PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Bayesian analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources
PubMed2006

Dissecting inflammation in ESRD: do cytokines and C-reactive protein have a complementary prognostic value for mortality in dialysis patients?

Because atherogenesis represents a type of chronic inflammation that involves multiple elements of the inflammatory-immune response, the simultaneous prediction power for death of C-reactive protein (CRP) and proinflammatory cytokines (IL-1 beta, IL-6, IL-18, and TNF-alpha) was tested in a cohort of 217 patients with ESRD. During the follow-up period (average 41 mo), 112 patients died. In an analysis that was adjusted for other risk factors, the relative risks for death of patients who were exposed to high levels of one, two, three, and four or more inflammation biomarkers were 1.48, 1.64, 2.76, and 3.05 times higher, respectively, than that of patients in the reference category (no inflammation). In this model, the explained variation in mortality that was attributable to overall inflammation burden (+9.1%) was marginally higher (P = 0.06) than that provided by IL-6 alone (+6.1%). In an alternative analysis based on the Bayesian approach (receiver operating characteristic curves analysis), the prediction power of the combined inflammatory burden was identical to that provided by the sole IL-6 (0.59 +/- 0.04 versus 0.59 +/- 0.04). IL-6 captures almost entirely the prediction power of the overall inflammation burden in patients with ESRD. IL-6 seems to be an almost ideal indicator of the severity of inflammation. The use of this biomarker can be recommended in clinical studies that aim to better the understanding of inflammation or to modify it in this population.

Adult↗
PubMed2005

Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method.

The increased complexity of HIV-1 genetic heterogeneity raises the issue for reliable classification and analysis of these sequences. Until now, bootscanning analysis has been the main method used for the analysis of potential HIV-1 intersubtype recombinants. We show evidence that in some cases of complex recombinants, where three or more segments with discordant phylogenetic signal may exist in protease (PR) and partial reverse transcriptase (RT) region, Bayesian scanning provides a clearer picture than bootscanning plots about the boundaries of potential recombination. Thus, a recently developed Bayesian scanning tool can facilitate the analysis and classification of HIV-1 mosaic sequences.

Africa, Central↗
PubMed2004

Likelihood ratio and a Bayesian approach were superior to standard noninferiority analysis when the noninferiority margin varied with the control event rate.

OBJECTIVE: To present and compare three statistical approaches for analyzing a noninferiority trial when the noninferiority margin depends on the control event rate. STUDY DESIGN AND SETTING: In noninferiority trials with a binary outcome, the noninferiority margin is often defined as a fixed delta, the largest clinically acceptable difference in event rates between treatment groups. An alternative and more flexible approach is to allow delta to vary according to the true event rate in the control group. The appropriate statistical method for evaluating noninferiority with a variable noninferiority margin is not apparent. Three statistical approaches are proposed and compared: an observed event rate (OER) approach based on equating the true control rate to the observed rate, a Bayesian approach, and a likelihood ratio test. RESULTS AND CONCLUSIONS: Simulations studies indicate that the proportion of trials in which noninferiority was erroneously demonstrated was higher for the OER approach than with the Bayesian and likelihood ratio approaches. In some cases, the Type I error rate exceeded 10% for the OER approach. The OER approach is not recommended for the analysis of noninferiority trials with a variable margin of equivalence. The Bayesian and likelihood ratio methods yielded better operating characteristics.

Bayes Theorem↗
PubMed2004

New approaches to enhance the accuracy of the diagnosis of reflux disease.

The accuracy of symptoms in diagnosing gastro-oesophageal reflux disease (GORD) is complicated by the lack of a gold standard test. Statistical techniques such as latent class and Bayesian analyses can estimate accuracy of symptoms without a gold standard. Both techniques require three independent diagnostic tests. Latent class analysis makes no assumptions about the performance of the tests. Bayesian analysis is useful when the accuracy of the other tests is known. These statistical techniques should be used in the future to validate GORD symptom questionnaires comparing them with endoscopy, oesophageal pH monitoring, and response to proton pump inhibitor therapy. Studies that evaluate GORD symptoms are usually done in secondary care. The prevalence of GORD in primary care will be lower and this reduces the positive predictive value of symptoms. There will be some bias in the type of patient referred for diagnosis and this usually decreases the specificity of symptom diagnosis.

