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Results for “Bayes factor”

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PubMed2001

Projecting cancer incidence and mortality using Bayesian age-period-cohort models.

BACKGROUND: We present a practical application of an age-period-cohort model in a Bayesian frame-work for making cancer-burden projections. METHODS: Second degree autoregressive smoothing was used on the age, period and cohort effects for estimating future incidence and mortality. RESULTS: We are able to demonstrate the feasibility, flexibility and strengths of this approach. Compared with previously used methods, it performed better for providing point estimates when past trends continued into the future. However, the extremely wide credible intervals need careful interpretation. DISCUSSION: Part of the uncertainty is attributable to the possible inadequacy of the model and not necessarily relevant in the prediction of what would happen if the present trends continue into the future.

Age Factors↗
PubMed2024

BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees.

Next-generation sequencing is widely applied to the investigation of pedigree data for gene discovery. However, identifying plausible disease-causing variants within a robust statistical framework is challenging. Here, we introduce BICEP: a Bayesian inference tool for rare variant causality evaluation in pedigree-based cohorts. BICEP calculates the posterior odds that a genomic variant is causal for a phenotype based on the variant cosegregation as well as a priori evidence such as deleteriousness and functional consequence. BICEP can correctly identify causal variants for phenotypes with both Mendelian and complex genetic architectures, outperforming existing methodologies. Additionally, BICEP can correctly down-weight common variants that are unlikely to be involved in phenotypic liability in the context of a pedigree, even if they have reasonable cosegregation patterns. The output metrics from BICEP allow for the quantitative comparison of variant causality within and across pedigrees, which is not possible with existing approaches.

Pedigree↗
PubMed1979

The Chatham Blood Pressure Study. An application of Bayesian growth curve models to a longitudinal study of blood pressure in children.

Recent developments in statistics have produced powerful methods that facilitate the analysis of longitudinal studies. These methods are illustrated by an analysis of a longitudinal study of blood pressure in children. The results of the study show a clear tendency for blood pressure to increase with age, and Asian children tend to have lower blood pressures than their Caucasian counterparts of the same age. There is evidence to support the hypothesis that blood pressures track.

Age Factors↗
PubMed2026

A systematic review and network meta-analysis of single nucleotide polymorphisms associated with oral submucous fibrosis risk.

BACKGROUND: Oral submucous fibrosis (OSF) is a chronic and insidious oral disease characterized by hyalinization of the subepithelial connective tissue and progressive fibrosis of the oral submucosa. It is a precancerous condition of oral squamous cell carcinoma. Studies have demonstrated that single nucleotide polymorphisms (SNPs) are closely associated with susceptibility to OSF. This study aims to comprehensively evaluate the association between SNPs and OSF risk and to rank the strength of the association between different genetic models and OSF susceptibility. METHODS: Literature related to OSF was comprehensively searched from PubMed, Web of Science, Embase, Cochrane Library, CNKI, and Wangfang databases up to July 2025. Full-text case-control studies with patients diagnosed with OSF were included. Quality assessment was performed to evaluate the risk of bias. RevMan 5.4, GeMTC 0.14.3, and STATA 17.0 were used for the pairwise and Bayesian network meta-analysis. RESULTS: A total of 24 studies with 2545 cases and 3772 controls, covering 13 SNPs in 11 genes, were included in our meta-analysis. We found that CYP1A1 rs4646903:T>C, CYP1A1 rs1048943:A>G, GSTT1 null genotype, GSTM1 null genotype, and XRCC3 rs861539:C>T were associated with an increased risk of OSF, while MMP2 rs243865:C>T and MMP3 rs3025058: 5A>6A were associated with a decreased risk of OSF. Further Bayesian network meta-analysis indicated the top 5 genetic models with the highest association with OSF risk in network group 1 were the dominant model, homozygous model, allelic model, and recessive model of CYP1A1 rs1048943:A>G (ranked 1-4), and the heterozygous/dominant model of CYP1A1 rs4646903:T>C (both ranked 5). While the allelic models of XRCC3 rs861539:C>T and MMP3 rs3025058: 5A>6A ranked first for predicting OSF in group 2 and group 3, respectively. CONCLUSION: Some specific SNPs are significantly related to the risk of OSF. Among them, the dominant model of CYP1A1 rs1048943:A>G may be the most strongly associated genetic model with OSF risk. Future large-sample, well-designed studies with detailed genotype data are needed to validate the roles of these SNPs in OSF risk.

