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Solorio MR, Milburn NG, Weiss RE, Batterham PJ. Newly homeless youth STD testing patterns over time. J Adolesc Health 2006; 39:443.e9-443.e16. [PMID: 16919810 DOI: 10.1016/j.jadohealth.2005.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 11/03/2005] [Accepted: 12/15/2005] [Indexed: 10/24/2022]
Abstract
PURPOSE To use the Behavioral Model for Vulnerable Populations to examine the predisposing and need characteristics of newly homeless youth that are associated with sexually transmitted disease (STD) testing over time. METHODS A longitudinal cohort of newly homeless youth from Los Angeles County (n = 261; ages 12-20 years) were followed for 24 months. Youth were interviewed at baseline, 3, 6, 12, 18, and 24 months, and asked about their background, housing situation, emotional distress (using the Brief-Symptom Inventory), substance use, sexual risk behaviors, and their STD testing rates. We modeled our longitudinal data using logistic random effects models. RESULTS Characteristics of homeless youth that were associated with STD testing in our multivariate model included time in study (odds ratio [OR] 1.3, 95% confidence interval [CI] 1.1-1.6), age at baseline (OR 1.2, 95% CI 1.1-1.4), being African-American (OR 2.7, 95% CI 1.4-5.3), being from a mixed race/ethnic group (OR 2.8, 95% CI 1.3-5.8), self-identifying as a gay/bisexual male (OR 2.9, 95% CI 1.2-6.9), self-identifying as a heterosexual female (OR 2.2, 95% CI 1.3-3.7), using amphetamines (OR 1.7, 95% CI 1.1-2.6), and history of having gotten someone/becoming pregnant (OR 2.3, 95% CI 1.4-3.9). Youth who lived in an apartment were less likely to have received an STD test than youth who lived in other types of housing (OR .4, 95% CI .2-.9). Sexual risk behaviors such as inconsistent condom use (OR 1.0, 95% CI .6-1.4) and number of sexual partners over past 3 months (OR 1.1, 95% CI 1.0-1.1) were not predictive of STD testing over time. CONCLUSIONS A need exists for interventions to target young newly homeless youth who engage in high-risk sexual behaviors to increase their STD testing rates and thereby decrease their risk for HIV infection.
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Marshall JM, Weiss RE. A Bayesian heterogeneous analysis of variance approach to inferring recent selective sweeps. Genetics 2006; 173:2357-70. [PMID: 16751672 PMCID: PMC1569732 DOI: 10.1534/genetics.105.053314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The distribution of microsatellite allele sizes in populations aids in understanding the genetic diversity of species and the evolutionary history of recent selective sweeps. We propose a heterogeneous Bayesian analysis of variance model for inferring loci involved in recent selective sweeps by analyzing the distribution of allele sizes at multiple loci in multiple populations. Our model is shown to be consistent with a multilocus test statistic, ln RV, proposed for identifying microsatellite loci involved in recent selective sweeps. Our methodology differs in that it accepts original allele size data rather than summary statistics and allows the incorporation of prior knowledge about allele frequencies using a hierarchical prior distribution consisting of log normal and gamma probability distributions. Interesting features of the model are its ability to simultaneously analyze allele size data for any number of populations and to cope with the presence of any number of selected loci. The utility of the method is illustrated by application to two sets of microsatellite allele size data for a group of West African Anopheles gambiae populations. The results are consistent with the suppressed-recombination model of speciation, and additional candidate loci on chromosomes 2 (079 and 175) and 3 (088) are discovered that escaped former analysis.
