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PubMedDate not supplied

Associative clustering for exploring dependencies between functional genomics data sets.

High-throughput genomic measurements, interpreted as cooccurring data samples from multiple sources, open up a fresh problem for machine learning: What is in common in the different data sets, that is, what kind of statistical dependencies are there between the paired samples from the different sets? We introduce a clustering algorithm for exploring the dependencies. Samples within each data set are grouped such that the dependencies between groups of different sets capture as much of pairwise dependencies between the samples as possible. We formalize this problem in a novel probabilistic way, as optimization of a Bayes factor. The method is applied to reveal commonalities and exceptions in gene expression between organisms and to suggest regulatory interactions in the form of dependencies between gene expression profiles and regulator binding patterns.

Algorithms↗
PubMedDate not supplied

Longitudinal random effects models for genetic analysis of binary data with application to mastitis in dairy cattle.

A Bayesian analysis of longitudinal mastitis records obtained in the course of lactation was undertaken. Data were 3341 test-day binary records from 329 first lactation Holstein cows scored for mastitis at 14 and 30 days of lactation and every 30 days thereafter. First, the conditional probability of a sequence for a given cow was the product of the probabilities at each test-day. The probability of infection at time t for a cow was a normal integral, with its argument being a function of "fixed" and "random" effects and of time. Models for the latent normal variable included effects of: (1) year-month of test + a five-parameter linear regression function ("fixed", within age-season of calving) + genetic value of the cow + environmental effect peculiar to all records of the same cow + residual. (2) As in (1), but with five parameter random genetic regressions for each cow. (3) A hierarchical structure, where each of three parameters of the regression function for each cow followed a mixed effects linear model. Model 1 posterior mean of heritability was 0.05. Model 2 heritabilities were: 0.27, 0.05, 0.03 and 0.07 at days 14, 60, 120 and 305, respectively. Model 3 heritabilities were 0.57, 0.16, 0.06 and 0.18 at days 14, 60, 120 and 305, respectively. Bayes factors were: 0.011 (Model 1/Model 2), 0.017 (Model 1/Model 3) and 1.535 (Model 2/Model 3). The probability of mastitis for an "average" cow, using Model 2, was: 0.06, 0.05, 0.06 and 0.07 at days 14, 60, 120 and 305, respectively. Relaxing the conditional independence assumption via an autoregressive process (Model 2) improved the results slightly.

Animals↗
PubMedDate not supplied

Cumulative t-link threshold models for the genetic analysis of calving ease scores.

In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t4 (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 +/-0.06, 0.11 +/- 0.04) and a direct maternal genetic correlation (-0.58 +/- 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 +/- 0.07, 0.14 +/- 0.04) and the genetic correlation (-0.55 +/- 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF.

Animals↗
PubMed2006

Visualizing gene determinants of disease in drug discovery.

Target discovery, subphenotype detection and the detection of human heterogeneity are major challenges in drug discovery and development on which genetic markers can have an impact. Visualizing gene determinants of traits in case-control study individuals during drug discovery using contrasts of empirically-derived log Bayes factors (LBFs) from whole-genome scan single nucleotide polymorphism (SNP) data is presented to aid this. Examples of the use of eigen analysis, covariate overlays and individualized aggregation to ontologies are included from disease research studies. Displays of individuals, or exposures of biological features of interest, can encompass unlimited numbers of markers in a single multivariate analysis without multiple testing. This filtering approach is aimed at nonspecialists who find themselves asked to undertake work such as that performed by the authors.

Animals↗
PubMed2005

Multiple-breed genetic inference using heavy-tailed structural models for heterogeneous residual variances.

