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At least 217 records · Page 12Linked to original sources
PubMed2006

The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes.

The Mekong giant catfish (Pangasianodon gigas) is the largest scale-less freshwater fish of the world, and a critically endangered species. We determined the complete nucleotide sequence (16,533 bp) of the mitochondrial genome of the Mekong giant catfish, and conducted phylogenetic analyses based on mitochondrial protein (the combined amino acid sequences of all 13 mitochondrial protein coding genes) and rRNA (the combined nucleotide sequences of mitochondrial 12S and 16S rRNA genes) data sets in order to further clarify the relative phylogenetic position of P. gigas, and to recover phylogenetic relationships among 15 out of the 33 families of Siluriformes. Phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, Bayesian inference) of the protein data set were congruent with a basal split of the order into Loricarioidei and Siluroidei, and supported a closer relationship of the Mekong giant catfish (family Pangasiidae) to Siluridae than to Bagridae. The rRNA-based Bayesian phylogeny recovered Callichthyidae as the sister group of all other analyzed non-diplomystid catfish families, rendering Loricarioidei paraphyletic. In addition, Loricariidae were recovered as paraphyletic due to the inclusion of Astroblepidae. However, none of the two relationships received bootstrap support in the maximum parsimony, minimum evolution, and maximum likelihood analyses, and should be interpreted with caution. The derived position of Cetopsidae within Siluroidei, the sister group relationship of Pseudopimelodidae and Pimelodidae, and a close relationship of Doradidae and Auchenipteridae to the exclusion of Mochokidae were strongly supported. Pangasiidae was placed as a single lineage without clear affinities.

Animals↗
PubMed2003

Robust inference of baseline optical properties of the human head with three-dimensional segmentation from magnetic resonance imaging.

We model the capability of a small (6-optode) time-resolved diffuse optical tomography (DOT) system to infer baseline absorption and reduced scattering coefficients of the tissues of the human head (scalp, skull, and brain). Our heterogeneous three-dimensional diffusion forward model uses tissue geometry from segmented magnetic resonance (MR) data. Handling the inverse problem by use of Bayesian inference and introducing a realistic noise model, we predict coefficient error bars in terms of detected photon number and assumed model error. We demonstrate the large improvement that a MR-segmented model can provide: 2-10% error in brain coefficients (for 2 x 10(6) photons, 5% model error). We sample from the exact posterior and show robustness to numerical model error. This opens up the possibility of simultaneous DOT and MR for quantitative cortically constrained functional neuroimaging.

Bayes Theorem↗
PubMed2000

The Bayesian approach improves the electrocardiographic diagnosis of broad complex tachycardia.

Despite numerous attempts at devising algorithms for diagnosing broad complex tachycardia (BCT) on the basis of the electrocardiogram (ECG), misdiagnosis is still common. The reason for this may lie with difficulty in implementing existent algorithms in practice, due to imperfect ascertainment of ECG features within them. An attempt was made to approach the problem afresh with the Bayesian inference by the construction of a diagnostic algorithm centered around the likelihood ratio (LR). Previously studied ECG features most effective in discriminating ventricular tachycardia (VT) from supraventricular tachycardia with aberrant conduction (SVTAC), according to their LR values, were selected for inclusion into a Bayesian diagnostic algorithm. A test set of 244 BCT ECGs was assembled and shown to three independent observers who were blinded to the diagnoses made at electrophysiological study. Their diagnostic accuracy by the Bayesian algorithm was compared against that by clinical judgement with the diagnoses from EPS as the criterial standard. Clinical judgement correctly diagnosed 35% of SVTAC, 85% of VT, and 47% of fascicular tachycardia. In comparison, by the Bayesian algorithm devised, 52% of SVTAC, 95% of VT, and 97% of fascicular tachycardia were correctly diagnosed. The Bayesian algorithm devised has proved to be superior to the clinical judgement of the observers who participated in this study, and theoretically will obviate the problem of imperfect ascertainment of ECG features. Hence, it holds the promise for being an effective tool for routine use in clinical practice.

