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Results for “Bayesian modelling”

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At least 991 records · Page 55Linked to original sources
PubMed1996

Estimating defibrillation efficacy using combined upper limit of vulnerability and defibrillation testing.

It is frequently necessary, both clinically and in the laboratory, to estimate how strong a stimulus is required to defibrillate. Current techniques for forming such estimates require the repeated induction of ventricular fibrillation (VF) and subsequent attempts at defibrillation (DF testing). DF testing can be time consuming and in the operating room may increase the patient risks. A novel scheme is presented which combines DF testing with upper limit of vulnerability (ULV) testing. ULV testing is a relatively safe procedure which yields data well correlated with defibrillation efficacy. A Bayesian statistical model of combined ULV/DF testing is presented which is both powerful and concise. The model is used in two examples to design minimum rms error protocols and estimators for the DF95 (the stimulus strength which defibrillates 95% of the time). A simulation for humans of one example solution shows that a single VF episode of combined ULV/DF testing (rms error = 23% of the mean DF95) is better than two VF episodes with DF testing alone (25%). The simulation results for a second example are directly compared with laboratory results from six pigs, showing a less than 1.0% average difference between the simulated and measured rms errors.

Algorithms↗
PubMed2005

Inferring figure-ground using a recurrent integrate-and-fire neural circuit.

Several theories of early visual perception hypothesize neural circuits that are responsible for assigning ownership of an object's occluding contour to a region which represents the "figure." Previously, we have presented a Bayesian network model which integrates multiple cues and uses belief propagation to infer local figure-ground relationships along an object's occluding contour. In this paper, we use a linear integrate-and-fire model to demonstrate how such inference mechanisms could be carried out in a biologically realistic neural circuit. The circuit maps the membrane potentials of individual neurons to log probabilities and uses recurrent connections to represent transition probabilities. The network's "perception" of figure-ground is demonstrated for several examples, including perceptually ambiguous figures, and compared qualitatively and quantitatively with human psychophysics.

Action Potentials↗
PubMed2006

Local environmental effects and spatial effects in macroecological studies using mapped abundance classes: the case of the rook Corvus frugilegus in Scotland.

1. The study of the spatial pattern of species abundance is complicated by statistical problems, such as spatial autocorrelation of the abundance data, which lead to the confusion of environmental effects and dispersal. 2. Atlas-derived data for the rook in Scotland are used as a case study to propose an approach for assessing the likely contribution of dispersal and local environmental effects, based on a Bayesian Conditional Autoregressive (CAR) approach. 3. The availability of moist grasslands is a key factor explaining the spatial pattern of abundance. This is influenced by a combination of climatic and soil-related factors. A direct link to soil properties is for the first time reported for the wide-scale distribution of a bird species. In addition, for this species, dispersal seems to contribute significantly to the spatial pattern and produces a smoother than expected decline in abundance at the north-western edge of its distribution range. Areas where dispersal is most likely to be important are highlighted. 4. The approach described can help ecologists make more efficient use of atlas data for the investigation of the structure of species abundance, and can highlight potential sink areas at the landscape and regional scale. 5. Bayesian spatial models can deal with data autocorrelation in atlas-type data, while clearly communicating uncertainty through the estimation of the full posterior probability distribution of all parameters.

Animals↗
PubMed2004

On the evolution of statistical methods as applied to clinical trials.

This paper describes how statistical methods have evolved in parallel with activities associated with randomized control trials. In particular we emphasize the pivotal role of two papers published in British Journal of Cancer, and the paper describing the Cox proportional hazards model. In addition, the importance of early papers on estimating the sample size required for trials is highlighted. Later developments including the increasing roles for competing risks, multilevel modelling and Bayesian methodologies are described. The interplay between computer software and statistical methodological developments is stressed. Finally some future directions are indicated.

Humans↗
PubMed2004

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore.

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Animals↗
PubMed2004

Admixture and diversity in West African cattle populations.

We present a population genetic analysis of microsatellite variation in 16 West African cattle populations. West Africa represents a unique juxtaposition of different climatic and ecological zones in a relatively small geographical area. While more humid coastal regions are inhabited by the tsetse fly, a vector which spreads trypanosomiasis among cattle, the disease is not transmitted in the drier areas outside this zone. This is the most thorough study of genetic diversity in cattle within this area, which contains genetically important trypanotolerant Bos taurus breeds. Genetic relationships among the many breeds are examined and levels of diversity are assessed. Admixture levels were determined using a variety of methods. Ancestry informative or population-associated alleles (PAAs) were selected using populations from India, the Near East and Europe. Multivariate analysis, the admix program and model-based Bayesian admixture analysis approaches were also employed. These analyses reveal the direct impact of ecological factors and the profound effect of admixture on the cattle of this region. They also highlight the importance of efforts to prevent further dilution of African taurine breeds by B. indicus cattle.

