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PubMed1995

Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probability-based criterion for comparing the results from diverse algorithms. To examine the usefulness of the method, the origin of the eukaryotes has been investigated by the analysis of ribosomal small subunit RNA sequences. Three common algorithms (paralinear distances, Jukes-Cantor distances, and Kimura distances) support the eocyte topology, whereas one (maximum parsimony) supports the archaebacterial topology, suggesting that the eocyte prokaryotes are the closest prokaryotic relatives of the eukaryotes.

Algorithms↗

PubMed2006

Green turtle (Chelonia mydas) foraging and nesting aggregations in the Caribbean and Atlantic: impact of currents and behavior on dispersal.

Although significant amounts of research have been dedicated to increasing the knowledge of the life history of green turtles (Chelonia mydas), large gaps exist in our understanding of juvenile migratory behavior. These gaps can be filled by genetic studies of foraging ground aggregations. Using mitochondrial DNA markers and Bayesian analyses, samples (n = 106) from a foraging aggregation in North Carolina indicated that animals from the east coast of the United States (54%) and Mexico (27%) dominate the composition with the remainder coming from other Caribbean and Atlantic nesting aggregations. These findings prompted a reanalysis of 4 regional foraging aggregations using Bayesian mixed stock analysis, analysis of molecular variance, and diversity measures. Significant regional population structure between northern and southern foraging aggregations in the Caribbean was detected (phiST = 0.27, P = 0.000) in addition to significant nesting aggregation structure (phiST = 0.87, P = 0.000). Haplotype diversity levels were highest at foraging aggregations located within the confluence of major current systems. These findings indicate that both currents and behavior have strong influences on the composition of foraging aggregations. In addition, our results provide evidence of juvenile homing to regional foraging grounds and highlight the difficulties of separating historical and current effects on recruitment patterns at foraging locations.

Animal Population Groups↗

PubMed2004

The Association of Coloproctology of Great Britain and Ireland study of large bowel obstruction caused by colorectal cancer.

BACKGROUND: This study was designed to investigate the early outcomes after surgical treatment of malignant large bowel obstruction (MBO) and to identify risk factors affecting operative mortality. METHODS: Data were prospectively collected from 1046 patients with MBO by 294 surgeons in 148 UK hospitals during a 12-month period from April 1998. A predictive model of in-hospital mortality was developed using a 3-level Bayesian logistic regression analysis. RESULTS: The median age of patients was 73 years (interquartile range 64-80). Of the 989 patients having surgery, 91.7% underwent bowel resection with an overall mortality of 15.7%. The multilevel model used the following independent risk factors to predict mortality: age (odds ratio [OR] 1.85 per 10 year increase), American Society of Anesthesiologists grade (OR for American Society of Anesthesiologists grade I versus II,III,IV-V = 3.3,11.7,22.2), Dukes' staging (OR for Dukes' A versus B,C,D = 2.0, 2.1, 6.0), and mode of surgery (OR for scheduled versus urgent, emergency = 1.6, 2.3). A significant interhospital variability in operative mortality was evident with increasing age (variance = 0.004, SE = 0.001, P < 0.001). No detectable caseload effect was demonstrated between specialist colorectal and other general surgeons. CONCLUSIONS: Using prognostic models, it was possible to develop a risk-stratification index that accurately predicted survival in patients presenting with malignant large bowel obstruction. The methodology and model for risk adjusted survival can set the reference point for more accurate and reliable comparative analysis and be used as an adjunct to the process of informed consent.

Adult↗

PubMed1998

Spatio-temporal fMRI analysis using Markov random fields.

Functional magnetic resonance images (fMRI's) provide high-resolution datasets which allow researchers to obtain accurate delineation and sensitive detection of activation areas involved in cognitive processes. To preserve the resolution of this noninvasive technique, refined methods are required in the analysis of the data. In this paper, we first discuss the widely used methods based on a statistical parameter map (SPM) analysis exposing the different shortcomings of this approach when considering high-resolution data. First, the often used Gaussian filtering results in a blurring effect and in delocalization of the activated area. Secondly, the SPM approach only considers false alarms due to noise but not rejections of activated voxels. We propose to embed the fMRI analysis problem into a Bayesian framework consisting of two steps: i) data restoration and ii) data analysis. We, therefore, propose two Markov random fields (MRF's) to solve these two problems. Results on three protocols (visual, motor and word recognition) are shown for two SPM approaches and compared with the proposed MRF approach.

Adult↗

PubMed2001

A physically based, probabilistic model for ultrasonic images incorporating shape, microstructure, and system characteristics.

