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https://www.readbyqxmd.com/read/28319254/a-bayesian-subgroup-analysis-using-collections-of-anova-models
#1
Jinzhong Liu, Siva Sivaganesan, Purushottam W Laud, Peter Müller
We develop a Bayesian approach to subgroup analysis using ANOVA models with multiple covariates, extending an earlier work. We assume a two-arm clinical trial with normally distributed response variable. We also assume that the covariates for subgroup finding are categorical and are a priori specified, and parsimonious easy-to-interpret subgroups are preferable. We represent the subgroups of interest by a collection of models and use a model selection approach to finding subgroups with heterogeneous effects...
March 20, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/28318586/prediction-and-repeatability-of-milk-coagulation-properties-and-curd-firming-modeling-parameters-of-ovine-milk-using-fourier-transform-infrared-spectroscopy-and-bayesian-models
#2
A Ferragina, C Cipolat-Gotet, A Cecchinato, M Pazzola, M L Dettori, G M Vacca, G Bittante
The aim of this study was to apply Bayesian models to the Fourier-transform infrared spectroscopy spectra of individual sheep milk samples to derive calibration equations to predict traditional and modeled milk coagulation properties (MCP), and to assess the repeatability of MCP measures and their predictions. Data consisted of 1,002 individual milk samples collected from Sarda ewes reared in 22 farms in the region of Sardinia (Italy) for which MCP and modeled curd-firming parameters were available. Two milk samples were taken from 87 ewes and analyzed with the aim of estimating repeatability, whereas a single sample was taken from the other 915 ewes...
March 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28318420/bayesian-penalized-log-likelihood-ratio-approach-for-dose-response-clinical-trial-studies
#3
Yuanyuan Tang, Chunyan Cai, Liangrui Sun, Jianghua He
In literature, there are a few unified approaches to test proof of concept and estimate a target dose, including the multiple comparison procedure using modeling approach, and the permutation approach proposed by Klingenberg. We discuss and compare the operating characteristics of these unified approaches and further develop an alternative approach in a Bayesian framework based on the posterior distribution of a penalized log-likelihood ratio test statistic. Our Bayesian approach is much more flexible to handle linear or nonlinear dose-response relationships and is more efficient than the permutation approach...
February 13, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28318286/asking-better-questions-how-presentation-formats-influence-information-search
#4
Charley M Wu, Björn Meder, Flavia Filimon, Jonathan D Nelson
While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information)...
March 20, 2017: Journal of Experimental Psychology. Learning, Memory, and Cognition
https://www.readbyqxmd.com/read/28317296/how-to-make-more-out-of-community-data-a-conceptual-framework-and-its-implementation-as-models-and-software
#5
Otso Ovaskainen, Gleb Tikhonov, Anna Norberg, F Guillaume Blanchet, Leo Duan, David Dunson, Tomas Roslin, Nerea Abrego
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities...
March 20, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28316883/middle-pleistocene-protein-sequences-from-the-rhinoceros-genus-stephanorhinus-and-the-phylogeny-of-extant-and-extinct-middle-late-pleistocene-rhinocerotidae
#6
Frido Welker, Geoff M Smith, Jarod M Hutson, Lutz Kindler, Alejandro Garcia-Moreno, Aritza Villaluenga, Elaine Turner, Sabine Gaudzinski-Windheuser
BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis)...
2017: PeerJ
https://www.readbyqxmd.com/read/28316255/a-bayesian-double-fusion-model-for-resting-state-brain-connectivity-using-joint-functional-and-structural-data
#7
Hakmook Kang, Hernando Ombao, Christopher Fonnesbeck, Zhaohua Ding, Victoria L Morgan
Current approaches separately analyze concurrently acquired diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) data. The primary limitation of these approaches is that they do not take advantage of the information from DTI that could potentially enhance estimation of resting state functional connectivity (FC) between brain regions. To overcome this limitation, we develop a Bayesian hierarchical spatio-temporal model that incorporates structural connectivity into estimating FC. In our proposed approach, structural connectivity (SC) based on DTI data is used to construct an informative prior for functional connectivity based on resting state fMRI data via the Cholesky decomposition...
March 19, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/28314238/paternity-testing-and-other-inference-about-relationships-from-dna-mixtures
#8
Peter J Green, Julia Mortera
We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. The evidence for such a relationship is evaluated as the likelihood ratio for the specified relationship versus the alternative that there is no relationship. We analyse real casework examples from a criminal case and a disputed paternity case; in both examples part of the evidence was from a DNA mixture...
February 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28314157/bayesian-updating-in-a-fault-tree-model-for-shipwreck-risk-assessment
#9
H Landquist, L Rosén, A Lindhe, T Norberg, I-M Hassellöv
Shipwrecks containing oil and other hazardous substances have been deteriorating on the seabeds of the world for many years and are threatening to pollute the marine environment. The status of the wrecks and the potential volume of harmful substances present in the wrecks are affected by a multitude of uncertainties. Each shipwreck poses a unique threat, the nature of which is determined by the structural status of the wreck and possible damage resulting from hazardous activities that could potentially cause a discharge...
