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Bayesian modeling

Kristina Weber, Rob Hemmings, Armin Koch
A common challenge for the development of drugs in rare diseases and special populations, eg, paediatrics, is the small numbers of patients that can be recruited into clinical trials. Extrapolation can be used to support development and licensing in paediatrics through the structured integration of available data in adults and prospectively generated data in paediatrics to derive conclusions that support licensing decisions in the target paediatric population. In this context, Bayesian analyses have been proposed to obtain formal proof of efficacy of a new drug or therapeutic principle by using additional information (data, opinion, or expectation), expressed through a prior distribution...
April 17, 2018: Pharmaceutical Statistics
Bernard X W Liew, Christopher C Drovandi, Samuel Clifford, Justin W L Keogh, Susan Morris, Kevin Netto
Background: There is convincing evidence for the benefits of resistance training on vertical jump improvements, but little evidence to guide optimal training prescription. The inability to detect small between modality effects may partially reflect the use of ANOVA statistics. This study represents the results of a sub-study from a larger project investigating the effects of two resistance training methods on load carriage running energetics. Bayesian statistics were used to compare the effectiveness of isoinertial resistance against speed-power training to change countermovement jump (CMJ) and squat jump (SJ) height, and joint energetics...
2018: PeerJ
Simon J Moore, James T MacDonald, Sarah Wienecke, Alka Ishwarbhai, Argyro Tsipa, Rochelle Aw, Nicolas Kylilis, David J Bell, David W McClymont, Kirsten Jensen, Karen M Polizzi, Rebekka Biedendieck, Paul S Freemont
Native cell-free transcription-translation systems offer a rapid route to characterize the regulatory elements (promoters, transcription factors) for gene expression from nonmodel microbial hosts, which can be difficult to assess through traditional in vivo approaches. One such host, Bacillus megaterium , is a giant Gram-positive bacterium with potential biotechnology applications, although many of its regulatory elements remain uncharacterized. Here, we have developed a rapid automated platform for measuring and modeling in vitro cell-free reactions and have applied this to B...
April 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
Sarah Tan, Susanna Makela, Daliah Heller, Kevin Konty, Sharon Balter, Tian Zheng, James H Stark
Existing methods to estimate the prevalence of chronic hepatitis C (HCV) in New York City (NYC) are limited in scope and fail to assess hard-to-reach subpopulations with highest risk such as injecting drug users (IDUs). To address these limitations, we employ a Bayesian multi-parameter evidence synthesis model to systematically combine multiple sources of data, account for bias in certain data sources, and provide unbiased HCV prevalence estimates with associated uncertainty. Our approach improves on previous estimates by explicitly accounting for injecting drug use and including data from high-risk subpopulations such as the incarcerated, and is more inclusive, utilizing ten NYC data sources...
February 3, 2018: Epidemics
Kingsley P Storer, George N Reeke
BACKGROUND: Propofol produces memory impairment at concentrations well below those abolishing consciousness. Episodic memory, mediated by the hippocampus, is most sensitive. Two potentially overlapping scenarios may explain how γ-aminobutyric acid receptor type A (GABAA) potentiation by propofol disrupts episodic memory-the first mediated by shifting the balance from excitation to inhibition while the second involves disruption of rhythmic oscillations. We use a hippocampal network model to explore these scenarios...
April 17, 2018: Anesthesiology
L Angela Mihai, Thomas E Woolley, Alain Goriely
Biological and synthetic materials often exhibit intrinsic variability in their elastic responses under large strains, owing to microstructural inhomogeneity or when elastic data are extracted from viscoelastic mechanical tests. For these materials, although hyperelastic models calibrated to mean data are useful, stochastic representations accounting also for data dispersion carry extra information about the variability of material properties found in practical applications. We combine finite elasticity and information theories to construct homogeneous isotropic hyperelastic models with random field parameters calibrated to discrete mean values and standard deviations of either the stress-strain function or the nonlinear shear modulus, which is a function of the deformation, estimated from experimental tests...
