Numerical study of thermal plume characteristics and entertainment in an enclosure with a point heat source

The structure of a buoyant plume above a point heat source in a ventilated enclosure has been investigated using large-eddy simulation (LES). The aim of the work is to assess the performance and the accuracy of LES for modelling buoyancy-driven displacement ventilation of an enclosure and investigate the role of coherent structures in the plume entrainment mechanism which is important in these flow types because, for example, entrainment determines the ventilation flow rate. The Smagorinsky subgrid-scale model is used for the unresolved small-scale turbulence. The Rayleigh number Ra is chosen in the range where spatial transition from laminar to turbulent flow takes place (Ra=1.5×109). The stratification height and temperature of the stratified layer deduced from the mean field of the LES data is in good agreement with the theory of Linden, Lane-Serff and Smeed (1990). The plume entrainment coefficient is in good agreement with experimental values determined by Morton, Taylor and Turner (1956), Rouse, Yih and Humphreys (1952), and Baines and Turner (1969). Instantaneously, the plume develops through expansion and contraction phases, where the expansion phase is associated with the existence of coherent large-scale structures leading to an outward stretching of the plume and the contraction occurs as a result of partial breakdown and/or loss of coherence of these structures. As a result, the instantaneous entrained mass (and thus the entrainment coefficient) at different heights below the mean interface height were found to fluctuate about a mean value. Visualization of the computed flow showed that the stretching mechanism of the large-scale structures, which governs the expansion-contraction behaviour of the plume, occurs in such a way that the coherent structure dominating the flow below the interface height takes a spiral shape

Exome-wide association study of pancreatic cancer risk

We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P=3.27x10(-6); exome-wide statistical significance threshold P<2.5x10(-6)). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35, P=.045). At the suggestive threshold (P<.001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distrib- uted national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia’s capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas—Tools, Data, Standards, Platforms, Compute and Training—are described in this article

Duality Invariant Actions and Generalised Geometry

We construct the non-linear realisation of the semi-direct product of E(11) and its first fundamental representation at lowest order and appropriate to spacetime dimensions four to seven. This leads to a non-linear realisation of the duality groups and introduces fields that depend on a generalised space which possess a generalised vielbein. We focus on the part of the generalised space on which the duality groups alone act and construct an invariant action.Comment: 59 pages (typos fixed and added comments

Semi-parametric risk prediction models for recurrent cardiovascular events in the LIPID study

Background: Traditional methods for analyzing clinical and epidemiological cohort study data have been focused on the first occurrence of a health outcome. However, in many situations, recurrent event data are frequently observed. It is inefficient to use methods for the analysis of first events to analyse recurrent event data

An open toolkit for tracking open science partnership implementation and impact.

Serious concerns about the way research is organized collectively are increasingly being raised. They include the escalating costs of research and lower research productivity, low public trust in researchers to report the truth, lack of diversity, poor community engagement, ethical concerns over research practices, and irreproducibility. Open science (OS) collaborations comprise of a set of practices including open access publication, open data sharing and the absence of restrictive intellectual property rights with which institutions, firms, governments and communities are experimenting in order to overcome these concerns. We gathered two groups of international representatives from a large variety of stakeholders to construct a toolkit to guide and facilitate data collection about OS and non-OS collaborations. Ultimately, the toolkit will be used to assess and study the impact of OS collaborations on research and innovation. The toolkit contains the following four elements: 1) an annual report form of quantitative data to be completed by OS partnership administrators; 2) a series of semi-structured interview guides of stakeholders; 3) a survey form of participants in OS collaborations; and 4) a set of other quantitative measures best collected by other organizations, such as research foundations and governmental or intergovernmental agencies. We opened our toolkit to community comment and input. We present the resulting toolkit for use by government and philanthropic grantors, institutions, researchers and community organizations with the aim of measuring the implementation and impact of OS partnership across these organizations. We invite these and other stakeholders to not only measure, but to share the resulting data so that social scientists and policy makers can analyse the data across projects

