Multi-species temporal network of livestock movements for disease spread

Introduction: The objective of this study is to show the importance of interspecies links and temporal network dynamics of a multi-species livestock movement network. Although both cattle and sheep networks have been previously studied, cattle-sheep multi-species networks have not generally been studied in-depth. The central question of this study is how the combination of cattle and sheep movements affects the potential for disease spread on the combined network. Materials and methods: Our analysis considers static and temporal representations of networks based on recorded animal movements. We computed network-based node importance measures of two single-species networks, and compared the top-ranked premises with the ones in the multi-species network. We propose the use of a measure based on contact chains calculated in a network weighted with transmission probabilities to assess the importance of premises in an outbreak. To ground our investigation in infectious disease epidemiology, we compared this suggested measure with the results of disease simulation models with asymmetric probabilities of transmission between species. Results: Our analysis of the temporal networks shows that the premises which are likely to drive the epidemic in this multi-species network differ from the ones in both the cattle and the sheep networks. Although sheep movements are highly seasonal, the estimated size of an epidemic is significantly larger in the multi-species network than in the cattle network, independently of the period of the year. Finally, we demonstrate that a measure based on contact chains allow us to identify around 30% of the key farms in a simulated epidemic, ignoring markets, whilst static network measures identify less than 10% of these farms. Conclusion: Our results ascertain the importance of combining species networks, as well as considering layers of temporal livestock movements in detail for the study of disease spread

Bardoxolone methyl: a potential therapeutic for the prevention of anti-psychotic drug-induced obesity?

Abstract of a presentation

The photodecomposition product μ-oxalato-1κ^2O,O′:2κ^2O″,O‴-bis{bis[2-(2-pyridyl)phenyl-κ^2C,N]iridium(III)}–acetone (1/1.974)

An attempt to grow crystals of [Ir(ppy)_2(vacac)], (I), from an acetone-d_6 solution formed instead crystals of [{Ir(ppy)_2}_2(μ-oxalato)] acetone solvate, (II), [Ir_2(C_(11)H_8N)_4(C_2O_4)]·1.974C_3H_6O, where ppy is the phenyl­pyridine anion and vacac is vin­ylacetyl­acetonate. Each Ir^(III) ion in (II) is in a pseudo-octa­hedral coordination environment, where the pyridine N atoms are trans to each other and the phen­yl C atoms are trans to the O atoms of the oxalate bridging ligand. There are two crystallographically independent dimer molecules, each lying on an inversion centre. It is suggested that the oxalate ligand is formed in a series of steps initiated by the aldol condensation of acetone with vacac

Predictors of Hospitals with Endemic Community-Associated Methicillin-Resistant Staphylococcus aureus

OBJECTIVE: We sought to identify hospital characteristics associated with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) carriage among inpatients. DESIGN: Prospective cohort study. SETTING: Orange County, California. PARTICIPANTS: Thirty hospitals in a single county. METHODS: We collected clinical MRSA isolates from inpatients in 30 of 31 hospitals in Orange County, California, from October 2008 through April 2010. We characterized isolates by spa typing to identify CA-MRSA strains. Using California’s mandatory hospitalization data set, we identified hospital-level predictors of CA-MRSA isolation. RESULTS: CA-MRSA strains represented 1,033 (46%) of 2,246 of MRSA isolates. By hospital, the median percentage of CA-MRSA isolates was 46% (range, 14%–81%). In multivariate models, CA-MRSA isolation was associated with smaller hospitals (odds ratio [OR], 0.97, or 3% decreased odds of CA-MRSA isolation per 1,000 annual admissions; P < .001), hospitals with more Medicaid-insured patients (OR, 1.2; P = .002), and hospitals with more patients with low comorbidity scores (OR, 1.3; P < .001). Results were similar when restricted to isolates from patients with hospital-onset infection. CONCLUSIONS: Among 30 hospitals, CA-MRSA comprised nearly half of MRSA isolates. There was substantial variability in CA-MRSA penetration across hospitals, with more CA-MRSA in smaller hospitals with healthier but socially disadvantaged patient populations. Additional research is needed to determine whether infection control strategies can be successful in targeting CA-MRSA influx

A high-resolution mRNA expression time course of embryonic development in zebrafish.

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3' ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl

The effects of lower-body compression garments on walking performance and perceived exertion in adults with CVD risk factors

Objectives Compression garments are used by athletes in attempts to enhance performance and recovery, although evidence to support their use is equivocal. Reducing the exertion experienced during exercise may encourage sedentary individuals to increase physical activity. The aim of this study was to assess the effect of compression garments on walking performance (self-paced and enforced pace) and rate of perceived exertion (RPE) in adults who presented with two or more CVD risk factors. Participants (n = 15, 10 female, 58.9 ± 11.5 years, BMI 27.5 ± 4.5 kg m2) were recruited. Design A repeated measures design. Methods Participants were randomised to Modified Bruce Protocol (enforced pace), or the 6 min walk test (self-paced), and completed the test wearing compression garments or normal exercise clothes (Control). Outcome measures included stage completed, gross efficiency (%) and RPE in Modified Bruce Protocol, and distance walked (m) and RPE in 6 min walk test. Results In the Modified Bruce Protcol participants had a higher RPE (15.5 ± 2.5 vs 14.3 ± 2.2) and a lower efficiency (19.1 ± 5.9 vs 21.1 ± 6.7) in the compression garment condition compared with control, p < 0.05. In the 6 min walk test participants walked 9% less in the compression garment condition (p < 0.05) but did not have a lower RPE. Conclusions Compared with previous studies reporting enhanced or no effects of compression garments on performance or RPE, this study shows adverse effects of such clothing in untrained individuals with CVD risk factors. The mechanisms underlying this negative effect require further exploration. Use of garments designed for the athletic individuals may not be suitable for the wider population

Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae

The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacteria populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated twelve major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan-genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of eleven populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation

FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of "following the science" are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline developed during the COVID-19 pandemic that allows easy annotation of data as they are consumed by analyses, while tracing the provenance of scientific outputs back through the analytical source code to data sources. Such a tool provides a mechanism for the public, and fellow scientists, to better assess the trust that should be placed in scientific evidence, while allowing scientists to support policy-makers in openly justifying their decisions. We believe that tools such as this should be promoted for use across all areas of policy-facing research