Africa↗
PubMed2006

Bayesian identification of admixture events using multilocus molecular markers.

Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals' genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Alleles↗
PubMed2006

Echinococcus multilocularis in Austrian foxes from 1991 until 2004.

The prevalence rates of Echinococcus multilocularis in foxes (n=5600) evaluated in several Austrian surveys conducted between 1991 and 2004 were analysed for spatial and temporal differences. Data from early studies (1993-1997) in which the intestinal scraping technique (IST) was utilized were compared with data from recent (1999-2004) investigations, which made use of the shaking in a vessel technique (SVT), and it was assessed whether or not the infection rates of Austrian foxes had increased between the investigated intervals. In total, data from 85 districts are presented and both the retrospective and recent data are available from 39 of these districts. A Bayesian hierarchical model of parasite prevalences is presented which (i) accounts for differences in the sensitivity of IST and SVT, (ii) incorporates spatial auto-correlation between neighbouring districts, (iii) investigates the possibility of a temporal shift in the infection status of foxes, and (iv) quantifies uncertainty at each level of the model. The national average prevalence rates in the mid-1990s and at the turn of the millennium were 2.4% (95% confidence intervals 1.1-4.8) and 3.9% (95% confidence intervals 1.5-8.4) respectively. Above average prevalence rates were observed in the western and the northern parts of the country. Evidence is also presented for a temporal augmentation of the prevalence rates in some districts in the northern and eastern parts of the country. These findings are in concordance with several investigations in other European states where both newly emerged areas and elevated levels of transmission in existing endemic areas have been found. None of the districts investigated here showed significant evidence of a drop in prevalence.

Animals↗
PubMed2006

Bayesian robust inference for differential gene expression in microarrays with multiple samples.

We consider the problem of identifying differentially expressed genes under different conditions using gene expression microarrays. Because of the many steps involved in the experimental process, from hybridization to image analysis, cDNA microarray data often contain outliers. For example, an outlying data value could occur because of scratches or dust on the surface, imperfections in the glass, or imperfections in the array production. We develop a robust Bayesian hierarchical model for testing for differential expression. Errors are modeled explicitly using a t-distribution, which accounts for outliers. The model includes an exchangeable prior for the variances, which allows different variances for the genes but still shrinks extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and it can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. The method is illustrated using two publicly available gene expression data sets. We compare our method to six other baseline and commonly used techniques, namely the t-test, the Bonferroni-adjusted t-test, significance analysis of microarrays (SAM), Efron's empirical Bayes, and EBarrays in both its lognormal-normal and gamma-gamma forms. In an experiment with HIV data, our method performed better than these alternatives, on the basis of between-replicate agreement and disagreement.

Bayes Theorem↗
PubMed2005

Multiple transatlantic introductions of the western corn rootworm.

The invasion of Europe by the western corn rootworm, North America's most destructive corn pest, is ongoing and represents a serious threat to European agriculture. Because this pest was initially introduced in Central Europe, it was believed that subsequent outbreaks in Western Europe originated from this area. Using model-based Bayesian analyses of the genetic variability of the western corn rootworm, we demonstrate that this belief is false: There have been at least three independent introductions from North America during the past two decades. This result raises questions about changing circumstances that have enabled a sudden burst of transatlantic introductions.

Animals↗
PubMed2005

Bayesian network analysis of signaling networks: a primer.

High-throughput proteomic data can be used to reveal the connectivity of signaling networks and the influences between signaling molecules. We present a primer on the use of Bayesian networks for this task. Bayesian networks have been successfully used to derive causal influences among biological signaling molecules (for example, in the analysis of intracellular multicolor flow cytometry). We discuss ways to automatically derive a Bayesian network model from proteomic data and to interpret the resulting model.

Algorithms↗
PubMed1978

Computer-assisted identification of anaerobic bacteria.

A computer program was developed to identify anaerobic bacteria by using simultaneous pattern recognition via a Bayesian probabilistic model. The system is intended for use as a rapid, precise, and reproducible aid in the identification of unknown isolates. The program operates on a data base of 28 genera comprising 238 species of anaerobic bacteria that can be separated by the program. Input to the program consists of biochemical and gas chromatographic test results in binary format. The system is flexible and yields outputs of: (i) most probable species, (ii) significant test results conflicting with established data, and (iii) differential tests of significance for missing test results.

Anaerobiosis↗
PubMed2003

Use of gene networks for identifying and validating drug targets.