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Gorbach PM, Sopheab H, Chhorvann C, Weiss RE, Vun MC. Changing Behaviors and Patterns Among Cambodian Sex Workers. J Acquir Immune Defic Syndr 2006; 42:242-7. [PMID: 16639348 DOI: 10.1097/01.qai.0000214817.03411.80] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Identify patterns and behaviors among direct and indirect female sex workers (DFSWs and IDFSWs, respectively) across Cambodia's 5 major cities from 1997 to 2003. METHODS Interviews with DFSWs and IDFSWs followed random selection from clusters in 5 cities. Individual characteristics and condom use with clients and other partners were assessed in univariate and multivariate analyses. RESULTS From 1997 to 2003, consistent condom use with clients increased from 53% to 96% among DFSWs and from 30% to 84% among IDFSWs. DFSWs reported staying in their profession longer, had fewer clients per day, stayed longer in each brothel, were in increasingly larger brothels, and were tested more for HIV. For IDFSWs, there were significant changes: more reported practicing commercial sex and testing for HIV. In adjusted models, reported condom use with clients was significantly higher among DFSWs in later survey years (odds ratio [OR], 2.17) and who were never married (OR, 1.69), were in larger brothels (OR, 1.02), and charged more for sex (OR, 1.27), but lower for DFSWs with sweethearts (OR, 0.68) and who reported abnormal vaginal discharge (OR, 0.52). For IDFSWs, in the adjusted models, reported condom use with clients was higher in later years (OR, 1.77) and for those reporting abnormal vaginal discharge (OR, 1.34) and HIV testing (OR, 1.46), and lower for those with sweethearts (OR, 0.49). CONCLUSIONS From 1997 to 2003, Cambodian direct and indirect sex workers increased their use of condoms each year with commercial as well as noncommercial partners, contributing to the evidence that HIV prevention programs can produce significant changes in risk behaviors.
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Grillenberger M, Neumann CG, Murphy SP, Bwibo NO, Weiss RE, Jiang L, Hautvast JGAJ, West CE. Intake of micronutrients high in animal-source foods is associated with better growth in rural Kenyan school children. Br J Nutr 2006; 95:379-90. [PMID: 16469157 DOI: 10.1079/bjn20051641] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Observational studies have shown that children in developing countries consuming diets containing high amounts of bioavailable nutrients, such as those found in animal-source foods, grow better. The present study investigated which specific nutrients from the diet of Kenyan school children predicted their growth. The children (n 544, median age 7 years) participated in a 2-year long food supplementation study with animal-source foods. Height gain during the intervention period was positively predicted by average daily intakes of energy from animal-source foods, haem Fe, preformed vitamin A, Ca and vitamin B12. Weight gain was positively predicted by average daily intakes of energy from animal-source foods, haem Fe, preformed vitamin A, Ca and vitamin B12. Gain in mid-upper-arm muscle area was positively predicted by average daily intakes of energy from animal-source foods and vitamin B12. Gain in mid-upper-arm fat area was positively predicted by average daily intakes of energy from animal-source foods. Gain in subscapular skinfold thickness was not predicted by any of the nutrient intakes. Negative predictors of growth were total energy and nutrients that are contained in high amounts in plant foods. The study shows that growth was positively predicted by energy and nutrients that are provided in high amounts and in a bioavailable form in meat and milk, and their inclusion into the diets of children in developing countries should be part of all food-based programmes in order to improve micronutrient status and growth.
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Suchard MA, Weiss RE, Sinsheimer JS. Models for estimating bayes factors with applications to phylogeny and tests of monophyly. Biometrics 2005; 61:665-73. [PMID: 16135017 DOI: 10.1111/j.1541-0420.2005.00352.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bayes factors comparing two or more competing hypotheses are often estimated by constructing a Markov chain Monte Carlo (MCMC) sampler to explore the joint space of the hypotheses. To obtain efficient Bayes factor estimates, Carlin and Chib (1995, Journal of the Royal Statistical Society, Series B57, 473-484) suggest adjusting the prior odds of the competing hypotheses so that the posterior odds are approximately one, then estimating the Bayes factor by simple division. A byproduct is that one often produces several independent MCMC chains, only one of which is actually used for estimation. We extend this approach to incorporate output from multiple chains by proposing three statistical models. The first assumes independent sampler draws and models the hypothesis indicator function using logistic regression for various choices of the prior odds. The two more complex models relax the independence assumption by allowing for higher-lag dependence within the MCMC output. These models allow us to estimate the uncertainty in our Bayes factor calculation and to fully use several different MCMC chains even when the prior odds of the hypotheses vary from chain to chain. We apply these methods to calculate Bayes factors for tests of monophyly in two phylogenetic examples. The first example explores the relationship of an unknown pathogen to a set of known pathogens. Identification of the unknown's monophyletic relationship may affect antibiotic choice in a clinical setting. The second example focuses on HIV recombination detection. For potential clinical application, these types of analyses must be completed as efficiently as possible.
