Efficient Bayesian model choice for partially observed processes: with application to an experimental transmission study of an infectious disease

Infectious diseases such as avian influenza pose a global threat to human health. Mathematical and statistical models can provide key insights into the mechanisms that underlie the spread and persistence of infectious diseases, though their utility is linked to the ability to adequately calibrate these models to observed data. Performing robust inference for these systems is challenging. The fact that the underlying models exhibit complex non-linear dynamics, coupled with practical constraints to observing key epidemiological events such as transmission, requires the use of inference techniques that are able to numerically integrate over multiple hidden states and/or infer missing information. Simulation-based inference techniques such as Approximate Bayesian Computation (ABC) have shown great promise in this area, since they rely on the development of suitable simulation models, which are often easier to code and generalise than routines that require evaluations of an intractable likelihood function. In this manuscript we make some contributions towards improving the efficiency of ABC-based particle Markov chain Monte Carlo methods, and show the utility of these approaches for performing both model inference and model comparison in a Bayesian framework. We illustrate these approaches on both simulated data, as well as real data from an experimental transmission study of highly pathogenic avian influenza in genetically modi fied chickens.This work was supported by the Biotechnology and Biological Sciences Research Council (grants BB/G00479X/1, BBS/B/00239, and BBS/B/00301) and by the Cambridge Infectious Diseases Consortium Department for Environment, Food and Rural Affairs-Higher Education Funding Council for England (grant VT0105). AJKC was supported by BBSRC grant BB/I024550/1

Phylogenetic patterns of foliar mineral nutrient accumulation among gypsophiles and their relatives in the Chihuahuan Desert

PREMISE OF THE STUDY: Gypsum endemism in plants (gypsophily) is common on gypsum outcrops worldwide, but little is known about the functional ecology of Chihuahuan Desert gypsophiles. We investigated whether leaf chemistry of gypsophile lineages from the northern Chihuahuan Desert are similar to leaves of related nonendemic (gypsovag) species relative to their soil chemistry. We expected widely distributed gypsophiles (hypothesized to be older lineages on gypsum) would have distinct leaf chemistry from narrowly distributed, relatively younger lineages endemic to gypsum and gypsovags, reflecting adaptation to gypsum. METHODS: We collected leaves from 23 gypsophiles and related nonendemic taxa growing on nongypsum soils. Soils and leaves were analyzed for Ca, S, Mg, K, N, and P. Leaf gypsum was assessed using Fourier transform infrared spectroscopy. KEY RESULTS: Most widespread gypsophile lineages that are hypothesized to be relatively old accumulate foliar S, Ca, and gypsum, but younger gypsophile lineages and closely related gypsovags do not. Young, narrowly distributed gypsophile lineages have leaf chemical signatures similar to nonendemic congeners and confamilials. CONCLUSIONS: Our data suggest multiple adaptive mechanisms support life on gypsum in Chihuahuan Desert gypsophiles. Most widespread gypsophiles are specialized for life on gypsum, likely due to shared abilities to accumulate and assimilate S and Ca in leaves. In contrast, narrowly distributed gypsophiles may have mechanisms to exclude excess S and Ca from their leaves, preventing toxicity. Future work will investigate the nutrient accumulation and exclusion patterns of other plant organs to determine at what level excess S and Ca uptake is restricted for young-lineage gypsophiles and gypsovags

The Cardiff self‐injury inventory (English version): convergent validity and psychometric properties

Background and Aims: The Cardiff Self‐Injury Inventory (CSII) is a short (1 min), relatively nonintrusive, measure of previous self‐injury behaviors written in English. It measures self‐injury with suicidal intent and without such intent, covers actions versus thoughts, and has two time periods (lifetime vs recent [defined as the last 3 months]). The study aimed to examine its psychometric properties and its relationship to more well‐established measures. Methods: A UK community sample of 184 participants completed the CSII and two other measures of self‐harming (Deliberate Self‐Harm Inventory [DSHI] and Suicidal Behaviors Questionnaire–Revised [SBQ‐R]) in March 2020–May 2020. Fifty participants also repeated these measurements 1–2 weeks later. Results: The CSII showed strong psychometric properties with internal reliability of 0.87 and a test–retest of 0.82. The subscales also showed strong psychometric properties. The CSII showed strong concurrent validity to the other measures of self‐injury (SBQ‐R, r = 0.70; DSHI, r = 0.81). A factor analysis supported the idea that there are two distinct components to the overall CSII score arising due to the distinction between suicidal and nonsuicidal behaviors. Conclusion: The CSII has good psychometric properties in this population and can be used as a fast, nonintrusive, measure of different self‐injurious behaviors for clinical or research purposes

