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

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

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

Testing General Relativity with Current Cosmological Data

Deviations from general relativity, such as could be responsible for the cosmic acceleration, would influence the growth of large scale structure and the deflection of light by that structure. We clarify the relations between several different model independent approaches to deviations from general relativity appearing in the literature, devising a translation table. We examine current constraints on such deviations, using weak gravitational lensing data of the CFHTLS and COSMOS surveys, cosmic microwave background radiation data of WMAP5, and supernova distance data of Union2. Markov Chain Monte Carlo likelihood analysis of the parameters over various redshift ranges yields consistency with general relativity at the 95% confidence level.Comment: 11 pages; 7 figures; typographical errors corrected; this is the published versio

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description ofﾠEscovopsis kreiseliiﾠsp. nov.

Since the formal description of fungi in the genus Escovopsis in 1990, only a few studies have focused on the systematics of this group. For more than two decades, only two Escovopsis species were described; however, in 2013, three additional Escovopsis species were formally described along with the genus Escovopsioides, both found exclusively in attine ant gardens. During a survey for Escovopsis species in gardens of the lower attine ant Mycetophylax morschi in Brazil, we found four strains belonging to the pink-colored Escovopsis clade. Careful examination of these strains revealed significant morphological differences when compared to previously described species of Escovopsis and Escovopsioides. Based on the type of conidiogenesis (sympodial), as well as morphology of conidiogenous cells (percurrent), non-vesiculated conidiophores, and DNA sequences, we describe the four new strains as a new species, Escovopsis kreiselii sp. nov. Phylogenetic analyses using three nuclear markers (Large subunit RNA; translation elongation factor 1-alpha; and internal transcribed spacer) from the new strains as well as available sequences in public databases confirmed that all known fungi infecting attine ant gardens comprise a monophyletic group within the Hypocreaceae family, with very diverse morphological characteristics. Specifically, Escovopsis kreiselii is likely associated with gardens of lower-attine ants and its pathogenicity remains uncertain

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

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

Core competencies for pain management: results of an interprofessional consensus summit.

ObjectiveThe objective of this project was to develop core competencies in pain assessment and management for prelicensure health professional education. Such core pain competencies common to all prelicensure health professionals have not been previously reported.MethodsAn interprofessional executive committee led a consensus-building process to develop the core competencies. An in-depth literature review was conducted followed by engagement of an interprofessional Competency Advisory Committee to critique competencies through an iterative process. A 2-day summit was held so that consensus could be reached.ResultsThe consensus-derived competencies were categorized within four domains: multidimensional nature of pain, pain assessment and measurement, management of pain, and context of pain management. These domains address the fundamental concepts and complexity of pain; how pain is observed and assessed; collaborative approaches to treatment options; and application of competencies across the life span in the context of various settings, populations, and care team models. A set of values and guiding principles are embedded within each domain.ConclusionsThese competencies can serve as a foundation for developing, defining, and revising curricula and as a resource for the creation of learning activities across health professions designed to advance care that effectively responds to pain

Emergency Department Clinicians’ Attitudes Toward Opioid Use Disorder and Emergency Department-initiated Buprenorphine Treatment: A Mixed-Methods Study

Introduction: Emergency department (ED) visits related to opioid use disorder (OUD) have increased nearly twofold over the last decade. Treatment with buprenorphine has been demonstrated to decrease opioid-related overdose deaths. In this study, we aimed to better understand ED clinicians’ attitudes toward the initiation of buprenorphine treatment in the ED.Methods: We performed a mixed-methods study consisting of a survey of 174 ED clinicians (attending physicians, residents, and physician assistants) and semi-structured interviews with 17 attending emergency physicians at a tertiary-care academic hospital.Results: A total of 93 ED clinicians (53% of those contacted) completed the survey. While 80% of respondents agreed that buprenorphine should be administered in the ED for patients requesting treatment, only 44% felt that they were prepared to discuss medication for addiction treatment. Compared to clinicians with fewer than five years of practice, those with greater experience were less likely to approve of ED-initiated buprenorphine. In our qualitative analysis, physicians had differing perspectives on the role that the ED should play in treating OUD. Most physicians felt that a buprenorphine-based intervention in the ED would be feasible with institutional support, including training opportunities, protocol support within the electronic health record, counseling and support staff, and a robust referral system for outpatient follow-up.Conclusion: ED clinicians’ perception of buprenorphine varied by years of practice and training level. Most ED clinicians did not feel prepared to initiate buprenorphine in the ED. Qualitative interviews identified several addressable barriers to ED-initiated buprenorphine