Using the High Productivity Language Chapel to Target GPGPU Architectures

It has been widely shown that GPGPU architectures offer large performance gains compared to their traditional CPU counterparts for many applications. The downside to these architectures is that the current programming models present numerous challenges to the programmer: lower-level languages, explicit data movement, loss of portability, and challenges in performance optimization. In this paper, we present novel methods and compiler transformations that increase productivity by enabling users to easily program GPGPU architectures using the high productivity programming language Chapel. Rather than resorting to different parallel libraries or annotations for a given parallel platform, we leverage a language that has been designed from first principles to address the challenge of programming for parallelism and locality. This also has the advantage of being portable across distinct classes of parallel architectures, including desktop multicores, distributed memory clusters, large-scale shared memory, and now CPU-GPU hybrids. We present experimental results from the Parboil benchmark suite which demonstrate that codes written in Chapel achieve performance comparable to the original versions implemented in CUDA.NSF CCF 0702260Cray Inc. Cray-SRA-2010-016962010-2011 Nvidia Research Fellowshipunpublishednot peer reviewe

Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P.

This is the published version. Copyright 2000 by the RNA Society.Ribonuclease P is the enzyme responsible for removing the 5'-leader segment of precursor transfer RNAs in all organisms. All eukaryotic nuclear RNase Ps are ribonucleoproteins in which multiple protein components and a single RNA species are required for activity in vitro as well as in vivo. It is not known, however, which subunits participate directly in phosphodiester-bond hydrolysis. The RNA subunit of nuclear RNase P is evolutionarily related to its catalytically active bacterial counterpart, prompting speculation that in eukaryotes the RNA may be the catalytic component. In the bacterial RNase P reaction, Mg(II) is required to coordinate the nonbridging phosphodiester oxygen(s) of the scissile bond. As a consequence, bacterial RNase P cannot cleave pre-tRNA in which the pro-Rp nonbridging oxygen of the scissile bond is replaced by sulfur. In contrast, the RNase P reaction in plant chloroplasts is catalyzed by a protein enzyme whose mechanism does not involve Mg(II) coordinated by the pro-Rp oxygen. To determine whether the mechanism of nuclear RNase P resembles more closely an RNA- or a protein-catalyzed reaction, we analyzed the ability of Saccharomyces cerevisiae nuclear RNase P to cleave pre-tRNA containing a sulfur substitution of the pro-Rp oxygen at the cleavage site. Sulfur substitution at this position prohibits correct cleavage of pre-tRNA. Cleavage by eukaryotic RNase P thus depends on the presence of a thio-sensitive ligand to the pro-Rp oxygen of the scissile bond, and is consistent with a common, RNA-based mechanism for the bacterial and eukaryal enzymes

Structural modification of the antidepressant mianserin suggests that its anti-inflammatory activity may be independent of 5-Hydroxytryptamine receptors

Antidepressants are increasingly recognized to have anti-inflammatory properties in addition to their ability to treat major depressive disorders. To explore if engagement of 5-hydroxytryptamine (5-HT) receptors was required for the anti-inflammatory effect of the tetracyclic antidepressant mianserin, a series of structural derivatives were generated with the aim of reducing 5-HT receptor binding. Primary human peripheral blood mononuclear cells were used to screen for anti-inflammatory activity. The lead compound demonstrated a significant loss in 5-HT receptor binding, as assessed by non-selective 5-HT binding of radiolabelled serotonin in rat cerebral cortex. However, it retained the ability to inhibit endosomal toll-like receptor 8 signaling in primary human macrophages and spontaneous cytokine production from human rheumatoid synovial tissue equivalent to that previously observed for mianserin. These data demonstrate that the anti-inflammatory mechanism of mianserin may be independent of 5-HT receptor activity. This research offers new insights into the mechanism and structural requirements for the anti-inflammatory action of mianserin

A laboratory investigation on thermal properties of virgin and aged asphalt mixture

