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PubMed2005

Spatial and management factors associated with exposure of smallholder dairy cattle in Tanzania to tick-borne pathogens.

A cross-sectional study of serum antibody responses of cattle to tick-borne pathogens (Theileria parva, Theileria mutans,Anaplasma marginale, Babesia bigemina and Babesia bovis) was conducted on smallholder dairy farms in Tanga and Iringa Regions of Tanzania. Seroprevalence was highest for T. parva (48% in Iringa and 23% in Tanga) and B. bigemina (43% in Iringa and 27% in Tanga) and lowest for B. bovis (12% in Iringa and 6% in Tanga). We use spatial and non-spatial models, fitted using classical and Bayesian methods, to explore risk factors associated with seroprevalence. These include both fixed effects (age, grazing history and breeding status) and random effects (farm and local spatial effects). In both regions, seroprevalence for all tick-borne pathogens increased significantly with age. Animals pasture grazed in the 3 months prior to the start of the sampling period were significantly more likely to be seropositive for Theileria spp. and Babesia spp. Pasture grazed animals were more likely to be seropositive than zero-grazed animals for A. marginale, but the relationship was weaker than that observed for the other four pathogens. This study did not detect any significant differences in seroprevalence associated with other management-related variables, including the method or frequency of acaricide application. After adjusting for age, there was weak evidence of localised (<5 km) spatial correlation in exposure to some of the tick borne diseases. However, this was small compared with the 'farm-effect', suggesting that risk factors specific to the farm were more important than those common to the local neighbourhood. Many animals were seropositive for more than one pathogen and the correlation between exposure to the different pathogens remained after adjusting for the identified risk factors. Identifying the determinants of exposure to multiple tick-borne pathogens and characterizing local variation in risk will assist in the development of more effective control strategies for smallholder dairy farms.

Anaplasma marginale↗
PubMed2003

Statistical decision theory and evolution.

Two recent articles by Geisler and Diehl use Bayesian statistical decision theory to model the co-evolution of predator and prey in a simple, game-like environment. The prey is characterized by its coloration. The predator is characterized by the chromatic sensitivity of its visual system and its willingness to attack. The authors demonstrate how the coloration of prey and the perceptual system of the predator co-evolve, converging to a Nash equilibrium for both species.

Journal Article↗
PubMed2005

Efficacy of inactivated hepatitis A vaccine in HIV-infected patients: a hierarchical bayesian meta-analysis.

Patients with human immunodeficiency virus-1 (HIV) have elevated risk for hepatitis A virus (HAV) coinfection. Sequelae from coinfection include increased risk of liver-related morbidity and mortality. This study synthesizes the results of trials measuring response to HAV vaccine in HIV-infected patients using Bayesian meta-analysis methodologies. PubMed, OhioLINK/Medline, and other sources were used to search for studies analyzing response to HAV vaccine in HIV-infected patients. Studies were evaluated for quality. A Bayesian hierarchical random-effects model was used to estimate overall response to vaccine. Between-study variance was calculated. Sensitivity analyses were conducted to determine the potential for bias. The literature search yielded eight studies for inclusion in the meta-analysis, with a combined total of 458 patients. Observed proportions of response in individual studies ranged from 50 to 95%. The intention-to-treat meta-analysis estimated a combined proportion of HIV+ patients responding to vaccine of 64% (95% CI 52-75%). Heterogeneity between studies was significant. The overall response rate to HAV vaccine in HIV-infected patients is lower than typically cited. Up to 1/2 of HIV-infected patients may be nonresponders. Future research will be required to better understand the correlates of response.

Bayes Theorem↗
PubMed2001

Interaction of visual prior constraints.

The visual system relies on two types of information to interpret a visual scene: the cues that can be extracted from the retinal images and prior constraints that are used to disambiguate the scene. Many studies have looked at how multiple visual cues are combined. We examined the interaction of multiple prior constraints. The particular constraints studied here are assumptions the observer makes concerning the location of the light source (for the shading cue to depth) and the orientation of a surface (for depth based on image contours). The reliability of each of the two cues was manipulated by changing the contrast of different parts of the stimuli. We developed a model based on elements of Bayesian decision theory that permitted us to track the weights applied to each of the prior constraints as a function of the cue reliabilities. The results provided evidence that prior constraints behave just like visual cues to depth: cues with more reliable information have higher weight attributed to their corresponding prior constraint.

Bayes Theorem↗
PubMed2006

[Incidence of lung cancer in Bas-Rhin, France: trends and projection for 2014].