March 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28306347/bayesian-modal-estimation-of-the-four-parameter-item-response-model-in-real-realistic-and-idealized-data-sets
#10
Niels G Waller, Leah Feuerstahler
In this study, we explored item and person parameter recovery of the four-parameter model (4PM) in over 24,000 real, realistic, and idealized data sets. In the first analyses, we fit the 4PM and three alternative models to data from three Minnesota Multiphasic Personality Inventory-Adolescent form factor scales using Bayesian modal estimation (BME). Our results indicated that the 4PM fits these scales better than simpler item Response Theory (IRT) models. Next, using the parameter estimates from these real data analyses, we estimated 4PM item parameters in 6,000 realistic data sets to establish minimum sample size requirements for accurate item and person parameter recovery...
March 17, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28304237/cervical-disc-arthroplasty-with-the-prestige-lp-disc-versus-anterior-cervical-discectomy-and-fusion-at-2-levels-results-of-a-prospective-multicenter-randomized-controlled-clinical-trial-at-24-months
#11
Matthew F Gornet, Todd H Lanman, J Kenneth Burkus, Scott D Hodges, Jeffrey R McConnell, Randall F Dryer, Anne G Copay, Hui Nian, Frank E Harrell
OBJECTIVE The authors compared the efficacy and safety of arthroplasty using the Prestige LP cervical disc with those of anterior cervical discectomy and fusion (ACDF) for the treatment of degenerative disc disease (DDD) at 2 adjacent levels. METHODS Patients from 30 investigational sites were randomized to 1 of 2 groups: investigational patients (209) underwent arthroplasty using a Prestige LP artificial disc, and control patients (188) underwent ACDF with a cortical ring allograft and anterior cervical plate...
March 17, 2017: Journal of Neurosurgery. Spine
https://www.readbyqxmd.com/read/28304219/surgical-or-transcatheter-aortic-valve-replacement-in-intermediate-risk-patients
#12
Michael J Reardon, Nicolas M Van Mieghem, Jeffrey J Popma, Neal S Kleiman, Lars Søndergaard, Mubashir Mumtaz, David H Adams, G Michael Deeb, Brijeshwar Maini, Hemal Gada, Stanley Chetcuti, Thomas Gleason, John Heiser, Rüdiger Lange, William Merhi, Jae K Oh, Peter S Olsen, Nicolo Piazza, Mathew Williams, Stephan Windecker, Steven J Yakubov, Eberhard Grube, Raj Makkar, Joon S Lee, John Conte, Eric Vang, Hang Nguyen, Yanping Chang, Andrew S Mugglin, Patrick W J C Serruys, Arie P Kappetein
Background Although transcatheter aortic-valve replacement (TAVR) is an accepted alternative to surgery in patients with severe aortic stenosis who are at high surgical risk, less is known about comparative outcomes among patients with aortic stenosis who are at intermediate surgical risk. Methods We evaluated the clinical outcomes in intermediate-risk patients with severe, symptomatic aortic stenosis in a randomized trial comparing TAVR (performed with the use of a self-expanding prosthesis) with surgical aortic-valve replacement...
March 17, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28303174/local-site-differences-in-survival-and-parasitism-of-periwinkles-littorina-sitkana-philippi-1846
#13
Mónica Ayala-Díaz, Jean M L Richardson, Bradley R Anholt
The periwinkle, Littorina sitkana, is found throughout the intertidal zone, often in isolated subpopulations. The majority of trematode parasites use snails as intermediate hosts, and decreased survivorship is often observed in snails infected with trematodes. Sampling L. sitkana from four sites in Barkley Sound, British Columbia, Canada, we test the effects of parasitic infection on snail survival using maximum likelihood and Bayesian approaches using the software MARK and WinBUGS. We found that survival of periwinkles and trematode community composition differed among sites, but survival and trematode prevalence were uncorrelated...
