Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease.

Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease-associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes

Looking inside the black box : a theory-based process evaluation alongside a randomised controlled trial of printed educational materials (the Ontario printed educational message, OPEM) to improve referral and prescribing practices in primary care in Ontario, Canada

Background: Randomised controlled trials of implementation strategies tell us whether (or not) an intervention results in changes in professional behaviour but little about the causal mechanisms that produce any change. Theory-based process evaluations collect data on theoretical constructs alongside randomised trials to explore possible causal mechanisms and effect modifiers. This is similar to measuring intermediate endpoints in clinical trials to further understand the biological basis of any observed effects (for example, measuring lipid profiles alongside trials of lipid lowering drugs where the primary endpoint could be reduction in vascular related deaths). This study protocol describes a theory-based process evaluation alongside the Ontario Printed Educational Message (OPEM) trial. We hypothesize that the OPEM interventions are most likely to operate through changes in physicians' behavioural intentions due to improved attitudes or subjective norms with little or no change in perceived behavioural control. We will test this hypothesis using a well-validated social cognition model, the theory of planned behaviour (TPB) that incorporates these constructs. Methods/design: We will develop theory-based surveys using standard methods based upon the TPB for the second and third replications, and survey a subsample of Ontario family physicians from each arm of the trial two months before and six months after the dissemination of the index edition of informed, the evidence based newsletter used for the interventions. In the third replication, our study will converge with the "TRY-ME" protocol (a second study conducted alongside the OPEM trial), in which the content of educational messages was constructed using both standard methods and methods informed by psychological theory. We will modify Dillman's total design method to maximise response rates. Preliminary analyses will initially assess the internal reliability of the measures and use regression to explore the relationships between predictor and dependent variable (intention to advise diabetic patients to have annual retinopathy screening and to prescribe thiazide diuretics for first line treatment of uncomplicated hypertension). We will then compare groups using methods appropriate for comparing independent samples to determine whether there have been changes in the predicted constructs (attitudes, subjective norms, or intentions) across the study groups as hypothesised, and will assess the convergence between the process evaluation results and the main trial results.The OPEM trial and OPEM process evaluation are funded by the Canadian Institute of Health Research (CIHR). The OPEM process evaluation study was developed as part of the CIHR funded interdisciplinary capacity enhancement team KT-ICEBeRG. Gaston Godin, Jeremy Grimshaw and France Légaré hold Canada Research Chairs. Louise Lemyre holds an R.S. McLaughlin Research Chair

Diverted from Landfill: Reuse of Single-Use Plastic Packaging Waste

Low-density polyethylene (LDPE) based packaging films mostly end up in landfill after single-use as they are not commonly recycled due to their flexible nature, low strength and low cost. Additionally, the necessity to separate and sort different plastic waste streams is the most costly step in plastics recycling, and is a major barrier to increasing recycling rates. This cost can be reduced through using waste mixed plastics (wMP) as a raw material. This research investigates the properties of PE-based wMP coming from film packaging wastes that constitutes different grades of PE with traces of polypropylene (PP). Their properties are compared with segregated individual recycled polyolefins and virgin LDPE. The plastic plaques are produced directly from the wMP shreds as well as after extruding the wMP shreds into a more uniform material. The effect of different material forms and processing conditions on the mechanical properties are investigated. The results of the investigation show that measured properties of the wMP fall well within the range of properties of various grades of virgin polyethylene, indicating the maximum possible variations between different batches. Addition of an intermediate processing step of extrusion before compression moulding is found to have no effect on the tensile properties but results in a noticeably different failure behaviour. The wMP does not show any thermal degradation during processing that was confirmed by thermogravimetric analysis. The results give a scientific insight into the adoption of wMP in real world products that can divert them from landfill creating a more circular economy