INTRODUCTION: In France lung cancer is the second most common cancer in men and the fourth most common in women. In the department of Bas-Rhin the incidence is increasing by 0.1% per annum in men and by 4.4% in women. The aim is to analyse and predict the trend of lung cancer incidence in Bas-Rhin from 1975 to 2014. METHODS: The incidence data from 1975 to 1999 were extracted from the Bas-Rhin cancer registry. Population estimates (2594 years) were made for the period 1975-2014. Predictions were based on a Bayesian age-period-cohort model. RESULTS: Between 1975 and 1999 the incidence of lung cancer increased by 4.5% p.a. in women. In men it increased by 1.6% p.a. between 1975 and 1989 and then diminished. For the periods 2000-2004, 2005-2009 and 2010-2014 respectively the rates should reach 25.6, 32.9 and 42.8 per 100,000 in women and 117.5, 111.6 and 110.1 per 100,000 in men. CONCLUSIONS: Increasing tobacco smoking among women and a reduction among men could be one of the reasons for the respective increasing and decreasing incidences.

Adult↗
PubMed2001

Estimating the number of opiate users in amsterdam by capture-recapture: the importance of case definition.

One of the objectives of Amsterdam's methadone maintenance treatment is maximising its coverage among problematic opiate users. In order to evaluate what proportion is reached, the capture-recapture method is conducted to estimate the prevalence of problematic opiate use. Samples of opiate users in contact with police, hospital or treatment are used. The treatment sample is limited to the low threshold treatment sample (treatment with minimal requirements to the clients). Based on differences of log likelihood ratio, Akaike's and Bayesian information criteria, log linear models are selected. The size of the population of problematic opiate users in 1997 is estimated to be 4130 (95% confidence interval: 3753-4566). Within 3 months 50% was registered: 16% at the police, 2.5% at the hospital and 40% at treatment. This study shows that the Amsterdam methadone treatment programs succeed in reaching a high proportion of problematic opiate users. The estimation of the prevalence of problematic opiate users is considered to be valid. However, if, instead of the low threshold treatment, the total treatment sample had been used, the population of interest and the sampled population would not match correctly, and prevalence would have been overestimated.

Bayes Theorem↗
PubMedDate not supplied

Descriptive spatial analysis of BSE in western France.

The spatial heterogeneity of Bovine Spongiform Encephalopathy (BSE) was analysed on the 84 cases confirmed in western France (WF) between August and December 2000, when both the Mandatory Reporting System and an active surveillance on cattle at risk were running. Ninety-four percent of these cases were born between June 1993 and June 1996, and we analysed the location at birth. One disease mapping and two clustering methods (Scan of Kulldorff and the method of Besag and Newell) were used. In order to attenuate the contrasts artificially created by the standard disease mapping method (over-dispersion), we estimated the Standard Incidence Ratio (SIR) with a Bayesian method (Poisson-Gamma model) allowing a smoothing of the estimators. The geographical location of interest was the "canton", that divided the total area into 526 geographical units. The background population (2.6 million cattle) was obtained from the Agricultural Census 2000. We tested the hypothesis of a homogenous spatial distribution of the BSE risk where the expected number of BSE cases per unit area was obtained by applying the overall BSE rate in WF to each "canton", standardised on the type of breed, dairy versus beef suckler. The SIR ranged from 0.80 to 2.18 and the spatial distribution of BSE cases was significantly heterogeneous. Two spatial clusters were detected with the spatial scan statistics of Kulldorff and the method of Besag and Newell (18 to 20 observed BSE-cases per cluster with a radius of 45 km) centred on the "département" of Côtes-d'Armor and Mayenne. Another cluster was detected with the method of Besag and Newell (9 observed BSE-cases) in the "département" of Finistère. The results proved that the risk of BSE is linked to the geographical location in the area of the study.

Animals↗
PubMed2006

cBrother: relaxing parental tree assumptions for Bayesian recombination detection.

UNLABELLED: Bayesian multiple change-point models accurately detect recombination in molecular sequence data. Previous Java-based implementations assume a fixed topology for the representative parental data. cBrother is a novel C language implementation that capitalizes on reduced computational time to relax the fixed tree assumption. We show that cBrother is 19 times faster than its predecessor and the fixed tree assumption can influence estimates of recombination in a medically-relevant dataset. AVAILABILITY: cBrother can be freely downloaded from http://www.biomath.org/dormanks/ and can be compiled on Linux, Macintosh and Windows operating systems. Online documentation and a tutorial are also available at the site.

Algorithms↗
PubMed2006

Bayesian logistic regression using a perfect phylogeny.

Haplotype data capture the genetic variation among individuals in a population and among populations. An understanding of this variation and the ancestral history of haplotypes is important in genetic association studies of complex disease. We introduce a method for detecting associations between disease and haplotypes in a candidate gene region or candidate block with little or no recombination. A perfect phylogeny demonstrates the evolutionary relationship between single-nucleotide polymorphisms (SNPs) in the haplotype blocks. Our approach extends the logic regression technique of Ruczinski and others (2003) to a Bayesian framework, and constrains the model space to that of a perfect phylogeny. Environmental factors, as well as their interactions with SNPs, may be incorporated into the regression framework. We demonstrate our method on simulated data from a coalescent model, as well as data from a candidate gene study of sarcoidosis.

