well when genes are highly correlated and many uninformative genes are included for clustering due to the high dimensionality. In this article, we introduce a novel subtype identification method in the Bayesian setting based on gene expression profiles...
March 25, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28343059/internal-cycling-not-external-loading-decides-the-nutrient-limitation-in-eutrophic-lake-a-dynamic-model-with-temporal-bayesian-hierarchical-inference
#7
Zhen Wu, Yong Liu, Zhongyao Liang, Sifeng Wu, Huaicheng Guo
Lake eutrophication is associated with excessive anthropogenic nutrients (mainly nitrogen (N) and phosphorus (P)) and unobserved internal nutrient cycling. Despite the advances in understanding the role of external loadings, the contribution of internal nutrient cycling is still an open question. A dynamic mass-balance model was developed to simulate and measure the contributions of internal cycling and external loading. It was based on the temporal Bayesian Hierarchical Framework (BHM), where we explored the seasonal patterns in the dynamics of nutrient cycling processes and the limitation of N and P on phytoplankton growth in hyper-eutrophic Lake Dianchi, China...
March 19, 2017: Water Research
https://www.readbyqxmd.com/read/28342962/intellectual-evaluation-of-children-exposed-to-phthalate-tainted-products-after-the-2011-taiwan-phthalate-episode
#8
Po-Chin Huang, Chih-Hsin Tsai, Chu-Chih Chen, Ming-Tsang Wu, Mei-Lien Chen, Shu-Li Wang, Bai-Hsiun Chen, Ching-Chang Lee, Jouni J K Jaakkola, Wen-Chiu Wu, Min-Kung Chen, Chao A Hsiung, Rapit Group
INTRODUCTION: Phthalate exposure may reduce intellectual development in young children. In 2011, numerous Taiwanese children had been reported to have consumed phthalate-tainted products. We investigated the effects of phthalate exposure on the intellectual development of these children after the 2011 Taiwan di-2-ethylhexyl phthalate (DEHP) episode. METHODS: We recruited 204 children, aged 3-12 y, from 3 hospitals in Taiwan between 2012 and 2013. First-morning urine samples were collected for analyzing 5 phthalate metabolites...
March 23, 2017: Environmental Research
https://www.readbyqxmd.com/read/28342072/statistical-properties-of-four-effect-size-measures-for-mediation-models
#9
Milica Miočević, Holly P O'Rourke, David P MacKinnon, Hendricks C Brown
This project examined the performance of classical and Bayesian estimators of four effect size measures for the indirect effect in a single-mediator model and a two-mediator model. Compared to the proportion and ratio mediation effect sizes, standardized mediation effect-size measures were relatively unbiased and efficient in the single-mediator model and the two-mediator model. Percentile and bias-corrected bootstrap interval estimates of ab/s Y , and ab(s X )/s Y in the single-mediator model outperformed interval estimates of the proportion and ratio effect sizes in terms of power, Type I error rate, coverage, imbalance, and interval width...
March 24, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28341048/genetic-analysis-of-coagulation-properties-curd-firming-modeling-milk-yield-composition-and-acidity-in-sarda-dairy-sheep
#10
G Bittante, C Cipolat-Gotet, M Pazzola, M L Dettori, G M Vacca, A Cecchinato
Sheep milk is an important source of food, especially in Mediterranean countries, and is used in large part for cheese production. Milk technological traits are important for the sheep dairy industry, but research is lacking into the genetic variation of such traits. Therefore the aim of this study was to estimate the heritability of traditional milk coagulation properties and curd firmness modeled on time t (CFt) parameters, and their genetic relationships with test-day milk yield, composition (fat, protein, and casein content), and acidity in Sarda dairy sheep...
January 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28340551/genomic-prediction-using-subsampling
#11
Alencar Xavier, Shizhong Xu, William Muir, Katy Martin Rainey
BACKGROUND: Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo...
March 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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