We propose a new data-augmentation strategy for fully Bayesian inference in models with binomial likelihoods. The approach appeals to a new class of Pólya–Gamma distributions, which are constructed ...in detail. A variety of examples are presented to show the versatility of the method, including logistic regression, negative binomial regression, nonlinear mixed-effect models, and spatial models for count data. In each case, our data-augmentation strategy leads to simple, effective methods for posterior inference that (1) circumvent the need for analytic approximations, numerical integration, or Metropolis–Hastings; and (2) outperform other known data-augmentation strategies, both in ease of use and in computational efficiency. All methods, including an efficient sampler for the Pólya–Gamma distribution, are implemented in the R package BayesLogit . Supplementary materials for this article are available online.
The global burden of disease (GBD) studies have derived detailed and comparable epidemiological and burden of disease estimates for schizophrenia. We report GBD 2016 estimates of schizophrenia ...prevalence and burden of disease with disaggregation by age, sex, year, and for all countries.
We conducted a systematic review to identify studies reporting the prevalence, incidence, remission, and/or excess mortality associated with schizophrenia. Reported estimates which met our inclusion criteria were entered into a Bayesian meta-regression tool used in GBD 2016 to derive prevalence for 20 age groups, 7 super-regions, 21 regions, and 195 countries and territories. Burden of disease estimates were derived for acute and residual states of schizophrenia by multiplying the age-, sex-, year-, and location-specific prevalence by 2 disability weights representative of the disability experienced during these states.
The systematic review found a total of 129 individual data sources. The global age-standardized point prevalence of schizophrenia in 2016 was estimated to be 0.28% (95% uncertainty interval UI: 0.24-0.31). No sex differences were observed in prevalence. Age-standardized point prevalence rates did not vary widely across countries or regions. Globally, prevalent cases rose from 13.1 (95% UI: 11.6-14.8) million in 1990 to 20.9 (95% UI: 18.5-23.4) million cases in 2016. Schizophrenia contributes 13.4 (95% UI: 9.9-16.7) million years of life lived with disability to burden of disease globally.
Although schizophrenia is a low prevalence disorder, the burden of disease is substantial. Our modeling suggests that significant population growth and aging has led to a large and increasing disease burden attributable to schizophrenia, particularly for middle income countries.
Attention-deficit/hyperactivity disorder (ADHD) and conduct disorder (CD) are common externalizing disorders. Despite previous research demonstrating that both are longitudinally associated with ...adverse outcomes, there have been no systematic reviews examining all of the available evidence linking ADHD and CD with a range of health and psychosocial outcomes.
Electronic databases (EMBASE, Medline, and PsycINFO) were searched for studies published from 1980 up to March 2015. Published cohort and case-control studies were included if they reported a longitudinal association between ADHD or CD and adverse outcomes with a minimum follow-up of 2 years. Outcomes with sufficient data were pooled in a random effects meta-analysis to give overall odds ratios (ORs) with corresponding 95% CIs.
Of the 278 studies assessed, 114 met inclusion criteria and 98 were used in subsequent meta-analyses. ADHD was associated with adverse outcomes including academic achievement (e.g. failure to complete high school; odds ratio OR = 3.7, 95% CIs 2.0-7.0), other mental and substance use disorders (e.g. depression; OR = 2.3, 1.5-3.7), criminality (e.g. arrest; OR = 2.4, 1.5-3.8), and employment (e.g., unemployment; OR = 2.0, 1.0-3.9). CD was associated with outcomes relating to academic achievement (e.g. failure to complete high school; OR = 2.7, 1.5-4.7), other mental and substance use disorders (e.g., illicit drug use; OR = 2.1, 1.7-2.6), and criminality (e.g. violence; OR = 3.5, 2.3-5.3).
This study demonstrated that ADHD and CD are associated with disability beyond immediate health loss. Although the analyses could not determine the mechanisms behind these longitudinal associations, they demonstrate the importance of addressing ADHD and CD early in life so as to potentially avert a wide range of future adverse outcomes.
It is unclear whether an evaluation incorporating coronary computed tomographic angiography (CCTA) is more effective than standard evaluation in the emergency department in patients with symptoms ...suggestive of acute coronary syndromes.
In this multicenter trial, we randomly assigned patients 40 to 74 years of age with symptoms suggestive of acute coronary syndromes but without ischemic electrocardiographic changes or an initial positive troponin test to early CCTA or to standard evaluation in the emergency department on weekdays during daylight hours between April 2010 and January 2012. The primary end point was length of stay in the hospital. Secondary end points included rates of discharge from the emergency department, major adverse cardiovascular events at 28 days, and cumulative costs. Safety end points were undetected acute coronary syndromes.