Multiple-breed genetic models recently have been demonstrated to account for the heterogenous genetic variances that exist between different beef cattle breed groups. We extend these models to allow for residual heteroskedasticity (heterogeneous residual variances), specified as a function of fixed effects (e.g., sex, breed proportion, breed group heterozygosity) and random effects such as contemporary groups (CG). We additionally specify the residual distributions to be either Gaussian or based on heavier-tailed alternatives such as the Student's t or Slash densities. For each of these three residual densities using either homoskedastic (homogeneous variance) or heteroskedastic error specifications, we analyzed 22,717 postweaning gain records from a Nelore-Hereford population based on a Markov chain Monte Carlo animal model implementation. The heteroskedastic Student's t error model (with estimated df = 7.33 +/- 0.48) was clearly the best-fitting model based on a pseudo-Bayes factor criterion. Breed group heterozygosity and, to a lesser extent, calf sex seemed to be marginally important sources of residual heteroskedasticity. Specifically, the residual variance in F1 animals was estimated to be 0.70 +/- 0.16 times that for purebreds, whereas the male residual variance was estimated to be 1.13 +/- 0.09 times that for females. The CG effects were important random sources of residual heteroskedasticity (i.e., the coefficient of variation of CG-specific residual variances was estimated to be 0.72 +/- 0.06). Purebred Nelores were estimated to have a larger genetic variance (124.84 +/- 21.75 kg2) compared with Herefords (40.89 +/- 6.70 kg2) under the heteroskedastic Student's t error model; however, the converse was observed from results based on a homoskedastic Student's t error model (46.24 +/- 10.90 kg2 and 60.11 +/- 8.54 kg2, respectively). These results indicate that allowing for robustness to outliers and accounting for heteroskedasticity of residual variances has potentially important implications for variance component and genetic parameter estimates from data on multiple-breed populations.

Animals↗
PubMed1991

[Tools for the evaluation of diagnostic techniques].

This presentation focuses on evaluation of the diagnostic value of clinical findings, laboratory test results and data provided by diagnostic technologies including imaging techniques. A sign S or indicant of a disease D is a datum which is more frequent (more likely) in patients with the disease D than in subjects free of the disease D. The ratio of these two conditional probabilities is the likelihood ratio or Bayes factor of S for D. For a given test T, the number of likelihood ratios is equal to the number of different result patterns obtained with test T. The likelihood ratio reflects the role of the test result in the predictive value, i.e., the likelihood that the disease is present given the test result observed. The likelihood ratio is the tool of choice for evaluating the diagnostic value of a test. The method proposed by Spiegelhalter and Knill-Jones is based on the likelihood ratio. Evaluation of an imaging technique rests on the characteristics of the "image-physician" combination. The rating method can be used to analyze Receiver Operating Characteristic curves in view of assessing either the imaging technique or the physician's diagnostic skills.

Clinical Laboratory Techniques↗
PubMed1985

A Bayesian analysis of the two-period crossover design for clinical trials.

Statisticians have been critical of the use of the two-period crossover designs for clinical trials because the estimate of the treatment difference is biased when the carryover effects of the two treatments are not equal. In the standard approach, if the null hypothesis of equal carryover effects is not rejected, data from both periods are used to estimate and test for treatment differences; if the null hypothesis is rejected, data from the first period alone are used. A Bayesian analysis based on the Bayes factor against unequal carryover effects is given. Although this Bayesian approach avoids the "all-or-nothing" decision inherent in the standard approach, it recognizes that with small trials it is difficult to provide unequivocal evidence that the carryover effects of the two treatments are equal, and thus that the interpretation of the difference between treatment effects is highly dependent on a subjective assessment of the reality or not of equal carryover effects.

Analysis of Variance↗
PubMed2002

A nuclear factor-kappaB inhibitor BAY 11-7082 suppresses endothelin-1 production in cultured vascular endothelial cells.

BAY 11-7082, an inhibitor of nuclear factor-kappaB (NF-kappaB), which prevents a step of the phosphorylation of inhibitory protein IkappaB bound to NF-kappaB, suppressed basal and tumor necrosis factor (TNF)-alpha-induced prepro endothelin (ET)-1 mRNA expression and NF-kappaB activation in cultured vascular endothelial cells. BAY 11-7082 significantly decreased basal and TNF-alpha-induced ET-1 release from endothelial cells. These results indicate that the inhibition of NF-kappaB activation contributes to the suppressive effect of BAY 11-7082 on ET-1 gene expression and ET-1 release, thereby suggesting that NF-kappaB plays an important role in the regulation of ET-1 production.

Animals↗
PubMed2005

In vitro and in vivo studies of the novel antithrombotic agent BAY 59-7939--an oral, direct Factor Xa inhibitor.