Bayes Theorem↗
PubMed2003

Temporal relation between the ADC and DC potential responses to transient focal ischemia in the rat: a Markov chain Monte Carlo simulation analysis.

Markov chain Monte Carlo simulation was used in a reanalysis of the longitudinal data obtained by Harris et al. (J Cereb Blood Flow Metab 20:28-36) in a study of the direct current (DC) potential and apparent diffusion coefficient (ADC) responses to focal ischemia. The main purpose was to provide a formal analysis of the temporal relationship between the ADC and DC responses, to explore the possible involvement of a common latent (driving) process. A Bayesian nonlinear hierarchical random coefficients model was adopted. DC and ADC transition parameter posterior probability distributions were generated using three parallel Markov chains created using the Metropolis algorithm. Particular attention was paid to the within-subject differences between the DC and ADC time course characteristics. The results show that the DC response is biphasic, whereas the ADC exhibits monophasic behavior, and that the two DC components are each distinguishable from the ADC response in their time dependencies. The DC and ADC changes are not, therefore, driven by a common latent process. This work demonstrates a general analytical approach to the multivariate, longitudinal data-processing problem that commonly arises in stroke and other biomedical research.

Animals↗
PubMed2001

New stopping criteria for segmenting DNA sequences.

We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian information criterion in the model selection framework. When this criterion is applied to telomere of S. cerevisiae and the complete sequence of E. coli, borders of biologically meaningful units were identified, and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.

Bayes Theorem↗
PubMedDate not supplied

Incorporating direct and indirect evidence using bayesian methods: an applied case study in ovarian cancer.

OBJECTIVE: To demonstrate the application of a Bayesian mixed treatment comparison (MTC) model to synthesize data from clinical trials to inform decisions based on all relevant evidence. METHODS: The value of an MTC model is demonstrated using a probabilistic decision-analytic model developed to assess the cost-effectiveness of second-line chemotherapy in ovarian cancer. Three clinical trials were found that each made a different pair-wise comparison of three treatments of interest in the overall patient population. As no common comparator existed between the three trials, an MTC model was used to assess the combined weight of evidence on survival from all three trials simultaneously. This analysis was compared to an alternative approach that combined two of the trials to make the same comparison of all three treatments using a common comparator, and an informal approach that did not synthesize the available evidence. RESULTS: By including all three trials using an MTC model, the credible intervals around estimated overall survival were reduced compared with making the same comparison using only two trials and a common comparator. Nevertheless, the survival estimates from the MTC model result in greater uncertainty around the optimal treatment strategy at a cost-effectiveness threshold of 30,000 pounds per quality-adjusted life-year. CONCLUSIONS: MTC models can be used to combine more data than would typically be included in a traditional meta-analysis that relies on a common comparator. They can formally quantify the combined uncertainty from all available evidence, and can be conducted using the same analytical approaches as standard meta-analyses.

Antineoplastic Agents↗
PubMed2026

Sugar kelp (Saccharina latissima) population genetics map onto geographic distance and oceanographic features across coastal Maine.

Sugar kelp (Saccharina latissima; order Laminariales) plays a vital role in kelp forest ecosystems, as well as an expanding kelp aquaculture industry, in the Gulf of Maine, United States. However, ocean warming is eroding the resilience of Maine's kelp forests and may be compromising their local genetic diversity, with impacts on population structure and gene flow. Here, we used genome-wide single nucleotide polymorphism (SNP) data to assess the genetic diversity, structure, and connectivity of S. latissima populations at 11 outer coastal sites spanning the historical range of kelp forests in Maine. Our analyses identified moderate genetic diversity and limited inbreeding within sites (average heterozygosity: 0.27). Further, they revealed that three clusters comprising four genetically distinct populations exist across the study region. Population structure was strongly associated with geographic distance and oceanographic features, as supported by principal coordinate analysis, FST calculations, Bayesian clustering, and spore dispersal modeling. Lastly, our outlier analysis identified genes potentially under selection. Thus, our findings highlight distinct, genetically unique kelp populations along Maine's coast and emphasize the need for regional management strategies that support both ecosystem resilience and sustainable aquaculture under climate change.

Gulf of Maine↗
PubMed2005

Using unsupervised learning with independent component analysis to identify patterns of glaucomatous visual field defects.

