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61 results for “Bayesian method”
Figure 6 in Global phylogeny of Hadrosauridae (Dinosauria: Ornithopoda) using parsimony and Bayesian methods
Figure 6. Strict reduced consensus tree of the 160 most parsimonious trees resulting from the parsimony analysis of 53 iguanodontian taxa. Posterior to the analysis, Claosaurus agilis, Barsboldia sicinskii, and Nipponosaurus sachalinensis were pruned from the data after implementation of REDCON 3.0 (Wilkinson, 2001b). At each node, the pair of numbers separated by a slash above or below a branch represents, from left to right, a decay index and a bootstrap proportion. Bootstrap proportions lower than 50 are indicted by a hyphen. The decimal number in italics that appears below a branch represents the P value of topology-dependant permutation tail probability (T-PTP) analysis.
Figure 1 in Global phylogeny of Hadrosauridae (Dinosauria: Ornithopoda) using parsimony and Bayesian methods
Figure 1. Dentaries of two specimens of Edmontosaurus in lateral view, showing evidence of postdepositional dorsoventral compression in the form of bending lines (arrows). A, left dentary of Edmontosaurus regalis, CMN 2289. B, right dentary of CMN 2289. C, right dentary of Edmontosaurus annectens, cast of AMNH 5730 (= 'Anatotitan copei').
Figure 2 in Global phylogeny of Hadrosauridae (Dinosauria: Ornithopoda) using parsimony and Bayesian methods
Figure 2. Signs of postdepositional dorsoventral compression (rectangle and arrow) in a specimen of Edmontosaurus annectens, cast of AMNH 5730 (type of 'Anatotitan copei'), lateral view. A, dorsal region of the left quadrate. B, left postorbital.
Figure 3 in Global phylogeny of Hadrosauridae (Dinosauria: Ornithopoda) using parsimony and Bayesian methods
Figure 3. Right prefrontal of Prosaurolophus maximus (MOR 454-6-24-6-2), part of the holotype of Prosaurolophus blackfeetensis, showing a concave surface (arrows) dorsomedial to the orbital margin, in (A) dorsal and (B) lateral views.
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
<p>This repository contains data to reproduce analysis presented in the paper:</p> <p>B. Mourguiart, B. Liquet, K. Mengersen, T. Couturier, J. Mansons, Y. Braud, A. Besnard . A new method to explicitly estimate the shift of optimum along gradients in multispecies studies. <em>Journal of Biogeography</em>, (in press).</p> <p>The paper introduces a new formulation of a Bayesian hierarchical linear model that explicitly estimates optimum shifts for multiple species having symmetrical response curves. This new formulation, called Explicit Hierarchical Model of Optimum Shifts (EHMOS), is compared to a mean comparison method and a Bayesian generalized linear mixed model (GLMM) using simulated and real datasets. Fitting the models to the simulated data took several days. Here we provide the models' outputs needed to reproduce the results presented in the paper without re-running the models. </p>
A Series of N-of-1 Trials of Traditional Chinese Medicine Based on Bayesian Method
ClinicalTrials.gov study NCT04601792. IPD Sharing: YES. Countries: 1. Publications: 6.
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
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Data from: Estimating age and age class of harvested hog deer from eye lens mass using frequentist and Bayesian methods
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Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
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Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets
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Data from: A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression
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Data from: Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf dataset
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Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods
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Data from: Quantifying demographic uncertainty: Bayesian methods for integral projection models (IPMs)
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Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model
<p>Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated <i>in vitro</i>; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 non-diseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for five phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors (TDVF). Toxicokinetic modeling was used for probabilistic <i>in vitro</i>-to-<i>in vivo </i>extrapolation in order to derive population-wide margins of safety (MOS) for pharmaceuticals and margins of exposure (MOE) for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. TDVF estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally-assumed default of ~3. Population variability-based MOS for pharmaceuticals were correctly predicted to be relatively narrow, between 10-100; however, MOE for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at general population exposures even to sensitive sub populations. This study represents a first of its kind human <i>in vitro</i> model that can be used to characterize toxicodynamic population variability in cardiotoxic risk.</p>
Data from: The impact of variable degrees of freedom and scale parameters in Bayesian methods for genomic prediction in Chinese Simmental beef cattle
Three conventional Bayesian approaches (BayesA, BayesB and BayesCπ) have been demonstrated to be powerful in predicting genomic merit for complex traits in livestock. A priori, these Bayesian models assume that the non-zero SNP effects (marginally) follow a t-distribution depending on two fixed hyperparameters, degrees of freedom and scale parameters. In this study, we performed genomic prediction in Chinese Simmental beef cattle and treated degrees of freedom and scale parameters as unknown with inappropriate priors. Furthermore, we compared the modified methods (BayesFA, BayesFB and BayesFCπ) with their corresponding counterparts using simulation datasets. We found that the modified methods with distribution assumed to the two hyperparameters were beneficial for improving the predictive accuracy. Our results showed that the predictive accuracies of the modified methods were slightly higher than those of their counterparts especially for traits with low heritability and a small number of QTLs. Moreover, cross-validation analysis for three traits, namely carcass weight, live weight and tenderloin weight, in 1136 Simmental beef cattle suggested that predictive accuracy of BayesFCπ noticeably outperformed BayesCπ with the highest increase (3.8%) for live weight using the cohort masking cross-validation.
Data from: A Bayesian method for analyzing lateral gene transfer
Lateral gene transfer (LGT)—which transfers DNA between two non-vertically related individuals belonging to the same or different species—is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most-parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications. Consequently, proposed LGT among specific gene families, and the rate of LGT in general remain debated. We present a Bayesian MCMC-based method that integrates gene duplication, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close species-LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events.
Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
The increasing ability to extract and sequence DNA from non-contemporaneous tissue offers biologists the opportunity to analyze ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. Here we provide a critical assessment of Bayesian MCMC analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates due to model misspecification when the data comes from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However when model misspecification is only mild, then the 95% HPD intervals provide adequate frequentist coverage of the true rates.
Data from: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics
Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g. matrix representation with parsimony (MRP). We investigated new implementations of ML and Bayesian SMs and compared these with some currently available alternative approaches. Comparisons include hypothetical examples previously used to investigate biases of SMs with respect to input tree shape and size, and empirical studies based either on trees harvested from the literature or on trees inferred from phylogenomic scale data. Our results provide no evidence of size or shape biases and demonstrate that the Bayesian method is a viable alternative to MRP and other non-parametric methods. Computation of input tree likelihoods allows the adoption of standard tests of tree topologies (e.g. the approximately unbiased test). The Bayesian approach is particularly useful in providing support values for supertree clades in the form of posterior probabilities.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.