Algorithms↗
PubMed2004

Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences.

Advanced frogs (Neobatrachia) are usually divided into two taxa, Ranoidea (the firmisternal frogs) and Hyloidea (all other neobatrachians). We investigated phylogenetic relationships among several groups of Hyloidea using 12S and 16S rRNA mitochondrial gene sequences and tested explicit relationships of certain problematic hyloid taxa using a sample of 93 neobatrachians. Parsimony, maximum likelihood, and Bayesian inference methods suggest that both the Ranoidea and Hyloidea are well-supported monophyletic groups. We reject three hypotheses using parametric bootstrap simulation: (1) Dendrobatidae lies within the Ranoidea; (2) The group containing Hylidae, Pseudidae, and Centrolenidae is monophyletic; and (3) Brachycephalus is part of Bufonidae.

Animals↗
PubMed2005

Introduction to Bayesian methods I: measuring the strength of evidence.

Bayesian inference is a formal method to combine evidence external to a study, represented by a prior probability curve, with the evidence generated by the study, represented by a likelihood function. Because Bayes theorem provides a proper way to measure and to combine study evidence, Bayesian methods can be viewed as a calculus of evidence, not just belief. In this introduction, we explore the properties and consequences of using the Bayesian measure of evidence, the Bayes factor (in its simplest form, the likelihood ratio). The Bayes factor compares the relative support given to two hypotheses by the data, in contrast to the P-value, which is calculated with reference only to the null hypothesis. This comparative property of the Bayes factor, combined with the need to explicitly predefine the alternative hypothesis, produces a different assessment of the strength of evidence against the null hypothesis than does the P-value, and it gives Bayesian procedures attractive frequency properties. However, the most important contribution of Bayesian methods is the way in which they affect both who participates in a scientific dialogue, and what is discussed. With the emphasis moved from "error rates" to evidence, content experts have an opportunity for their input to be meaningfully incorporated, making it easier for regulatory decisions to be made correctly.

Bayes Theorem↗
PubMed2003

New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences.

Annelid systematics and the ingroup relationships of polychaete annelids are matter of ongoing debates in recent analyses. For the investigation of sedentary polychaete relationships a molecular phylogenetic analysis was conducted based on 94 sequences of 18S rDNA, including unpublished sequences of 13 polychaete species. The data set was analyzed with maximum parsimony and maximum likelihood methods, as wells as Bayesian inference. As in previous molecular analyses the monophyly of many traditional polychaete families is confirmed. No evidence has been found for a possible monophyly of Canalipalpata or Scolecida. In all analyses a placement of the Echiura as a derived polychaete ingroup with a close relationship to the Capitellidae is confirmed. The orbiniids appear paraphyletic with regard to Questa. Travisia is transferred from Opheliidae to Scalibregmatidae. The remaining opheliids include a yet undescribed ctenodrilid species from Elba, whereas the other investigated ctenodrilid Ctenodrilus serratus groups with the Cirratulidae and shows a close affinity to the cirratulid genus Dodecaceria. A common ancestry of Branchiomaldane and Arenicola, which has been predicted on morphological data, is confirmed by the analysis and a sistergroup relationship between Arenicolidae and Maldanidae is also recovered. These results support our assumption that on the basis of a broader taxon sampling the phylogenetic position of controversially discussed taxa can be inferred by using 18S rDNA sequence data.

Animals↗
PubMed1988

The diagnosis of polyarteritis nodosa. I. A literature-based decision analysis approach.