Bayes Theorem↗
PubMed2005

Bayesian regression models for cost-effectiveness analysis.

Recent studies have shown how cost-effectiveness analysis can be undertaken in a regression framework. This contribution explores the use of practical regression models for estimating cost-effectiveness from a Bayesian perspective. Two different Bayesian models are described. The first considers the outcome measure to be a quantitative variable. In the second model the individual outcome measure is a binary variable with value 1 if any objective has been achieved. We describe the implementation of the model using data from a trial that compares two highly active antiretroviral therapies in HIV asymptomatic patients. Data on direct cost and data effectiveness (percentage of patients with undetectable viral load and quality of life) were recorded. If we consider the quality of life as an effectiveness measure, the new treatment is preferred for a willingness to pay more than Euro 142.3 for an increase in the quality of life. For illustrative purposes, if we compare the results with an analogous model that does not include covariates, the critical value becomes Euro 247.4. For the binary measure of effectiveness the control treatment dominates the new treatment.

Antiretroviral Therapy, Highly Active↗
PubMed2006

Bayesian methods for pharmacokinetic models in dynamic contrast-enhanced magnetic resonance imaging.

This paper proposes a new method for estimating kinetic parameters of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) based on adaptive Gaussian Markov random fields. Kinetic parameter estimates using neighboring voxels reduce the observed variability in local tumor regions while preserving sharp transitions between heterogeneous tissue boundaries. Asymptotic results for standard errors from likelihood-based nonlinear regression are compared with those derived from the posterior distribution using Bayesian estimation with and without neighborhood information. Application of the method to the analysis of breast tumors based on kinetic parameters has shown that the use of Bayesian analysis combined with adaptive Gaussian Markov random fields provides improved convergence behavior and more consistent morphological and functional statistics.

Algorithms↗
PubMed1993

Outcomes of bacterial meningitis in children: a meta-analysis.

We abstracted the results of all English language reports of the outcomes of bacterial meningitis published after 1955. We used hierarchical Bayesian meta-analysis to determine the overall and organism-specific frequencies of death and persistent neurologic sequelae in children 2 months to 19 years of age. A total of 4920 children with acute bacterial meningitis were included in 45 reports that met the inclusion criteria. Children described in the 19 reports of prospectively enrolled cohorts from developed countries had lower mortality (4.8% vs. 8.1%) and were more likely to have no sequelae (82.5% vs. 73.9%). In these 19 studies 1602 children were evaluated for at least 1 sequela after hospital discharge. The mean probabilities of these sequelae were: deafness, 10.5%; bilateral severe or profound deafness, 5.1%; mental retardation, 4.2%; spasticity and/or paresis, 3.5%; seizure disorder, 4.2%; and no detectable sequelae, 83.6%. Mean probabilities of outcomes varied significantly by etiologic bacteria, e.g. mortality: Haemophilus influenzae, 3.8%; Neisseria meningitis, 7.5%; Streptococcus pneumoniae, 15.3%.

Adolescent↗
PubMed2002

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.

Animals↗
PubMedDate not supplied

Differentiation among Spanish sheep breeds using microsatellites.

Genetic variability at 18 microsatellites was analysed on the basis of individual genotypes in five Spanish breeds of sheep--Churra, Latxa, Castellana, Rasa-Aragonesa and Merino--with Awassi also being studied as a reference breed. The degree of population subdivision calculated between Spanish breeds from F(ST) diversity indices was around 7% of total variability. A high degree of reliability was obtained for individual-breed assignment from the 18 loci by using different approaches among which the Bayesian method provided to be the most efficient, with an accuracy for nine microsatellites of over 99%. Analysis of the Bayesian assignment criterion illustrated the divergence between any one breed and the others, which was highest for Awassi sheep, while no great differences were evident among the Spanish breeds. Relationships between individuals were analysed from the proportion of shared alleles. The resulting dendrogram showed a remarkable breed structure, with the highest level of clustering among members of the Spanish breeds in Latxa and the lowest in Merino sheep, the latter breed exhibiting a peculiar pattern of clustering, with animals grouped into several closely set nodes. Analysis of individual genotypes provided valuable information for understanding intra- and inter-population genetic differences and allowed for a discussion with previously reported results using populations as taxonomic units.

