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Bayesian modeling

Fitsum Abadi, Christophe Barbraud, Olivier Gimenez
Early-life demographic traits are poorly known, impeding our understanding of population processes and sensitivity to climate change. Survival of immature individuals is a critical component of population dynamics and recruitment in particular. However, obtaining reliable estimates of juvenile survival (i.e., from independence to first year) remains challenging, as immatures are often difficult to observe and to monitor individually in the field. This is particularly acute for seabirds, in which juveniles stay at sea and remain undetectable for several years...
October 22, 2016: Global Change Biology
Georgie Powell, Zoe Meredith, Rebecca McMillin, Tom C A Freeman
According to Bayesian models, perception and cognition depend on the optimal combination of noisy incoming evidence with prior knowledge of the world. Individual differences in perception should therefore be jointly determined by a person's sensitivity to incoming evidence and his or her prior expectations. It has been proposed that individuals with autism have flatter prior distributions than do nonautistic individuals, which suggests that prior variance is linked to the degree of autistic traits in the general population...
October 21, 2016: Psychological Science
Bram Thijssen, Tjeerd M H Dijkstra, Tom Heskes, Lodewyk F A Wessels
BACKGROUND: Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. RESULTS: We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers...
October 21, 2016: BMC Systems Biology
Ruifeng Liu, Xueping Yu, Anders Wallqvist
Chemical toxicity is conventionally evaluated in animal models. However, animal models are resource intensive; moreover, they face ethical and scientific challenges because the outcomes obtained by animal testing may not correlate with human responses. To develop an alternative method for assessing chemical toxicity, we investigated the feasibility of using chemical-induced genome-wide expression changes in cultured human cells to predict the potential of a chemical to cause specific organ injuries in humans...
October 21, 2016: Chemical Research in Toxicology
Claire Montlahuc, Emmanuel Curis, Sarah Flora Jonas, Frank Bellivier, Sylvie Chevret
Gaussian mixture analysis is frequently used to model the age-at-onset (AAO) in bipolar I disorder and identify homogeneous subsets of patients. This study aimed to examine whether, using admixture analysis of AAO, cross-sectional designs (which cause right truncation), unreliable diagnosis for individuals younger than 10 years old (which causes left truncation) and the selection criterion used for admixture analysis impact the number of identified subsets. A simulation study was performed. Different criteria - the likelihood ratio test (LRT), the Akaike information criterion (AIC), and the Bayesian information criterion (BIC) - were compared using no, left and/or right truncation simulated data...
October 21, 2016: International Journal of Methods in Psychiatric Research
Xue Li, Jianfeng Feng, Christopher Wellen, Yuqiu Wang
In this study, a modeling framework based on the theory of SPAtially Referenced Regression On Watershed attributes (SPARROW) model was developed to identify impaired river reaches with respect to total nitrogen (TN) and estimate the TN sources in the Xin'anjiang River basin, which had limited monitoring sites. A Bayesian approach was applied to estimate the mean values and uncertainties of parameters, including land use export coefficients and in-stream attention rates. Based on the parameters, the midranges (25-75 %) of annual TN concentrations were assessed by the model and 4...
October 20, 2016: Environmental Science and Pollution Research International
Shasha Yuan, Weidong Zhou, Junhui Li, Qi Wu
Epilepsy is a serious chronic neurological disorder, which affects more than 50 million people worldwide, and automatic seizure detection on EEG recordings is extremely required in the diagnosis and monitoring of epilepsy. This paper presents a novel seizure detection method using sparse representation-based Earth Mover's Distance (SR-EMD). In the proposed algorithm, wavelet decomposition is executed on the original EEG recordings with five scales, and the scales 3, 4 and 5 are selected to structure the distributions of EEG signals...