February 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28303148/differentiating-wheat-genotypes-by-bayesian-hierarchical-nonlinear-mixed-modeling-of-wheat-root-density
#14
Anton P Wasson, Grace S Chiu, Alexander B Zwart, Timothy R Binns
Ensuring future food security for a growing population while climate change and urban sprawl put pressure on agricultural land will require sustainable intensification of current farming practices. For the crop breeder this means producing higher crop yields with less resources due to greater environmental stresses. While easy gains in crop yield have been made mostly "above ground," little progress has been made "below ground"; and yet it is these root system traits that can improve productivity and resistance to drought stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28301833/persistent-environmental-toxicants-in-breast-milk-and-rapid-infant-growth
#15
Rachel Criswell, Virissa Lenters, Siddhartha Mandal, Hein Stigum, Nina Iszatt, Merete Eggesbø
BACKGROUND/AIMS: Many environmental toxicants are passed to infants in utero and through breast milk. Exposure to toxicants during the perinatal period can alter growth patterns, impairing growth or increasing obesity risk. Previous studies have focused on only a few toxicants at a time, which may confound results. We investigated levels of 26 toxicants in breast milk and their associations with rapid infant growth, a risk factor for later obesity. METHODS: We used data from the Norwegian HUMIS study, a multi-center cohort of 2,606 mothers and newborns enrolled between 2002 and 2008...
March 17, 2017: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/28301606/usefulness-of-bone-scintigraphy-for-the-diagnosis-of-complex-regional-pain-syndrome-1-a-systematic-review-and-bayesian-meta-analysis
#16
Maria M Wertli, Florian Brunner, Johann Steurer, Ulrike Held
BACKGROUND: Since 2007, the Budapest criteria are recommended for the diagnosis of Complex Regional Pain Syndrome (CRPS) 1. The usefulness of bone scintigraphy (BS, index test) for the diagnosis of CRPS 1 remains controversial. Imperfect reference tests (RT) result in underestimation of the diagnostic accuracy of BS. Further, biased results can occur when a dependency between the RT and BS exists. The objective was to assess the impact of different RTs, specifically the Budapest criteria, and the assumed imperfect nature of the RT on the diagnostic accuracy of BS...
2017: PloS One
https://www.readbyqxmd.com/read/28301540/tight-species-cohesion-among-sympatric-insular-wild-gingers-asarum-spp-aristolochiaceae-on-continental-islands-highly-differentiated-floral-characteristics-versus-undifferentiated-genotypes
#17
Junshi Matsuda, Yoshiyuki Maeda, Junichi Nagasawa, Hiroaki Setoguchi
The Amami Island group of the Ryukyu Archipelago, Japan, harbors extensive species diversity of Asarum in a small landmass. The fine-scale population genetic structure and diversity of nine insular endemic Asarum species were examined using nuclear DNA microsatellite loci and ITS sequences. High population genetic diversity (HS = 0.45-0.79) was estimated based on the microsatellites, implying outcrossing of Asarum species within populations accompanied by inbreeding. Bayesian clustering analyses revealed that species were divided into three robust genetic clusters and that the species within each cluster had a homogeneous genetic structure, indicating incomplete lineage sorting...
2017: PloS One
https://www.readbyqxmd.com/read/28301529/applying-diffusion-based-markov-chain-monte-carlo
#18
Radu Herbei, Rajib Paul, L Mark Berliner
We examine the performance of a strategy for Markov chain Monte Carlo (MCMC) developed by simulating a discrete approximation to a stochastic differential equation (SDE). We refer to the approach as diffusion MCMC. A variety of motivations for the approach are reviewed in the context of Bayesian analysis. In particular, implementation of diffusion MCMC is very simple to set-up, even in the presence of nonlinear models and non-conjugate priors. Also, it requires comparatively little problem-specific tuning. We implement the algorithm and assess its performance for both a test case and a glaciological application...
2017: PloS One
https://www.readbyqxmd.com/read/28300991/spatial-analysis-of-tuberculosis-in-rio-de-janeiro-in-the-period-from-2005-to-2008-and-associated-socioeconomic-factors-using-micro-data-and-global-spatial-regression-models
#19
Monica de Avelar Figueiredo Mafra Magalhães, Roberto de Andrade Medronho
The present study analyses the spatial pattern of tuberculosis (TB) from 2005 to 2008 by identifying relevant socioeconomic variables for the occurrence of the disease through spatial statistical models. This ecological study was performed in Rio de Janeiro using new cases. The census sector was used as the unit of analysis. Incidence rates were calculated, and the Local Empirical Bayesian method was used. The spatial autocorrelation was verified with Moran's Index and local indicators of spatial association (LISA)...
March 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28298201/the-patterns-of-genomic-variances-and-covariances-across-genome-for-milk-production-traits-between-chinese-and-nordic-holstein-populations
#20
Xiujin Li, Mogens Sandø Lund, Luc Janss, Chonglong Wang, Xiangdong Ding, Qin Zhang, Guosheng Su
BACKGROUND: With the development of SNP chips, SNP information provides an efficient approach to further disentangle different patterns of genomic variances and covariances across the genome for traits of interest. Due to the interaction between genotype and environment as well as possible differences in genetic background, it is reasonable to treat the performances of a biological trait in different populations as different but genetic correlated traits. In the present study, we performed an investigation on the patterns of region-specific genomic variances, covariances and correlations between Chinese and Nordic Holstein populations for three milk production traits...
March 15, 2017: BMC Genetics
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