We investigated diagnostic testing in polyarteritis nodosa (PAN) by calculating, from published data, the sensitivity and specificity of visceral angiography and muscle, nerve, testicle, kidney, and liver biopsy. Test sequence strategies were constructed by Bayesian inference using a computer program written for this purpose. Test sequences were compared with an aggressive strategy consisting of repeated tests until there was a positive finding or until the available tests were exhausted, and a conservative strategy consisting of 1 biopsy procedure plus angiography. The Bayesian analysis agreed most closely with the conservative approach for most prior probabilities (degree of suspicion) that a patient had PAN. The aggressive strategy had an overall sensitivity of 90% and specificity of 91%, whereas the conservative strategy was 85% sensitive and 96% specific. Furthermore, the aggressive strategy was more costly ($2,986 versus $1,961) and had a higher rate of morbidity (3.8 versus 2.7 days of hospitalization per patient evaluated) than did the conservative strategy. The mortality rates of both strategies were equivalent (approximately 0.05 deaths per hundred patients evaluated). The per-case cost of diagnosis increased as prevalence decreased, and at 10% prevalence, the aggressive strategy cost more than $17,000 per case diagnosed. Sensitivity analysis revealed that the strategies were moderately affected by the test characteristics, within reasonable assumptions, but that the differences in conservative and aggressive approaches remained. Thus, our analysis based on available data and the assumption of test independence suggests that the preferred diagnostic evaluation of patients with symptoms suggestive of PAN consists, in most cases, of a single biopsy procedure, with angiographic evaluation if necessary.

Costs and Cost Analysis↗
PubMed1998

Generalized linear mixed models in dairy cattle breeding.

Fitness and fertility traits of dairy cattle are of increasing importance and are often measured on a discrete scale. The development and application of generalized linear mixed models to the genetic analysis of these traits are reviewed. Because current genetic evaluation systems are predominantly based on animal models, the inferential challenges of highly parameterized generalized linear mixed models are discussed. Development and adoption of new methods for drawing appropriate inferences on dispersion parameters are essential. Recent hierarchical extensions have been proposed for generalized linear mixed models, allowing for complex dispersion patterns that accommodate heteroscedasticity and outlier robustness. Steady advances in available computing power have facilitated multiple-trait analyses involving continuous and discrete measures. Full Bayesian inference via the development of Markov Chain Monte Carlo methods will continue to allow even greater generality and dimensions in the genetic model.

Animals↗
PubMed2006

Unified method for Bayesian calculation of genetic risk.

Bayesian inference has been used for genetic risk calculation. In this traditional method, inheritance events are divided into a number of cases under the inheritance model, and some elements of the inheritance model are usually disregarded. We developed a genetic risk calculation program, GRISK, which contains an improved Bayesian risk calculation algorithm to express the outcome of inheritance events with inheritance vectors, a set of ordered genotypes of founders, and mutation vectors, which represent a new idea for description of mutations in a pedigree. GRISK can calculate genetic risk in a common format that allows users to execute the same operation in every case, whereas the traditional risk calculation method requires construction of a calculation table in which the inheritance events are variously divided in each respective case. In addition, GRISK does not disregard any possible events in inheritance. This program was developed as a Japanese macro for Excel to run on Windows.

Algorithms↗
PubMed2005

Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences.

The catfish family Clariidae comprises species in which the body shape ranges from fusiform to anguilliform. Recent studies have shown that this body elongation is the result of convergent evolution. This paper aims to study the evolution towards anguilliformity in a phylogenetic framework. Sequences of 29 taxa were analyzed using the neighbor-joining, maximum-likelihood, maximum-parsimony, and Bayesian inference algorithms and the parsimony algorithm in POY. The study yields phylogenetic hypotheses showing well-supported clades. Anguilliformity appears to have arisen at least four times, each time having a sister group relation with a fusiform Clarias-like ancestor. Divergence time estimation indicates that the African Clariidae started radiating between 123 and 56 My ago.

Africa↗
PubMed2000

Baseline risk as predictor of treatment benefit: three clinical meta-re-analyses.

