Christopher Fonnesbeck

EFFICIENT ESTIMATION OF ABUNDANCE FOR PATCHILY DISTRIBUTED POPULATIONS VIA TWO-PHASE, ADAPTIVE SAMPLING

Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of abundance of rare and patchily distributed species and is particularly appropriate when sampling in all patches is impossible, but a global estimate of abundance is required.

Adaptive Management and the Value of Information: Learning Via Intervention in Epidemiology

This Research Article explores the benefits of applying Adaptive Management approaches to disease outbreaks, finding that formally integrating science and policy allows one to reduce uncertainty and improve disease management outcomes.

Pharmacologic Interventions for Infantile Hemangioma: A Meta-analysis.

CONTEXT: Infantile hemangiomas (IH) may be associated with significant functional impact. OBJECTIVE: The objective of this study was to meta-analyze studies of pharmacologic interventions for children with IH. DATA SOURCES: Data sources were Medline and other databases from 1982 to June 2015. STUDY SELECTION: Two reviewers assessed studies using predetermined inclusion criteria. DATA EXTRACTION: One reviewer extracted data with review by a second. RESULTS: We included 18 studies in a network meta-analysis assessing relative expected rates of IH clearance associated with β-blockers and steroids. Oral propranolol had the largest mean estimate of expected clearance (95%; 95% Bayesian credible interval [BCI]: 88%–99%) relative to oral corticosteroids (43%, 95% BCI: 21%–66%) and control (6%, 95% BCI: 1%–11%). Strength of evidence (SOE) was high for propranolol’s effects on reducing lesion size compared with observation/placebo. Corticosteroids demonstrated moderate effectiveness at reducing size/volume (moderate SOE for improvement in IH). SOE was low for effects of topical timolol versus placebo. LIMITATIONS: Methodologic limitations of available evidence may compromise SOE. Validity of meta-analytic estimates relies on the assumption of exchangeability among studies, conditional on effects of the intervention. Results rely on assumed lack of reporting bias. CONCLUSIONS: Propranolol is effective at reducing IH size compared with placebo, observation, and other treatments including steroids in most studies. Corticosteroids demonstrate moderate effectiveness at reducing IH size/volume. The meta-analysis estimates provide a relative ranking of anticipated rates of lesion clearance among treatments. Families and clinicians making treatment decisions should also factor in elements such as lesion size, location, number, and type, and patient and family preferences.

Randomized, double-blind comparison of standard-dose vs. high-dose trivalent inactivated influenza vaccine in pediatric solid organ transplant patients

Children who have undergone SOT mount a lower immune response after vaccination with TIV compared to healthy controls. HD or SD TIV in pediatric SOT was given to subjects 3–17 yr and at least six months post‐transplant. Subjects were randomized 2:1 to receive either the HD (60 μg) or the SD (15 μg) TIV. Local and systemic reactions were solicited after each vaccination, and immune responses were measured before and after each vaccination. Thirty‐eight subjects were enrolled. Mean age was 11.25 yr; 68% male, 45% renal, 26% heart, 21% liver, 5% lung, and 5% intestinal. Twenty‐three subjects were given HD and 15 SD TIV. The median time since transplant receipt was 2.2 yr. No severe AEs or rejection was attributed to vaccination. The HD group reported more tenderness and local reactions, fatigue, and body ache when compared to the SD cohort, but these were considered mild and resolved within three days. Subjects in the HD group demonstrated a higher percentage of four‐fold titer rise to H3N2 compared to the SD group. HD influenza vaccine was well tolerated and may have increased immunogenicity. A phase 2 trial is needed to confirm.

Early life establishment of site-specific microbial communities in the gut

Fecal sampling is widely utilized to define small intestinal tissue-level microbial communities in healthy and diseased newborns. However, this approach may lead to inaccurate assessments of disease or therapeutics in newborns because of the assumption that the taxa in the fecal microbiota are representative of the taxa present throughout the gastrointestinal tract. To assess the stratification of microbes in the newborn gut and to evaluate the probable shortcoming of fecal sampling in place of tissue sampling, we simultaneously compared intestinal mucosa and fecal microbial communities in 15 neonates undergoing intestinal resections. We report three key results. First, when the site of fecal and mucosal samples are further apart, their microbial communities are more distinct, as indicated by low mean Sørensen similarity indices for each patients fecal and tissue microbiota. Second, two distinct niches (intestinal mucosa and fecal microbiota) are evident by principal component analyses, demonstrating the critical role of sample source in defining microbial composition. Finally, in contrast to adult studies, intestinal bacterial diversity was higher in tissue than in fecal samples. This study represents an unprecedented map of the infant microbiota from intestinal mucosa and establishes discernable biogeography throughout the neonatal gastrointestinal tract. Our results question the reliance on fecal microbiota as a proxy for the developing intestinal microbiota. Additionally, the robust intestinal tissue-level bacterial diversity we detected at these early ages may contribute to the maturation of mucosal immunity.