Recent successes with Bayesian methods for analysis of shape in medical images have motivated our development of a shape-based data likelihood for ultrasound, the foundation of which is a computationally feasible, pixel-based, probabilistic image model. Previous probabilistic models for ultrasound generally assume an analytic form, e.g., Rayleigh, Rician, K, Generalized K, etc., then attempt to fit data to the model. Assumptions and intensive computation inherent in such an approach make it unsuitable for our purposes. In the pursuit of a new model, we have described previously a physical model for image formation that incorporates the imaging system characteristics, the surface shape, and the surface microstructure. That physical model was validated via a visual comparison of simulated and actual images of a cadaveric vertebra. In this work, a random phasor sum representation of the physical model provides the basis for a probabilistic form. In contrast to existing probabilistic models, we compute the amplitude mean and variance directly from the physical model. These statistics can be displayed as images to characterize the tissue, but, more importantly, they permit the subsequent assignment of a suitable density function to each pixel for the purposes of constructing a data likelihood. The order of these steps, i.e., first computing the statistics and then assigning a density function, permits the inclusion of the local surface shape, the surface microstructure, and the system characteristics at every image pixel without violating the physical model. Currently, the value of the SNR0, the ratio of the mean to the standard deviation, is used to estimate whether a pixel is Rayleigh- or non-Rayleigh-distributed. This assessment forms the basis for a data likelihood constructed as a product of Rayleigh and Gaussian density functions describing the individual image pixels.

Humans↗

PubMed2003

Binomial regression with misclassification.

Motivated by a study of human papillomavirus infection in women, we present a Bayesian binomial regression analysis in which the response is subject to an unconstrained misclassification process. Our iterative approach provides inferences for the parameters that describe the relationships of the covariates with the response and for the misclassification probabilities. Furthermore, our approach applies to any meaningful generalized linear model, making model selection possible. Finally, it is straightforward to extend it to multinomial settings.

Bayes Theorem↗

PubMed2026

Nature-based meaning-focused photography intervention enhances subjective well-being: A three-arm randomized controlled study.

Gaining meaning from nature contact can promote subjective well-being. However, few studies have validated the effectiveness of nature-based meaning interventions in enhancing subjective well-being. This study consisted of a 7-day online intervention to examine the effects of nature-based meaning-focused photography on well-being by comparing a photo-only group, a photo + writing group, and a waiting list control group and how meaning in life mediates the relationship between nature contact and well-being. A pre-registered three-arm randomized controlled trial (groups: photo + writing group vs. photo-only group vs. control group) * (time: pre-test vs. post-test vs. 1-month follow-up) was conducted with 219 college students. In the photo + writing group, participants captured nature scenes and wrote 100-word reflections. The photo-only group only took nature photos. The primary outcomes were meaning in life and well-being, and the secondary outcome was life satisfaction. A conservative Bayesian causal forest analysis based on machine learning was used to detect both treatment and heterogeneous intervention effects. Compared with the control group, the photo + writing group showed positive effects on meaning in life, subjective well-being, and life satisfaction, with average treatment effects of 0.36, 0.27, and 0.66 standard deviations (SD), respectively. The photo-only group also showed generally positive effects on these outcomes, with average treatment effects of 0.27, 0.24, and 0.54 SD, respectively. However, these effects were not sustained after 1 month. The intervention was especially beneficial for participants from lower subjective socioeconomic status, with limited prior nature exposure, or lower baseline psychological well-being. Importantly, enhanced meaning in life helped explain how the intervention improved well-being and life satisfaction. This study also demonstrated that combining nature-based photography and reflective writing can improve well-being.

Humans↗

PubMed2006

Geographical partitioning of goat diversity in Europe and the Middle East.

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.

Animals↗

PubMed2006

Speaking the truth in maritime risk assessment.

Several major risk studies have been performed in recent years in the maritime transportation domain. These studies have had significant impact on management practices in the industry. The first, the Prince William Sound risk assessment, was reviewed by the National Research Council and found to be promising but incomplete, as the uncertainty in its results was not assessed. The difficulty in assessing this uncertainty is the different techniques that need to be used to model risk in this dynamic and data-scarce application area. In previous articles, we have developed the two pieces of methodology necessary to assess uncertainty in maritime risk assessment, a Bayesian simulation of the occurrence of situations with accident potential and a Bayesian multivariate regression analysis of the relationship between factors describing these situations and expert judgments of accident risk. In this article, we combine the methods to perform a full-scale assessment of risk and uncertainty for two case studies. The first is an assessment of the effects of proposed ferry service expansions in San Francisco Bay. The second is an assessment of risk for the Washington State Ferries, the largest ferry system in the United States.

Journal Article↗

PubMed2006

Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland.