In this paper, the thermal properties of three dense graded asphalt mixtures, 20 mm DBM, AC 14, and AC 6, are presented. Density and air voids of the compacted specimens are also shown. Thermal conductivity was measured in the laboratory for non-aged, short-term aged and long-term aged asphalt mixtures at three different temperatures 19 (±1) oC, 65 (±5) oC, and 80 (±5) oC. Specific heat capacity and thermal diffusivity were calculated from equations derived from the literature. Heat penetration depth was also calculated and shows the heat from the thermal conductivity instrument heat source that dissipates into the asphalt specimens. The results were analysed to determine the effect of air voids content, transient line source (TLS) method, temperature and aggregate size in thermal conductivity and the effect of aging on the thermal properties of the asphalt mixtures studied. It was concluded that there is a minimal effect in thermal conductivity for 4% to 6.5% air voids. The method of measurement and temperature affect considerably thermal conductivity. However, the results were inconclusive in the effect of aggregate size on thermal conductivity. The effect of asphalt aging in thermal conductivity and thermal diffusivity varied between the asphalt mixtures studied and was relative to the temperature. Asphalt aging did not affect specific heat capacity

An innovative asphalt patch repair pre–heating method using dynamic heating

In hot mix asphalt patch repair, inadequate temperature at the interfaces is one of the influencing factors for inferior compaction and poor interface bonding. To enhance repair performance, a precisely controlled infrared pre-heating method for patch repair has been investigated. Asphalt slabs with 45 mm, 75 mm and 100 mm deep pothole excavations were subjected to dynamic heating with infrared heater operating power from 6.6 kW to 7.7 kW. The heater was kept either stationary or moving slowly across the excavations at 130 mm and 230 mm offsets. The tests included evaluating temperature increase throughout the excavations and inside the slab, recording heat power of infrared heater and heating time to avoid burning the asphalt. Irrespective of excavation depth, heating power and offset, the temperature distribution was found non-uniform in the pothole excavations and into the asphalt slab. The temperatures were higher at the faces of the excavation than inside the slab. Dynamic heating for approximately 10 min yielded better heat distribution while minimising the possibility of asphalt overheating and long pre-heating time. It has been concluded that 45 mm and 100 mm deep pothole excavations can be pre-heated with 6.6 kW and stationary heater or 7.5 kW and moving heater at 230 mm and 130 mm offset respectively. 75 mm deep excavation can be pre-heated with 7.1 kW and stationary heater at 230 mm offset

Results of the Cooperative Uniform Soybean Tests, 1948 Part I. North Central States

United States Department of Agriculture, Agricultural Research Administration; Bureau of Plant Industry, Soils, and Agricultural Engineering, Division of Forage Crops and Diseases Cooperating with State Agricultural Experiment Station

Results of the Cooperative Uniform Soybean Tests Part I. North Central States 1949

United States Department of Agriculture, Agricultural Research Administration; Bureau of Plant Industry, Soils, and Agricultural Engineering, Division of Forage Crops and Diseases Cooperating with State Agricultural Experiment Station

Clinical Advances in Obsessive Compulsive Disorder: A Position Statement by the International College of Obsessive Compulsive Spectrum Disorders

© 2020 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CC-BY-NC-ND - https://creativecommons.org/licenses/by-nc-nd/4.0/), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.In this position statement, developed by The International College of Obsessive-Compulsive Spectrum Disorders, a group of international experts responds to recent developments in the evidence-based management of obsessive-compulsive disorder (OCD). The article presents those selected therapeutic advances judged to be of utmost relevance to the treatment of OCD, based on new and emerging evidence from clinical and translational science. Areas covered include refinement in the methods of clinical assessment, the importance of early intervention based on new staging models and the need to provide sustained well-being involving effective relapse prevention. The relative benefits of psychological, pharmacological and somatic treatments are reviewed and novel treatment strategies for difficult to treat OCD, including neurostimulation, as well as new areas for research such as problematic internet use, novel digital interventions, immunological therapies, pharmacogenetics and novel forms of psychotherapy are discussed.Peer reviewe

A multi-tissue atlas of regulatory variants in cattle:Cattle Genotype-Tissue Expression Atlas

Characterization of genetic regulatory variants acting on the livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 7,180 RNA-Seq samples. We describe the transcriptomic landscape of over 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle