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Bayesian model

Benjamin Stich, Delphine Van Inghelandt
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy...
2018: Frontiers in Plant Science
Zaneta M Thayer, Meredith A Wilson, Andrew W Kim, Adrian V Jaeggi
Prenatal exposure to maternal stress is commonly associated with variation in Hypothalamic Pituitary Adrenal (HPA)-axis functioning in offspring. However, the strength or consistency of this response has never been empirically evaluated across vertebrate species. Here we meta-analyzed 114 results from 39 studies across 14 vertebrate species using Bayesian phylogenetic mixed-effects models. We found a positive overall effect of prenatal stress on offspring glucocorticoids (d' = 0.43) though the 95% Highest Posterior Density Interval overlapped with 0 (-0...
March 21, 2018: Scientific Reports
Timothy M Rawson, Esmita Charani, Luke Sp Moore, Mark Gilchrist, Pantelis Georgiou, William Hope, Alison H Holmes
BackgroundC-reactive protein (CRP) pharmacodynamic (PD) models have the potential to provide adjunctive methods for predicting the individual exposure-response to antimicrobial therapy. We investigated CRP PD linked to a vancomycin pharmacokinetics (PK) model using routinely collected data from non-critical care adults in secondary care.MethodsPatients receiving intermittent intravenous vancomycin therapy in secondary care were identified. A two-compartment vancomycin PK model was linked to a previously described PD model describing CRP response...
March 20, 2018: Therapeutic Drug Monitoring
Claire O'Callaghan, Julie M Hall, Alessandro Tomassini, Alana J Muller, Ishan C Walpola, Ahmed A Moustafa, James M Shine, Simon J G Lewis
BACKGROUND: Models of hallucinations emphasize imbalance between sensory input and top-down influences over perception, as false perceptual inference can arise when top-down predictions are afforded too much precision (certainty) relative to sensory evidence. Visual hallucinations in Parkinson's disease (PD) are associated with lower-level visual and attentional impairments, accompanied by overactivity in higher-order association brain networks. PD therefore provides an attractive framework to explore contributions of bottom-up versus top-down disturbances in hallucinations...
November 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Francisco Javier Navas González, Jordi Jordana Vidal, María Esperanza Camacho Vallejo, Jose Manuel León Jurado, Manuel Rafael de la Haba Giraldo, Cecilio Barba Capote, Juan Vicente Delgado Bermejo
Cutaneous habronematidosis (CH) is a highly prevalent seasonally recurrent skin disease that affects donkeys as a result from the action of spirurid stomach worm larvae. Carrier flies mistakenly deposit these larvae on previous skin lesions or on the moisture of natural orifices, causing distress and inflicting relapsing wounds to the animals. First, we carried out a meta-analysis of the predisposing factors that could condition the development of CH in Andalusian donkeys. Second, basing on the empirical existence of an inter and intrafamilial variation previously addressed by owners, we isolated the genetic background behind the hypersensibility to this parasitological disease...
March 15, 2018: Veterinary Parasitology
Kelson Zawack, Will Love, Cristina Lanzas, James G Booth, Yrjö T Gröhn
The growth of antimicrobial resistance presents a significant threat to human and animal health. Of particular concern is multi-drug resistance, as this increases the chances an infection will be untreatable by any antibiotic. In order to understand multi-drug resistance, it is essential to understand the association between drug resistances. Pairwise associations characterize the connectivity between resistances and are useful in making decisions about courses of treatment, or the design of drug cocktails...
April 1, 2018: Preventive Veterinary Medicine
Oswaldo Santos Baquero, Fernando Ferreira, Marcelo Robis, José Soares Ferreira Neto, Jason Ardila Onell
Animal abuse adversely affects animal health and welfare and has been associated with interpersonal violence in studies of individuals. However, if that association also depends on sociocultural contexts and can be detected on a geographic scale, a wider source of data can be used to identify risk areas to support the surveillance of both types of violence. In this study, we evaluated the association between interpersonal violence notifications, animal abuse notifications and an index of social vulnerability in São Paulo City, on a geographic scale, using Bayesian spatial models...