Artificial nighttime light changes aphid-parasitoid population dynamics

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Artificial light at night (ALAN) is recognized as a widespread and increasingly important anthropogenic environmental pressure on wild species and their interactions. Understanding of how these impacts translate into changes in population dynamics of communities with multiple trophic levels is, however, severely lacking. In an outdoor mesocosm experiment we tested the effect of ALAN on the population dynamics of a plant-aphid-parasitoid community with one plant species, three aphid species and their specialist parasitoids. The light treatment reduced the abundance of two aphid species by 20% over five generations, most likely as a consequence of bottom-up effects, with reductions in bean plant biomass being observed. For the aphid Megoura viciae this effect was reversed under autumn conditions with the light treatment promoting continuous reproduction through asexuals. All three parasitoid species were negatively affected by the light treatment, through reduced host numbers and we discuss induced possible behavioural changes. These results suggest that, in addition to direct impacts on species behaviour, the impacts of ALAN can cascade through food webs with potentially far reaching effects on the wider ecosystem.The research leading to this paper was funded by the European Research council under the European Union’s Seventh Framework programme (FP7/2007-2013)/ERC grant agreement no. 268504 to KJG, and by NERC (grant no. NE/K005650/1) to FJFvV

Atomic Scale Structure and Chemical Composition across Order-Disorder Interfaces

Through a combination of aberration-corrected high-resolution scanning transmission electron microscopy and three-dimensional atom probe tomography, the true atomic-scale structure and change in chemical composition across the complex order-disorder interface in a metallic alloy has been determined. The study reveals the presence of two interfacial widths, one corresponding to an order-disorder transition, and the other to the compositional transition across the interface, raising fundamental questions regarding the definition of the interfacial width in such systems

Associations between early-life growth pattern and body size and follicular lymphoma risk and survival: a family-based case-control study

Background: The influence of early-life growth pattern and body size on follicular lymphoma (FL) risk and survival is unclear. In this study, we aimed to investigate the association between gestational age, growth during childhood, body size, changes in body shape over time, and FL risk and survival. Methods: We conducted a population-based family case-control study and included 706 cases and 490 controls. We ascertained gestational age, growth during childhood, body size and body shape using questionnaires and followed-up cases (median=83 months) using record linkage with national death records. We used a group-based trajectory modeling approach to identify body shape trajectories from ages 5–70. We examined associations with FL risk using unconditional logistic regression and used Cox regression to assess the association between body mass index (BMI) and all-cause and FL-specific mortality among cases. Results: We found no association between gestational age, childhood height and FL risk. We observed a modest increase in FL risk with being obese 5 years prior to enrolment (OR=1.43, 95 %CI=0.99–2.06; BMI ≥30 kg/m2) and per 5-kg/m2 increase in BMI 5 years prior to enrolment (OR=1.14, 95 %CI=0.99–1.31). The excess risk for obesity 5 years prior to enrolment was higher for ever-smokers (OR=2.00, 95 %CI=1.08–3.69) than never-smokers (OR=1.14, 95 %CI=0.71–1.84). We found no association between FL risk and BMI at enrolment, BMI for heaviest lifetime weight, the highest categories of adult weight or height, trouser size, body shape at different ages or body shape trajectory. We also observed no association between all-cause or FL-specific mortality and excess adiposity at or prior to enrolment. Conclusion: We observed a weak association between elevated BMI and FL risk, and no association with all-cause or FL-specific mortality, consistent with previous studies. Future studies incorporating biomarkers are needed to elucidate possible mechanisms underlying the role of body composition in FL etiology