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Nurzia MJ, Hwang J, Cummings KB, Weiss RE. 39: The Utility and Cost of Outside Pathology Review after Transurethral Resection for Carcinoma of the Bladder. J Urol 2005. [DOI: 10.1016/s0022-5347(18)34304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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157
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Aksoy DY, Gurlek A, Ringkananont U, Weiss RE, Refetoff S. Resistance to thyroid hormone associated with autoimmune thyroid disease in a Turkish family. J Endocrinol Invest 2005; 28:379-83. [PMID: 15966514 DOI: 10.1007/bf03347207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The syndrome of resistance to thyroid hormone (RTH) is characterized by impaired tissue responses to thyroid hormone. Hashimoto's thyroiditis is the most common thyroid autoimmune disease. We present a Turkish family with both RTH and Hashimoto's thyroiditis. RTH was detected through the presence of point mutation in thyroid hormone receptor (TR), and Hashimoto's thyroiditis was diagnosed due to the presence of thyroid autoantibodies. The proposita, her affected mother as well as her unaffected sister have thyroid autoantibodies consistent with Hashimoto's thyroiditis, and a heterozygous point mutation in exon 10 encoding the ligand (3,3',5-L-T3)-binding domain of the TRbeta gene was detected in both the proposita and the mother. The mutation is a replacement of cytosine for guanine in codon 453 (CCT->GCT) producing a missense mutation substituting a normal proline with an alanine (P453A), which reduces the affinity for T3 to 17% of that of the normal TRbeta. Both also have modest elevation of serum TSH levels. In severe RTH, marked elevation of thyroid hormone concentrations in the absence of suppressed TSH supports the laboratory diagnosis of RTH. However, when RTH is mild and associated with thyroiditis, even a modest thyroid gland insufficiency can obliterate the serum T4 and T3 elevations, typical of RTH. This will manifest as elevated serum TSH. Demonstration of TRbeta gene mutation is then necessary to establish the diagnosis. In addition, under these circumstances, treatment with thyroid hormone should be considered.
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Newman PA, Rhodes F, Weiss RE. Correlates of sex trading among drug-using men who have sex with men. Am J Public Health 2004; 94:1998-2003. [PMID: 15514243 PMCID: PMC1448575 DOI: 10.2105/ajph.94.11.1998] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We examined correlates of trading sex for money, drugs, and shelter, or food among drug-using men who have sex with men (MSM). METHODS Audio computer-assisted self-interviewing questionnaires were completed by 387 MSM. The association of predictors with sex trading was assessed with chi(2) tests and multiple logistic regression. RESULTS Sex-trading prevalence was 62.5% (95% confidence interval=57.7%, 67.4%). Sex trading was associated with crack use, injection drug use, childhood maltreatment, non-gay self-identification, and homelessness (adjusted odds ratios=3.72, 2.28, 2.62, 2.21, and 1.88, respectively). CONCLUSIONS Multiple risk factors are associated with sex trading among MSM. Interventions may need to address crack and injection drug use, homelessness, and childhood maltreatment and target non-gay-identified MSM who engage in sex trading.
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Rotheram-Borus MJ, Swendeman D, Comulada WS, Weiss RE, Lee M, Lightfoot M. Prevention for substance-using HIV-positive young people: telephone and in-person delivery. J Acquir Immune Defic Syndr 2004; 37 Suppl 2:S68-77. [PMID: 15385902 PMCID: PMC2843590 DOI: 10.1097/01.qai.0000140604.57478.67] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SUMMARY HIV risky behaviors and health practices were examined among young people living with HIV (YPLH) in Los Angeles, San Francisco, and New York over 15 months in response to receiving a preventive intervention. YPLH aged 16 to 29 years (n = 175; 26% black and 42% Latino; 69% gay men) were randomly assigned to a 3-module intervention totaling 18 sessions delivered by telephone, in person, or a delayed-intervention condition. Intention-to-treat analyses found that the in-person intervention resulted in a significantly higher proportion of sexual acts protected by condoms overall and with HIV-seronegative partners. Pre- and postanalyses of YPLH in the delayed-intervention condition alone found that YPLH tended to have fewer sexual partners, used fewer drugs, reported less emotional distress, and decreased their use of antiretroviral therapies. Prevention programs can be delivered in alternative formats while retaining efficacy. When YPLH are using hard drugs, drug treatment may be needed before delivery of preventive interventions.