Humans↗
PubMed2006

Children use categories to maximize accuracy in estimation.

The present study tests a model of category effects upon stimulus estimation in children. Prior work with adults suggests that people inductively generalize distributional information about a category of stimuli and use this information to adjust their estimates of individual stimuli in a way that maximizes average accuracy in estimation (see Huttenlocher, Hedges & Vevea, 2000). However, little is known about the developmental origin of this cognitive process. In the present study, 5- and 7-year-old children viewed stimuli that varied in size and reproduced each from memory. Consistent with the predictions of a Bayesian model of category effects on estimation, responses were adjusted toward the central value of the stimulus distribution. Additionally, the dispersion of the stimulus distribution affected the pattern of bias and variability of responses in a way that is predicted by the model. The results suggest that, like adults, children use categories for increasing average accuracy in estimating inexact stimuli.

Age Factors↗
PubMed2005

MLE and Bayesian inference of age-dependent sensitivity and transition probability in periodic screening.

This article extends previous probability models for periodic breast cancer screening examinations. The specific aim is to provide statistical inference for age dependence of sensitivity and the transition probability from the disease free to the preclinical state. The setting is a periodic screening program in which a cohort of initially asymptomatic women undergo a sequence of breast cancer screening exams. We use age as a covariate in the estimation of screening sensitivity and the transition probability simultaneously, both from a frequentist point of view and within a Bayesian framework. We apply our method to the Health Insurance Plan of Greater New York study of female breast cancer and give age-dependent sensitivity and transition probability density estimates. The inferential methodology we develop is also applicable when analyzing studies of modalities for early detection of other types of progressive chronic diseases.

Adult↗
PubMed2026

Programmed cell death and risk of diabetic retinopathy: a Mendelian randomization study.

BACKGROUND: Programmed cell death (PCD) plays an important role in diabetic retinopathy (DR); however, the underlying genetic mechanisms remain unclear. We used Mendelian randomization (MR) to investigate the causal relationships between PCD-related genes and DR. This study aimed to investigate the effects of PCD on the risk of DR by conducting MR analysis. METHODS: Summary statistics from gene expression quantitative trait loci (eQTL) studies (31,684 Europeans) were analyzed. Genetic instrumental variables were selected using cis-eQTL single-nucleotide polymorphisms (SNPs; P&#x2009;<&#x2009;5&#x2009;&#xd7;&#x2009;10-&#x2009;8). Summary data-based MR (SMR) was employed to assess causal associations between PCD-related genes and DR, with three additional MR methods used for sensitivity testing. Bayesian colocalization was used to examine the shared regulatory mechanisms between PCD QTLs and DR risk loci. RESULTS: Sensitivity and colocalization analyses revealed six genes that affected DR: cathepsin H (CTSH), NAD(P)H: quinone oxidoreductase 1 (NQO1), tribbles pseudokinase 3 (TRIB3), and phosphoglycerate mutase 5 (PGAM5), which increased DR risk, and iron-responsive element binding protein 2 (IREB2) and tumor necrosis factor (TNF), which exhibited protective effects. Multivariate MR confirmed significant causal effects for CTSH, IREB2, and PGAM5 (p&#x2009;<&#x2009;0.050). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis (including 10 STRING-derived genes) revealed that 13 genes were enriched in necroptosis, apoptosis, mitophagy, and TNF signaling pathways in DR. CONCLUSIONS: This MR study supports the causal involvement of PCD in DR and identifies candidate genes (CTSH, IREB2, PGAM5, NQO1, TRIB3, and TNF) for therapeutic targeting or biomarker development in DR prevention or diagnosis.