A relationship between baseline risk and treatment effect is increasingly investigated as a possible explanation of between-study heterogeneity in clinical trial meta-analysis. An approach that is still often applied in the medical literature is to plot the estimated treatment effects against the estimated measures of risk in the control groups (as a measure of baseline risk), and to compute the ordinary weighted least squares regression line. However, it has been pointed out by several authors that this approach can be seriously flawed. The main problem is that the observed treatment effect and baseline risk measures should be viewed as estimates rather than the true values. In recent years several methods have been proposed in the statistical literature to potentially deal with the measurement errors in the estimates. In this article we propose a vague priors Bayesian solution to the problem which can be carried out using the 'Bayesian inference using Gibbs sampling' (BUGS) implementation of Markov chain Monte Carlo numerical integration techniques. Different from other proposed methods, it uses the exact rather than an approximate likelihood, while it can handle many different treatment effect measures and baseline risk measures. The method differs from a recently proposed Bayesian method in that it explicitly models the distribution of the underlying baseline risks. We apply the method to three meta-analyses published in the medical literature and compare the results with the outcomes of the other recently proposed methods. In particular we compare our approach to McIntosh's method, for which we show how it can be carried out using standard statistical software. We conclude that our proposed method offers a very general and flexible solution to the problem, which can be carried out relatively easily with existing Bayesian analysis software. A confidence band for the underlying relationship between true effect measure and baseline risk and a confidence interval for the value of the baseline risk measure for which there is no treatment effect are easily obtained by-products of our approach.

Bayes Theorem↗
PubMed2006

How and when did Old World ratsnakes disperse into the New World?

To examine Holarctic snake dispersal, we inferred a phylogenetic tree from four mtDNA genes and one scnDNA gene for most species of the Old World (OW) and New World (NW) colubrid group known as ratsnakes. Ancestral area distributions are estimated for various clades using divergence-vicariance analysis and maximum likelihood on trees produced using Bayesian inference. Dates of divergence for the same clades are estimated using penalized likelihood with statistically crosschecked calibration references obtained from the Miocene fossil record. With ancestral areas and associated dates estimated, various hypotheses concerning the age and environment associated with the origin of ratsnakes and the dispersal of NW taxa from OW ancestors were tested. Results suggest that the ratsnakes originated in tropical Asia in the late Eocene and subsequently dispersed to the Western and Eastern Palearctic by the early Oligocene. These analyses also suggest that the monophyletic NW ratsnakes (the Lampropeltini) diverged from OW ratsnakes and dispersed through Beringia in the late Oligocene/early Miocene when this land bridge was mostly composed of deciduous and coniferous forests.

Animals↗
PubMed2003

Inference and computation with population codes.

In the vertebrate nervous system, sensory stimuli are typically encoded through the concerted activity of large populations of neurons. Classically, these patterns of activity have been treated as encoding the value of the stimulus (e.g., the orientation of a contour), and computation has been formalized in terms of function approximation. More recently, there have been several suggestions that neural computation is akin to a Bayesian inference process, with population activity patterns representing uncertainty about stimuli in the form of probability distributions (e.g., the probability density function over the orientation of a contour). This paper reviews both approaches, with a particular emphasis on the latter, which we see as a very promising framework for future modeling and experimental work.

Animals↗
PubMed1990

Hypermedia and randomized algorithms for medical expert systems.

KNET is an environment for constructing probabilistic, knowledge-intensive systems within the axiomatic framework of decision theory. The KNET architecture defines a complete separation between the hypermedia user interface on the one hand, and the representation and management of expert opinion on the other. KNET offers a choice of algorithms for probabilistic inference. We and our coworkers have used KNET to build consultation systems for lymph-node pathology, bone-marrow transplantation therapy, clinical epidemiology, and alarm management in the intensive-care unit. Most important, KNET contains a randomized approximation scheme (RAS) for the difficult and almost certainly intractable problem of Bayesian inference. Our algorithm can, in many circumstances, perform efficient approximate inference in large and richly interconnected models of medical diagnosis. In this article, we describe the architecture of KNET, construct a randomized algorithm for probabilistic inference, and analyze the algorithm's performance. Finally, we characterize our algorithms' empiric behavior and explore its potential for parallel speedups. From design to implementation, then, KNET demonstrates the crucial interaction between theoretical computer science and medical informatics.