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Mannavola D, Moeller LC, Beck-Peccoz P, Persani L, Weiss RE, Refetoff S. A novel splice variant involving the 5' untranslated region of thyroid hormone receptor beta1 (TRbeta1). J Endocrinol Invest 2004; 27:318-22. [PMID: 15233549 DOI: 10.1007/bf03351055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The thyroid hormone receptor beta (TRbeta) gene generates two different proteins by use of a different promoter (beta1 and beta2). We now report a novel short TRbeta1 RNA splice variant in humans lacking 35 nucleotides at the 3' end of the non-coding exon 1 due to an alternative 5' splice donor site. This short variant was first identified in sequences of cDNA obtained from cultured human fibroblasts. Both variants were found in human fibroblasts, brain, pituitary, adrenal gland, placenta, muscle, thyroid and lymphocytes. These TRbeta1 variants possess splice donor sites with a sequence score slightly favoring the TRbeta1 long variant. Variant-specific real-time polymerase chain reaction (PCR) showed that their relative proportions were equal except in pituitary and muscle, in which the long form was 3- and 5-fold in excess. T3 treatment of fibroblasts grown in thyroid hormone depleted medium did not affect the absolute or relative expression of the two variants. Furthermore, the expression level in fibroblasts from patients with resistance to thyroid hormone with or without TRbeta gene mutations was not different to that in fibroblasts from normal controls.
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161
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Ankem MK, Han KR, Hartanto V, Perrotti M, Decarvalho VS, Cummings KB, Weiss RE. Routine pouchograms are not necessary after continent urinary diversion. Urology 2004; 63:435-7. [PMID: 15028432 DOI: 10.1016/j.urology.2003.10.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2003] [Accepted: 10/23/2003] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Pouchograms are routinely performed before catheter removal after continent urinary diversion at our institution. Our aim was to determine the necessity of pouchograms based on a review of our experience. METHODS A retrospective review of patient records and radiographic studies was done for patients undergoing radical cystectomy and continent urinary diversions between 1991 and 2001. RESULTS Seventy-two patients underwent continent urinary diversion (orthotopic, n = 59; cutaneous, n = 13) during the study period. All underwent pouchogram postoperatively (median 22 days; range 20 to 27). Six patients (8.3%) had a demonstrable radiographic leak; in 5 of the 6 patients, the urine leak was suspected on clinical grounds. Three patients (4.7%) developed urosepsis after pouchogram. CONCLUSIONS Our findings indicate that routine pouchograms before pouch activation after continent urinary diversion may not be necessary.
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162
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Ye Z, Weiss RE. Using the Bootstrap to Select One of a New Class of Dimension Reduction Methods. J Am Stat Assoc 2003. [DOI: 10.1198/016214503000000927] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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163
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Neumann CG, Bwibo NO, Murphy SP, Sigman M, Whaley S, Allen LH, Guthrie D, Weiss RE, Demment MW. Animal Source Foods Improve Dietary Quality, Micronutrient Status, Growth and Cognitive Function in Kenyan School Children: Background, Study Design and Baseline Findings. J Nutr 2003; 133:3941S-3949S. [PMID: 14672294 DOI: 10.1093/jn/133.11.3941s] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A previous longitudinal three-country study in Egypt, Kenya and Mexico found significant positive associations between intake of animal source foods (ASF) and growth, cognitive development and physical activity. To test for a causal relationship, a controlled school feeding intervention study was designed to test the hypotheses that ASF would improve micronutrient status, growth and cognitive function in Kenyan primary school children. Twelve rural Kenyan schools with 554 children were randomized to four feeding interventions using a local vegetable stew as the vehicle. The groups were designated as Meat, Milk, Energy and Control, who received no feedings. Feeding was carried out on school days for seven terms during 21 mo. Preintervention baseline measures included nutritional status, home food intake, anthropometry, biochemical measures of micronutrient status, malaria, intestinal parasites, health status and cognitive and behavioral measures. The measurements of each child were repeated at intervals over 2 y. Baseline data revealed stunting and underweight in approximately 30% of children and widespread inadequate intakes and/or biochemical evidence of micronutrient deficiencies, particularly of iron, zinc, vitamins A and B-12, riboflavin and calcium. Little or no ASF were eaten and fat intake was low. Malaria was present in 31% of children, and hookworm, amebiasis and giardia were widely prevalent. The outcomes measured were rates of change or increase during the intervention in cognitive function, growth, physical activity and behavior and micronutrient status. Hierarchical linear random effects modeling was used for analysis of outcomes.