BAY 59-7939 is an oral, direct Factor Xa (FXa) inhibitor in development for the prevention and treatment of arterial and venous thrombosis. BAY 59-7939 competitively inhibits human FXa (K(i) 0.4 nm) with > 10 000-fold greater selectivity than for other serine proteases; it also inhibited prothrombinase activity (IC(50) 2.1 nm). BAY 59-7939 inhibited endogenous FXa more potently in human and rabbit plasma (IC(50) 21 nm) than rat plasma (IC(50) 290 nm). It demonstrated anticoagulant effects in human plasma, doubling prothrombin time (PT) and activated partial thromboplastin time at 0.23 and 0.69 microm, respectively. In vivo, BAY 59-7939 reduced venous thrombosis (fibrin-rich, platelet-poor thrombi) dose dependently (ED(50) 0.1 mg kg(-1) i.v.) in a rat venous stasis model. BAY 59-7939 reduced arterial (fibrin- and platelet-rich) thrombus formation in an arteriovenous (AV) shunt in rats (ED(50) 5.0 mg kg(-1) p.o.) and rabbits (ED(50) 0.6 mg kg(-1) p.o.). Slight inhibition of FXa (32% at ED(50)) reduced thrombus formation in the venous model; to affect arterial thrombosis in the rat and rabbit, stronger inhibition of FXa (74%, 92% at ED(50)) was required. Calculated plasma levels in rabbits at the ED(50) were 14-fold lower than in the rat AV shunt model, correlating with the 14-fold lower IC(50) of FXa inhibition in rabbit compared with rat plasma; this may suggest a correlation between FXa inhibition and antithrombotic activity. Bleeding times in rats and rabbits were not significantly affected at antithrombotic doses (3 mg kg(-1) p.o., AV shunt). Based on these results, BAY 59-7939 was selected for clinical development.

Animals↗
PubMed2004

Phase I clinical and pharmacokinetic study of the Novel Raf kinase and vascular endothelial growth factor receptor inhibitor BAY 43-9006 in patients with advanced refractory solid tumors.

PURPOSE: BAY 43-9006 is a novel dual-action Raf kinase and vascular endothelial growth factor receptor inhibitor that inhibits tumor cell proliferation and angiogenesis. This study established the safety and pharmacokinetics of BAY 43-9006 in 69 patients with advanced refractory solid tumors. PATIENTS AND METHODS: BAY 43-9006 (50 to 800 mg) was administered once or twice daily on a varying weekly schedule. Pharmacokinetic sampling was performed in all patients; preliminary tumor response was also assessed. The effect of BAY 43-9006 on phorbol myristate acetate-stimulated ERK phosphorylation in peripheral blood lymphocytes was studied using flow cytometry. RESULTS: Mild to moderate diarrhea was the most common (55%) treatment-related adverse event. The maximum-tolerated dose was 400 mg bid continuous. Dose-limiting toxicities were grade 3 diarrhea and fatigue at 800 mg bid, and grade 3 skin toxicity at 600 mg bid. BAY 43-9006 pharmacokinetics were highly variable for single and multiple dosing, and toxicity did not appear to be dose dependent. Significant decreases of phorbol myristate acetate-stimulated ERK phosphorylation (P < .01) were identified at doses >/= 200 mg bid continuous. Forty-five patients were assessable for efficacy; one patient had a partial response (hepatocellular carcinoma at 400 mg bid continuous), 25 patients had stable disease, with eight lasting > 6 months and five for >12 months. Eighteen patients had progressive disease, and tumor response could not be evaluated in one patient. CONCLUSION: Oral BAY 43-9006 was well tolerated and appeared to provide some clinical benefits. Based on the results of this study, BAY 43-9006 at 400 mg bid continuous is recommended for ongoing and future studies.

Adolescent↗
PubMed2005

Safety and pharmacokinetics of the dual action Raf kinase and vascular endothelial growth factor receptor inhibitor, BAY 43-9006, in patients with advanced, refractory solid tumors.

PURPOSE: BAY 43-9006, a novel multikinase inhibitor, prevents tumor growth by combining two antitumor activities: inhibition of both tumor cell proliferation and tumor angiogenesis. This phase I, open-label, nonrandomized, noncontrolled, single-arm, dose escalation study was done to determine the maximum tolerated dose (MTD), safety profile, pharmacokinetic variables, effect on biomarkers, and tumor response with BAY 43-9006 in 19 patients with advanced, refractory solid tumors. EXPERIMENTAL DESIGN: BAY 43-9006 was given orally in repeated cycles of 1-week on/1-week off. The study comprised five dose levels, ranging from 100 mg twice daily (bid) to 800 mg bid. Treatment of each patient continued until unacceptable toxicity, tumor progression, or death. RESULTS: Rash and hypertension were the dose-limiting toxicities at the 800 mg bid dose requiring study drug discontinuation; therefore, the MTD of BAY 43-9006 in this study was determined to be 600 mg bid. BAY 43-9006 was generally well tolerated, with mild to moderate toxicities. Pharmacokinetic analysis showed early absorption followed by delayed secondary peaks and slow terminal elimination. Stable disease was achieved in five patients: one patient showed reduced tumor activity (positron emission tomography scan) and reduced mitogen-activated protein kinase signaling (lower phospho-ERK); one patient remained on treatment until study end point. CONCLUSIONS: The results confirm the favorable safety profile of BAY 43-9006 and support the development of this compound for the treatment of solid tumors.

