Experiences in porting mini-applications to OpenACC and OpenMP on heterogeneous systems

This article studies mini-applications—Minisweep, GenASiS, GPP, and FF—that use computational methods commonly encountered in HPC. We have ported these applications to develop OpenACC and OpenMP versions, and evaluated their performance on Titan (Cray XK7 with K20x GPUs), Cori (Cray XC40 with Intel KNL), Summit (IBM AC922 with Volta GPUs), and Cori-GPU (Cray CS-Storm 500NX with Intel Skylake and Volta GPUs). Our goals are for these new ports to be useful to both application and compiler developers, to document and describe the lessons learned and the methodology to create optimized OpenMP and OpenACC versions, and to provide a description of possible migration paths between the two specifications. Cases where specific directives or code patterns result in improved performance for a given architecture are highlighted. We also include discussions of the functionality and maturity of the latest compilers available on the above platforms with respect to OpenACC or OpenMP implementations

Contrasting the effects of intra-uterine smoking and one-carbon micronutrient exposures on offspring DNA methylation

Maternal smoking and micronutrient intake during pregnancy are two strong biological candidates for impacting the developing epigenome. The extent to which DNA methylation in offspring is modified by these intrauterine exposures has not been presented in parallel. In this review, we summarize human studies which have investigated genome-wide DNA methylation in the offspring in relation to maternal smoking and one-carbon micronutrient exposure during pregnancy. We contrast the primarily independent efforts for these two categories of exposure, and potential explanations for these differences. We emphasize methodological considerations such as power to detect methylation signals, exposure assessment, control of sources of variability, causal inference and the role of observed methylation changes in mediating downstream outcomes in the offspring

A one-hour universal protocol for mouse genotyping

Introduction Transgenic animals are widely used for research and for most of them, genotyping is unavoidable. Published protocols may be powerful but may also present disadvantages such as their cost or the requirement of additional steps/equipment. Moreover, if more than one strain must be genotyped, several protocols may need to be developed. Methods we adapted the existing amplification‐resistant mutation protocol to develop the 1‐hour universal genotyping protocol (1‐HUG), which allows the robust genotyping of genetically modified mice in 1 h from sample isolation to PCR gel running. Results This protocol allows the genotyping of different mouse models including mdx mouse, and FLExDUX4 and HSA‐MerCreMer alone or in combination. It can be applied to different types of genomic modifications and to sexing. Discussion The 1‐HUG protocol can be used routinely in any laboratory using mouse models for neuromuscular diseases

Inhalation therapy during acute asthma : the role of a combined steroid and beta-stimulant preparation

CITATION: Joubert, J. R., Burger, G. & Shephard, E. 1985. Inhalation therapy during acute asthma : the role of a combined steroid and beta-stimulant preparation. South African Medical Journal, 68:381-384.The original publication is available at http://www.samj.org.zaA compound consisting of a β-stimulant, salbutamol (100 μg/puff), and a steroid, beclomethasone diproprionate (50 μg/puff), was studied to test the hypothesis that the corticosteroid could enhance the bronchodilator proporties of the β-stimulant during chronic asthma and simulated acute attacks (antigen challenge). Conventional doses (200 μg and 100 μg of salbutamol and beclomethasone respectively) were compared using a schedule which included a second administration 1 hour later. The results obtained on the baseline bronchial responsiveness of chronic asthmatics and during the delayed asthmatic response (simulated acute asthma) were similar. The compound was as effective as salbutamol alone but not more so. A significantly greater bronchodilator response was recorded in all patients after the second administration of both the compound and salbutamol alone. The practical advantages of having one rather than two inhalers are evident, but the appropriate application of this compound agent, probably in a prophylactic role, must be defined.Publisher’s versio

Simulation as an educational strategy to deliver interprofessional education

Background. Various educational methods are available to deliver interprofessional education (IPE) to prepare healthcare students for collaborative practice. One such method is simulation-based health education.Objectives. To identify current IPE methods used in undergraduate programmes in the Faculty of Health Sciences at the University of the Free State, Bloemfontein, South Africa, and to determine the opinions of module leaders on using simulation as a particular IPE teaching strategy.Methods. A quantitative, cross-sectional descriptive study design was employed. Structured interviews were conducted with 47 module leaders of the undergraduate programmes in the Faculty of Health Sciences. These programmes cover 66 modules in the Schools for Allied Health Professions (nutrition and dietetics, occupational therapy, physiotherapy and optometry), nursing and medicine.Results. At the time of the study, IPE activities were used in 29 (43.9%) of the modules, of which 17 (58.6%) were coincidental.  Respondents’ opinions on the potential use of simulation to address formalised IPE activities included the challenge of ‘scheduling’ (73.9%) and ‘logistical and high cost issues’ (19.6%). The most prominent advantage that was foreseen (41.3%) was better clarification of roles among the different professions.Conclusions. The module leaders had a positive attitude towards simulation and its potential use for IPE, with their major concern being logistical challenges. To improve role clarification, a scenario should be developed to engage students from all the relevant professions. The proposed type of simulation was to use standardised patients in a role-play scenario. The outcomes of these activities should be aligned with the principles of IPE

On-the-fly memory compression for multibody algorithms.

