Using a multifrontal sparse solver in a high performance, finite element code

We consider the performance of the finite element method on a vector supercomputer. The computationally intensive parts of the finite element method are typically the individual element forms and the solution of the global stiffness matrix both of which are vectorized in high performance codes. To further increase throughput, new algorithms are needed. We compare a multifrontal sparse solver to a traditional skyline solver in a finite element code on a vector supercomputer. The multifrontal solver uses the Multiple-Minimum Degree reordering heuristic to reduce the number of operations required to factor a sparse matrix and full matrix computational kernels (e.g., BLAS3) to enhance vector performance. The net result in an order-of-magnitude reduction in run time for a finite element application on one processor of a Cray X-MP

Solar Panel Installation on ECU Warehouse Campus

2013 Online Presentations RCA

Rural general practice training: experience of a rural general practice team and a postgraduate year two registrar

INTRODUCTION: Undertaking training in rural areas is a recognised way of helping recruit staff to work in rural communities. Postgraduate year two medical doctors in New Zealand have been able to undertake a three-month placement in rural practice as part of their pre-vocational training experience since November 2010. AIM: To describe the experience of a rural general practice team providing training to a postgraduate year two medical trainee, and to describe the teaching experience and range of conditions seen by the trainee. METHODS: A pre- and post-placement interview with staff, and analysis of a logbook of cases and teaching undertaken in the practice. RESULTS: The practice team's experience of having the trainee was positive, and the trainee was exposed to a wide range of conditions over 418 clinical encounters. The trainee received 22.5 hours of formal training over the three-month placement. DISCUSSION: Rural general practice can provide a wide range of clinical experience to a postgraduate year two medical trainee. Rural practices in New Zealand should be encouraged to offer teaching placements at this training level. Exposure to rural practice at every level of training is important to encourage doctors to consider rural practice as a career

Variation on a theme: the structures and biosynthesis of specialized fatty acid natural products in plants

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly elaborate and unique structural features that have novel bioproduct functionalities. Furthermore, although recent work has shed light on multiple new fatty acid natural product biosynthesis pathways and products in diverse plant species, these discoveries have not been reviewed. The aims of this work, therefore, are to (i) review and systematize our current knowledge of the structures and biosynthesis of fatty acid-derived natural products that are not seed oils or jasmonate-type oxylipins, specifically, polyacetylenic, very-long-chain, and aromatic fatty acid-derived natural products, and (ii) suggest priorities for future investigative steps that will bring our knowledge of fatty acid-derived natural products closer to the levels of knowledge that we have attained for other phytochemical classes

Basement-cover relations and internal structure of the Cape Smith klippe: A 1.9 Ga greenstone belt in northern Quebec, Canada

The Cape Smith Belt is a 380x60 km tectonic klippe composed of greenschistto amphibolite-grade mafic and komatiitic lava flows and fine-grained quartzose sediment, intruded by minor syn- to post-tectonic granitoids. Previously studied transects in areas of relatively high structural level show that the belt is constructed of seven or more north-dipping thrust sheets which verge toward the Superior Province (Archean) foreland in the south and away from an Archean basement massif (Kovik Antiform) external to the Trans-Hudson Orogen (Early Proterozoic) in the north. A field project (mapping and structural-stratigraphic-metamorphic studies) directed by MRS was begun in 1985 aimed at the structurally deeper levels of the belt and underlying basement, which are superby exposed in oblique cross-section (12 km minimum structural relief) at the west-plunging eastern end of the belt. Mapping now complete of the eastern end of the belt confirms that all of the metavolcanic and most of the metasedimentary rocks are allochthonous with respect to the Archean basement, and that the thrusts must have been rooted north of Kovik Antiform. The main findings follow

Interaction Tree Specifications: A Framework for Specifying Recursive, Effectful Computations That Supports Auto-Active Verification (Artifact)

This paper presents a specification framework for monadic, recursive, interactive programs that supports auto-active verification, an approach that combines user-provided guidance with automatic verification techniques. This verification tool is designed to have the flexibility of a manual approach to verification along with the usability benefits of automatic approaches. We accomplish this by augmenting Interaction Trees, a Coq datastructure for representing effectful computations, with logical quantifier events. We show that this yields a language of specifications that are easy to understand, automatable, and are powerful enough to handle properties that involve non-termination. Our framework is implemented as a library in Coq. We demonstrate the effectiveness of this framework by verifying real, low-level code

Interaction Tree Specifications: A Framework for Specifying Recursive, Effectful Computations That Supports Auto-Active Verification

This paper presents a specification framework for monadic, recursive, interactive programs that supports auto-active verification, an approach that combines user-provided guidance with automatic verification techniques. This verification tool is designed to have the flexibility of a manual approach to verification along with the usability benefits of automatic approaches. We accomplish this by augmenting Interaction Trees, a Coq datastructure for representing effectful computations, with logical quantifier events. We show that this yields a language of specifications that are easy to understand, automatable, and are powerful enough to handle properties that involve non-termination. Our framework is implemented as a library in Coq. We demonstrate the effectiveness of this framework by verifying real, low-level code

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase.

In meiotic prophase, chromosomes are organized into compacted loop arrays to promote homolog pairing and recombination. Here, we probe the architecture of the mouse spermatocyte genome in early and late meiotic prophase using chromosome conformation capture (Hi-C). Our data support the established loop array model of meiotic chromosomes, and infer loops averaging 0.8-1.0 megabase pairs (Mb) in early prophase and extending to 1.5-2.0 Mb in late prophase as chromosomes compact and homologs undergo synapsis. Topologically associating domains (TADs) are lost in meiotic prophase, suggesting that assembly of the meiotic chromosome axis alters the activity of chromosome-associated cohesin complexes. While TADs are lost, physically separated A and B compartments are maintained in meiotic prophase. Moreover, meiotic DNA breaks and interhomolog crossovers preferentially form in the gene-dense A compartment, revealing a role for chromatin organization in meiotic recombination. Finally, direct detection of interhomolog contacts genome-wide reveals the structural basis for homolog alignment and juxtaposition by the synaptonemal complex

Demographic characteristics and opportunistic diseases associated with attrition during preparation for antiretroviral therapy in primary health centres in Kibera, Kenya.

Using routine data from HIV-positive adult patients eligible for antiretroviral therapy (ART), we report on routinely collected demographic characteristics and opportunistic diseases associated with pre-ART attrition (deaths and loss to follow-up). Among 2471 ART eligible patients, enrolled between January 2005 and November 2008, 446 (18%) were lost to attrition pre-ART. Adjusted risk factors significantly associated with pre-ART attrition included age <35 years (Odds Ratio, OR 1.4, 95% Confidence Interval, CI 1.1-1.8), severe malnutrition (OR 1.5, 95% CI 1.1-2.0), active pulmonary tuberculosis (OR 1.6, 95% CI 1.1-2.4), severe bacterial infections including severe bacterial pneumonia (OR 1.9, 95% CI 1.2-2.8) and prolonged unexplained fever (>1 month), (OR 2.6, 95% CI 1.3-5.2). This study highlights a number of clinical markers associated with pre-ART attrition that could serve as 'pointers' or screening tools to identify patients who merit fast-tracking onto ART and/or closer clinical attention and follow-up