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Whaley SE, Sigman M, Neumann C, Bwibo N, Guthrie D, Weiss RE, Alber S, Murphy SP. The Impact of Dietary Intervention on the Cognitive Development of Kenyan School Children. J Nutr 2003; 133:3965S-3971S. [PMID: 14672297 DOI: 10.1093/jn/133.11.3965s] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Previous observational studies in developing countries have suggested that diet quality, particularly increased animal source food (ASF) consumption, is positively associated with child cognitive development. This report presents findings from a study in rural Kenya, designed to test the impact of three different diets on the cognitive development of school children. Twelve schools with a total of 555 Standard 1 children (equivalent to U.S. Grade 1) were randomized to one of four feeding interventions: Meat, Milk, Energy or Control (no feeding). Feeding continued for seven school terms (21 mo), and cognitive tests were administered before the commencement of feeding and during every other term of feeding. Hierarchical linear random effects models and associated methods were used to examine the effects of treatment group on changes in cognitive performance over time. Analyses revealed that children receiving supplemental food with meat significantly outperformed all other children on the Raven's Progressive Matrices. Children supplemented with meat, and children supplemented with energy, outperformed children in the Control group on tests of arithmetic ability. There were no group differences on tests of verbal comprehension. Results suggest that supplementation with animal source food has positive effects on Kenyan children's cognitive performance. However, these effects are not equivalent across all domains of cognitive functioning, nor did different forms of animal source foods produce the same beneficial effects. Implications of these findings for supplementation programs in developing countries are discussed.
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165
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Suchard MA, Kitchen CMR, Sinsheimer JS, Weiss RE. Hierarchical Phylogenetic Models for Analyzing Multipartite Sequence Data. Syst Biol 2003; 52:649-64. [PMID: 14530132 DOI: 10.1080/10635150390238879] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Debate exists over how to incorporate information from multipartite sequence data in phylogenetic analyses. Strict combined-data approaches argue for concatenation of all partitions and estimation of one evolutionary history, maximizing the explanatory power of the data. Consensus/independence approaches endorse a two-step procedure where partitions are analyzed independently and then a consensus is determined from the multiple results. Mixtures across the model space of a strict combined-data approach and a priori independent parameters are popular methods to integrate these methods. We propose an alternative middle ground by constructing a Bayesian hierarchical phylogenetic model. Our hierarchical framework enables researchers to pool information across data partitions to improve estimate precision in individual partitions while permitting estimation and testing of tendencies in across-partition quantities. Such across-partition quantities include the distribution from which individual topologies relating the sequences within a partition are drawn. We propose standard hierarchical priors on continuous evolutionary parameters across partitions, while the structure on topologies varies depending on the research problem. We illustrate our model with three examples. We first explore the evolutionary history of the guinea pig (Cavia porcellus) using alignments of 13 mitochondrial genes. The hierarchical model returns substantially more precise continuous parameter estimates than an independent parameter approach without losing the salient features of the data. Second, we analyze the frequency of horizontal gene transfer using 50 prokaryotic genes. We assume an unknown species-level topology and allow individual gene topologies to differ from this with a small estimable probability. Simultaneously inferring the species and individual gene topologies returns a transfer frequency of 17%. We also examine HIV sequences longitudinally sampled from HIV+ patients. We ask whether posttreatment development of CCR5 coreceptor virus represents concerted evolution from middisease CXCR4 virus or reemergence of initial infecting CCR5 virus. The hierarchical model pools partitions from multiple unrelated patients by assuming that the topology for each patient is drawn from a multinomial distribution with unknown probabilities. Preliminary results suggest evolution and not reemergence.
