Heterogeneous Computing on Mixed Unstructured Grids with PyFR

PyFR is an open-source high-order accurate computational fluid dynamics solver for mixed unstructured grids that can target a range of hardware platforms from a single codebase. In this paper we demonstrate the ability of PyFR to perform high-order accurate unsteady simulations of flow on mixed unstructured grids using heterogeneous multi-node hardware. Specifically, after benchmarking single-node performance for various platforms, PyFR v0.2.2 is used to undertake simulations of unsteady flow over a circular cylinder at Reynolds number 3 900 using a mixed unstructured grid of prismatic and tetrahedral elements on a desktop workstation containing an Intel Xeon E5-2697 v2 CPU, an NVIDIA Tesla K40c GPU, and an AMD FirePro W9100 GPU. Both the performance and accuracy of PyFR are assessed. PyFR v0.2.2 is freely available under a 3-Clause New Style BSD license (see www.pyfr.org).Comment: 21 pages, 9 figures, 6 table

Crystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue

peer reviewedThe structures of the, class C beta-lactamase from Enterobacter cloacae 908R alone and in complex with a baronic acid transition-state analogue were determined by X-ray crystallography at 2.1 and 2.3 Angstrom, respectively. The structure of the enzyme resembles those of other class C beta-lactamases. The structure of the. complex with the transition-state analogue, iodo-acetamido-phenyl boronic acid, shows that the inhibitor is covalently, bound to the active-site serine (Ser64). Binding of the inhibitor within the active site is compared with previously determined structures of complexes with other class C enzymes. The structure of the boronic acid adduct indicates ways to improve the affinity of this class of inhibitors. This structure of 908R class C beta-lactamase in complex with a transitionstate analogue provides further insights into the mechanism of action of these hydrolases

Temporal Stabilisation of Flux Reconstruction on Linear Problems

Filtering is often used in Large Eddy Simulation with a global filter width, instead here a filter width in the reference domain of high order Flux Reconstruction is considered. It is shown via Von Neumann analysis how filtering effects the dispersion and dissipation of the scheme when spatially and temporally discretised. With it being shown that filtering stabilises the scheme temporally by upto $25\%$ for forth order FR. The impact of filtering on error production is calculated, highlighting the reduction in convective velocity caused and showing numerically the impact on order of accuracy. Finally, the turbulent Taylor-Green case is used to understand the effect of reference domain filtering on the transition to turbulence, and a filter Reynolds number is defined that is shown to be useful in understanding the effect of filtering on simulations.Comment: AIAA Aviation Forum June 201

Analysis of different preferences for the EU's regulatory options forendocrine disruptor identification criteria using argumentation theory

What criteria are most suitable to identify endocrine disrupting substances (EDSs) for regulatory purposes in the EU? The results of the European Commission's public consultation, as part of the process to establish identification criteria for EDSs, show that different regulatory options are supported. Some respondents prefer an option including hazard characterization considerations, whereas others prefer an option that avoids these considerations and introduces several hazard-identification based weight-of-evidence categories. In this study, the argumentation underlying the different preferences for identification criteria are analyzed and compared using pragma-dialectical argumentation theory (PDAT). All responses of non-anonymous, national governments that submitted a response in English (n = 17) were included. Responses of other stakeholder organizations were included if a Google News search returned an opinionated presence in the media on the subject (n = 9). Five topical themes and 21 underlying issues were identified. The themes are 1) mechanistic understanding of EDSs, 2) regulatory considerations related to the identification of EDSs, 3) consistency with existing regulatory frameworks, and 4) evaluations of specific issues related to a category approach and 5) related to including potency. We argue that two overarching (implicit) ‘advocacy coalitions’ can be discerned, that adopted contrasting positions towards the identified themes and issues. Among these ‘coalitions’, there appears to be consensus about the necessity of having ‘science-based’ criteria, though different perspectives exist as to what the most accurate mechanistic understanding of EDSs entails. To move the discussion forward, we argue that a societal dialogue would be beneficial, where EDS science and regulation are discussed as interrelated themes

