73 research outputs found
Hyper-g Priors for Generalized Linear Models
We develop an extension of the classical Zellner's g-prior to generalized
linear models. The prior on the hyperparameter g is handled in a flexible way,
so that any continuous proper hyperprior f(g) can be used, giving rise to a
large class of hyper-g priors. Connections with the literature are described in
detail. A fast and accurate integrated Laplace approximation of the marginal
likelihood makes inference in large model spaces feasible. For posterior
parameter estimation we propose an efficient and tuning-free
Metropolis-Hastings sampler. The methodology is illustrated with variable
selection and automatic covariate transformation in the Pima Indians diabetes
data set.Comment: 30 pages, 12 figures, poster contribution at ISBA 201
Approximate Bayesian Model Selection with the Deviance Statistic
Bayesian model selection poses two main challenges: the specification of
parameter priors for all models, and the computation of the resulting Bayes
factors between models. There is now a large literature on automatic and
objective parameter priors in the linear model. One important class are
-priors, which were recently extended from linear to generalized linear
models (GLMs). We show that the resulting Bayes factors can be approximated by
test-based Bayes factors (Johnson [Scand. J. Stat. 35 (2008) 354-368]) using
the deviance statistics of the models. To estimate the hyperparameter , we
propose empirical and fully Bayes approaches and link the former to minimum
Bayes factors and shrinkage estimates from the literature. Furthermore, we
describe how to approximate the corresponding posterior distribution of the
regression coefficients based on the standard GLM output. We illustrate the
approach with the development of a clinical prediction model for 30-day
survival in the GUSTO-I trial using logistic regression.Comment: Published at http://dx.doi.org/10.1214/14-STS510 in the Statistical
Science (http://www.imstat.org/sts/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Bayesian fractional polynomials
This paper sets out to implement the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms. Fractional polynomials widen the class of ordinary polynomials and offer an additive and transportable modelling approach. The methodology is based on a Bayesian linear model with a quasi-default hyper-g prior and combines variable selection with parametric modelling of additive effects. AMarkov chain Monte Carlo algorithm for the exploration of the model space is presented. This theoretically well-founded stochastic search constitutes a substantial improvement to ad hoc stepwise procedures for the fitting of fractional polynomial models. The method is applied to a data set on the relationship between ozone levels and meteorological parameters, previously analysed in the literatur
Ankle sprain versus muscle strain injury in professional men's basketball: a 9-year prospective follow-up study
Peer ReviewedPostprint (author's final draft
Pilot study on HTR2A promoter polymorphism, −1438G/A (rs6311) and a nearby copy number variation showed association with onset and severity in early onset obsessive-compulsive disorder
A previous study showed that a single nucleotide polymorphism (SNP), −1438G/A (rs6311), found in the transcriptional control region of the gene that encodes the serotonin-receptor 2A (HTR2A) was associated with obsessive-compulsive disorder (OCD) in a sample of children and adolescents. In this study, we reanalyzed the association of this SNP with OCD in an enlarged population of 136 cases (55 previous+81 new cases) and compared them to 106 newly recruited, healthy, age-matched controls. We also investigated whether this SNP or its copy number variations (CNV) was associated with OCD severity and age of onset. The CNV was analyzed in a DNA region located near rs6311. The results confirmed the association between the A-allele and early onset OCD in children and adolescents, with an odds ratio (OR) of 1.69 [95% CI (1.17, 2.46); p=0.005]. Strikingly, we found that carriers of one copy (deletion) of the CNV were associated with a very early onset OCD (2.5years earlier than the typical onset), and they had increased CY-BOCS scores (8.7 points higher compared to "normal” CNV and duplications); which is related to increased severity of OCD symptoms (p=0.031; p=0.004, respectively). Compared to the normal CNV and duplications, the association between the deletion and OCD showed an OR of 7.56 [95% CI (1.32, 142.84); p=0.020]. These results pointed to the functional importance of this promoter region of HTR2A; it influenced the occurrence, the onset, and the severity of OC
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. (Résumé d'auteur
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus
Vector population control using insecticides is a key element of current strategies to prevent
malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate
pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance
driven by the highly diverse Anopheles genomes. Here, we use a population genomic
approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors
Anopheles gambiae and A. coluzzii. A combination of copy number variation and a single
non-synonymous substitution in the acetylcholinesterase gene, Ace1, provides the key
resistance diagnostic in an A. coluzzii population from Coˆte d’Ivoire that we used for
sequence-based association mapping, with replication in other West African populations.
The Ace1 substitution and duplications occur on a unique resistance haplotype that evolved
in A. gambiae and introgressed into A. coluzzii, and is now common in West Africa primarily
due to selection imposed by other organophosphate or carbamate insecticides. Our findings
highlight the predictive value of this complex resistance haplotype for phenotypic resistance
and clarify its evolutionary history, providing tools to for molecular surveillance of the current
and future effectiveness of pirimiphos-methyl based interventions
International collaborative study to assess cardiovascular risk and evaluate long-term health in cats with preclinical hypertrophic cardiomyopathy and apparently healthy cats:The REVEAL Study
Background: Hypertrophic cardiomyopathy is the most prevalent heart disorder in cats and principal cause of cardiovascular morbidity and mortality. Yet, the impact of preclinical disease is unresolved. Hypothesis/Objectives: Observational study to characterize cardiovascular morbidity and survival in cats with preclinical nonobstructive (HCM) and obstructive (HOCM) hypertrophic cardiomyopathy and in apparently healthy cats (AH). Animals: One thousand seven hundred and thirty client-owned cats (430 preclinical HCM; 578 preclinical HOCM; 722 AH). Methods: Retrospective multicenter, longitudinal, cohort study. Cats from 21 countries were followed through medical record review and owner or referring veterinarian interviews. Data were analyzed to compare long-term outcomes, incidence, and risk for congestive heart failure (CHF), arterial thromboembolism (ATE), and cardiovascular death. Results: During the study period, CHF, ATE, or both occurred in 30.5% and cardiovascular death in 27.9% of 1008 HCM/HOCM cats. Risk assessed at 1, 5, and 10 years after study entry was 7.0%/3.5%, 19.9%/9.7%, and 23.9%/11.3% for CHF/ATE, and 6.7%, 22.8%, and 28.3% for cardiovascular death, respectively. There were no statistically significant differences between HOCM compared with HCM for cardiovascular morbidity or mortality, time from diagnosis to development of morbidity, or cardiovascular survival. Cats that developed cardiovascular morbidity had short survival (mean \ub1 standard deviation, 1.3 \ub1 1.7 years). Overall, prolonged longevity was recorded in a minority of preclinical HCM/HOCM cats with 10% reaching 9-15 years. Conclusions and Clinical Importance: Preclinical HCM/HOCM is a global health problem of cats that carries substantial risk for CHF, ATE, and cardiovascular death. This finding underscores the need to identify therapies and monitoring strategies that decrease morbidity and mortality
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