March 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Jian Zeng, Ronald de Vlaming, Yang Wu, Matthew R Robinson, Luke R Lloyd-Jones, Loic Yengo, Chloe X Yap, Angli Xue, Julia Sidorenko, Allan F McRae, Joseph E Powell, Grant W Montgomery, Andres Metspalu, Tonu Esko, Greg Gibson, Naomi R Wray, Peter M Visscher, Jian Yang
We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance...
April 16, 2018: Nature Genetics
Michael A Lyons
Pretomanid is a nitroimidazole antibiotic in late phase clinical testing as a component of several novel antituberculosis (anti-TB) regimens. A population pharmacokinetic model for pretomanid was constructed using a Bayesian analysis of data from two phase 2 studies, PA-824-CL-007 and PA-824-CL-010, conducted with newly diagnosed adult (median age 27 years) pulmonary TB patients in Cape Town, South Africa. Combined, these studies included 63 males and 59 females administered once daily oral pretomanid doses of 50, 100, 150, 200, 600, 1000, or 1200 mg for 14 days...
April 16, 2018: Antimicrobial Agents and Chemotherapy
Heng Zhou, Ying Yuan, Lei Nie
A number of novel model-based and model-assisted designs have been proposed to find the maximum tolerated dose (MTD) in phase I clinical trials, but their differences and relative pros and cons are not clear to many practitioners. We review three model-based designs, including the continual reassessment method (CRM), dose escalation with overdose control (EWOC), and Bayesian logistic regression model (BLRM), and three model-assisted designs, including the modified toxicity probability interval (mTPI), Bayesian optimal interval (BOIN), and keyboard designs...
April 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Xiulan Han, Junming Li, Nannan Wang
BACKGROUND: Most countries are experiencing growth in the number and proportion of their ageing populations and this issue is posing challenges for economies and societies worldwide. The most populated country in the world, China, is experiencing a dramatic increase in its ageing population. As China is the world's largest developing country, its serious ageing issue may have far-reaching effects not only domestically but also in other countries and even globally. METHODS: In order to overcome the weaknesses of traditional statistical models and reveal further detail regarding the local area evolution, an improved Bayesian space-time model is presented in this paper and used to estimate the spatiotemporal evolution of Chinese ageing from 1992 to 2015...
April 16, 2018: BMC Public Health
Peter Milanov, Gergana Koroleova, Radoslav Mavrevski, Nevena Pencheva
PURPOSE: The aim of this study was to investigate the curve fitting and model selection problem of the torque-velocity relationship of elbow flexors and extensors in untrained females. The second goal was to determine the optimal models in different function classes and the best, among the optimal ones. Lastly, test the best models to predict the torque were tested. METHODS: Using the polynomials (second - fourth degree) and Boltzmann sigmoid functions, and a different presentation of data points (averages, a point cloud, etc...
2018: Acta of Bioengineering and Biomechanics
Yi-Hsien Cheng, Jim E Riviere, Nancy A Monteiro-Riviere, Zhoumeng Lin
This study aimed to conduct an integrated and probabilistic risk assessment of gold nanoparticles (AuNPs) based on recently published in vitro and in vivo toxicity studies coupled to a physiologically based pharmacokinetic (PBPK) model. Dose-response relationships were characterized based on cell viability assays in various human cell types. A previously well-validated human PBPK model for AuNPs was applied to quantify internal concentrations in liver, kidney, skin, and venous plasma. By applying a Bayesian-based probabilistic risk assessment approach incorporating Monte Carlo simulation, probable human cell death fractions were characterized...
April 14, 2018: Nanotoxicology
C M Pooley, G Marion
While model evidence is considered by Bayesian statisticians as a gold standard for model selection (the ratio in model evidence between two models giving the Bayes factor), its calculation is often viewed as too computationally demanding for many applications. By contrast, the widely used deviance information criterion (DIC), a different measure that balances model accuracy against complexity, is commonly considered a much faster alternative. However, recent advances in computational tools for efficient multi-temperature Markov chain Monte Carlo algorithms, such as steppingstone sampling (SS) and thermodynamic integration schemes, enable efficient calculation of the Bayesian model evidence...
