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Bayesian modeling

Duncan Taylor, Bas Kokshoorn, Alex Biedermann
The evaluation of results of forensic genetic analyses given activity level propositions is an emerging discipline in forensic genetics. Although it is a topic with a long history, it has never been considered to be such a critically important topic for the field, as today. With the increasing sensitivity of analysis techniques, and advances in data interpretation using probabilistic models ('probabilistic genotyping'), there is an increasing demand on forensic biologists to share specialised knowledge to help recipients of expert information address mode and timing of transfer and persistence of traces in court...
June 7, 2018: Forensic Science International. Genetics
James P Corsetti, Tanzy M Love, Charles E Sparks, Stephan J L Bakker, Robin P F Dullaart
OBJECTIVE: Familial dysbetalipoproteinemia (FD) or Type III hyperlipoproteinemia is closely associated with the ε2ε2 genotype of the common APOE polymorphism although not all ε2 homozygotes develop FD indicating that additional factors play a role including insulin resistance (IR). The current study was undertaken to explore relationships and influences among factors, especially IR, that might elucidate FD progression pathways. METHODS: Bayesian network (BN) modeling, a probabilistic graphical exploratory data analysis tool that portrays relationships and influences among variables as simple diagrams, was applied to 52 e2e2 subjects...
June 18, 2018: Clinical Biochemistry
F Schwendicke, G Göstemeyer, M Stolpe, J Krois
We aimed to assess the cost-effectiveness of amalgam alternatives-namely, incrementally placed composites (IComp), composites placed in bulk (BComp), and glass ionomer cements (GIC). In a sensitivity analysis, we also included composite inlays (CompI) and incrementally placed bulk-fills (IBComp). Moreover, the value of information (VOI) regarding the effectiveness of all strategies was determined. A mixed public-private-payer perspective in the context of Germany was adopted. Bayesian network meta-analyses were performed to yield effectiveness estimates (relative risk [RR] of failure)...
June 1, 2018: Journal of Dental Research
Lukasz Huminiecki
Understanding how regulatory elements control mammalian gene expression is a challenge of post-genomic era. We previously reported that size of proximal promoter architecture predicted the breadth of expression (fraction of tissues in which a gene is expressed). Herein, the contributions of individual transcription factors (TFs) were quantified. Several technologies of statistical modelling were utilized and compared: tree models, generalized linear models (GLMs, without and with regularization), Bayesian GLMs and random forest...
2018: PloS One
Erica J Weinstein, Jacob L Levene, Marc S Cohen, Doerthe A Andreae, Jerry Y Chao, Matthew Johnson, Charles B Hall, Michael H Andreae
BACKGROUND: Regional anaesthesia may reduce the rate of persistent postoperative pain (PPP), a frequent and debilitating condition. This review was originally published in 2012 and updated in 2017. OBJECTIVES: To compare local anaesthetics and regional anaesthesia versus conventional analgesia for the prevention of PPP beyond three months in adults and children undergoing elective surgery. SEARCH METHODS: We searched CENTRAL, MEDLINE, and Embase to December 2016 without any language restriction...
June 20, 2018: Cochrane Database of Systematic Reviews
Corinna Pehrs, Jamil Zaki, Liila Taruffi, Lars Kuchinke, Stefan Koelsch
People are better able to empathize with others when they are given information concerning the context driving that person's experiences. This suggests that people draw on prior memories when empathizing, but the mechanisms underlying this connection remain largely unexplored. The present study investigates how variations in episodic information shape the emotional response towards a movie character. Episodic information is either absent or provided by a written context preceding empathic film clips. It was shown that sad context information increases empathic concern for a movie character...
June 20, 2018: Scientific Reports
Kevin Phan, Declan Lloyd, Ash Wilson-Smith, Vannessa Leung, Marko Andric
BACKGROUND/AIM: To clarify the nature of the relationship between novel oral anticoagulants (NOACs) and traditional anticoagulation in respect to intraocular bleeding. METHODS: A comprehensive literature search up to October 2017 yielded 12 randomised controlled trials. Bayesian Markov chain Monte Carlo analysis was employed to investigate the relationship across multiple trials with varying NOACs. Random effects (informative priors) ORs were applied for the risk of intraocular bleeding due to various treatment measures...
