One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE

Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open‐source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N‐mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block‐sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one‐size‐fits‐all best strategy, but rather problem‐specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10–12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model‐generic MCMC procedures in open‐source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim.     

Focus: Preventive Medicine: Undiagnosed Hypertension and Undiagnosed Type 2 Diabetes among Overweight and Obese Marshallese Participants in a Diabetes Prevention Program

Hypertension and type 2 diabetes (T2D) are major public health issues that disproportionately affect minority communities, including Native Hawaiians and Pacific Islanders (NHPI). Minority communities are also more likely to have undiagnosed hypertension and T2D. Marshallese Pacific Islanders have been shown to have high proportions of diagnosed and undiagnosed hypertension and T2D. Using survey and biometric data collected from 378 overweight/obese Marshallese Pacific Islander adults, this study documents the prevalence of hypertension and T2D, as well as the prevalence of undiagnosed hypertension and T2D. The study also examines associations between undiagnosed hypertension and undiagnosed T2D and age group, sex, health care access (defined by foregone care due to cost and health insurance status), and body mass index (BMI). Among participants with blood pressure readings indicative of hypertension, 68.4% were undiagnosed, and among participants with HbA1c indicative of T2D, 31.6% were undiagnosed. A quarter of participants (24.5%) had blood pressure and HbA1c measures indicative of both undiagnosed hypertension and undiagnosed T2D. Undiagnosed hypertension was significantly associated with age group (p’s<0.0001) and sex (p=0.028). Undiagnosed T2D was significantly associated with age group (p’s<0.05), forgone care due to cost (p=0.018), health insurance status (p=0.035), and BMI (p=0.001). Participants in this study had high proportions of undiagnosed hypertension and undiagnosed T2D. These findings will be immediately useful for those working to address hypertension and T2D disparities among Marshallese and other NHPI populations.     

Thermal sensitivity of juvenile rabbitfishes Siganus doliatus and S. lineatus (Siganidae): a key role for habitat?

The majority of our understanding of the effects of climate change on coral reef fishes are currently based on studies of small-bodied species such as damselfishes. By contrast, we know little about the potential impacts of ocean warming on larger species of herbivorous and detritivorous reef fish, despite them being a critical functional group and an essential source of food protein for millions of people. In addition, we know little of the role of habitat in determining species’ thermal sensitivity and the legitimacy of extrapolating thermal performance across closely-related species from different habitat types. Here we test the effect of exposure to increased water temperature during juvenile development on key physiological and behavioral traits of two species of rabbitfish typically associated with different habitats: Siganus doliatus (reef-associated) and S. lineatus (estuarine). Wild-caught juveniles were reared for 14 weeks at temperatures representing present-day ambient conditions (28.0 °C), late-summer ambient conditions (30.0 °C), or those projected on reefs under future global warming scenarios (31.5 °C). We then measured the somatic (growth, condition, immune response) and behavioral (feeding rate, latency to feed and activity level) traits of individuals within each treatment to determine the sensitivity of each species to elevated water temperatures. Overall, both species showed comparatively robust levels of thermal tolerance, based on previously-documented responses of small-bodied reef fishes. However, two very different patterns emerged. The reef-associated S. doliatus showed a greater physiological response to temperature, with negative effects on hepatosomatic condition and immune function observed in individuals exposed to the 31.5 °C treatment. By contrast, there were no negative physiological effects of temperature observed in S. lineatus and instead we recorded behavioral changes, with individuals at 30 °C and 31.5 °C displaying altered feeding behavior (increased feeding rate and decreased latency to feed). These distinct responses observed between congeners are likely due to their evolutionary history and flag the potential inaccuracies that could arise from extrapolating effects of ocean warming across even closely-related species adapted to different habitats.

     

Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764

We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ ¹H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 10³ M^?1 s^?1) is less than stellar.     

Undergraduate Music Program Alumni's Career Path,Retrospective Institutional Satisfaction,and Financial Status

The purpose of this study was to examine undergraduate music education and performance alumni's career path, retrospective institutional satisfaction, and financial status. Data for this study were drawn from respondents from the 2010 administration of the nationwide, multi-institutional survey conducted by the Strategic National Arts Alumni Project (SNAAP). Regarding career path, nearly half of the music performance degree graduates reported performing as their current job, and slightly more than half of the music education degree graduates reported working in K–12 schools. Participants were generally satisfied with their institutional experiences, although relatively low levels of satisfaction were reported for networking and career advising services. The respondents reported being most satisfied with aspects of their current jobs that reflected the intrinsic benefits of contributing to a greater good, satisfying personal interests and values, and opportunities to be creative. The majority of the sample reported accruing student loan debt ranging between $10,000 and $30,000; however, no significant differences were found between groups, and 40 percent of the participants reported having accrued no debt at all. The reported annual income of the participants varied significantly, with music educators reporting higher earnings than performers.     

Business‐to‐Business Information Technology User Practices at End of Life in the United Kingdom,Germany, and France

Business‐to‐business (B2B) electronics account for a significant volume of the electrical and electronic equipment (EEE) put on the market. Very little B2B waste electrical and electronic equipment (WEEE) is reported as collected in the European Union (EU) in compliance with the WEEE Directive, which uses the policy principle of extended producer responsibility (EPR) to ensure that WEEE is managed correctly. This presents a barrier to parties looking for access to the waste. Company practice dictates the channels into which B2B WEEE flows following primary use. This article presents a study that engaged with company actors directly to get a better understanding of business information technology (IT) EEE asset management. Data were collected to determine the barriers current practice could present to the collection of B2B IT EEE at end of life and the implications of these for the development of policies and strategies for EPR. A questionnaire was developed and data were gathered from organizations in three EU countries—the United Kingdom, Germany, and France—stratified by size. Some notable findings were that there are several routes by which end‐of‐life B2B WEEE can flow. The recycling and refurbishment of B2B IT units at end of use was shown to be commonplace, but it is likely that these units enter streams where they are not reported. The actors disposing of their units did not have information on the management or disposition of these streams. It is concluded that to achieve the goals of EPR for B2B IT WEEE, the networks and the operational practices of these streams need to be better understood when developing strategies and policies.