We propose a new method for identifying and validating drug targets by using gene networks, which are estimated from cDNA microarray gene expression profile data. We created novel gene disruption and drug response microarray gene expression profile data libraries for the purpose of drug target elucidation. We use two types of microarray gene expression profile data for estimating gene networks and then identifying drug targets. The estimated gene networks play an essential role in understanding drug response data and this information is unattainable from clustering methods, which are the standard for gene expression analysis. In the construction of gene networks, we use the Bayesian network model. We use an actual example from analysis of the Saccharomyces cerevisiae gene expression profile data to express a concrete strategy for the application of gene network information to drug discovery.

Algorithms↗
PubMed2006

Vision and touch are automatically integrated for the perception of sequences of events.

The purpose of the present experiment was to investigate the integration of sequences of visual and tactile events. Subjects were presented with sequences of visual flashes and tactile taps simultaneously and instructed to count either the flashes (Session 1) or the taps (Session 2). The number of flashes could differ from the number of taps by +/-1. For both sessions, the perceived number of events was significantly influenced by the number of events presented in the task-irrelevant modality. Touch had a stronger influence on vision than vision on touch. Interestingly, touch was the more reliable of the two modalities-less variable estimates when presented alone. For both sessions, the perceptual estimates were less variable when stimuli were presented in both modalities than when the task-relevant modality was presented alone. These results indicate that even when one signal is explicitly task irrelevant, sensory information tends to be automatically integrated across modalities. They also suggest that the relative weight of each sensory channel in the integration process depends on its relative reliability. The results are described using a Bayesian probabilistic model for multimodal integration that accounts for the coupling between the sensory estimates.

Adult↗
PubMed1986

How to construct a subjective index.

We present a method of constructing quantitative indices, which is based on the subjective opinions of a panel of experts, and discuss how a Bayesian probability model and panel opinions can be used together to produce an index. Among the advantages of the method are its face validity and ease of construction. Research shows that when expert opinions are solicited according to certain guidelines, subjective methods may be as accurate as the more objective ones. Guidelines along with a brief report of a recent application are also discussed.

Abstracting and Indexing↗
PubMedDate not supplied

Validity of criteria used to evaluate fingerstick devices that assess international normalized ratio.

BACKGROUND: Investigators commonly rely on unvalidated, mainly arithmetic criteria to predict if point-of-care fingerstick devices that assess International Normalized Ratio (INR) lead to the same warfarin dosing decisions as a standard measure. METHODS: Criteria that predict warfarin dosing agreement between 2 INR measurements were evaluated using clinicians' actual dosing decisions as the standard. Bayesian hierarchical modeling was used to rank the criteria by the proportion of correct dosing predictions and the magnitude of difference between actual and predicted dosing agreement. RESULTS: The prediction criteria misclassified dosing agreement for between 19% and 38% of paired INR values (x: 27%). The magnitude of misclassification varied inconsistently throughout the INR scale. CONCLUSION: The unvalidated criteria used to predict warfarin dosing agreement between 2 INR measurements are associated with large error. Warfarin dosing decisions should be measured directly in such assessments.

Anticoagulants↗
PubMedDate not supplied

Medical decision making in the choice of a thrombolytic agent for acute myocardial infarction. Quebec Acute Coronary Care Working Group.

Little is known about how physicians make decisions when the evidence is incomplete or controversial. While thrombolysis improves survival following acute myocardial infarction (AMI), conflicting evidence exists as to any specific agent's superiority, particularly if cost-effectiveness is considered. Using a Bayesian hierarchical model, the authors examined the patient, physician, and hospital characteristics that are related to the decision-making process concerning the choice of thrombolytic agent in a prospective registry of 1,165 AMI patients receiving thrombolysis. Tissue plasminogen activator (t-PA) was administered to 432 patients (31.8%) and streptokinase (SK) to the remainder. The presence of an anterior infarction, a previous myocardial infarction, low blood pressure, a cardiologist decision maker, younger age, and receiving treatment within six hours after the start of symptoms were independent predictors of receiving t-PA. The levels of importance that physicians accorded to these patient characteristics differed according to their practicing institutions. Generally, they followed evidence-based medicine and reasonably targeted high-risk patients to receive the more expensive t-PA. However, they also preferentially treated younger patients, where only a small absolute advantage appears to exist.

Aged↗
PubMed2006

A meta-analytic assessment of a thyroglobulin marker for marbling in beef cattle.

A meta-analysis was undertaken reporting on the association between a polymorphism in the Thyroglobulin gene (TG5) and marbling in beef cattle. A Bayesian hierarchical model was adopted, with alternative representations assessed through sensitivity analysis. Based on the overall posterior means and posterior probabilities, there is substantial support for an additive association between the TG5 marker and marbling. The marker effect was also assessed across various breed groups, with each group displaying a high probability of positive association between the T allele and marbling. The WinBUGS program code used to simulate the model is included as an Appendix available online at www.edpsciences.org/gse.

Adipose Tissue↗