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Suchard MA, Weiss RE, Sinsheimer JS, Dorman KS, Patel M, McCabe ERB. Evolutionary Similarity Among Genes. J Am Stat Assoc 2003. [DOI: 10.1198/016214503000000558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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167
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Comulada WS, Swendeman DT, Rotheram-Borus MJ, Mattes KM, Weiss RE. Use of HAART among young people living with HIV. Am J Health Behav 2003; 27:389-400. [PMID: 12882433 PMCID: PMC2819811 DOI: 10.5993/ajhb.27.4.11] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To examine HAART use. METHODS HIV+ youth, aged 14-29 (n=253; 71% male; 74% ethnic minority), were recruited in Los Angeles, San Francisco, and New York. RESULTS Almost all youth had been offered HAART (84%); 77% had ever used it, 54% were currently using, and 63% of users adhered to 90% of their medications. Compared to non-users, users were more likely to be female, Latino or African American. Users were also more likely to have the following: AIDS, positive coping styles, social support, and a high quality of life. Users were less likely to: do jail time, perform sexual-risk acts, and use substances. CONCLUSIONS HIV+ youth self-select to use HAART.
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Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Inferring Spatial Phylogenetic Variation Along Nucleotide Sequences. J Am Stat Assoc 2003. [DOI: 10.1198/016214503000215] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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169
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Chen MH, Ibrahim JG, Shao QM, Weiss RE. Prior elicitation for model selection and estimation in generalized linear mixed models. J Stat Plan Inference 2003. [DOI: 10.1016/s0378-3758(02)00285-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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170
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Suchard MA, Weiss RE, Sinsheimer JS. Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework. Syst Biol 2003; 52:48-54. [PMID: 12554439 DOI: 10.1080/10635150390132713] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We propose a Bayesian method for testing molecular clock hypotheses for use with aligned sequence data from multiple taxa. Our method utilizes a nonreversible nucleotide substitution model to avoid the necessity of specifying either a known tree relating the taxa or an outgroup for rooting the tree. We employ reversible jump Markov chain Monte Carlo to sample from the posterior distribution of the phylogenetic model parameters and conduct hypothesis testing using Bayes factors, the ratio of the posterior to prior odds of competing models. Here, the Bayes factors reflect the relative support of the sequence data for equal rates of evolutionary change between taxa versus unequal rates, averaged over all possible phylogenetic parameters, including the tree and root position. As the molecular clock model is a restriction of the more general unequal rates model, we use the Savage-Dickey ratio to estimate the Bayes factors. The Savage-Dickey ratio provides a convenient approach to calculating Bayes factors in favor of sharp hypotheses. Critical to calculating the Savage-Dickey ratio is a determination of the prior induced on the modeling restrictions. We demonstrate our method on a well-studied mtDNA sequence data set consisting of nine primates. We find strong support against a global molecular clock, but do find support for a local clock among the anthropoids. We provide mathematical derivations of the induced priors on branch length restrictions assuming equally likely trees. These derivations also have more general applicability to the examination of prior assumptions in Bayesian phylogenetics.
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Sinsheimer JS, Suchard MA, Dorman KS, Fang F, Weiss RE. Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains. APPLIED BIOINFORMATICS 2003; 2:131-44. [PMID: 15130798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Reconstructing evolutionary relationships using Bayesian inference has become increasingly popular due to the ability of Bayesian inference to handle complex models of evolution. In this review we concentrate on inference of recombination events between strains of viruses when these events are sporadic, ie rare relative to point mutations. Bayesian inference is especially attractive in the detection of recombination events because it allows for simultaneous inferences about the presence, number and location of crossover points and the identification of parental sequences. Current frequentist recombination identification falls into a sequential testing trap. The most likely parental sequences and crossover points are identified using the data and then the certainty of recombination is assessed conditional on this identification. After briefly outlining basic phylogenetic models, Bayesian inference and Markov chain Monte Carlo (MCMC) computation, we summarise three different approaches to recombination detection and discuss current challenges in applying Bayesian phylogenetic inference of recombination.