June 20, 2018: British Journal of Ophthalmology
Mahmoud Shirali, Patrick Francis Varley, Just Jensen
BACKGROUND: This study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for average daily feed consumption (ADFI), average daily weight gain (ADG), lean meat percentage (LMP) along with the derived traits of RFI and FCR; and (3) deriving Bayesian estimates of direct and correlated responses to selection on RFI, FCR, ADG, ADFI, and LMP. Response to selection was defined as the difference in additive genetic mean of the selected top individuals, expected to be parents of the next generation, and the total population after integrating genetic trends out of the posterior distribution of selection responses...
June 20, 2018: Genetics, Selection, Evolution: GSE
Chi-Jui Feng, Balamurugan Dhayalan, Andrei Tokmakoff
Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR) spectroscopy has picosecond time resolution to freeze structural ensembles as needed for probing disordered-protein ensembles and conformational dynamics. Also, developments in amide I computational spectroscopy now allow a quantitative and direct prediction of amide I spectra based on conformational distributions drawn from molecular dynamics simulations, providing a route to ensemble refinement against experimental spectra...
June 19, 2018: Biophysical Journal
Kim Scribner, Iyob Tsehaye, Travis Brenden, Wendylee Stott, Jeannette Kanefsky, James Bence
Recent assessments indicate the emergence of naturally produced lake trout (Salvelinus namaycush) recruitment throughout Lake Huron in the North American Laurentian Great Lakes (>50% of fish <7 yrs). Because naturally produced fish derived from different stocked hatchery strains are unmarked, managers cannot distinguish strains contributing to natural recruitment. We used 15 microsatellite loci to identify strains of naturally produced lake trout (N=1567) collected in assessment fisheries during early (2002-2004) and late (2009-2012) sampling periods...
June 19, 2018: Journal of Heredity
Jin Jin, Lin Zhang, Ethan Leng, Gregory J Metzger, Joseph S Koopmeiners
Multiparametric magnetic resonance imaging (mpMRI), which combines traditional anatomic and newer quantitative MRI methods, has been shown to result in improved voxel-wise classification of prostate cancer as compared with any single MRI parameter. While these results are promising, substantial heterogeneity in the mpMRI parameter values and voxel-wise prostate cancer risk has been observed both between and within regions of the prostate. This suggests that classification of prostate cancer can potentially be improved by incorporating structural information into the classifier...
June 19, 2018: Statistics in Medicine
Michael J Kofler, Jamie A Spiegel, Elia F Soto, Lauren N Irwin, Erica L Wells, Kristin E Austin
Reading problems are common in children with ADHD and show strong covariation with these children's underdeveloped working memory abilities. In contrast, working memory training does not appear to improve reading performance for children with ADHD or neurotypical children. The current study bridges the gap between these conflicting findings, and combines dual-task methodology with Bayesian modeling to examine the role of working memory for explaining ADHD-related reading problems. Children ages 8-13 (M = 10...
June 19, 2018: Journal of Abnormal Child Psychology
Stuart K Watson, Gillian L Vale, Lydia M Hopper, Lewis G Dean, Rachel L Kendal, Elizabeth E Price, Lara A Wood, Sarah J Davis, Steven J Schapiro, Susan P Lambeth, Andrew Whiten
Studies of transmission biases in social learning have greatly informed our understanding of how behaviour patterns may diffuse through animal populations, yet within-species inter-individual variation in social information use has received little attention and remains poorly understood. We have addressed this question by examining individual performances across multiple experiments with the same population of primates. We compiled a dataset spanning 16 social learning studies (26 experimental conditions) carried out at the same study site over a 12-year period, incorporating a total of 167 chimpanzees...