The rate of acute coronary syndromes among 1000 patients with a mean (±SD) age of 54±8 years (47% women) was 8%. After early CCTA, as compared with standard evaluation, the mean length of stay in the hospital was reduced by 7.6 hours (P<0.001) and more patients were discharged directly from the emergency department (47% vs. 12%, P<0.001). There were no undetected acute coronary syndromes and no significant differences in major adverse cardiovascular events at 28 days. After CCTA, there was more downstream testing and higher radiation exposure. The cumulative mean cost of care was similar in the CCTA group and the standard-evaluation group ($4,289 and $4,060, respectively; P=0.65).
In patients in the emergency department with symptoms suggestive of acute coronary syndromes, incorporating CCTA into a triage strategy improved the efficiency of clinical decision making, as compared with a standard evaluation in the emergency department, but it resulted in an increase in downstream testing and radiation exposure with no decrease in the overall costs of care. (Funded by the National Heart, Lung, and Blood Institute; ROMICAT-II ClinicalTrials.gov number, NCT01084239.).
To evaluate three coronary artery calcification (CAC) scoring methods to assess risk of coronary heart disease (CHD) death and all-cause mortality in National Lung Screening Trial (NLST) participants ...across levels of CAC scores.
The NLST was approved by the institutional review board at each participating institution, and informed consent was obtained from all participants. Image review was HIPAA compliant. Five cardiothoracic radiologists evaluated 1575 low-dose computed tomographic (CT) scans from three groups: 210 CHD deaths, 315 deaths not from CHD, and 1050 participants who were alive at conclusion of the trial. Radiologists used three scoring methods: overall visual assessment, segmented vessel-specific scoring, and Agatston scoring. Weighted Cox proportional hazards models were fit to evaluate the association between scoring methods and outcomes.
In multivariate analysis of time to CHD death, Agatston scores of 1-100, 101-1000, and greater than 1000 (reference category 0) were associated with hazard ratios of 1.27 (95% confidence interval: 0.69, 2.53), 3.57 (95% confidence interval: 2.14, 7.48), and 6.63 (95% confidence interval: 3.57, 14.97), respectively; hazard ratios for summed segmented vessel-specific scores of 1-5, 6-11, and 12-30 (reference category 0) were 1.72 (95% confidence interval: 1.05, 3.34), 5.11 (95% confidence interval: 2.92, 10.94), and 6.10 (95% confidence interval: 3.19, 14.05), respectively; and hazard ratios for overall visual assessment of mild, moderate, or heavy (reference category none) were 2.09 (95% confidence interval: 1.30, 4.16), 3.86 (95% confidence interval: 2.02, 8.20), and 6.95 (95% confidence interval: 3.73, 15.67), respectively.
By using low-dose CT performed for lung cancer screening in older, heavy smokers, a simple visual assessment of CAC can be generated for risk assessment of CHD death and all-cause mortality, which is comparable to Agatston scoring and strongly associated with outcome.
Proximal algorithms are useful for obtaining solutions to difficult optimization problems, especially those involving nonsmooth or composite objective functions. A proximal algorithm is one whose ...basic iterations involve the proximal operator of some function, whose evaluation requires solving a specific optimization problem that is typically easier than the original problem. Many familiar algorithms can be cast in this form, and this "proximal view" turns out to provide a set of broad organizing principles for many algorithms useful in statistics and machine learning. In this paper, we show how a number of recent advances in this area can inform modern statistical practice. We focus on several main themes: (1) variable splitting strategies and the augmented Lagrangian; (2) the broad utility of envelope (or variational) representations of objective functions; (3) proximal algorithms for composite objective functions; and (4) the surprisingly large number of functions for which there are closed-form solutions of proximal operators. We illustrate our methodology with regularized Logistic and Poisson regression incorporating a nonconvex bridge penalty and a fused lasso penalty. We also discuss several related issues, including the convergence of nondescent algorithms, acceleration and optimization for nonconvex functions. Finally, we provide directions for future research in this exciting area at the intersection of statistics and optimization.
Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot ...properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process.
In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects of all experimental factors on the expression of every gene. The Poisson-based model allows for the correct specification of the mean-variance relationship of the PCR amplification process, and can also glean information from instances of no amplification (zero counts). Our method is very flexible with respect to control genes: any prior knowledge about the expected degree of their stability can be directly incorporated into the model. Yet the method provides sensible answers without such assumptions, or even in the complete absence of control genes. We also present a natural Bayesian analogue of the "classic" analysis, which uses standard data pre-processing steps (logarithmic transformation and multi-gene normalization) but estimates all gene expression changes jointly within a single model. The new methods are considerably more flexible and powerful than the standard delta-delta Ct analysis based on pairwise t-tests.
Our methodology expands the applicability of the relative-quantification analysis protocol all the way to the lowest-abundance targets, and provides a novel opportunity to analyze qRT-PCR data without making any assumptions concerning target stability. These procedures have been implemented as the MCMC.qpcr package in R.
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