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Ansell BJ, Watson KE, Weiss RE, Fonarow GC. hsCRP and HDL effects of statins trial (CHEST): rapid effect of statin therapy on C-reactive protein and high-density lipoprotein levels A clinical investigation. HEART DISEASE (HAGERSTOWN, MD.) 2003; 5:2-7. [PMID: 12549983 DOI: 10.1097/01.hdx.0000050407.62572.de] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inflammation contributes to the pathogenesis of coronary heart disease and elevated serum levels of C-reactive protein (CRP) are independently associated with increased coronary risk. This study assessed whether there were differences in the effects on CRP and high-density lipoprotein (HDL) cholesterol levels among patients treated with three common statins. In a prospective, observational study, 80 dyslipidemic adults without evidence of cardiovascular disease were treated with 10 mg atorvastatin (A), 20 mg simvastatin (S), or 40 mg pravastatin (P) daily. CRP and lipid profiles were assayed before and after 12 weeks of therapy; in 21 patients, CRP levels were also measured after 1 and 4 weeks. The three treatment groups experienced comparable reductions in CRP (A: 33%, S: 42%, and P: 30%) and statistically insignificant changes in HDL cholesterol levels. CRP began to decrease after 1 week of treatment, and decreased further at 4 and 12 weeks of therapy. The change in the log-transformed CRP concentration correlated with the change in the log-transformed LDL cholesterol concentration. Subjects had similar baseline CRP levels, lipid profiles, and coronary risk factors. The authors conclude that at doses achieving similar reductions in LDL cholesterol, the three statins were associated with comparable decreases in CRP without significant changes in HDL cholesterol levels. The correlation between the reductions in CRP and LDL cholesterol differs from the findings of other published studies, and should prompt further investigation of the mechanism by which statins reduce CRP.
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Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst Biol 2002; 51:715-28. [PMID: 12396586 DOI: 10.1080/10635150290102384] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Current methods to identify recombination between subtypes of human immunodeficiency virus 1 (HIV-1) fall into a sequential testing trap, in which significance is assessed conditional on parental representative sequences and crossover points (COPs) that maximize the same test statistic. We overcame this shortfall by testing for recombination while inferring parental heritage and COPs using an extended Bayesian multiple change-point model. The model assumes that aligned molecular sequence data consist of an unknown number of contiguous segments that may support alternative topologies or varying evolutionary pressures. We allowed for heterogeneity in the substitution process and specifically tested for intersubtype recombination using Bayes factors. We also developed a new class of priors to assess significance across a wide range of support for recombination in the data. We applied our method to three putative gag gene recombinants. HIV-1 isolate RW024 decisively supported recombination with an inferred parental heritage of AD and a COP 95% Bayesian credible interval of (1,152, 1,178) using the HXB2 numbering scheme. HIV-1 isolate VI557 barely supported recombination. HIV-1 isolate RF decisively rejected recombination as expected, given that the sequence is commonly used as a reference sequence for subtype B. We employed scaled regeneration quantile plots to assess convergence and found this approach convenient to use even for our variable dimensional model parameter space.