Adult↗
PubMed2006

Application of the nuclear factor-kappaB inhibitor BAY 11-7085 for the treatment of endometriosis: an in vitro study.

Most of the current medical treatments for endometriosis aim to downregulate estrogen activity. However, a high recurrence rate after medical treatment has been the most significant problem. BAY 11-7085, a soluble inhibitor of NK-kappaB activation, has been shown to inhibit cell proliferation and induce apoptosis of a variety of cells. To examine the potential application of BAY 11-7085 in the treatment of endometriosis, we investigated the effects of this agent on the cell proliferation and apoptosis of cultured ovarian endometriotic cyst stromal cells (ECSCs) by a modified methylthiazole tetrazolium assay, a 5-bromo-2'-deoxyuridine incorporation assay, and internucleosomal DNA fragmentation assays. The effect of BAY 11-7085 on the cell cycle of ECSCs was also determined by flow cytometry. The expression of apoptosis-related molecules was examined in ECSCs with Western blot analysis. BAY 11-7085 significantly inhibited the cell proliferation and DNA synthesis of ECSCs and induced apoptosis and the G0/G1 phase cell cycle arrest of these cells. Additionally, downregulation of the B-cell lymphoma/leukemia-2 (Bcl-2) and Bcl-X(L) expression with simultaneous activation of caspase-3, -8, and -9 was observed in ECSCs after treatment with BAY 11-7085. These results suggest that BAY 11-7085 induces apoptosis of ECSCs by suppressing antiapoptotic proteins, and that caspase-3-, -8-, and -9-mediated cascades are involved in this mechanism. Therefore, BAY 11-7085 could be used as a therapeutic agent for the treatment of endometriosis.

Apoptosis↗
PubMed2006

A once-daily, oral, direct Factor Xa inhibitor, rivaroxaban (BAY 59-7939), for thromboprophylaxis after total hip replacement.

BACKGROUND: Rivaroxaban (BAY 59-7939)--an oral, direct Factor Xa inhibitor--could be an alternative to heparins and warfarin for the prevention and treatment of thromboembolic disorders. METHODS AND RESULTS: This randomized, double-blind, double-dummy, active-comparator-controlled, multinational, dose-ranging study assessed the efficacy and safety of once-daily rivaroxaban relative to enoxaparin for prevention of venous thromboembolism in patients undergoing elective total hip replacement. Patients (n=873) were randomized to once-daily oral rivaroxaban doses of 5, 10, 20, 30, or 40 mg (initiated 6 to 8 hours after surgery) or a once-daily subcutaneous enoxaparin dose of 40 mg (given the evening before and > or = 6 hours after surgery). Study drugs were continued for an additional 5 to 9 days; mandatory bilateral venography was performed the following day. The primary end point (composite of any deep vein thrombosis, objectively confirmed pulmonary embolism, and all-cause mortality) was observed in 14.9%, 10.6%, 8.5%, 13.5%, 6.4%, and 25.2% of patients receiving 5, 10, 20, 30, and 40 mg rivaroxaban, and 40 mg enoxaparin, respectively (n=618, per-protocol population). No significant dose-response relationship was found for efficacy (P=0.0852). Major postoperative bleeding was observed in 2.3%, 0.7%, 4.3%, 4.9%, 5.1%, and 1.9% of patients receiving 5, 10, 20, 30, and 40 mg rivaroxaban, and 40 mg enoxaparin, respectively (n=845, safety population), representing a significant dose-response relationship (P=0.0391). CONCLUSIONS: Rivaroxaban showed efficacy and safety similar to enoxaparin for thromboprophylaxis after total hip replacement, with the convenience of once-daily oral dosing and without the need for coagulation monitoring. When both efficacy and safety are considered, these results suggest that 10 mg rivaroxaban once daily should be investigated in phase III studies.

Administration, Oral↗
PubMed2006

Oral, direct Factor Xa inhibition with BAY 59-7939 for the prevention of venous thromboembolism after total hip replacement.