April 1, 2018: Preventive Veterinary Medicine
Shaheen A Abdulkareem, Ellen-Wien Augustijn, Yaseen T Mustafa, Tatiana Filatova
BACKGROUND: Millions of people worldwide are exposed to deadly infectious diseases on a regular basis. Breaking news of the Zika outbreak for instance, made it to the main media titles internationally. Perceiving disease risks motivate people to adapt their behavior toward a safer and more protective lifestyle. Computational science is instrumental in exploring patterns of disease spread emerging from many individual decisions and interactions among agents and their environment by means of agent-based models...
March 20, 2018: International Journal of Health Geographics
Yanyong Guo, Zhibin Li, Yao Wu, Chengcheng Xu
Bicyclists running the red light at crossing facilities increase the potential of colliding with motor vehicles. Exploring the contributing factors could improve the prediction of running red-light probability and develop countermeasures to reduce such behaviors. However, individuals could have unobserved heterogeneities in running a red light, which make the accurate prediction more challenging. Traditional models assume that factor parameters are fixed and cannot capture the varying impacts on red-light running behaviors...
March 17, 2018: Accident; Analysis and Prevention
Ida Robertsen, Jean Debord, Anders Åsberg, Pierre Marquet, Jean-Baptiste Woillard
BACKGROUND AND OBJECTIVE: Intracellular exposure of everolimus may be a better marker of therapeutic effect than trough whole blood concentrations. We aimed to develop pharmacokinetic population models and Bayesian estimators based on a limited sampling strategy for estimation of dose interval exposures of everolimus in whole blood and peripheral blood mononuclear cells (PBMCs) in renal transplant recipients. METHODS: Full whole blood and PBMC concentration-time profiles of everolimus were obtained from 12 stable renal transplant recipients on two different occasions, 4 weeks apart...
March 20, 2018: Clinical Pharmacokinetics
Miguel Ángel Lozada Aguilar, Andrei Khrennikov, Klaudia Oleschko
As was recently shown by the authors, quantum probability theory can be used for the modelling of the process of decision-making (e.g. probabilistic risk analysis) for macroscopic geophysical structures such as hydrocarbon reservoirs. This approach can be considered as a geophysical realization of Hilbert's programme on axiomatization of statistical models in physics (the famous sixth Hilbert problem). In this conceptual paper , we continue development of this approach to decision-making under uncertainty which is generated by complexity, variability, heterogeneity, anisotropy, as well as the restrictions to accessibility of subsurface structures...
April 28, 2018: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Hayley Treloar Padovano, Robert Miranda
OBJECTIVE: The present study used youth's in vivo reports of subjective responses to cannabis while smoking in their natural environments to identify real-world mechanisms of topiramate treatment for cannabis misuse. METHOD: Participants were 40 cannabis users (≥ twice weekly in past 30 days), ages 15-24 years (47.5% female), with at least one cannabis use episode during the final 3 weeks of a 6-week, randomized clinical trial. Youth reported subjective "high" while smoking, stimulation, sedation, stress, craving, and grams of marijuana used in the natural environment via wireless electronic devices...
March 2018: Journal of Studies on Alcohol and Drugs
Dong Leng, Ran Miao, Xiaoxi Huang, Ying Wang
Octamer-binding protein 2 (Oct2) binds to the ATGCAAAT octamer on the IgH enhancer and stimulates IgH expression in human multiple myeloma (MM). Cysteine-rich secreted protein 3 (CRISP3) possesses the ATGCAAAT sequence and thus is activated by Oct2 in mouse B cells, suggesting that CRISP3 may be activated in and be a potential biomarker for MM. The present study involved a meta-analysis of the gene expression profiling data of human MM peripheral blood. Significantly expressed genes were analyzed on merged super array microarray data and selected sample data with significantly expressed genes were additionally analyzed by principal component analysis and Bayesian probit regression...