March 2018: Royal Society Open Science
Famke Jansen, Pierre Dorny, Sarah Gabriël, Ramon Marc Eichenberger, Dirk Berkvens
A Bayesian model was developed to estimate values for the prevalence and diagnostic test characteristics of bovine cysticercosis (Taenia saginata) by combining results of four imperfect tests. Samples of 612 bovine carcases that were found negative for cysticercosis during routine meat inspection collected at three Belgian slaughterhouses, underwent enhanced meat inspection (additional incisions in the heart), dissection of the predilection sites, B158/B60 Ag-ELISA and ES Ab-ELISA. This Bayesian approach allows for the combination of prior expert opinion with experimental data to estimate the true prevalence of bovine cysticercosis in the absence of a gold standard test...
April 30, 2018: Veterinary Parasitology
F Alarid-Escudero, E A Enns, R F MacLehose, J Parsonnet, J M Torres, K M Kuntz
Helicobacter pylori (H. pylori) is present in the stomach of half of the world's population. The force of infection describes the rate at which susceptibles acquire infection. In this article, we estimated the age-specific force of infection of H. pylori in Mexico. Data came from a national H. pylori seroepidemiology survey collected in Mexico in 1987-88. We modelled the number of individuals with H. pylori at a given age as a binomial random variable. We assumed that the cumulative risk of infection by a given age follows a modified exponential catalytic model, allowing some fraction of the population to remain uninfected...
April 16, 2018: Epidemiology and Infection
Chiara Bulgarelli, Anna Blasi, Simon Arridge, Samuel Powell, Carina de Klerk, Victoria Southgate, Sabrina Brigadoi, William Penny, Sungho Tak, Antonia Hamilton
Tracking the connectivity of the developing brain from infancy through childhood is an area of increasing research interest, and fNIRS provides an ideal method for studying the infant brain as it is compact, safe and robust to motion. However, data analysis methods for fNIRS are still underdeveloped compared to those available for fMRI. Dynamic causal modelling (DCM) is an advanced connectivity technique developed for fMRI data, that aims to estimate the coupling between brain regions and how this might be modulated by changes in experimental conditions...
April 12, 2018: NeuroImage
Tomer D Ullman, Andreas Stuhlmüller, Noah D Goodman, Joshua B Tenenbaum
Humans acquire their most basic physical concepts early in development, and continue to enrich and expand their intuitive physics throughout life as they are exposed to more and varied dynamical environments. We introduce a hierarchical Bayesian framework to explain how people can learn physical parameters at multiple levels. In contrast to previous Bayesian models of theory acquisition (Tenenbaum, Kemp, Griffiths, & Goodman, 2011), we work with more expressive probabilistic program representations suitable for learning the forces and properties that govern how objects interact in dynamic scenes unfolding over time...
April 10, 2018: Cognitive Psychology
Christopher J Brown, Michael T Brett, Maria Fernanda Adame, Ben Stewart-Koster, Stuart E Bunn
Mixing models have become requisite tools for analyzing biotracer data, most commonly stable isotope ratios, to infer dietary contributions of multiple sources to a consumer. However, Bayesian mixing models will always return a result that defaults to their priors if the data poorly resolve the source contributions, and thus, their interpretation requires caution. We describe an application of information theory to quantify how much has been learned about a consumer's diet from new biotracer data. We apply the approach to two example data sets...
April 12, 2018: Oecologia
Heena Ambreen, Shivendra Kumar, Amar Kumar, Manu Agarwal, Arun Jagannath, Shailendra Goel
Carthamus tinctorius L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index ( H = 0...
2018: Frontiers in Plant Science
Daniel Magee, Jesse E Taylor, Matthew Scotch
The use of generalized linear models in Bayesian phylogeography has enabled researchers to simultaneously reconstruct the spatiotemporal history of a virus and quantify the contribution of predictor variables to that process. However, little is known about the sensitivity of this method to the choice of the discrete state partition. Here we investigate this question by analyzing a data set containing 299 sequences of the West Nile virus envelope gene sampled in the United States and fifteen predictors aggregated at four spatial levels...
April 12, 2018: Scientific Reports
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