BACKGROUND: Joint replacement surgery is an appropriate model for dose-ranging studies investigating new anticoagulants. OBJECTIVES: To assess the efficacy and safety of a novel, oral, direct factor Xa (FXa) inhibitor--BAY 59-7939--relative to enoxaparin in patients undergoing elective total hip replacement. METHODS: In this double-blind, double-dummy, dose-ranging study, patients were randomized to oral BAY 59-7939 (2.5, 5, 10, 20, or 30 mg b.i.d.), starting 6-8 h after surgery, or s.c. enoxaparin 40 mg once daily, starting on the evening before surgery. Treatment was continued until mandatory bilateral venography was performed 5-9 days after surgery. RESULTS: Of 706 patients treated, 548 were eligible for the primary efficacy analysis. The primary efficacy endpoint was the incidence of any deep vein thrombosis, non-fatal pulmonary embolism, and all-cause mortality; rates were 15%, 14%, 12%, 18%, and 7% for BAY 59-7939 2.5, 5, 10, 20, and 30 mg b.i.d., respectively, compared with 17% for enoxaparin. The primary efficacy analysis did not demonstrate any significant trend in dose-response relationship for BAY 59-7939. The primary safety endpoint was major, postoperative bleeding; there was a significant increase in the frequency of events with increasing doses of BAY 59-7939 (P = 0.045), but no significant differences between individual BAY 59-7939 doses and enoxaparin. CONCLUSIONS: When efficacy and safety were considered together, the oral, direct FXa inhibitor BAY 59-7939, at 2.5-10 mg b.i.d., compared favorably with enoxaparin for the prevention of venous thromboembolism in patients undergoing elective total hip replacement.

Adult↗
PubMed1995

Respiratory symptoms and environmental factors in schoolchildren in the Bay of Plenty.

AIMS: To determine the prevalence of respiratory symptoms in children and to examine associations with environmental factors in the Bay of Plenty. METHODS: International Study of Asthma and Allergies in Childhood (ISAAC) questionnaires were distributed to 13-14 year old children and to care-givers of 6-7 year old children as part of the ISAAC study. RESULTS: Completed questionnaires were received for 2614 primary and 2752 secondary students. Analysis by district showed no consistent association with exposure to industrial emissions from paper mills, natural sulphur fumes, or climatic variation. All districts are subject to high levels of pollen. Symptom prevalence was close to the mean for New Zealand centres participating in the ISAAC survey. Night cough and nasal symptoms were more common in secondary pupils exposed to smoking in the home, but there was no consistent association between passive smoking and wheeze or diagnosed asthma. Children from larger households reported less wheezy symptoms and less diagnosed asthma. CONCLUSIONS: There was no consistent evidence of an effect on respiratory morbidity from natural fumes, industrial air pollution, or climate. The indoor environment is probably of greater importance in this population.

Adolescent↗
PubMed2002

Bay 11-7082 inhibits transcription factor NF-kappaB and induces apoptosis of HTLV-I-infected T-cell lines and primary adult T-cell leukemia cells.

Human T-cell leukemia virus type I (HTLV-I) is the causative agent of an aggressive form of leukemia designated adult T-cell leukemia (ATL). We have previously demonstrated that all T-cell lines infected with HTLV-I and primary leukemic cells from ATL patients display constitutively high activity of transcription factor NF-kappaB. In this study we showed that Bay 11-7082, an inhibitor of NF-kappaB, induced apoptosis of HTLV-I-infected T-cell lines but only negligible apoptosis of HTLV-I-negative T cells. Bay 11-7082 rapidly and efficiently reduced the DNA binding of NF-kappaB in HTLV-I-infected T-cell lines and down-regulated the expression of the antiapoptotic gene, Bcl-x(L), regulated by NF-kappaB, whereas it had little effect on the DNA binding of another transcription factor, AP-1. Although the viral protein Tax is an activator of NF-kappaB, Bay 11-7082-induced apoptosis of HTLV-I-infected cells was not associated with reduced expression of Tax. Furthermore, Bay 11-7082- induced apoptosis of primary ATL cells was more prominent than that of normal peripheral blood mononuclear cells, and apoptosis of these cells was also associated with down-regulation of NF-kappaB activity. Our results indicate that NF-kappaB plays a crucial role in the pathogenesis and survival of HTLV-I-infected leukemic cells and that it is a suitable target for the prevention and treatment of ATL.

Adult↗