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

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

Clinical effect of mirikizumab treatment on bowel urgency in patients with moderately to severely active ulcerative colitis and the clinical relevance of bowel urgency improvement for disease remission

Background: Bowel urgency reduces ulcerative colitis patients' quality of life. Mirikizumab, a p19-directed anti-IL-23 antibody, demonstrates ulcerative colitis efficacy. Mirikizumab efficacy to reduce bowel urgency and bowel urgency association with other endpoints were analyzed in 2 Phase 3 trials. Methods: LUCENT-1 (Induction): 1162 patients randomized 3:1 to intravenous 300 mg mirikizumab or placebo every 4 weeks for 12 weeks. LUCENT-2 (Maintenance): 544 mirikizumab responders during induction were re-randomized 2:1 to subcutaneous mirikizumab 200 mg or placebo every 4 weeks for 40 weeks (52 weeks of continuous treatment). Bowel urgency was measured using the Urgency Numeric Rating Scale (0–10); for patients with LUCENT-1 baseline score ≥3, bowel urgency clinically meaningful improvement (≥3-point decrease) and remission (score ≤1) rates in mirikizumab versus placebo groups were compared at Weeks 12 and 52. Associations between bowel urgency and other efficacy endpoints were assessed at Weeks 12 and 52. Results: A significantly higher proportion of mirikizumab patients versus placebo achieved clinically meaningful improvement in bowel urgency and remission at Weeks 12 and 52. Significantly higher percentages of patients achieving bowel urgency clinically meaningful improvement or remission, compared with those who did not, also achieved endpoints for clinical, corticosteroid-free, endoscopic, and symptomatic remission; clinical response; normalized fecal calprotectin and C-reactive protein; and improved quality of life. Conclusions: In patients with ulcerative colitis, bowel urgency improvement was associated with better clinical outcomes than in patients without improvement during induction and maintenance. A greater proportion of mirikizumab patients achieved sustainable bowel urgency improvement and remission compared to placebo patients

DOP17 Identification of biomarkers and mechanistic insight for upadacitinib in ulcerative colitis: Analysis of serum inflammatory mediators in the phase 2b U-ACHIEVE study

Abstract Background The U-ACHIEVE trial evaluated upadacitinib (UPA), an oral JAK1 selective inhibitor, in patients with moderately to severely active ulcerative colitis (UC). Patient-reported and endoscopic outcomes improved after UPA treatment. This analysis used pharmacodynamic profiling to link changes in serum biomarkers to changes in UC disease activity, and to assess the UPA mechanism of action in UC. Methods U-ACHIEVE (NCT02819635) was a randomised, double-blind, placebo (PBO)-controlled phase 2b clinical trial. Adults with an inadequate response, loss of response, or intolerance to corticosteroids, immunosuppressants, or biologic therapies were randomised to receive 7.5, 15, 30, or 45 mg UPA once daily or PBO for 8 weeks (weeks). Serum samples (baseline [BL], weeks 2, 4, and 8) were analysed by OLINK® inflammation panel (92 proteins) and by Singulex immunoassay for interleukin-1b (IL-1b), IL-17A, IL-17F, and IL-22. Protein-level changes were analysed by a mixed-effect model; BL protein level was adjusted as a covariate; treatment group, time point, and their interaction were included as fixed effects. Spearman rank-correlation coefficients were used to determine the relationship between changes of serum biomarker levels and improvements in adapted Mayo scores and endoscopic subscores. Multiplicity adjusted P values were calculated using 1000 runs of random permutations. Results Paired BL and week 8 serum samples were available from 114 patients (PBO, n = 17; UPA 7.5 mg, n = 21; UPA 15 mg, n = 21; UPA 30 mg, n = 29; UPA 45 mg, n = 26). UPA treatment reduced expression of pro-inflammatory mediators associated with immune cell migration, type I/II IFN responses, T-cell responses, macrophage and dendritic cell activity and increased expression of biomarkers associated with haematopoiesis, neuroprotection and mucosal repair in a dose-dependent manner. Improvements in adapted Mayo score, endoscopic subscore, and stool frequency correlated with increases in CX3CL1, DNER and FLt3L (p < 0.05 for all). Endoscopic improvements correlated with reductions in OSM, and improvements in fatigue correlated with increases in CCL25 and NT-3. There was a substantial overlap in biomarkers modulated by UPA in patients with UC and Crohn's disease (Figure). Conclusion UPA modulated expression of serum pro-inflammatory mediators found in pathways associated with the pathogenesis of UC, including immune cell migration, type I/II IFN responses, T-cell responses, macrophage and dendritic cell activity, haematopoiesis, neuroprotection, and mucosal repair. Consistent correlations were observed between changes in biomarker expression and improvements in disease activity and symptoms of UC