Alleles↗
PubMed2006

Sensitivity analysis of misclassification: a graphical and a Bayesian approach.

PURPOSE: Misclassification can produce bias in measures of association. Sensitivity analyses have been suggested to explore the impact of such bias, but do not supply formally justified interval estimates. METHODS: To account for exposure misclassification, recently developed Bayesian approaches were extended to incorporate prior uncertainty and correlation of sensitivity and specificity. Under nondifferential misclassification, a contour plot is used to depict relations among the corrected odds ratio, sensitivity, and specificity. RESULTS: Methods are illustrated by application to a case-control study of cigarette smoking and invasive pneumococcal disease while varying the distributional assumptions about sensitivity and specificity. Results are compared with those of conventional methods, which do not account for misclassification, and a sensitivity analysis, which assumes fixed sensitivity and specificity. CONCLUSION: By using Bayesian methods, investigators can incorporate uncertainty about misclassification into probabilistic inferences.

Bayes Theorem↗
PubMed1998

A Bayesian framework for intent-to-treat analysis with missing data.

In longitudinal clinical trials, one analysis of interest is an intention-to-treat analysis, which groups subjects according to the randomized treatment regardless of whether they stayed on that treatment or not. When in addition to going off the randomized treatment subjects may also drop out of the study and be lost to follow-up, it is unclear what an intention-to-treat analysis should be. If measurements are made after treatment drop-out on a random sample of subjects who drop the treatment, then Hogan and Laird (1996, Biometrics 52, 1002-1017) present a random effects model, well suited to this type of analysis, which fits a two-piece linear spline to the data with the knot at the time the assigned treatment is dropped. This article presents a Bayesian approach to fitting a similar two-piece linear spline model and shows how the model can be applied to data that have no off-treatment observations.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Bayesian reconstruction of PET images: methodology and performance analysis.

We describe a practical statistical methodology for the reconstruction of PET images. Our approach is based on a Bayesian formulation of the imaging problem. The data are modelled as independent Poisson random variables and the image is modelled using a Markov random field smoothing prior. We describe a sequence of calibration procedures which are performed before reconstruction: (i) calculation of accurate attenuation correction factors from re-projected Bayesian reconstructions of the transmission image; (ii) estimation of the mean of the randoms component in the data; and (iii) computation of the scatter component in the data using a Klein-Nishina-based scatter estimation method. The Bayesian estimate of the PET image is then reconstructed using a pre-conditioned conjugate gradient method. We performed a quantitation study with a multi-compartment chest phantom in a Siemens/CTI ECAT931 system. Using 40 1 min frames, we computed the ensemble mean and variance over several regions of interest from images reconstructed using the Bayesian and a standard filtered backprojection (FBP) protocol. The values for the region of interest were compared with well counter data for each compartment. These results show that the Bayesian protocol can produce substantial improvements in relative quantitation over the standard FBP protocol, particularly when short transmission scans are used. An example showing the application of the method to a clinical chest study is also given.

Algorithms↗
PubMed2006

Modeling the relation between socioeconomic status and mortality in a mixture of majority and minority ethnic groups.

Ethnic variation in mortality and whether this variation can be explained by socioeconomic status are of substantive interest to social epidemiologists. The authors consider the analysis of mortality data for a mixture of majority and minority ethnic groups. Such data are likely to be coarsely cross-classified by age and socioeconomic status and yet, even then, in some cells of this cross-classification the observed mortality rate will be an imprecise estimate of the underlying rate. The authors illustrate conventional and Bayesian approaches to analysis with data from the 1996 census used by the New Zealand Census-Mortality Study. A conventional approach is exploratory data analysis first followed by Poisson regression. The authors use spline smoothing within a generalized additive model framework as an exploratory data analysis, following a strategy of adding just enough model structure to gain a sensible picture. A Bayesian approach is modeling first and then a description of posterior estimates using exploratory data analysis techniques. The authors use hierarchical Poisson regression and then illustrate their posterior estimates of the mortality rate using the same spline smoothing as before. The advantage of the hierarchical Bayesian approach is that it assesses uncertainty about a Poisson regression model proposed a priori; the conventional approach assumes that the fitted Poisson regression model is correct. All analyses use software that is available at no cost.

