Inference of epidemiological parameters from household stratified data

We consider a continuous-time Markov chain model of SIR disease dynamics with two levels of mixing. For this so-called stochastic households model, we provide two methods for inferring the model parameters---governing within-household transmission, recovery, and between-household transmission---from data of the day upon which each individual became infectious and the household in which each infection occurred, as would be available from first few hundred studies. Each method is a form of Bayesian Markov Chain Monte Carlo that allows us to calculate a joint posterior distribution for all parameters and hence the household reproduction number and the early growth rate of the epidemic. The first method performs exact Bayesian inference using a standard data-augmentation approach; the second performs approximate Bayesian inference based on a likelihood approximation derived from branching processes. These methods are compared for computational efficiency and posteriors from each are compared. The branching process is shown to be an excellent approximation and remains computationally efficient as the amount of data is increased

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice

The authors gratefully acknowledge Doctoral Training Partnership funding from the BBSRC (M.J.D.) and funding from the Scottish Government (P.J.M., A.W.R., and A.W.W.). We also thank the Centre for Genome-Enabled Biology and Medicine for help with next-generation sequencing and Karen Garden and the Rowett’s Analytical Services for SCFA analysis. SUPPLEMENTAL INFORMATION Supplemental Information includes four figures and two tables and can be found with this article online at https://doi.org/10.1016/j.celrep.2017.10.056.Peer reviewedPublisher PD

Racing with a purpose:Sustainability in Formula E

This study examined the seasonal sustainability reporting of Formula E for its content, variation, and linearity. Formula E was chosen since it was built as a sustainable sport enterprise rather than one which integrated sustainability into existing operations and for the accessibility of its annual sustainability reports. Using an exploratory approach for content and variation, and the Green Waves of sport sustainability for linearity, eight seasons of sustainability reports from Formula E were collected and examined via content analysis. Findings revealed the major content areas for Formula E concerned event management, car design, and community engagement with these initiatives classified as internal or external efforts. Reports were inconsistent in their structure, language, scope, and focus. The Green Waves suggest that while some efforts progress, others may regress according to strategy or the initiative’s life cycle. Formula E is progressing overall in their sustainability efforts, but exemplifies the lack of an end point to sustainability efforts. It is suggested that better coordination could yield higher strategic success and recognition

Presenilin complexes in Arabidopsis: Novel plant cell-signalling components?

Intercellular signalling is essential for multicellular organisms to coordinate growth and development, and is mediated by a huge variety of proteins. Some signalling pathways rely on the proteolytic cleavage of membrane proteins by a relatively newly discovered process of regulated intramembrane proteolysis (RIP), the cleavage of proteins within a transmembrane domain. There are four classes of intramembrane cleaving proteases (ICliPs) – Rhomboids, Site-2-proteases, Signal peptide peptidases and γ-secretase. Of all the ICliPs studied to date, γ-secretase is unique, as it is comprised of a four-protein complex, and is only found in multicellular organisms. A vast amount of research is carried out on the γ-secretase complex, not just because of its role in developmentally important pathways, such as NOTCH signalling, but also due to its role in Alzheimer’s disease. The β-amyloid precursor protein (APP) is cleaved by γ-secretase, and defects in this process result in the release of abnormal peptides that form the senile plaques in the brains of Alzheimer’s disease patients. Homologues of the four components of γ-secretase (PRESENILIN (PS), NICASTRIN (NCT), ANTERIOR PHARYNX DEFECTIVE-1 (APH-1) and PRESENILIN ENHANCER-2 (PEN-2)) are found in plants. The aim of this thesis was to characterise the potential γ-secretase components in Arabidopsis thaliana, to determine whether they form a complex, and to analyse what role, if any, they play in plant signalling. The members of the putative Arabidopsis γ-secretase complex (AtPS1 and 2, AtNCT, AtAPH1 and AtPEN2) were identified through BLAST searches, and found to be uniformly expressed. Analysis of T-DNA insertion mutants in each of these genes, and combinations there of, revealed no gross morphological differences to wild type under normal growth conditions and when subjected to a range of stresses. Protein fusions to GFP under the control of the 35S promoter were constructed and stably transformed into plants. AtPEN2:GFP is expressed throughout the plant, and accumulates in BFA sensitive Golgi bodies in roots. AtPS1:GFP, only accumulates strongly in developing seeds. Native blue PAGE was used to look for high molecular weight complexes (HMW) containing AtPEN2:GFP and AtPS1:GFP. Both fusion proteins were found in similar sized HMW complexes. A variety of methods were used to look for substrates of the iv putative γ-secretase complex in Arabidopsis, and although no specific substrates were identified, a potential role in seed development has been established

Inference of epidemiological parameters from household stratified data

We consider a continuous-time Markov chain model of SIR disease dynamics with two levels of mixing. For this so-called stochastic households model, we provide two methods for inferring the model parameters-governing within-household transmission, recovery, and between-household transmission-from data of the day upon which each individual became infectious and the household in which each infection occurred, as might be available from First Few Hundred studies. Each method is a form of Bayesian Markov Chain Monte Carlo that allows us to calculate a joint posterior distribution for all parameters and hence the household reproduction number and the early growth rate of the epidemic. The first method performs exact Bayesian inference using a standard data-augmentation approach; the second performs approximate Bayesian inference based on a likelihood approximation derived from branching processes. These methods are compared for computational efficiency and posteriors from each are compared. The branching process is shown to be a good approximation and remains computationally efficient as the amount of data is increased.James N. Walker, Joshua V. Ross, Andrew J. Blac

Resident gut microbiota community determines the efficacy of soluble fiber in reducing adiposity

The authors also thank Lynn Thomson and the Rowett’s Analytical Services for SCFA analysis and CGEBM for sequence analysisPeer reviewe

Changes in the capacity of visual working memory in 5- to 10-year-olds

Using the Luck and Vogel change detection paradigm, we sought to investigate the capacity of visual working memory in 5-, 7-, and 10-year-olds. We found that performance on the task improved significantly with age and also obtained evidence that the capacity of visual working memory approximately doubles between 5 and 10 years of age, where it reaches adult levels of approximately three to four items