Memory and bandwidth demands challenge developers of particle-based codes that have to scale on new architectures, as the growth of concurrency outperforms improvements in memory access facilities, as the memory per core tends to stagnate, and as communication networks cannot increase bandwidth arbitrary. We propose to analyse each particle of such a code to find out whether a hierarchical data representation storing data with reduced precision caps the memory demands without exceeding given error bounds. For admissible candidates, we perform this compression and thus reduce the pressure on the memory subsystem, lower the total memory footprint and reduce the data to be exchanged via MPI. Notably, our analysis and transformation changes the data compression dynamically, i.e. the choice of data format follows the solution characteristics, and it does not require us to alter the core simulation code

Relational experiences of community members participating in a rural health initiative with interprofessional students

Background. A South African faculty of health sciences created a forum for the community to voice their relational experiences with interprofessional students through visual projections. No other studies that explore such experiences using the Mmogo method could be located. Objective. To gain an understanding of the relational experiences of community members participating in Lifestyle-groups as part of a rural health initiative with interprofessional student groups. Methods. The Mmogo method is a qualitative, structured, observation technique. Participants constructed visual projections representing specific relationships. Thereafter, during a group discussion, participants explained the meaning of their projections. The visual data were analysed according to their literal presentation and subjective, symbolic meaning. A thematic analysis was used for the transcribed data. Results. Thirteen of the 24 visual projections were of a quality that allowed visual analysis; all 24 members participated in the discussions. Light was identified as an overarching theme to represent the community-student interaction. Sub-themes and categories associated with light were healthier lifestyles (knowledge sharing, lifestyle transformation, improved health outcomes), solidarity (reciprocity, collaboration, person centredness, multidimensional approach) and affirmation (gratitude and acceptance). Conclusion. Though some statements by participants related to health education as opposed to health dialogue highlighted areas requiring improvement, the findings correlated with the outcomes prescribed for students by this rural health initiative. Emotional connections in relational experiences could facilitate higher levels of self-efficacy in communities. The question is whether a stronger emphasis on health dialogue can be a catalyst for improved self-efficacy

Nutritional status of HIV-infected adults on antiretroviral therapy and the impact of nutritional supplementation in the Northern Cape Province, South Africa

Objectives: The study aimed to describe the nutritional status and determine the impact of current nutrition intervention strategies on weightchanges in adult HIV-infected patients on antiretroviral (ARV) therapy.Design: A descriptive, prospective trial was performed.Setting: The investigation was conducted at ARV roll-out centres in Kimberley, Upington, Kuruman, Prieska and Springbok in the NorthernCape Province of South Africa.Subjects: Adult HIV-infected patients receiving ARV therapy were included in the study. Outcome measures: Each participants’s body mass index (BMI) was determined before and after a four-month intervention period ofnutritional supplementation with an instant, enriched maize product.Results: Data from 98 patients (mean age 39.7 years; standard deviation 8.9 years) were assessed. Prior to intervention, the median BMI was 20 kg/m2 (range 12.6–29.7 kg/m2); the patients from Kuruman had a greater incidence of underweight compared to the other towns, with a median BMI of 17.9 kg/m2. Of the 87 patients assessed during the final week, 49.4% experienced weight gain and 40.2% lost weight. Eighteen (20.7%) patients gained more than 5% of their baseline weight, which was significant. Only eight (9.2%) patients lost more than 5% of their baseline weight. Twenty-two patients who presented with a BMI 18.5 kg/m2 presented with no change in median weight.Conclusions: Nutritional supplementation, provided according to provincial policy and combined with ARVs, nutritionally benefitted about half of the patients in the ARV programme in the Northern Cape.Keywords: nutrition supplementation; HIV-infection; ARV; adults; nutritional statu

Nano-bio Interactions

Due to there extremely small size, nanoparticles display a unique set of characteristics, which differ significantly form bigger moieties. These characteristics also shape their interaction with biological entities. There large surface-to-volume area, for instance, makes particles in the nano- and micro-range very reactive. Clubmoss spores are an example of naturally occurring microparticles