A horizon scan of issues affecting UK forest management within 50 years

Forests are in the spotlight: they are expected to play a pivotal role in our response to society’s greatest challenges, such as the climate and biodiversity crises. Yet, the forests themselves, and the sector that manages them, face a range of interrelated threats and opportunities. Many of these are well understood, even if the solutions remain elusive. However, there are also emerging trends that are currently less widely appreciated. We report here the results of a horizon scan to identify developing issues likely to affect UK forest management within the next 50 years. These are issues that are presently under-recognized but have potential for significant impact across the sector and beyond. As the forest management sector naturally operates over long timescales, the importance of using good foresight is self-evident. We followed a tried-and-tested horizon scanning methodology involving a diverse Expert Panel to collate and prioritize a longlist of 180 issues. The top 15 issues identified are presented in the Graphical Abstract. The issues represent a diverse range of themes, within a spectrum of influences from environmental shocks and perturbations to changing political and socio-economic drivers, with complex emerging interactions between them. The most highly ranked issue was ‘Catastrophic forest ecosystem collapse’, reflecting agreement that not only is such collapse a likely prospect but it would also have huge implications across the sector and wider society. These and many of the other issues are large scale, with far-reaching implications. We must be careful to avoid inaction through being overwhelmed, or indeed to merely focus on ‘easy wins’ without considering broader ramifications. Our responses to each of the challenges and opportunities highlighted must be synergistic and coherent, involving landscape-scale planning. A more adaptive approach to forest management will be essential, encouraging continual innovation and learning. The 15 horizon scan issues presented here are a starting point on which to build further research, prompt debate and action, and develop evidence-based policy and practice. We hope that this stimulates greater recognition of how our forests and sector may need to change to be fit for the future. In some cases, these changes will need to be fundamental and momentous

Modelling the risk of Taenia solium exposure from pork produced in western Kenya

The tapeworm Taenia solium is the parasite responsible for neurocysticercosis, a neglected tropical disease of public health importance, thought to cause approximately 1/3 of epilepsy cases across endemic regions. The consumption of undercooked infected pork perpetuates the parasite’s life-cycle through the establishment of adult tapeworm infections in the community. Reducing the risk associated with pork consumption in the developing world is therefore a public health priority. The aim of this study was to estimate the risk of any one pork meal in western Kenya containing a potentially infective T. solium cysticercus at the point of consumption, an aspect of the parasite transmission that has not been estimated before. To estimate this, we used a quantitative food chain risk assessment model built in the @RISK add-on to Microsoft Excel. This model indicates that any one pork meal consumed in western Kenya has a 0.006 (99% Uncertainty Interval (U.I). 0.0002–0.0164) probability of containing at least one viable T. solium cysticercus at the point of consumption and therefore being potentially infectious to humans. This equates to 22,282 (99% U.I. 622–64,134) potentially infective pork meals consumed in the course of one year within Busia District alone. This model indicates a high risk of T. solium infection associated with pork consumption in western Kenya and the work presented here can be built upon to investigate the efficacy of various mitigation strategies for this locality

Immunocompetent 3D Model of Human Upper Airway for Disease Modeling and In Vitro Drug Evaluation

The development of more complex in vitro models for the assessment of novel drugs and chemicals is needed because of the limited biological relevance of animal models to humans as well as ethical considerations. Although some human-cell-based assays exist, they are usually 2D, consist of single cell type, and have limited cellular and functional representation of the native tissue. In this study, we have used biomimetic porous electrospun scaffolds to develop an immunocompetent 3D model of the human respiratory tract comprised of three key cell types present in upper airway epithelium. The three cell types, namely, epithelial cells (providing a physical barrier), fibroblasts (extracellular matrix production), and dendritic cells (immune sensing), were initially grown on individual scaffolds and then assembled into the 3D multicell tissue model. The epithelial layer was cultured at the air–liquid interface for up to four weeks, leading to formation of a functional barrier as evidenced by an increase in transepithelial electrical resistance (TEER) and tight junction formation. The response of epithelial cells to allergen exposure was monitored by quantifying changes in TEER readings and by assessment of cellular tight junctions using immunostaining. It was found that epithelial cells cocultured with fibroblasts formed a functional epithelial barrier at a quicker rate than single cultures of epithelial cells and that the recovery from allergen exposure was also more rapid. Also, our data show that dendritic cells within this model remain viable and responsive to external stimulation as evidenced by their migration within the 3D construct in response to allergen challenge. This model provides an easy to assemble and physiologically relevant 3D model of human airway epithelium that can be used for studies aiming at better understanding lung biology, the cross-talk between immune cells, and airborne allergens and pathogens as well as drug delivery