Increased prevalence of sleep disturbances and daytime sleepiness in subjects with bronchial asthma: a population study of young adults in three European countries

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldThe aim of this study was to investigate whether asthma is associated with decreased quality of sleep and increased daytime sleepiness. The study involved a random population of 2,202 subjects supplemented by 459 subjects with suspected asthma, aged 20-45 yrs. The subjects were from Reykjavik (Iceland), Uppsala and Göteborg (Sweden) and Antwerp (Belgium), and participated in the European Community Respiratory Health Survey. The investigation included a structured interview, methacholine challenge, skinprick tests and a questionnaire on sleep disturbances. Participants in Iceland and Sweden also estimated their sleep times and made peak expiratory flow (PEF) recordings during a period of 1 week. Asthma was defined as self-reported physician-diagnosed asthma with current asthma-related symptoms (n = 267). Difficulties inducing sleep (DIS) and early morning awakenings (EMA) were about twice as common, and daytime sleepiness 50% more common, in asthmatics compared with subjects without asthma. After adjusting for possible confounders, a positive association was found between asthma and: DIS (odds ratio (OR) = 1.8); EMA (OR = 2.0); daytime sleepiness (OR = 1.6); snoring (OR = 1.7); and self reported apnoeas (OR = 3.7). Allergic rhinitis, which was reported by 71% of subjects with asthma, was independently related to DIS (OR = 2.0) and daytime sleepiness (OR = 1.3). A significant correlation was found between the number of asthma-related symptoms and sleep disturbances (p < 0.001). Asthma is associated with decreased subjective quality of sleep and increased daytime sleepiness. Concurrent allergic rhinitis may be an important underlying cause of sleep impairment in asthmatic patients

Relationship between emergency presentation, systemic inflammatory response, and cancer-specific survival in patients undergoing potentially curative surgery for colon cancer

Background Emergency presentation is recognized to be associated with poorer cancer-specific survival following curative resection for colorectal cancer. The present study examined the hypothesis that an enhanced systemic inflammatory response, prior to surgery, might explain the impact of emergency presentation on survival. Methods In all, 188 patients undergoing potentially curative resection for colorectal cancer were studied. Of these, 55 (29&#37;) presented as emergencies. The systemic inflammatory response was assessed using the Glasgow Prognostic Score (mGPS), which is the combination of an elevated C-reactive protein (&gt;10 mg/L) and hypoalbuminemia (&lt;35 g/L). Results In the emergency group, tumor stage was greater (P &lt; 0.01), more patients received adjuvant therapy (P &lt; 0.01) more patients had an elevated mGPS (P &lt; 0.01), and more patients died of their disease (P &lt; 0.05). The minimum follow-up was 12 months; the median follow-up of the survivors was 48 months. Emergency presentation was associated with poorer 3-year cancer-specific survival in those patients aged 65 to 74 years (P &lt; 0.01), in both males and females (P &lt; 0.05), in the deprived (P &lt; 0.01), in patients with tumor-node-metastasis (TNM) stage II disease (P &lt; 0.01), in those who received no adjuvant therapy (P &lt; 0.01), and in the mGPS 0 and 1 groups (P &lt; 0.05) groups. On multivariate survival analysis of patients undergoing potentially curative surgery for TNM stage II colon cancer, emergency presentation (P &lt; 0.05) and mGPS (P &lt; 0.05) were independently associated with cancer-specific survival. Conclusions These results suggest that emergency presentation and the presence of systemic inflammatory response prior to surgery are linked and account for poorer cancer-specific survival in patients undergoing potentially curative surgery for colon cancer. Both emergency presentation and an elevated mGPS should be taken into account when assessing the likely outcome of these patients