June 19, 2018: Animal Cognition
Peida Zhan, Manqian Liao, Yufang Bian
In joint models for item response times (RTs) and response accuracy (RA), local item dependence is composed of local RA dependence and local RT dependence. The two components are usually caused by the same common stimulus and emerge as pairs. Thus, the violation of local item independence in the joint models is called paired local item dependence. To address the issue of paired local item dependence while applying the joint cognitive diagnosis models (CDMs), this study proposed a joint testlet cognitive diagnosis modeling approach...
2018: Frontiers in Psychology
Seung Eun Jung, Seoyoun Kim, Alex Bishop, Janice Hermann
BACKGROUND: Understanding of the mechanisms of how food insecurity and poor physical and mental health status are interrelated with nutritional status among older adults is needed due to their unique health and social needs. OBJECTIVE: To examine the complex relationships between self-care capacity, depressive symptoms, food insecurity, and nutritional status among low-income older adults. DESIGN: The cross-sectional study was conducted from February 2017 to May 2017...
June 16, 2018: Journal of the Academy of Nutrition and Dietetics
Zuyao Liu, Guoling Chen, Tianqi Zhu, Zhaochi Zeng, Zhitong Lyu, Jian Wang, Kevin Messenger, Anthony J Greenberg, Zixiao Guo, Ziheng Yang, Suhua Shi, Yingyong Wang
Diversity and distributions of cryptic species have long been a vexing issue. Identification of species boundaries is made difficult by the lack of obvious morphological differences. Here, we investigate the cryptic diversity and evolutionary history of an underappreciated group of Asian frog species (Megophrys) to explore the pattern and dynamic of amphibian cryptic species. We sequenced four mitochondrial genes and five nuclear genes and delineated species using multiple approaches, combining DNA and mating-call data...
June 16, 2018: Molecular Phylogenetics and Evolution
Gary Napier, Duncan Lee, Chris Robertson, Andrew Lawson
Population-level disease risk across a set of non-overlapping areal units varies in space and time, and a large research literature has developed methodology for identifying clusters of areal units exhibiting elevated risks. However, almost no research has extended the clustering paradigm to identify groups of areal units exhibiting similar temporal disease trends. We present a novel Bayesian hierarchical mixture model for achieving this goal, with inference based on a Metropolis-coupled Markov chain Monte Carlo ((MC)$^3$) algorithm...
June 18, 2018: Biostatistics
Yasuhiro Horita, Abdullah Alsultan, Awewura Kwara, Sampson Antwi, Antony Enimil, Antoinette Orstin, Albert Dompreh, Hongmei Yang, Lubbe Wiesner, Charles A Peloquin
Optimal doses for anti-tuberculosis (TB) drugs in children have yet to be established. In 2010, the World Health Organization (WHO) recommended revised dosages of the first-line anti-TB drugs for children. Pharmacokinetic (PK) studies that investigated the adequacy of the WHO revised dosages to date have yielded conflicting results. We performed population PK modeling using data from one of these studies to identify optimal dosages ranges. Ghanaian children with tuberculosis on recommended therapy with rifampin (RIF), isoniazid (INH), pyrazinamide (PZA) and ethambutol (EMB) for at least 4 weeks had blood samples collected at pre-dose, 1, 2, 4, and 8-hours post-dose...
June 18, 2018: Antimicrobial Agents and Chemotherapy
Bo Hu
The long-term care system in China relies heavily on informal care provided by family members. This study makes projections on the demand for informal care among Chinese older people between 2015 and 2035 and quantifies the level of long-term care resources needed to meet their needs. The data come from longitudinal information in a nationally representative sample, China Health and Retirement Longitudinal Survey 2011 and 2013. The macrosimulation approach (PSSRU model) and the Markov approach are integrated into one Bayesian modelling framework...
June 19, 2018: Health Economics, Policy, and Law
Ali Toosi, Rohan L Fernando, Jack C M Dekkers
BACKGROUND: Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to model these confounding factors and minimize their impact on the results of genome-wide association studies. In most of these methods, a two-stage approach is applied where: (1) methods are used to determine if there is a population structure in the sample dataset and (2) the effects of population structure are corrected either by modeling it or by running a separate analysis within each sub-population...
June 19, 2018: Genetics, Selection, Evolution: GSE
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