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174
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Cunningham JM, Buxton OM, Weiss RE. Circadian variation in Cushing's disease and pseudo-Cushing states by analysis of F and ACTH pulsatility. J Endocrinol Invest 2002; 25:791-9. [PMID: 12398238 DOI: 10.1007/bf03345514] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Distinguishing pituitary-dependent Cushing's disease from pseudo-Cushing's states can present a diagnostic challenge. Although many studies potentially discriminate between the 2, only the dexamethasone-suppressed corticotropin-releasing hormone (CRF) stimulation test at 15 minutes is 100% sensitive or specific. We measured baseline profiles of F and ACTH in 31 Cushing's disease patients, 11 with pseudo-Cushing's and 17 controls. Venous blood was collected at 30 minute intervals for 24-h. Subjects also had CRF stimulation tests and 2.0 mg/day dexamethasone suppression tests. F and ACTH profiles were analyzed for circadian rhythmicity, variability, and pulsatility. Relative circadian amplitude was decreased in Cushing's disease compared to both pseudo-Cushing's and normal states. Relative pulse amplitude was reduced in Cushing's disease. Because of this dampening of circadian and pulsatile variations, the overall variability of F and ACTH levels around their mean levels as quantified by the intra-series coefficient of variation (CV), was also decreased in Cushing's disease compared to pseudo-Cushing's and normal states. A F 24-h CV<40% was able to distinguish Cushing's disease from pseudo-Cushing's with 100% sensitivity (95% confidence interval (CI), 88-100%) and specificity (CI, 71-100%). An ACTH CV<40% had 97% sensitivity (CI, 83-100%) and 100% specificity (CI, 71-100%). An overnight 8-h F CV <40% also distinguished Cushing's disease from pseudo-Cushing's with 100% sensitivity (CI, 88-100%) and specificity (CI, 71-100%). These data show that a simple index of total temporal variability (the intra-series CV) derived from the analysis of basal F profiles, provides a useful method to distinguish Cushing's disease from pseudo-Cushing's. A F or ACTH CV <40% discriminates Cushing's disease from pseudo-Cushing's and reflects reduced circadian and pulsatile variations.
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Ankem MK, DeCarvalho VS, Harangozo AM, Hartanto VH, Perrotti M, Han KR, Shih WJ, Malka E, White EC, Maggio R, Ioffreda R, Goldsmith JW, Weiss RE. Implications of radioactive seed migration to the lungs after prostate brachytherapy. Urology 2002; 59:555-9. [PMID: 11927313 DOI: 10.1016/s0090-4295(01)01660-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To review the incidence and the impact of pulmonary seed migration after prostate brachytherapy on lung function. Isolated reports of seed migration to the lungs after prostate brachytherapy have been published; however, the clinical consequences of this pulmonary migration have not been adequately evaluated. METHODS We performed a retrospective review of patients undergoing prostate brachytherapy from 1998 to 2000. Pulmonary imaging with chest x-ray was performed 15 to 90 days (median 45) after the procedure. The chest radiographs were reviewed by a single radiologist (V.S.D.), and patients with seed migration to the lungs were evaluated by a single pulmonologist (A.M.H.) using a questionnaire, chest radiography, and pulmonary function tests. Computed tomography of the prostate after seed implantation was performed to check seed position and dosimetry. Odds ratio, confidence intervals, chi-square tests, and logistic regression analysis were performed to evaluate the relationship between the type and number of seeds used, the incidence of pulmonary migration, and the effects on pulmonary function. RESULTS A total of 83 patients underwent prostate brachytherapy during the study period and 58 patients underwent chest radiography. Seed migration occurred in 21 (36.2%) of 58 patients (95% confidence interval 23.8% to 48.6%). Thirty-four (0.71%) of 4755 seeds used migrated to the lungs. Nine patients had single seed migration to the right lung and three to the left lung. Nine patients had multiple (maximum of 4) and bilateral seed migration. No consistent relationship was found between seed migration and the type of seeds used (P = 0.24). Borderline statistical significance suggested an increased incidence of seed migration with an increasing number of implanted seeds (P = 0.054). Repeat chest radiography in 21 patients revealed no delayed migration at a median follow-up of 16 months. Clinical and pulmonary function testing revealed no consistent abnormality attributable to seed migration. CONCLUSIONS Radioactive seed migration occurred in 36.2% of brachytherapy patients who had chest radiographs done in our series. Pulmonary seed migration may be influenced by the number of implanted seeds and does not appear to be influenced by the seed type. Additional study of this observed phenomenon is required. A thorough pulmonary workup failed to reveal any short-term harmful side effects; however, long-term follow-up is needed. Healthcare providers should discuss the possibility of pulmonary seed migration with patients with prostate cancer considering prostate brachytherapy.
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