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P D S N Somarathna, Budiman Minasny, Brendan P Malone, Uta Stockmann, Alex B McBratney
Spatial modelling of environmental data commonly only considers spatial variability as the single source of uncertainty. In reality however, the measurement errors should also be accounted for. In recent years, infrared spectroscopy has been shown to offer low cost, yet invaluable information needed for digital soil mapping at meaningful spatial scales for land management. However, spectrally inferred soil carbon data are known to be less accurate compared to laboratory analysed measurements. This study establishes a methodology to filter out the measurement error variability by incorporating the measurement error variance in the spatial covariance structure of the model...
March 8, 2018: Science of the Total Environment
Xulong Wang, Vivek M Philip, Guruprasad Ananda, Charles C White, Ankit Malhotra, Paul J Michalski, Krishna R Murthy Karuturi, Sumana R Chintalapudi, Casey Acklin, Michael Sasner, David A Bennett, Philip L De Jager, Gareth R Howell, Gregory W Carter
Recent technical and methodological advances have greatly enhanced genome-wide association studies (GWAS). The advent of low-cost whole-genome sequencing facilitates high-resolution variant identification, and the development of linear mixed models (LMM) allows improved identification of putatively causal variants. While essential for correcting false positive associations due to sample relatedness and population stratification, LMMs have commonly been restricted to quantitative variables. However, phenotypic traits in association studies are often categorical, coded as binary case-control or ordered variables describing disease stages...
March 5, 2018: Genetics
Sabrina N Portelli, Andrés S Quinteros
The genus Liolaemus comprises more than 260 species and can be divided in two subgenera: Eulaemus and Liolaemus sensu stricto . In this paper, we present a phylogenetic analysis, divergence times, and ancestral distribution ranges of the Liolaemus alticolor-bibronii group ( Liolaemus sensu stricto subgenus). We inferred a total evidence phylogeny combining molecular ( Cytb and 12S genes) and morphological characters using Maximum Parsimony and Bayesian Inference. Divergence times were calculated using Bayesian MCMC with an uncorrelated lognormal distributed relaxed clock, calibrated with a fossil record...
2018: PeerJ
Milan Malinsky, Emiliano Trucchi, Daniel John Lawson, Daniel Falush
Powerful approaches to inferring recent or current population structure based on nearest neighbour haplotype 'coancestry' have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in non-model organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure - a complete, easy to use, and fast population inference package for RADseq data (https://github...
February 20, 2018: Molecular Biology and Evolution
Jeremy M Brown, Robert C Thomson
Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior distributions can result from a variety of factors, including unmodeled variation in evolutionary processes and unrecognized variation in the true topology across sites or genes...
February 15, 2018: Systematic Biology
C Edson Utazi, Julia Thorley, Victor A Alegana, Matthew J Ferrari, Saki Takahashi, C Jessica E Metcalf, Justin Lessler, Andrew J Tatem
BACKGROUND: The expansion of childhood vaccination programs in low and middle income countries has been a substantial public health success story. Indicators of the performance of intervention programmes such as coverage levels and numbers covered are typically measured through national statistics or at the scale of large regions due to survey design, administrative convenience or operational limitations. These mask heterogeneities and 'coldspots' of low coverage that may allow diseases to persist, even if overall coverage is high...
February 14, 2018: Vaccine
Arunabha Majumdar, Tanushree Haldar, Sourabh Bhattacharya, John S Witte
Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy). For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes) that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus...
February 2018: PLoS Genetics
Alberto Pessia, Jukka Corander, Bonnie Berger
Motivation: Estimation of the hidden population structure is an important step in many genetic studies. Often the aim is also to identify which sequence locations are the most discriminative between groups of samples for a given data partition. Automated discovery of interesting patterns that are present in the data can help to generate new biological hypotheses. Results: We introduce Kpax3, a Bayesian method for bi-clustering multiple sequence alignments. Influence of individual sites will be determined in a supervised manner by using informative prior distributions for the model parameters...
February 7, 2018: Bioinformatics
Stanisław Adaszewski, David Slater, Lester Melie-Garcia, Bogdan Draganski, Piotr Bogorodzki
We introduce a new approach to Bayesian pRF model estimation using Markov Chain Monte Carlo (MCMC) sampling for simultaneous estimation of pRF and hemodynamic parameters. To obtain high performance on commonly accessible hardware we present a novel heuristic consisting of interpolation between precomputed responses for predetermined stimuli and a large cross-section of receptive field parameters. We investigate the validity of the proposed approach with respect to MCMC convergence, tuning and biases. We compare different combinations of pRF - Compressive Spatial Summation (CSS), Dumoulin-Wandell (DW) and hemodynamic (5-parameter and 3-parameter Balloon-Windkessel) models within our framework with and without the usage of the new heuristic...
January 30, 2018: NeuroImage
Grant D Brown, Aaron T Porter, Jacob J Oleson, Jessica A Hinman
Approximate Bayesia n Computation (ABC) provides an attractive approach to estimation in complex Bayesian inferential problems for which evaluation of the kernel of the posterior distribution is impossible or computationally expensive. These highly parallelizable techniques have been successfully applied to many fields, particularly in cases where more traditional approaches such as Markov chain Monte Carlo (MCMC) are impractical. In this work, we demonstrate the application of approximate Bayesian inference to spatially heterogeneous Susceptible-Exposed-Infectious-Removed (SEIR) stochastic epidemic models...