In a survey of Phytophthora associated with alder decline in Poland, several isolates of a homothallic Phytophthora sp., which could not be assigned to other taxa including Phytophthora alni subspecies, were consistently recovered from rhizosphere soil samples. Their morphology and pathogenicity, as well as sequence data for three nuclear regions (internal transcribed spacer rDNA, elongation factor-1alpha and beta-tubulin) and a coding mitochondrial DNA region (nadh1), were examined. The new Phytophthora species is characterized by the moderate to slow growth rate of its colony in carrot agar at 20 degrees C, high optimal (c. 30 degrees C) and maximum (c. 38 degrees C) growth temperatures, formation of catenulate, often lateral, hyphal swellings, large chlamydospores in agar media and in soil extract, persistent, ovoid to ellipsoid nonpapillate sporangia and large oogonia with paragynous and sometimes amphigynous antheridia. Phytophthora polonica was slightly pathogenic to alder twigs and not pathogenic to trunks of several tree species. In a phylogenetic analysis using either Bayesian inference or maximum likelihood methods, P. polonica falls in clade 8 'sensu Kroon et al. (2004)' of Phytophthora.

Alnus↗

PubMed2005

Ancient differentiation of the H and I haplomes in diploid Hordeum species based on 5S rDNA.

5S rDNA clones from 12 South American diploid Hordeum species containing the HH genome and 3 Eurasian diploid Hordeum species containing the II genome, including the cultivated barley Hordeum vulgare, were sequenced and their sequence diversity was analyzed. The 374 sequenced clones were assigned to "unit classes", which were further assigned to haplomes. Each haplome contained 2 unit classes. The naming of the unit classes reflected the haplomes, viz. both the long H1 and short I1 unit classes were identified with II genome diploids, and both the long H2 and long Y2 unit classes were recognized in South American HH genome diploids. Based upon an alignment of all sequences or alignments of representative sequences, we tested several evolutionary models, and then subjected the parameters of the models to a series of maximum likelihood (ML) analyses and various tests, including the molecular clock, and to a Bayesian evolutionary inference analysis using Markov chain Monte Carlo (MCMC). The best fitting model of nucleotide substitution was the HKY+G (Hasegawa, Kishino, Yano 1985 model with the Gamma distribution rates of nucleotide substitutions). Results from both ML and MCMC imply that the long H1 and short I unit classes found in the II genome diploids diverged from each other at the same rate as the long H2 and long Y2 unit classes found in the HH genome diploids. The divergence among the unit classes, estimated to be circa 7 million years, suggests that the genus Hordeum may be a paleopolyploid.

DNA, Plant↗

PubMed2003

Multiple genome-wide analyses of smoking behavior in the Framingham Heart Study.

BACKGROUND: Cigarette smoking behavior may have a genetic basis. We assessed evidence for quantitative trait loci (QTLs) affecting the maximum number of cigarettes smoked per day, a trait meant to quantify this behavior, using data collected over 40 years as part of the Framingham Heart Study's original and offspring cohorts. RESULTS: Heritability was estimated to be approximately 21% using variance components (VC) methods (SOLAR), while oligogenic linkage and segregation analysis based on Bayesian Markov chain Monte Carlo (MCMC) methods (LOKI) estimated a mean of two large QTLs contributing approximately 28% and 20%, respectively, to the trait's variance. Genome-wide parametric (FASTLINK) and VC linkage analyses (SOLAR) revealed several LOD scores greater than 1.0, with peak LOD scores using both methods on chromosomes 2, 17, and 20; multi-point MCMC methods followed up on these chromosomes. The most robust linkage results were for a QTL between 65 and 84 cM on chromosome 20 with signals from multiple sex- and age-adjusted analyses including two-point LOD scores of 1.30 (parametric) and 1.07 (heritability = 0.17, VC) at 70.51 cM, a multi-point LOD score of 1.50 (heritability = 0.20, VC) at 84 cM, and an intensity ratio of 12.0 (MCMC) at 65 cM. CONCLUSION: Familial aggregation of the maximum number of cigarettes smoked per day was consistent with a genetic component to this behavior, and oligogenic segregation analyses using MCMC suggested two important QTLs. Linkage signals on chromosome 20 between 65 and 84 cM were seen using multiple analytical methods. No linkage result, however, met genome-wide statistical significance criteria, and the true relationship between these regions and smoking behavior remains unclear.

Adolescent↗

PubMed2004

In vivo MRS measurement of liver lipid levels in mice.