Age Factors↗
PubMed1995

Robust Bayesian methods for monitoring clinical trials.

Bayesian methods for the analysis of clinical trials data have received increasing attention recently as they offer an approach for dealing with difficult problems that arise in practice. A major criticism of the Bayesian approach, however, has focused on the need to specify a single, often subjective, prior distribution for the parameters of interest. In an attempt to address this criticism, we describe methods for assessing the robustness of the posterior distribution to the specification of the prior. The robust Bayesian approach to data analysis replaces the prior distribution with a class of prior distributions and investigates how the inferences might change as the prior varies over this class. The purpose of this paper is to illustrate the application of robust Bayesian methods to the analysis of clinical trials data. Using two examples of clinical trials taken from the literature, we illustrate how to use these methods to help a data monitoring committee decide whether or not to stop a trial early.

Bayes Theorem↗
PubMed2004

A Bayesian morphometry algorithm.

Most methods for structure-function analysis of the brain in medical images are usually based on voxel-wise statistical tests performed on registered magnetic resonance (MR) images across subjects. A major drawback of such methods is the inability to accurately locate regions that manifest nonlinear associations with clinical variables. In this paper, we propose Bayesian morphological analysis methods, based on a Bayesian-network representation, for the analysis of MR brain images. First, we describe how Bayesian networks (BNs) can represent probabilistic associations among voxels and clinical (function) variables. Second, we present a model-selection framework, which generates a BN that captures structure-function relationships from MR brain images and function variables. We demonstrate our methods in the context of determining associations between regional brain atrophy (as demonstrated on MR images of the brain), and functional deficits. We employ two data sets for this evaluation: the first contains MR images of 11 subjects, where associations between regional atrophy and a functional deficit are almost linear; the second data set contains MR images of the ventricles of 84 subjects, where the structure-function association is nonlinear. Our methods successfully identify voxel-wise morphological changes that are associated with functional deficits in both data sets, whereas standard statistical analysis (i.e., t-test and paired t-test) fails in the nonlinear-association case.

Aged↗
PubMed2026

Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT.

The advent of single-cell lineage-tracing technologies has enabled the simultaneous profiling of gene expression and lineage barcodes. However, accurate, high-resolution reconstruction of cell lineage trees remains challenging because most existing approaches treat these modalities separately and therefore fail to fully exploit their complementary information. Here we present BiLinT, a Bayesian framework that jointly models multimodal single-cell lineage-tracing data for lineage tree reconstruction. BiLinT integrates barcode evolution (a continuous-time Markov chain) with gene expression dynamics (an Ornstein-Uhlenbeck process) within a unified probabilistic model. Across synthetic and real data sets, BiLinT provides accurate lineage-tree reconstruction and reveals differentiation-associated clonal structure and developmental fate biases.

Journal Article↗
PubMed2003

Software to compute and conduct sequential Bayesian phase I or II dose-ranging clinical trials with stopping rules.

The aim of dose-ranging phase I (resp. phase II) clinical trials is to rapidly identify the maximum tolerated dose (MTD) (resp., minimal effective dose (MED)) of a new drug or combination. For the conduct and analysis of such trials, Bayesian approaches such as the Continual Reassessment Method (CRM) have been proposed, based on a sequential design and analysis up to a completed fixed sample size. To optimize sample sizes, Zohar and Chevret have proposed stopping rules (Stat. Med. 20 (2001) 2827), the computation of which is not provided by available softwares. We present in this paper a user-friendly software for the design and analysis of these Bayesian Phase I (resp. phase II) dose-ranging Clinical Trials (BPCT). It allows to carry out the CRM with stopping rules or not, from the planning of the trial, with choice of model parameterization based on its operating characteristics, up to the sequential conduct and analysis of the trial, with estimation at stopping of the MTD (resp. MED) of the new drug or combination.

Bayes Theorem↗