Diverted from landfill: reuse of single-use plastic packaging waste

Low-density polyethylene (LDPE) based packaging films mostly end up in landfill after single-use as they are not commonly recycled due to their flexible nature, low strength and low cost. Additionally, the necessity to separate and sort different plastic waste streams is the most costly step in plastics recycling, and is a major barrier to increasing recycling rates. This cost can be reduced through using waste mixed plastics (wMP) as a raw material. This research investigates the properties of PE-based wMP coming from film packaging wastes that constitutes different grades of PE with traces of polypropylene (PP). Their properties are compared with segregated individual recycled polyolefins and virgin LDPE. The plastic plaques are produced directly from the wMP shreds as well as after extruding the wMP shreds into a more uniform material. The effect of different material forms and processing conditions on the mechanical properties are investigated. The results of the investigation show that measured properties of the wMP fall well within the range of properties of various grades of virgin polyethylene, indicating the maximum possible variations between different batches. Addition of an intermediate processing step of extrusion before compression moulding is found to have no effect on the tensile properties but results in a noticeably different failure behaviour. The wMP does not show any thermal degradation during processing that was confirmed by thermogravimetric analysis. The results give a scientific insight into the adoption of wMP in real world products that can divert them from landfill creating a more circular economy.ye

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Pulmonary endothelial permeability and tissue fluid balance depend on the viscosity of the perfusion solution

Fluid filtration in the pulmonary microcirculation depends on the hydrostatic and oncotic pressure gradients across the endothelium and the selective permeability of the endothelial barrier. Maintaining normal fluid balance depends both on specific properties of the endothelium and of the perfusing blood. Although some of the essential properties of blood needed to prevent excessive fluid leak have been identified and characterized, our understanding of these remains incomplete. The role of perfusate viscosity in maintaining normal fluid exchange has not previously been examined. We prepared a high-viscosity perfusion solution (HVS) with a relative viscosity of 2.5, i.e., within the range displayed by blood flowing in vessels of different diameters in vivo (1.5–4.0). Perfusion of isolated murine lungs with HVS significantly reduced the rate of edema formation compared with perfusion with a standard solution (SS), which had a lower viscosity similar to plasma (relative viscosity 1.5). HVS did not alter capillary filtration pressure. Increased endothelial shear stress produced by increasing flow rates of SS, to mimic the increased shear stress produced by HVS, did not reduce edema formation. HVS significantly reduced extravasation of Evans bluelabeled albumin compared with SS, indicating that it attenuated endothelial leak. These findings demonstrate for the first time that the viscosity of the solution perfusing the pulmonary microcirculation is an important physiological property contributing to the maintenance of normal fluid exchange. This has significant implications for our understanding of fluid homeostasis in the healthy lung, edema formation in disease, and reconditioning of donor organs for transplantation

Trash into Treasure: Value-Added composites from waste plastic packaging and carbon nanotubes

This work explores the use of low-value packaging film-based waste mixed plastics (wMP) and carbon nanotubes (CNT) to produce value-added composites. The performance of the composites is assessed through mechanical testing, UV ageing, and electrical conductivity measurement. Reinforcing wMP with 5 wt% CNT increased the tensile strength and tensile modulus by 46 % and 23 %, respectively. There were similar increases in flexural modulus (53 %), compressive strength (131 %), and compressive modulus (89 %) compared to unreinforced wMP. UV ageing for 500 h had no measurable effect on unreinforced wMP but decreased the flexural modulus of wMP/5 wt% CNT by 23 %. An average electrical conductivity of 1.65 × 10−2 S/m was measured for wMP/CNT, with unreinforced wMP showing no measurable electrical conductivity, as expected. This research provides valuable scientific insights into the application of mixed waste plastics in composites, aiding the creation of a more circular economy for plastic waste and leading to second-generation products with a wide range of potential applications

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing

The Curious Case of the Flood in the Night Time

The Curious Case of the Flood in the Night Time was a brand new immersive theatrical performance created by the authors and performed for the first time in the Albany Theatre, Deptford, London, in February 2018 as part of the SMASHfestUK 2018: Flood! festival (see p24 of brochure for listing). In the play, which was designed for a young audience (Key stage 2 + parents/guardians/family), the audience play the role of the Jury in an inquest into the death of a local man, who was found dead on his houseboat in Deptford Creek. As the inquest proceeds, the audience/jury are shown evidence and testimony from witnesses about the events of the night of the death. This includes forensic tests and other forms of evidence which come together to form a picture of what happened that night. At the end of the performance the Jury have to vote on whether they believe the death was by foul play or natural causes. The evidence points them towards a mosquito-borne disease, the likes of which will become more prevalent in the UK due to the effects of climate change. The play was performed on 2 occasions during SMASHfestUK 2018: Flood! and both performances were sold-out, with 80 tickets available for each showing