A magnetic resonance spectroscopy (MRS) procedure for in vivo measurement of lipid levels in mouse liver is described and validated. The method uses respiratory-gated, localized spectroscopy to collect proton spectra from voxels within the mouse liver. Bayesian probability theory analysis of these spectra allows the relative intensities of the lipid and water resonances within the liver to be accurately measured. All spectral data were corrected for measured spin-spin relaxation. A total of 48 mice were used in this study, including wild-type mice and two different transgenic mouse strains. Different groups of these mice were fed high-fat or low-fat diets or liquid diets with and without the addition of alcohol. Proton spectra were collected at baseline and, subsequently, every 4 weeks for up to 16 weeks. Immediately after the last MRS measurement, mice were killed and their livers analyzed for triglyceride level by conventional wet-chemistry methods. The excellent correlation between in vivo MRS and ex vivo wet-chemistry determinations of liver lipids validates the MRS method. These results clearly demonstrate that in vivo MRS will be an extremely valuable technique for longitudinal studies aimed at providing important insights into the genetic, environmental, and dietary factors affecting fat deposition and accumulation within the mouse liver.

Animals↗

PubMed2002

Pharmacokinetic model for tobramycin in acinetobacter meningitis.

OBJECTIVE: To report a case of acinetobacter meningitis treated with a once-daily intravenous dose of tobramycin and to propose a pharmacokinetic model for the drug disposition. CASE SUMMARY: A 28-year-old man with chronic hydrocephalus was admitted with a diagnosis of intracranial hypertension. Acinetobacter spp. was detected in the cerebrospinal fluid (CSF); it was sensitive to tobramycin, ampicillin/sulbactam, and colistin. Based on the culture report, multiple daily-dose therapy with tobramycin was started. As the infectious symptoms remained, once-daily therapy was recommended; the optimal dose was calculated with nonlinear regression by least-squares analysis and a Bayesian method, using plasma and CSF samples. The infection was resolved, tobramycin therapy was discontinued, and the patient was discharged from the intensive care unit. DISCUSSION: We use once-daily intravenous tobramycin therapy because, although the intrathecal administration of drugs is generally well tolerated, the presence of preservatives may be a source of central nervous system adverse effects. Pharmacokinetic parameters were calculated with plasma and CSF concentration values obtained during the first once-daily dose by using a compartment-effect model which allows fitting of simultaneous plasma and CSF concentrations. The prediction level was determined by the estimation of drug concentrations during the fourth once-daily dose. CSF concentrations of drug were enough to eradicate the clinical signs of infection. CONCLUSIONS: Therapy using once-daily intravenous administration of tobramycin may be an adequate alternative for acinetobacter infections in neurosurgical patients when an intrathecal route is initially not recommended. The development of a compartment-effect model can be useful to predict drug concentrations.

Acinetobacter Infections↗

PubMed2005

Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers.

Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.

Chromosome Mapping↗

PubMed2005

Setting site-specific water-quality standards by using tissue residue criteria and bioaccumulation data. Part 1. Methodology.

We have developed a method for determining site-specific water-quality standards (SSWQSs) for substances regulated based on tissue residues. The method uses a multisite regression model to solve for the conditional prior probability density function (PDF) on water concentration, given that tissue concentration equals a tissue residue threshold. The method then uses site-specific water and tissue concentration data to update the probabilities on a Monte Carlo sample of the prior PDF by using Bayesian Monte Carlo analysis. The resultant posterior PDF identifies the water concentration that, if met at the site, would provide a desired level of confidence of meeting the tissue residue threshold contingent on model assumptions. This allows for derivation of a SSWQS. The method is fully reproducible, statistically rigorous, and easily implemented. A useful property of the method is that the model is sensitive to the amount of site-specific data available, that is, a more conservative or protective number (water concentration) is derived when the data set is small or the variance is large. Likewise, as the site water concentration increases above the water-quality standard, more site-specific information is needed to demonstrate a safe concentration at the site. A companion paper demonstrates the method by using selenium as an example.

Animals↗

PubMed1989

Bayesian forecasting of serum lithium concentrations. Comparison with traditional methods.

Twelve pharmacokinetic methods of estimating lithium maintenance dosage requirements were compared in 21 patients with bipolar illness. Methods which were compared included the single- and multiple-point methods of Perry, 4 non-linear regression and 6 Bayesian methods. The REVOL algorithm was employed for converging on to estimates of clearance and apparent volume of distribution for the non-linear regression and Bayesian methods. Data analysis was based on an evaluation of prediction error as a measure of bias, and absolute prediction error as a measure of precision. In a direct comparison, there were no statistically significant differences in bias or precision between any of the methods.

Adolescent↗

PubMed2001

[Therapeutic monitoring by blood concentrations with the focus on cyclosporin A].

Cyclosporin A therapeutic drug monitoring with through concentrations results in a high frequency of toxicity or therapeutic failure. There is no simple relation between the through and the mean concentration, and thus the therapeutic effect. Estimation of the AUC on sparse sampling or population pharmacokinetic analysis and the Bayesian fit of the parameters are discussed.

Bayes Theorem↗