Humans↗
PubMed1995

Premarketing population pharmacokinetic study of levofloxacin in normal subjects and patients with infectious diseases.

The population pharmacokinetics of levofloxacin (LVFX), the l-enantiomer of ofloxacin, were studied in 522 subjects, including normal subjects and patients with infectious diseases. Altogether, 1572 LVFX serum concentrations were obtained following a single oral administration during clinical trials. The influences of renal function, age, meals and concurrent drug administration on the pharmacokinetic parameters of LVFX were examined by the likelihood ratio test using a nonlinear mixed-effect model (NONMEM). In patients with renal insufficiency, the total body clearance (CL) of LVFX was related to creatinine clearance (Ccr) and body weight (WT), as expressed by CL = 0.0836 Ccr + 0.013 WT. The CL with normal renal function was 0.178 (l/h/kg). The apparent volume of distribution (Vd) was calculated to be 1.46 (l/kg). The elderly subjects, aged 65 years old or over, exhibited, on average, a 32% reduction in CL and 6% greater Vd. LVFX was rapidly absorbed in the gastrointestinal tract, but the concurrent administration of antacids (magnesium, aluminum, etc.) decreased the bioavailability of LVFX by 15-52%. The recommended dose of LVFX was decided on the basis of current pharmacokinetic information and the minimum inhibitory concentrations. Population pharmacokinetic parameters are also useful for the individualization of a dosage regimen by means of the Bayesian forecasting method.

Age Factors↗
PubMed2006

Natriuretic peptides in the diagnosis and management of heart failure.

The natriuretic peptides are a family of related hormones that play a crucial role in cardiovascular homeostasis. They have recently emerged as potentially important clinical markers in heart failure. Recent data have suggested an important role for these markers in establishing the diagnosis of heart failure in patients with unexplained dyspnea in both acute care and ambulatory settings. Other clinical uses of the natriuretic peptides, such as screening for asymptomatic ventricular dysfunction, establishing prognosis or guiding titration of drug therapy, are under investigation but have not yet sufficiently been validated for widespread clinical use.

Atrial Natriuretic Factor↗
PubMedDate not supplied

A Bayesian approach to estimate the prevalence of low height-for-age from the prevalence of low weight-for-age.

Victora et al. (1998) proposed the use of low weight-for-age prevalence to estimate the prevalence of height-for-age deficit in Brazilian children. This procedure was justified by the need to simplify methods used in the context of community health programs. From the same perspective, the present article broadens this proposal by using a Bayesian approach (based on Markov Chain Monte Carlo (MCMC) methods) to deal with the imprecision resulting from Victora et al.'s model. In order to avoid invalid estimated prevalence values which can occur with the original linear model, truncation or a logit transformation of the prevalences are suggested. The Bayesian approach is illustrated using a community study as an example. Imprecision arising from methodological complexities in the community study design, such as multi-stage sampling and clustering, is easily handled within the Bayesian framework by introducing a hierarchical or multilevel model structure. Since growth deficit was also evaluated in the community study, the article may also serve to validate the procedure proposed by Victora et al.

Age Factors↗
PubMed2004

Surgeon-directed ultrasound for trauma is a predictor of intra-abdominal injury in children.