Algorithms↗
PubMed2003

Fitting genetic models to twin data with binary and ordered categorical responses: a comparison of structural equation modelling and Bayesian hierarchical models.

We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a "correct" model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.

Bayes Theorem↗
PubMed2005

Molecular phylogenetic analysis of nycteribiid and streblid bat flies (Diptera: Brachycera, Calyptratae): implications for host associations and phylogeographic origins.

Bat flies are a small but diverse group of highly specialized ectoparasitic, obligatory bloodsucking Diptera. For the first time, the phylogenetic relationships of 26 species and five subfamilies were investigated using four genes (18S rDNA, 16S rDNA, COII, and cytB) under three optimality criteria (maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference). Tree topology tests of previous hypotheses were conducted under likelihood (Shimodaira-Hasegawa test). Major findings include the non-monophyly of the Streblidae and the recovery of an Old World- and a New World-Clade of bat flies. These data ambiguously resolve basal relationships between Hippoboscidae, Glossinidae, and bat flies. Recovered phylogenies resulted in either monophyly (Bayesian approach) or paraphyly (MP/ML topologies) of the bat flies, thus obscuring the potential number of possible associations with bats throughout the history of this group. Dispersal-vicariance analysis suggested the Neotropical region as the possible ancestral distribution area of the New World Streblidae and the Oriental region for the Old World bat flies. The genes examined show conflicting support across the nodes of the tree, particularly in the basal positions. Additionally, there is poor character support among all genes for the nodes associated with early hippoboscoid diversification. This results in extremely short basal branches, adding support to the idea of a rapid radiation among the four major groups of Hippoboscoidea.

Animals↗
PubMed2005

A statistical framework for haplotype block inference.

The existence of haplotype blocks transmitted from parents to offspring has been suggested recently. This has created an interest in the inference of the block structure and length. The motivation is that haplotype blocks that are characterized well will make it relatively easier to quickly map all the genes carrying human diseases. To study the inference of haplotype block systematically, we propose a statistical framework. In this framework, the optimal haplotype block partitioning is formulated as the problem of statistical model selection; missing data can be handled in a standard statistical way; population strata can be implemented; block structure inference/hypothesis testing can be performed; prior knowledge, if present, can be incorporated to perform a Bayesian inference. The algorithm is linear in the number of loci, instead of NP-hard for many such algorithms. We illustrate the applications of our method to both simulated and real data sets.

Algorithms↗
PubMed2005

Estimating diversifying selection and functional constraint in the presence of recombination.

Models of molecular evolution that incorporate the ratio of nonsynonymous to synonymous polymorphism (dN/dS ratio) as a parameter can be used to identify sites that are under diversifying selection or functional constraint in a sample of gene sequences. However, when there has been recombination in the evolutionary history of the sequences, reconstructing a single phylogenetic tree is not appropriate, and inference based on a single tree can give misleading results. In the presence of high levels of recombination, the identification of sites experiencing diversifying selection can suffer from a false-positive rate as high as 90%. We present a model that uses a population genetics approximation to the coalescent with recombination and use reversible-jump MCMC to perform Bayesian inference on both the dN/dS ratio and the recombination rate, allowing each to vary along the sequence. We demonstrate that the method has the power to detect variation in the dN/dS ratio and the recombination rate and does not suffer from a high false-positive rate. We use the method to analyze the porB gene of Neisseria meningitidis and verify the inferences using prior sensitivity analysis and model criticism techniques.

Bayes Theorem↗