Scalable computation of thermomechanical turbomachinery problems

A commonly held view in the turbomachinery community is that finite element methods are not well-suited for very large-scale thermomechanical simulations. We seek to dispel this notion by presenting performance data for a collection of realistic, large-scale thermomechanical simulations. We describe the necessary technology to compute problems with $O(10^7)$ to $O(10^9)$ degrees-of-freedom, and emphasise what is required to achieve near linear computational complexity with good parallel scaling. Performance data is presented for turbomachinery components with up to 3.3 billion degrees-of-freedom. The software libraries used to perform the simulations are freely available under open source licenses. The performance demonstrated in this work opens up the possibility of system-level thermomechanical modelling, and lays the foundation for further research into high-performance formulations for even larger problems and for other physical processes, such as contact, that are important in turbomachinery analysis.The support of Mitsubishi Heavy Industries is gratefully acknowledged. CNR is supported by EPSRC Grant EP/N018877/1

Uplift histories of Africa and Australia from linear inverse modeling of drainage inventories

We describe and apply a linear inverse model which calculates spatial and temporal patterns of uplift rate by minimizing the misfit between inventories of observed and predicted longitudinal river profiles. Our approach builds upon a more general, non-linear, optimization model, which suggests that shapes of river profiles are dominantly controlled by upstream advec- tion of kinematic waves of incision produced by spatial and temporal changes in regional uplift rate. Here, we use the method of characteristics to solve a version of this problem. A damped, non-negative, least squares approach is developed that permits river profiles to be inverted as a function of up- lift rate. An important benefit of a linearized treatment is low computational cost. We have tested our algorithm by inverting 957 river profiles from both Africa and Australia. For each continent, the drainage network was constructed from a digital elevation model. The fidelity of river profiles extracted from this network was carefully checked using satellite imagery. River profiles were inverted many times to systematically investigate the trade-off between model misfit and smoothness. Spatial and temporal patterns of both uplift rate and cumulative uplift were calibrated using independent geologic and geophys- ical observations. Uplift patterns suggest that the topography of Africa and Australia grew in Cenozoic times. Inverse modeling of large inventories of river profiles demonstrates that drainage networks contain coherent signals that record the regional growth of elevation.This is the final version. It first appeared at http://onlinelibrary.wiley.com/wol1/doi/10.1002/2014JF003297/abstract

Construction of Arbitrary Order Finite Element Degree-of-Freedom Maps on Polygonal and Polyhedral Cell Meshes

We develop a method for generating degree-of-freedom maps for arbitrary order finite element spaces for any cell shape. The approach is based on the composition of permutations and transformations by cell sub-entity. Current approaches to generating degree-of-freedom maps for arbitrary order problems typically rely on a consistent orientation of cell entities that permits the definition of a common local coordinate system on shared edges and faces. However, while orientation of a mesh is straightforward for simplex cells and is a local operation, it is not a strictly local operation for quadrilateral cells and in the case of hexahedral cells not all meshes are orientable. The permutation and transformation approach is developed for a range of element types, including Lagrange, and divergence- and curl-conforming elements, and for a range of cell shapes. The approach is local and can be applied to cells of any shape, including general polytopes and meshes with mixed cell types. A number of examples are presented and the developed approach has been implemented in an open-source finite element library

Hypothalamic arcuate nucleus glucokinase regulates insulin secretion and glucose homeostasis

Aims Glucokinase (GK) serves as a glucose sensor in several tissues including glucose‐sensitive neurons of the arcuate nucleus within the hypothalamus. We have previously demonstrated a role for arcuate GK in the regulation of food and glucose intake. However, its role in the regulation of glucose homeostasis is less clear. We therefore sought to investigate the role of arcuate GK in the regulation of glucose homeostasis. Materials and Methods Recombinant adeno‐associated virus expressing either GK or an antisense GK construct was used to alter GK activity specifically in the hypothalamic arcuate nucleus. GK activity in this nucleus was also increased by stereotactic injection of the GK activator, compound A. The effect of altered arcuate nucleus GK activity on glucose homeostasis was subsequently investigated using glucose and insulin tolerance tests. Results Increased GK activity specifically within the arcuate nucleus increased insulin secretion and improved glucose tolerance in rats during oral glucose tolerance tests. Decreased GK activity in this nucleus reduced insulin secretion and increased glucose levels during the same tests. Insulin sensitivity was not affected in either case. The effect of arcuate nucleus glucokinase was maintained in a model of type 2 diabetes. Conclusions These results demonstrate a role for arcuate nucleus GK in systemic glucose homeostasis

Protecting U.S. temporary waterways

International audienc

NuMA Overexpression in Epithelial Ovarian Cancer

Highly aneuploid tumours are common in epithelial ovarian cancers (EOC). We investigated whether NuMA expression was associated with this phenomenon

Consensus-based antimicrobial resistance and stewardship competencies for UK undergraduate medical students.