Progestogens for Preterm Birth Prevention A Systematic Review and Meta-Analysis

OBJECTIVE: We systematically reviewed the effectiveness of progestogens for prevention of preterm birth among women with prior spontaneous preterm birth, multiple gestations, preterm labor, short cervix, or other indications. DATA SOURCES: We searched MEDLINE and EMBASE databases for English language articles published from January 1966 to October 2011. METHODS OF STUDY SELECTION: We excluded publications that were not randomized controlled trials or had fewer than 20 participants, identifying 34 publications, of which 19 contained data for Bayesian meta-analysis. TABULATION, INTEGRATION, AND RESULTS: Two reviewers independently extracted data and assigned overall quality ratings based on predetermined criteria. Among women with prior preterm birth and a singleton pregnancy (five randomized controlled trials), progestogen treatment decreased the median risk of preterm birth by 22% (relative risk [RR] 0.78, 95% Bayesian credible interval 0.68–0.88) and neonatal death by 42% (RR 0.58, 95% Bayesian credible interval 0.27–0.98). The evidence suggests progestogen treatment does not prevent prematurity (RR 1.02, 95% Bayesian credible interval 0.87–1.17) or neonatal death (RR 1.44, 95% Bayesian credible interval 0.46–3.18) in multiple gestations. Limited evidence suggests progestogen treatment may prevent prematurity in women with preterm labor (RR 0.62, 95% Bayesian credible interval 0.47–0.79) and short cervix (RR 0.52, 95% Bayesian credible interval 0.36–0.70). Across indications, evidence about maternal, fetal, or neonatal health outcomes, other than reducing preterm birth and neonatal mortality, is inconsistent, insufficient, or absent. CONCLUSION: Progestogens prevent preterm birth when used in singleton pregnancies for women with a prior preterm birth. In contrast, evidence suggests lack of effectiveness for multiple gestations. Evidence supporting all other uses is insufficient to guide clinical care. Overall, clinicians and patients lack longer-term information to understand whether intervention has the ultimately desired outcome of preventing morbidity and promoting normal childhood development.

Magnetic Resonance Imaging for Locating Nonpalpable Undescended Testicles: A Meta-analysis

BACKGROUND AND OBJECTIVE: Preoperative imaging techniques may guide management of nonpalpable, cryptorchid testicles. We evaluated conventional MRI for identifying and locating nonpalpable testicles in prepubescent boys via meta-analysis. METHODS: Databases including Medline were searched from 1980 to February 2012. Eligible studies included ≥10 boys with cryptorchidism/suspected cryptorchidism and reported data on testicular presence/absence and position (abdominal, inguinal, or scrotal) as determined by imaging and surgery. Two investigators independently reviewed studies against inclusion criteria. We captured the number of testicles that were correctly and incorrectly identified and located, relative to surgically verified status, and estimated sensitivity and specificity by using a random-effects model. RESULTS: Eight unique prospective case series included 171 boys with 193 nonpalpable testicles (22 with bilateral testicles). Surgery identified 158 testicles (81.9%) present and 35 absent. MRI correctly identified testicles with an estimated median sensitivity of 0.62 (95% Bayesian credible interval [BCI]: 0.47–0.77) and a specificity of 1.0 (95% BCI: 0.99–1.0). MRI located intraabdominal testicles with a sensitivity of 0.55 (95% BCI: 0.09–1.0) and inguino-scrotal testicles with a sensitivity of 0.86 (95% BCI: 0.67–1.0). We were not able to obtain estimates for MRI sensitivity or specificity for locating atrophied testicles. The estimated specificity for location-specific testicles reached almost 100%. CONCLUSIONS: Conventional MRI has low sensitivity for estimating the population sensitivity for identifying the presence of nonpalpable cryptorchid testicles. When testicles are identified, MRI is poor at locating both atrophied and intraabdominal testicles but performs modestly well in locating those in the inguino-scrotal regions.

Human Metapneumovirus Infection in Jordanian Children: Epidemiology and Risk Factors for Severe Disease.

Background: Human metapneumovirus (HMPV) is a leading cause of acute respiratory tract infection in young children. Our objectives were to define HMPV epidemiology and circulating strains and determine markers of severe disease in Jordanian children. Methods: We conducted a prospective study from March 16, 2010 to March 31, 2013 using quantitative reverse transcription-polymerase chain reaction to determine the frequency of HMPV infection among children <2 years old admitted with fever and/or acute respiratory illness to a major government hospital in Amman, Jordan. Results: HMPV was present in 273 of 3168 (8.6%) of children presenting with acute respiratory tract infection. HMPV A2, B1 and B2, but not A1, were detected during the 3-year period. HMPV-infected children were older and more likely to be diagnosed with bronchopneumonia than HMPV-negative children. HMPV-infected children with lower respiratory tract infection had higher rates of cough and shortness of breath than children with lower respiratory tract infection infected with other or no identifiable viruses. Symptoms and severity were not different between children with HMPV only compared with HMPV coinfection. Children with HMPV subgroup A infection were more likely to require supplemental oxygen. In a multivariate analysis, HMPV subgroup A and age <6 months were independently associated with supplemental oxygen requirement. Conclusions: HMPV is a leading cause of acute respiratory tract disease in Jordanian children <2 years old. HMPV A and young age were associated with severe disease. Ninety percent of HMPV-infected hospitalized children were full term and otherwise healthy, in contrast to high-income nations; thus, factors contributing to disease severity likely vary depending on geographic and resource differences.

Modeling regional waterfowl harvest rates using markov chain monte carlo

Abstract We developed models for simultaneous inference on movement and harvest rates, and of factors influencing harvest rates, using band-recovery data and Markov chain Monte Carlo (MCMC) modeling. We modeled variation in harvest rates for American black ducks (Anas rubripes) during 1971–1994 using recoveries of ducks banded in 3 breeding regions and recovered in 6 harvest regions in Canada and the United States. Models based on season length or bag limit together with season length, and incorporating a random year- and area-specific effect, were superior to other models as gauged by information criteria, fit statistics, and cross-validation. We used these models to generate posterior predictive distributions for harvest rates as a function of harvest regulations, for application to adaptive harvest management.

Decision-making for foot-and-mouth disease control: objectives matter

Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.