A class of Poisson-Nijenhuis structures on a tangent bundle

Equipping the tangent bundle TQ of a manifold with a symplectic form coming from a regular Lagrangian L, we explore how to obtain a Poisson-Nijenhuis structure from a given type (1,1) tensor field J on Q. It is argued that the complete lift of J is not the natural candidate for a Nijenhuis tensor on TQ, but plays a crucial role in the construction of a different tensor R, which appears to be the pullback under the Legendre transform of the lift of J to co-tangent manifold of Q. We show how this tangent bundle view brings new insights and is capable also of producing all important results which are known from previous studies on the cotangent bundle, in the case that Q is equipped with a Riemannian metric. The present approach further paves the way for future generalizations.Comment: 22 page

Fungal and Bacterial Loads: Noninvasive Inflammatory Bowel Disease Biomarkers for the Clinical Setting

Malaltia inflamatòria intestinal; Càrrega microbiana; PrediccióEnfermedad inflamatoria intestinal; Carga microbiana; PredicciónInflammatory bowel disease; Microbial load; PredictionMicrobiome sequence data have been used to characterize Crohn's disease (CD) and ulcerative colitis (UC). Based on these data, we have previously identified microbiomarkers at the genus level to predict CD and CD relapse. However, microbial load was underexplored as a potential biomarker in inflammatory bowel disease (IBD). Here, we sought to study the use of fungal and bacterial loads as biomarkers to detect both CD and UC and CD and UC relapse. We analyzed the fecal fungal and bacterial loads of 294 stool samples obtained from 206 participants using real-time PCR amplification of the ITS2 region and the 16S rRNA gene, respectively. We combined the microbial data with demographic and standard laboratory data to diagnose ileal or ileocolonic CD and UC and predict disease relapse using the random forest algorithm. Fungal and bacterial loads were significantly different between healthy relatives of IBD patients and nonrelated healthy controls, between CD and UC patients in endoscopic remission, and between UC patients in relapse and non-UC individuals. Microbial load data combined with demographic and standard laboratory data improved the performance of the random forest models by 18%, reaching an average area under the receiver operating characteristic curve (AUC) of 0.842 (95% confidence interval [CI], 0.65 to 0.98), for IBD diagnosis and enhanced CD and UC discrimination and CD and UC relapse prediction. Our findings show that fecal fungal and bacterial loads could provide physicians with a noninvasive tool to discriminate disease subtypes or to predict disease flare in the clinical setting. IMPORTANCE Next-generation sequence data analysis has allowed a better understanding of the pathophysiology of IBD, relating microbiome composition and functions to the disease. Microbiome composition profiling may provide efficient diagnosis and prognosis tools in IBD. However, the bacterial and fungal loads of the fecal microbiota are underexplored as potential biomarkers of IBD. Ulcerative colitis (UC) patients have higher fecal fungal and bacterial loads than patients with ileal or ileocolonic CD. CD patients who relapsed harbor more-unstable fungal and bacterial loads than those of relapsed UC patients. Fecal fungal and bacterial load data improved prediction performance by 18% for IBD diagnosis based solely on clinical data and enhanced CD and UC discrimination and prediction of CD and UC relapse. Combined with existing laboratory biomarkers such as fecal calprotectin and C-reactive protein (CRP), microbial loads may improve the diagnostic accuracy of IBD and of ileal CD and UC disease activity and prediction of UC and ileal CD clinical relapse.This work was funded by Instituto de Salud Carlos III, grant PI17/00614, cofinanced by the European Regional Development Fund (ERDF) and by the PERIS (SLT002/16). F. Casellas has received research funding from AbbVie, Ferring, MSD, Shire, and Zambon and speaker fees from AbbVie, Chiesi, Ferring, Gebro, MSD, Shire, Takeda, and Zambon. S. Vermeire has received grant support from AbbVie, MSD, Pfizer, J&J, and Takeda; received speaker fees from AbbVie, MSD, Takeda, Ferring, Dr. Falk Pharma, Hospira, Pfizer Inc., and Tillots; and served as a consultant for AbbVie, MSD, Takeda, Ferring, Genentech/Roche, Robarts clinical trials, Gilead, Celgene, Prometheus, Avaxia, Prodigest, Shire, Pfizer Inc, Galapagos, Mundipharma, Hospira, Celgene, Second Genome, and Janssen. C. Manichanh has received financial support for research from Danone