BACKGROUND: In the UK there is limited coverage of antimicrobial stewardship across postgraduate curricula and evidence that final year medical students have insufficient and inconsistent antimicrobial stewardship teaching. A national undergraduate curriculum for antimicrobial resistance and stewardship is required to standardize an adequate level of understanding for all future doctors. OBJECTIVES: To provide a UK national consensus on competencies for antimicrobial resistance and stewardship for undergraduate medical education. METHODS: Using the modified Delphi method over two online survey rounds, an expert panel comprising leads for infection teaching from 25 UK medical schools reviewed competency descriptors for antimicrobial resistance and stewardship education. RESULTS: There was a response rate of 100% with all 28 experts who agreed to take part completing both survey rounds. Following the first-round survey, of the initial 55 descriptors, 43 reached consensus (78%). The second-round survey included the 12 descriptors from the first round in which agreement had not been reached, four amended descriptors and 12 new descriptors following qualitative feedback from the panel members. Following the second-round survey, a total of 58 consensus-based competency descriptors within six overarching domains were identified. CONCLUSIONS: The consensus-based competency descriptors defined here can be used to inform standards, design curricula, develop assessment tools and direct UK undergraduate medical education

When Does an Alien Become a Native Species? A Vulnerable Native Mammal Recognizes and Responds to Its Long-Term Alien Predator

The impact of alien predators on native prey populations is often attributed to prey naiveté towards a novel threat. Yet evolutionary theory predicts that alien predators cannot remain eternally novel; prey species must either become extinct or learn and adapt to the new threat. As local enemies lose their naiveté and coexistence becomes possible, an introduced species must eventually become ‘native’. But when exactly does an alien become a native species? The dingo (Canis lupus dingo) was introduced to Australia about 4000 years ago, yet its native status remains disputed. To determine whether a vulnerable native mammal (Perameles nasuta) recognizes the close relative of the dingo, the domestic dog (Canis lupus familiaris), we surveyed local residents to determine levels of bandicoot visitation to yards with and without resident dogs. Bandicoots in this area regularly emerge from bushland to forage in residential yards at night, leaving behind tell-tale deep, conical diggings in lawns and garden beds. These diggings were less likely to appear at all, and appeared less frequently and in smaller quantities in yards with dogs than in yards with either resident cats (Felis catus) or no pets. Most dogs were kept indoors at night, meaning that bandicoots were not simply chased out of the yards or killed before they could leave diggings, but rather they recognized the threat posed by dogs and avoided those yards. Native Australian mammals have had thousands of years experience with wild dingoes, which are very closely related to domestic dogs. Our study suggests that these bandicoots may no longer be naïve towards dogs. We argue that the logical criterion for determining native status of a long-term alien species must be once its native enemies are no longer naïve

Integrating an internet-mediated walking program into family medicine clinical practice: a pilot feasibility study

<p>Abstract</p> <p>Background</p> <p>Regular participation in physical activity can prevent many chronic health conditions. Computerized self-management programs are effective clinical tools to support patient participation in physical activity. This pilot study sought to develop and evaluate an online interface for primary care providers to refer patients to an Internet-mediated walking program called Stepping Up to Health (SUH) and to monitor participant progress in the program.</p> <p>Methods</p> <p>In Phase I of the study, we recruited six pairs of physicians and medical assistants from two family practice clinics to assist with the design of a clinical interface. During Phase II, providers used the developed interface to refer patients to a six-week pilot intervention. Provider perspectives were assessed regarding the feasibility of integrating the program into routine care. Assessment tools included quantitative and qualitative data gathered from semi-structured interviews, surveys, and online usage logs.</p> <p>Results</p> <p>In Phase I, 13 providers used SUH and participated in two interviews. Providers emphasized the need for alerts flagging patients who were not doing well and the ability to review participant progress. Additionally, providers asked for summary views of data across all enrolled clinic patients as well as advertising materials for intervention recruitment. In response to this input, an interface was developed containing three pages: 1) a recruitment page, 2) a summary page, and 3) a detailed patient page. In Phase II, providers used the interface to refer 139 patients to SUH and 37 (27%) enrolled in the intervention. Providers rarely used the interface to monitor enrolled patients. Barriers to regular use of the intervention included lack of integration with the medical record system, competing priorities, patient disinterest, and physician unease with exercise referrals. Intention-to-treat analyses showed that patients increased walking by an average of 1493 steps/day from pre- to post-intervention (<it>t </it>= (36) = 4.13, <it>p </it>< 0.01).</p> <p>Conclusions</p> <p>Providers successfully referred patients using the SUH provider interface, but were less willing to monitor patient compliance in the program. Patients who completed the program significantly increased their step counts. Future research is needed to test the effectiveness of integrating SUH with clinical information systems over a longer evaluation period.</p

Accurate Strand-Specific Quantification of Viral RNA

The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR) assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR) step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV) that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (−) strand RNA with this assay when higher levels of cDNA generated from the (+) strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (−) strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR® Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV), the recent cause of large outbreaks of disease in the Indian Ocean region