PURPOSE: Clustering by unsupervised learning with machine learning classifiers was shown to segment clusters of patterns in standard automated perimetry (SAP) for glaucoma in previous publications. In this study, unsupervised learning by independent component analysis decomposed SAP field patterns into axes, and the information represented by these axes was evaluated. METHODS: SAP fields were used that were obtained with the Humphrey Visual Field Analyzer (Carl Zeiss Meditec, Dublin, CA) from 189 normal eyes and 156 eyes with glaucomatous optic neuropathy (GON) determined by masked review with stereoscopic optic disc photographs. The variational Bayesian independent component analysis mixture model (vB-ICA-mm) partitioned the SAP fields into the most informative number of clusters. Simultaneously, the model learned an optimal number of maximally independent axes for each cluster. RESULTS: The most informative number of clusters in the SAP set was two. vB-ICA-mm placed 68.6% of the eyes with GON in a cluster labeled G and 98.4% of the eyes with normal optic discs in a cluster labeled N. Cluster G optimally contained six axes. Post hoc analysis of patterns generated at -1 SD and +2 SD from the cluster G mean on the six axes revealed defects similar to those identified by experts as indicative of glaucoma. SAP fields associated with an axis showed increasing severity, as they were located farther in the positive direction from the cluster G mean. CONCLUSIONS: vB-ICA-mm represented the SAP fields with patterns that were meaningful for glaucoma experts. This process also captured severity in the patterns uncovered. These findings should validate vB-ICA-mm as a data-mining technique for new and unfamiliar complex tests.

Artificial Intelligence↗
PubMed2005

Unsupervised machine learning with independent component analysis to identify areas of progression in glaucomatous visual fields.

PURPOSE: To determine whether a variational Bayesian independent component analysis mixture model (vB-ICA-mm), a form of unsupervised machine learning, can be used to identify and quantify areas of progression in standard automated perimetry fields. METHODS: In an earlier study, it was shown that a model using vB-ICA-mm can separate normal fields from fields with six different patterns of visual field loss related to glaucomatous optic neuropathy (GON) along maximally independent axes. In the present study, an independent group of 191 patient eyes (66 with ocular hypertension (OHT), 12 with suspected glaucoma by field, 61 with suspected glaucoma by disc, and 52 with glaucoma) with five or more standard visual fields under observation for a mean of 6.24 +/- 2.65 years and 8.11 +/- 2.42 visual fields were evaluated with the vB-ICA-mm. In addition, eyes with progressive GON (PGON) were identified (n = 39). Each participant had a series of fields tested, with each field entered independently and placed along the axes of the previously developed model. This allowed change in one pattern of visual field defect (along one axis) to be assessed relative to results other areas of that same field (no change along other axes). Progression was based on a slope falling outside the 5th and the 95th percentile limits of all slopes, with at least two axes not showing such a deviation in a given individual's series of fields. Fields were also scored using Advanced Glaucoma Intervention Study (AGIS) and the Early Manifest Glaucoma Treatment Trial (EMGT) criteria. RESULTS: Thirty-two of 191 eyes progressed on vB-ICA-mm by this definition. Of the 32, 22 had field loss at baseline, 7 had only GON, 3 were OHTs and 12 were from the 39 eyes (31%) with PGON. The vB-ICA-mm identified a higher percentage of progressing eyes in each diagnostic category than did AGIS or and the EMGT. CONCLUSIONS: The vB-ICA-mm can quantitatively identify progression in eyes with glaucoma by evaluating change in one or more patterns of the visual field loss while other areas or patterns remain stable. This may enable each eye to contribute to the determination of whether change is caused by true progression or by variability.

Adult↗
PubMedDate not supplied

A Bayesian approach to aid in formulary decision making: incorporating institution-specific cost-effectiveness data with clinical trial results.

Pharmacy and therapeutics committees commonly cite a lack of generalizability as a reason for not incorporating cost-effectiveness information into decision making. To address this concern, many committees undertake site-specific economic evaluations, which are often limited by small sample sizes and nonrandomized designs. We show how 2 complementary approaches were used to minimize these limitations in an economic evaluation of abciximab at 1 institution. Using a propensity score methodology, we selected patients who did not receive abciximab for the comparison cohort. Then, we adopted a Bayesian, hierarchical, random-effects model to integrate site-specific and clinical trial data. We applied the posterior distributions of effectiveness with local cost data in a traditional decision-analytic model. In 74% of the simulations, abciximab was cost-effective at 1 institution at the $50,000 per life year saved threshold, assuming a 50:50 split of patients undergoing coronary stenting and angioplasty. Among patients undergoing coronary stenting, the cost-effectiveness ratio of the addition of abciximab was at or below the $50,000 per life year saved threshold in 66.0% of the simulations.

Abciximab↗
PubMed2006

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle.

We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D'. Estimates of D' from the two approaches were in close agreement (r = 0.91). The mean estimates of D' for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e ( approximately 37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.

Animals↗
PubMed2006

OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.

BACKGROUND: Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. RESULTS: OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. CONCLUSION: Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

Algorithms↗