Forum: Critical Decision Dates for Drought Management in Centraland Northern Great Plains Rangeland

Ranchers and other land managers of central and northern Great Plains rangelands face recurrent droughts that negatively influence economic returns and environmental resources for ranching enterprises. Accurately estimating annual forage production and initiating drought decision-making actions proactively early in the growing season are both critical to minimize financial losses and degradation to rangeland soil and plant resources. Long-term forage production data sets from Alberta, Kansas, Montana, Nebraska, North Dakota, South Dakota, and Wyoming demonstrated that precipitation in April, May, and June (or some combination of these months) robustly predict annual forage production. Growth curves from clipping experiments and ecological site descriptions (ESDs) indicate that maximum monthly forage growth rates occur 1 mo after the best spring month (April to June) precipitation prediction variable. Key for rangeland managers is that the probability of receiving sufficient precipitation after 1 July to compensate for earlier spring precipitation deficits is extremely low. The complexity of human dimensions of drought decision-making necessitates that forage prediction tools account for uncertainty in matching animal demand to forage availability, and that continued advancements in remote sensing applications address both spatial and temporal relationships in forage production to inform critical decision dates for drought management in these rangeland ecosystems

Left gaze bias in humans, rhesus monkeys and domestic dogs

While viewing faces, human adults often demonstrate a natural gaze bias towards the left visual field, that is, the right side of the viewee’s face is often inspected first and for longer periods. Using a preferential looking paradigm, we demonstrate that this bias is neither uniquely human nor limited to primates, and provide evidence to help elucidate its biological function within a broader social cognitive framework. We observed that 6-month-old infants showed a wider tendency for left gaze preference towards objects and faces of different species and orientation, while in adults the bias appears only towards upright human faces. Rhesus monkeys showed a left gaze bias towards upright human and monkey faces, but not towards inverted faces. Domestic dogs, however, only demonstrated a left gaze bias towards human faces, but not towards monkey or dog faces, nor to inanimate object images. Our findings suggest that face- and species-sensitive gaze asymmetry is more widespread in the animal kingdom than previously recognised, is not constrained by attentional or scanning bias, and could be shaped by experience to develop adaptive behavioural significance

Identification of the Transgenic Integration Site in Immunodeficient tgε26 Human CD3ε Transgenic Mice

A strain of human CD3ε transgenic mice, tgε26, exhibits severe immunodeficiency associated with early arrest of T cell development. Complete loss of T cells is observed in homozygous tgε26 mice, but not in heterozygotes, suggesting that genomic disruption due to transgenic integration may contribute to the arrest of T cell development. Here we report the identification of the transgenic integration site in tgε26 mice. We found that multiple copies of the human CD3ε transgene are inserted between the Sstr5 and Metrn loci on chromosome 17, and that this is accompanied by duplication of the neighboring genomic region spanning 323 kb. However, none of the genes in this region were abrogated. These results suggest that the severe immunodeficiency seen in tgε26 mice is not due to gene disruption resulting from transgenic integration