This study investigated the efficacy of surgeon-directed focused assessment with sonography for trauma (FAST) in conjunction with physical exam (PEx) as a predictor of intra-abdominal injury in children. Injured children (ages < or = 17) presenting to a level I trauma center with abdominal trauma were evaluated in the emergency department (ED) by the trauma team of surgical attendings and residents. PEx and FAST were performed immediately upon arrival to the ED and results compared to CT, the standard exam for presence of intra-abdominal injury. Data was collected prospectively from July 1, 2000, until April 30, 2002. One hundred and twenty injured children underwent evaluation of abdominal trauma with PEx, FAST, and abdominal CT. Two patients had false-negative CT scans. Bayesian analysis was applied to the results of the remaining 118 patients. FAST compared with CT findings revealed sensitivity 70 per cent, specificity 100 per cent, positive predictive value 100 per cent, and negative predictive value 92 per cent. FAST results were combined with PEx findings such that either suggestive of intra-abdominal injury was regarded as a "positive exam." Sensitivity was 100 per cent, specificity 74 per cent, positive predictive value 53 per cent, and negative predictive value 100 per cent. Surgeon-directed FAST with consideration of PEx is a predictor of intra-abdominal injury in children.

Abdominal Injuries↗
PubMed2004

New data on ecological analysis of possible relationship between magnesium in drinking water and liver cancer.

Based on extensive ecological data and conducted Bayesian modeling, this paper reports on epidemiological findings concerning a possible relationship between magnesium in drinking water and carcinogenesis in human liver. Relative contributions of water quality to endemic waterborne disease for particular categories of magnesium concentration and for age groups of patients were ascertained, i.e. the smaller liver cancer morbidity is referred with a greater magnesium concentration in drinking water, both in males and females. The achieved outcomes provide statistically significant evidence of positive health effects of magnesium water supplies on this lethal disease.

Age Factors↗
PubMed1989

An analysis of pathology knowledge and decision making for the development of artificial intelligence-based consulting systems.

This paper partly addresses the question "What artificial intelligence (AI) tools are appropriate for which parts of pathology?" by analyzing the structure and components of knowledge in pathology (e.g., observations plus archival and reference data) and which aspects of that knowledge should be expressible in an AI consulting system. The different aspects of uncertainty (observational, prevalence and validity) play an important role in both human and computer-based decision-making processes, as do relationships between the components of knowledge. The design of an AI consultant system is discussed in terms of the way uncertainty is expressed and in how many parameters, the way uncertainty is propagated (Bayes, certainty factors, Dempster-Schafer, logic or Pathfinder heuristic methods), whether the system reasons from data to a conclusion or vice versa and what the aim of the system is. The suitability of an AI tool is determined by the knowable facts of the pathology subfield, by the match with its knowledge structure and by its requirements. While the success of an AI tool will partly depend on an appropriate definition of its scope, the appropriate combinatoric also depends on the expertise of the user.

Artificial Intelligence↗
PubMed2001

Variations in food intake of Pecten maximus (L.) from the Bay of Brest (France): influence of environmental factors and phytoplankton species composition.

Previous studies carried out in the bay of Brest on daily shell growth of Pecten maximus have demonstrated that temperature is a major control on daily shell growth in contrast to food supply. However, repeated events of slow growth have been observed during diatom and dinoflagellate blooms. The aim of this study was to determine how fluctuations in environmental parameters influence P. maximus food intake and daily shell growth rate. In 1995, P. maximus food intake and growth were highest when Cerataulina pelagica (diatom) blooms occurred and lowest during Gymnodinium cf. nagasakiense (dinoflagellate) blooms. During blooms of other diatom species, P. maximus food intake and growth were high when the algal concentration did not exceed a critical threshold, dependent upon the dominant species and sedimentation rate of diatoms. These results demonstrate that the morphological and physiological features of phytoplankton bloom species strongly affect benthic microphytophagy, a component of benthic-pelagic coupling.

Animals↗
PubMed2005

Discovery of the novel antithrombotic agent 5-chloro-N-({(5S)-2-oxo-3- [4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene- 2-carboxamide (BAY 59-7939): an oral, direct factor Xa inhibitor.