October 20, 2016: Medical & Biological Engineering & Computing
Erich Kummerfeld, Joseph Ramsey
Many scientific research programs aim to learn the causal structure of real world phenomena. This learning problem is made more difficult when the target of study cannot be directly observed. One strategy commonly used by social scientists is to create measurable "indicator" variables that covary with the latent variables of interest. Before leveraging the indicator variables to learn about the latent variables, however, one needs a measurement model of the causal relations between the indicators and their corresponding latents...
2016: KDD: Proceedings
Ilhem Guesmi-Mzoughi, Antonio Archidona-Yuste, Carolina Cantalapiedra-Navarrete, Hajer Regaieg, Najet Horrigue-Raouani, Juan E Palomares-Rius, Pablo Castillo
Spiral nematode species of the genus Rotylenchus have been reported on olive (Olea europaea L.) in several Mediterranean countries (Castillo et al., 2010; Ali et al., 2014). Nematological surveys for plant-parasitic nematodes on olive trees were carried out in Tunisia between 2013 and 2014, and two nematode species of Rotylenchus were collected from the rhizosphere of olive cv. Chemlali in several localities of Tunisia (Tables 1,2 [Table: see text] [Table: see text] ). Twenty-two soil samples of 3 to 4 kg were collected with a shovel from the upper 50 cm of soil from arbitrarily chosen olive trees...
September 2016: Journal of Nematology
Marie-Charlotte Desseroit, Florent Tixier, Wolfgang Andreas Weber, Barry Alan Siegel, Catherine Cheze Le Rest, Dimitris Visvikis, Mathieu Hatt
PURPOSE: The main purpose of this study was to assess the reliability of shape and heterogeneity features in both PET and low-dose CT components of PET/CT. A secondary objective was to investigate the impact of image quantization. MATERIAL AND METHODS: A HIPAA-compliant secondary analysis of deidentified prospectively acquired PET/CT test-retest datasets of 74 patients from multi-center Merck and ACRIN trials was performed. Metabolically active volumes were automatically delineated on PET with Fuzzy Locally Adaptive Bayesian (FLAB) algorithm...
October 20, 2016: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
Ronny Hedell, Olga Stephansson, Petter Mostad, Mats Gunnar Andersson
Efficient and correct evaluation of sampling results with respect to hypotheses about the concentration or distribution of bacteria generally requires knowledge about the performance of the detection method. To assess the sensitivity of the detection method an experiment is usually performed where the target matrix is spiked (i.e. artificially contaminated) with different concentrations of the bacteria, followed by analyses of the samples using the pre-enrichment method and the analytical detection method of interest...
October 11, 2016: International Journal of Food Microbiology
Ben L Gilby, Andrew D Olds, Rod M Connolly, Tim Stevens, Christopher J Henderson, Paul S Maxwell, Ian R Tibbetts, David S Schoeman, David Rissik, Thomas A Schlacher
Management authorities seldom have the capacity to comprehensively address the full suite of anthropogenic stressors, particularly in the coastal zone where numerous threats can act simultaneously to impact reefs and other ecosystems. This situation requires tools to prioritise management interventions that result in optimum ecological outcomes under a set of constraints. Here we develop one such tool, introducing a Bayesian Belief Network to model the ecological condition of inshore coral reefs in Moreton Bay (Australia) under a range of management actions...
2016: PloS One
Shuai Liu, Licheng Jiao, Shuyuan Yang
During the acquisition process hyperspectral images (HSI) are inevitably corrupted by various noises, which greatly influence their visual impression and subsequent applications. In this paper, a novel Bayesian approach integrating hierarchical sparse learning and spectral-spatial information is proposed for HSI denoising. Based on the structure correlations, spectral bands with similar and continuous features are segmented into the same band-subset. To exploit local similarity, each subset is then divided into overlapping cubic patches...