February 2018: Spatial and Spatio-temporal Epidemiology
Masaki Takahashi, Koo Nagasawa, Koichi Saito, Shun-Ichi Maisawa, Kiyotaka Fujita, Koichi Murakami, Makoto Kuroda, Akihide Ryo, Hirokazu Kimura
We performed detailed genetic analyses of the partial hemagglutinin-neuraminidase (HN) gene in 34 human respirovirus 3 (HRV3) strains from children with acute respiratory illness during 2013-2015 in Iwate Prefecture, Japan. In addition, we performed analyses of the evolutionary timescale of the gene using the Bayesian Markov chain Monte Carlo (MCMC) method. Furthermore, we analyzed pairwise distances and performed selective pressure analyses followed by linear B-cell epitope mapping and N-glycosylation and phylodynamic analyses...
February 2, 2018: Infection, Genetics and Evolution
Qiaolin Chen, Catherine A Sugar, Robert E Weiss
Researchers collected multiple measurements on patients with schizophrenia and their relatives, as well as control subjects and their relatives, to study vulnerability factors for schizophrenics and their near relatives. Observations across individuals from the same family are correlated, and also the multiple outcome measures on the same individuals are correlated. Traditional data analyses model outcomes separately and thus do not provide information about the interrelationships among outcomes. We propose a novel Bayesian family factor model (BFFM), which extends the classical confirmatory factor analysis model to explain the correlations among observed variables using a combination of family-member and outcome factors...
February 5, 2018: Statistics in Medicine
Riddhi Singh, Julianne D Quinn, Patrick M Reed, Klaus Keller
Many coupled human-natural systems have the potential to exhibit a highly nonlinear threshold response to external forcings resulting in fast transitions to undesirable states (such as eutrophication in a lake). Often, there are considerable uncertainties that make identifying the threshold challenging. Thus, rapid learning is critical for guiding management actions to avoid abrupt transitions. Here, we adopt the shallow lake problem as a test case to compare the performance of four common data assimilation schemes to predict an approaching transition...
2018: PloS One
Ruth Lazkoz, Iker Leanizbarrutia, Vincenzo Salzano
The cosmological redshift drift could lead to the next step in high-precision cosmic geometric observations, becoming a direct and irrefutable test for cosmic acceleration. In order to test the viability and possible properties of this effect, also called Sandage-Loeb (SL) test, we generate a model-independent mock data set in order to compare its constraining power with that of the future mock data sets of Type Ia Supernovae (SNe) and Baryon Acoustic Oscillations (BAO). The performance of those data sets is analyzed by testing several cosmological models with the Markov chain Monte Carlo (MCMC) method, both independently as well as combining all data sets...
2018: European Physical Journal. C, Particles and Fields
Fernando Racimo, Jeremy J Berg, Joseph K Pickrell
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred...
January 18, 2018: Genetics
Kan Shao, Andrew J Shapiro
BACKGROUND: Benchmark dose (BMD) modeling is an important step in human health risk assessment and is used as the default approach to identify the point of departure for risk assessment. A probabilistic framework for dose-response assessment has been proposed and advocated by various institutions and organizations; therefore, a reliable tool is needed to provide distributional estimates for BMD and other important quantities in dose-response assessment. OBJECTIVES: We developed an online system for Bayesian BMD (BBMD) estimation and compared results from this software with U...
January 11, 2018: Environmental Health Perspectives
Xiaodan Sun, Yanni Xiao, Zhihang Peng, Ning Wang
Intervention measures among men who have sex with men (MSM) are usually designed to reduce the frequency of high risk behaviors (within-community level), but unfortunately may change the contact network and consequently increase the opportunity for them to have sex with new partners (between-community level). A multi-community periodic model on complex network is proposed to study the two-side effects of interventions on HIV transmission among MSM in China, in which the wanning process of the impacts of interventions are modelled...
January 11, 2018: Scientific Reports
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
Toshihiro Shida, Yuji Endo, Tadashi Shiraishi, Takashi Yoshioka, Kaoru Suzuki, Yuka Kobayashi, Yuki Ono, Toshinori Ito, Tadao Inoue
 We evaluated four representative chemotherapy regimens for unresectable advanced or recurrent KRAS-wild type colorectal cancer: mFOLFOX6, mFOLFOX6+bevacizumab (Bmab), cetuximab (Cmab), or panitumumab (Pmab). We employed a decision analysis method in combination with clinical and economic evidence. The health outcomes of the regimens were analyzed on the basis of overall and progression-free survival. The data were drawn from the literature on randomized controlled clinical trials of the above-mentioned drugs...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
Andrew J Myrick, Thomas C Baker
Gas-chromatography-electroantennographic detection (GC-EAD) is a technique used in the identification of volatile organic compounds (VOCs), such as pheromones and plant host odors, which are physiologically relevant to insects. Although pheromones often elicit large EAD responses, other behaviorally relevant odors may elicit responses that are difficult to discern from noise. Lock-in amplification has long been used to reduce noise in a wide range of applications. Its utility when incorporated with GC-EAD was demonstrated previosuly by chopping (or pulsing) effluent-laden air that flowed over an insect antenna...
January 6, 2018: Journal of Chemical Ecology
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