April 2018: Oncology Letters
Heidi L Tessmer, Kimihito Ito, Ryosuke Omori
To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, R 0 , is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly R 0 . In this paper, we explore various machine learning approaches, the multi-layer perceptron, convolutional neural network, and long-short term memory, to learn and estimate the parameters. Further, we compare the accuracy of the estimates and time requirements for machine learning and the approximate Bayesian computation methods on both simulated and real-world epidemiological data from outbreaks of influenza A(H1N1)pdm09, mumps, and measles...
2018: Frontiers in Microbiology
Luis M Castro, Wan-Lun Wang, Victor H Lachos, Vanda Inácio de Carvalho, Cristian L Bayes
In biomedical studies, the analysis of longitudinal data based on Gaussian assumptions is common practice. Nevertheless, more often than not, the observed responses are naturally skewed, rendering the use of symmetric mixed effects models inadequate. In addition, it is also common in clinical assays that the patient's responses are subject to some upper and/or lower quantification limit, depending on the diagnostic assays used for their detection. Furthermore, responses may also often present a nonlinear relation with some covariates, such as time...
January 1, 2018: Statistical Methods in Medical Research
Tanja Stadler, Alexandra Gavryushkina, Rachel C M Warnock, Alexei J Drummond, Tracy A Heath
A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model - also referred to as the fossilized birth-death (FBD) model - gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects...
March 14, 2018: Journal of Theoretical Biology
H Song, L Li, P Ma, S Zhang, G Su, M S Lund, Q Zhang, X Ding
This study investigated the efficiency of genomic prediction with adding the markers identified by genome-wide association study (GWAS) using a data set of imputed high-density (HD) markers from 54K markers in Chinese Holsteins. Among 3,056 Chinese Holsteins with imputed HD data, 2,401 individuals born before October 1, 2009, were used for GWAS and a reference population for genomic prediction, and the 220 younger cows were used as a validation population. In total, 1,403, 1,536, and 1,383 significant single nucleotide polymorphisms (SNP; false discovery rate at 0...
March 14, 2018: Journal of Dairy Science
M P L Calus, M E Goddard, Y C J Wientjes, P J Bowman, B J Hayes
Genomic prediction is applicable to individuals of different breeds. Empirical results to date, however, show limited benefits in using information on multiple breeds in the context of genomic prediction. We investigated a multitask Bayesian model, presented previously by others, implemented in a Bayesian stochastic search variable selection (BSSVS) model. This model allowed for evidence of quantitative trait loci (QTL) to be accumulated across breeds or for both QTL that segregate across breeds and breed-specific QTL...
March 14, 2018: Journal of Dairy Science
Marcello Mezzasalma, Mirko Di Febbraro, Fabio Maria Guarino, Gaetano Odierna, Danilo Russo
In this work, we performed a biogeographic analysis with Bayesian binary MCMC (BBM) statistical dispersal-vicariance analysis (S-DIVA) and species distribution models (SDM) on three phylogenetically closely related Mediterranean whipsnakes (Hierophis gemonensis, H. carbonarius, H. viridiflavus), to investigate the pathways of their geographical diversification and locate putative refugial areas in the last glacial maximum (LGM). Our analysis suggests that the diversification processes between the studied species overall followed an east-west route, from eastern Greece to the Iberian Peninsula and continental France, highlighting a significant role of dispersal and vicariance processes at both inter- and intraspecific levels...
February 1, 2018: Zoology: Analysis of Complex Systems, ZACS
Robert T Keys, Anina N Rich, Regine Zopf
Tracking one's own body is essential for environmental interaction, and involves integrating multisensory cues with stored information about the body's typical features. Exactly how multisensory information is integrated in own-body perception is still unclear. For example, Ide and Hidaka (Exp Brain Res 228:43-50, 2013) found that participants made less precise visuo-tactile temporal order judgments (TOJ) when viewing hands in a plausible orientation (upright; typical for one's own hand) compared to an implausible orientation (rotated 180°)...
March 15, 2018: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
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