HDArray: Parallel Array Interface for Distributed Heterogeneous Devices

Heterogeneous clusters with nodes containing one or more accelerators, such as GPUs, have become common. While MPI provides a mechanism and management of interaddress space communication, and OpenCL provides a way to manage computation and communication within a process with access to heterogeneous computational resources, programmers are forced to write hybrid programs that manage the interaction of both of these systems. This paper describes an array programming interface that provides users with automatic or manual distributions of data and work. Using the distribution and information about what data is used and defined by kernels, communication among processes and among devices in a process is performed automatically. The interface provides a unified programming model to the user, thus simplifying program development

Three dimensional numerical relativity: the evolution of black holes

We report on a new 3D numerical code designed to solve the Einstein equations for general vacuum spacetimes. This code is based on the standard 3+1 approach using cartesian coordinates. We discuss the numerical techniques used in developing this code, and its performance on massively parallel and vector supercomputers. As a test case, we present evolutions for the first 3D black hole spacetimes. We identify a number of difficulties in evolving 3D black holes and suggest approaches to overcome them. We show how special treatment of the conformal factor can lead to more accurate evolution, and discuss techniques we developed to handle black hole spacetimes in the absence of symmetries. Many different slicing conditions are tested, including geodesic, maximal, and various algebraic conditions on the lapse. With current resolutions, limited by computer memory sizes, we show that with certain lapse conditions we can evolve the black hole to about $t=50M$, where $M$ is the black hole mass. Comparisons are made with results obtained by evolving spherical initial black hole data sets with a 1D spherically symmetric code. We also demonstrate that an ``apparent horizon locking shift'' can be used to prevent the development of large gradients in the metric functions that result from singularity avoiding time slicings. We compute the mass of the apparent horizon in these spacetimes, and find that in many cases it can be conserved to within about 5\% throughout the evolution with our techniques and current resolution.Comment: 35 pages, LaTeX with RevTeX 3.0 macros. 27 postscript figures taking 7 MB of space, uuencoded and gz-compressed into a 2MB uufile. Also available at http://jean-luc.ncsa.uiuc.edu/Papers/ and mpeg simulations at http://jean-luc.ncsa.uiuc.edu/Movies/ Submitted to Physical Review

Regulation of the Human Taurine Transporter by Oxidative Stress in Retinal Pigment Epithelial Cells Stably Transformed to Overexpress Aldose Reductase

In diabetes, overexpression of aldose reductase (AR) and consequent glucose-induced impairment of antioxidant defense systems may predispose to oxidative stress and the development of diabetic complications, but the mechanisms are poorly understood. Taurine (2-aminoethanesulfonic acid) functions as an antioxidant, osmolyte, and calcium modulator such that its intracellular depletion could promote cytotoxicity in diabetes. The relationships of oxidative stress and basal AR gene expression to Na+-taurine cotransporter (TT) gene expression, protein abundance, and TT activity were therefore explored in low AR-expressing human retinal pigment epithelial (RPE) 47 cells and RPE 47 cells stably transformed to overexpress AR (RPE 75). Changes in TT gene expression were determined using a 4.6-kb TT promoter-luciferase fusion gene. Compared with RPE 47 cells, in high AR-expressing RPE 75 cells, TT promoter activity was decreased by 46%, which was prevented by an AR inhibitor. TT promoter activity increased up to 900% by prooxidant exposure, which was associated with increased TT peptide abundance and taurine transport. However, induction of TT promoter activity by oxidative stress was attenuated in high AR-expressing cells and partially corrected by AR inhibitor. Finally, exposure of RPE 75 cells to high glucose increased oxidative stress, but down-regulated TT expression. These studies demonstrate for the first time that the TT is regulated by oxidative stress and that overexpression of AR and high glucose impair this response. Abnormal expression of AR may therefore impair antioxidant defense, which may determine tissue susceptibility to chronic diabetic complications. Antioxid. Redox Signal. 7, 1530–1542.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63284/1/ars.2005.7.1530.pd

Biochemistry Instructors’ Views toward Developing and Assessing Visual Literacy in Their Courses

Biochemistry instructors are inundated with various representations from which to choose to depict biochemical phenomena. Because of the immense amount of visual know-how needed to be an expert biochemist in the 21st century, there have been calls for instructors to develop biochemistry students’ visual literacy. However, visual literacy has multiple aspects, and determining which area to develop can be quite daunting. Therefore, the goals of this study were to determine what visual literacy skills biochemistry instructors deem to be most important and how instructors develop and assess visual literacy skills in their biochemistry courses. In order to address these goals, a needs assessment was administered to a national sample of biochemistry faculty at four-year colleges and universities. Based on the results of the survey, a cluster analysis was conducted to group instructors into categories based on how they intended to develop visual literacy in their courses. A misalignment was found between the visual literacy skills that were most important and how instructors developed visual literacy. In addition, the majority of instructors assumed these skills on assessments rather than explicitly testing them. Implications focus on the need for better measures to assess visual literacy skills directly

Validating Chemistry Faculty Members’ Self-Reported Familiarity with Assessment Terminology

With the increasing emphasis placed upon chemistry instructors and departments to assess and evaluate their courses and curricula, understanding the structure of chemistry faculty members’ knowledge and use of assessment terms and concepts can shed light on potential areas for targeted professional development. Survey research that might accomplish this objective often relies on self-reported responses from the target audience, and such information is sometimes difficult to assess in terms of validity. As an example of an internal mechanism to help establish validity, it is possible to include an “internal standard” item early in the survey. For the sake of understanding faculty members’ familiarity with assessment terminology, an item that asked participants to identify analogous pairs of terms comparing assessment measures (assessment validity and assessment reliability) to laboratory measures (accuracy and precision) served this purpose. Using ordered logistic regression, participants who answered the analogy question completely correctly were more likely to report higher levels of familiarity with the assessment terms. Because the self-reported data appears to be valid, these data can be further used in subsequent analyses in order to determine the general familiarity trends among chemistry faculty regarding assessment terminology

Mothers' perceptions of child weight status and the subsequent weight gain of their children : a population based longitudinal study

BACKGROUND: There is a plethora of cross sectional work on maternal perceptions of child weight status showing that mothers typically do not classify their overweight child as being overweight according to commonly used clinical criteria. Awareness of overweight in their child is regarded as an important prerequisite for mothers to initiate appropriate action. The gap in the literature is determining whether, if mothers do classify their overweight child's weight status correctly, this is associated with a positive outcome for the child's body mass index (BMI) at a later stage. OBJECTIVE: To explore longitudinal perceptions of child weight status from mothers of a contemporary population-based birth cohort (Gateshead Millennium Study) and relationships of these perceptions with future child weight gain. METHODS: Data collected in the same cohort at 7, 12 and 15 years of age: mothers' responses to two items concerning their child's body size; child's and mother's BMI; pubertal maturation; demographic information. RESULTS: Mothers' perceptions of whether their child was overweight did not change markedly over time. Child BMI was the only significant predictor of mothers' classification of overweight status, and it was only at the extreme end of the overweight range and in the obese range that mothers reliably described their child as overweight. Even when mothers did appropriately classify their child as overweight at an earlier stage, this was not related to relatively lower child BMI a few years later. CONCLUSIONS: Mothers tend to classify their child as overweight in only more extreme cases. It is an important finding that no beneficial impact was shown on later child BMI in overweight children whose mothers classified their child's weight status as overweight at an earlier stage.International Journal of Obesity accepted article preview online, 25 January 2017. doi:10.1038/ijo.2017.20