Despite recent progress in antithrombotic therapy, there is still an unmet medical need for safe and orally available anticoagulants. The coagulation enzyme Factor Xa (FXa) is a particularly promising target, and recent efforts in this field have focused on the identification of small-molecule inhibitors with good oral bioavailability. We identified oxazolidinone derivatives as a new class of potent FXa inhibitors. Lead optimization led to the discovery of BAY 59-7939 (5), a highly potent and selective, direct FXa inhibitor with excellent in vivo antithrombotic activity. The X-ray crystal structure of 5 in complex with human FXa clarified the binding mode and the stringent requirements for high affinity. The interaction of the neutral ligand chlorothiophene in the S1 subsite allows for the combination of good oral bioavailability and high potency for nonbasic 5. Compound 5 is currently under clinical development for the prevention and treatment of thromboembolic diseases.

Administration, Oral↗
PubMed2002

Risk factors for diabetic retinopathy in the Cree of James Bay.

BACKGROUND: The purpose of this project was to evaluate risk factors for diabetic retinopathy in the Cree population of James Bay, Ontario. METHODS: A retrospective cohort design was employed. The cohort was made up of all known individuals who had previously been diagnosed with diabetes in the communities of Moose Factory and Moosonee, Ontario. Hypertension, body-mass index, serum lipid levels, renal function status, and hemoglobin A1C were the main exposures of interest. Values for these variables were determined from a retrospective chart review and were sought for each individual for a five-year interval beginning one year following the diagnosis of diabetes. Relative risks for the association of these variables with diabetic retinopathy were determined through both univariate and multivariate Poisson regression. The main outcome of interest in this study was the presence or absence of any diabetic retinopathy in either eye, as determined by a retinal specialist. RESULTS: Significant univariate risks for the development of retinopathy included duration of diabetes, body-mass index, hemoglobin A1C, fasting blood glucose, insulin treatment, and serum cholesterol levels. In multivariate analyses, predictors of diabetic retinopathy included body-mass index, insulin treatment, and serum cholesterol levels. An increase in body-mass index reduced the risk of diabetic retinopathy (Relative Risk [RR] 0.64 per five kg/m( 2), 95% Confidence Interval [CI] 0.04 to 1.00). Insulin therapy was associated with an increased risk of retinopathy when compared to individuals on dietary therapy alone (Relative Risk [RR] 4.71, 95% Confidence Interval [CI] 1.16 to 19.16). For individuals with serum cholesterol levels above the average for the cohort, 5.2 mmol/L, the risk of retinopathy was increased (Relative Risk [RR] 2.38, 95% Confidence Interval [CI] 0.98 to 5.79). INTERPRETATION: Elevated serum cholesterol, lower body-mass index and insulin treatment were all associated with an increased risk of diabetic retinopathy in the Cree of James Bay, Ontario.

Body Mass Index↗
PubMed2003

Stimulation of defense factors for oysters deployed to contaminated sites in Pensacola Bay, Florida.

A positive association between chemical contaminants and defense factors has been established for eastern oysters (Crassostrea virginica) from Florida, but it is unknown whether such factors can be stimulated through short-term exposure to contaminants in the field. Hatchery oysters were deployed at two contaminated sites and one reference site near Pensacola, Florida, during spring and summer in 1998. Putative defense measurements, notably hemocyte count and bactericidal activity, were significantly elevated after 12-week deployment during summer at the most contaminated site. This site exhibited a dramatic increase in chemical concentrations in oyster tissue relative to both the initial concentrations in hatchery oysters and to oysters deployed at the reference site. Hemocyte activity was not stimulated after 16-week deployment of hatchery oysters in spring, despite similar increases in tissue chemical concentrations, so defense activation by short-term exposure may covary with other unmeasured environmental or physiological parameters. Using the converse approach, Pensacola Bay oysters were collected from two contaminated sites and deployed at the reference site for 16 weeks during spring. Results from this converse deployment were ambiguous; serum lysozyme concentrations were reduced for oysters transplanted from both sites, but hemocyte activities were not significantly changed. The principal outcome from this study was the demonstration of enhanced defense activities for oysters upon short-term summer deployment at a contaminated site.

Adaptation, Physiological↗