October 17, 2016: Sensors
Gabriella Juhasz, Eva Csepany, Mate Magyar, Andrea Edit Edes, Nora Eszlari, Gabor Hullam, Peter Antal, Gyongyi Kokonyei, Ian Muir Anderson, John Francis William Deakin, Gyorgy Bagdy
One of the main effects of the endocannabinoid system in the brain is stress adaptation with presynaptic endocannabinoid receptor 1 (CB1 receptors) playing a major role. In the present study, we investigated whether the effect of the CB1 receptor coding CNR1 gene on migraine and its symptoms is conditional on life stress. In a cross-sectional European population (n = 2426), recruited from Manchester and Budapest, we used the ID-Migraine questionnaire for migraine screening, the Life Threatening Experiences questionnaire to measure recent negative life events (RLE), and covered the CNR1 gene with 11 SNPs...
October 19, 2016: Genes, Brain, and Behavior
Xu Steven Xu, Min Yuan, Haitao Yang, Yan Feng, Jinfeng Xu, Jose Pinheiro
Covariate analysis based on population pharmacokinetics (PPK) is used to identify clinically relevant factors. The likelihood ratio test (LRT) based on nonlinear mixed effect model fits is currently recommended for covariate identification, whereas individual empirical Bayesian estimates (EBEs) are considered unreliable due to the presence of shrinkage. The objectives of this research were to investigate the type I error for LRT and EBE approaches, to confirm the similarity of power between the LRT and EBE approaches from a previous report and to explore the influence of shrinkage on LRT and EBE inferences...
October 19, 2016: AAPS Journal
Atsushi Kubo, Jota Kanda
Total organic carbon (TOC), total nitrogen (TN) contents, their stable C and N isotope ratio (δ(13)C and δ(15)N), and chlorophyll a ([Chl a]sed) of surface sediments were investigated monthly to identify the seasonal variations and sources of organic matter in Tokyo Bay. The sedimentary TOC (TOCsed) and TN (TNsed) contents, and the sedimentary δ(13)C and δ(15)N (δ(13)Csed and δ(15)Nsed) values were higher in summer than other seasons. The seasonal variations were controlled by high primary production in the water column and hypoxic water in the bottom water during summer...
October 16, 2016: Marine Pollution Bulletin
Peter Brommesson, Uno Wennergren, Tom Lindström
The structure of contacts that mediate transmission has a pronounced effect on the outbreak dynamics of infectious disease and simulation models are powerful tools to inform policy decisions. Most simulation models of livestock disease spread rely to some degree on predictions of animal movement between holdings. Typically, movements are more common between nearby farms than between those located far away from each other. Here, we assessed spatiotemporal variation in such distance dependence of animal movement contacts from an epidemiological perspective...
2016: PloS One
Yoonsik Shim, Andrew Philippides, Kevin Staras, Phil Husbands
We propose a biologically plausible architecture for unsupervised ensemble learning in a population of spiking neural network classifiers. A mixture of experts type organisation is shown to be effective, with the individual classifier outputs combined via a gating network whose operation is driven by input timing dependent plasticity (ITDP). The ITDP gating mechanism is based on recent experimental findings. An abstract, analytically tractable model of the ITDP driven ensemble architecture is derived from a logical model based on the probabilities of neural firing events...
October 2016: PLoS Computational Biology
M J Pérez-Alvarez, C Olavarría, R Moraga, C S Baker, R M Hamner, E Poulin
The complementarity of historical and contemporary processes contributes to understanding the genetic structure of continuously distributed marine species with high dispersal capabilities. Cephalorhynchus eutropia, has a continuous coastal distribution with strong genetic differentiation identified by nuclear DNA markers. We explored the historical dimension of this genetic differentiation between northern and southern populations to evaluate phylogeographic structure. Additionally, we conducted mtDNA and microsatellite analyses to detect past and recent demographic changes...
October 19, 2016: Scientific Reports
Michael A Grillo, Stephane De Mita, Patricia V Burke, Kathryn L S Solórzano-Lowell, Katy D Heath
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin...
October 19, 2016: Evolution; International Journal of Organic Evolution
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