GPU-TLS: an efficient runtime for speculative loop parallelization on GPUs

Recently GPUs have risen as one important parallel platform for general purpose applications, both in HPC and cloud environments. Due to the special execution model, developing programs for GPUs is difficult even with the recent introduction of high-level languages like CUDA and OpenCL. To ease the programming efforts, some research has proposed automatically generating parallel GPU codes by complex compile-time techniques. However, this approach can only parallelize loops 100% free of inter-iteration dependencies (i.e., DOALL loops). To exploit runtime parallelism, which cannot be proven by static analysis, in this work, we propose GPU-TLS, a runtime system to speculatively parallelize possibly-parallel loops in sequential programs on GPUs. GPU-TLS parallelizes a possibly-parallel loop by chopping it into smaller sub-loops, each of which is executed in parallel by a GPU kernel, speculating that no inter-iteration dependencies exist. After dependency checking, the buffered writes of iterations without mis-speculations are copied to the master memory while iterations encountering mis-speculations are re-executed. GPU-TLS addresses several key problems of speculative loop parallelization on GPUs: (1) The larger mis-speculation rate caused by larger number of threads is reduced by three approaches: the loop chopping parallelization approach, the deferred memory update scheme and intra-warp value forwarding method. (2) The larger overhead of dependency checking is reduced by a hybrid scheme: eager intra-warp dependency checking combined with lazy inter-warp dependency checking. (3) The bottleneck of serial commit is alleviated by a parallel commit scheme, which allows different iterations to enter the commit phase out of order but still guarantees sequential semantics. Extensive evaluations using both microbenchmarks and reallife applications on two recent NVIDIA GPU cards show that speculative loop parallelization using GPU-TLS can achieve speedups ranging from 5 to 160 for sequential programs with possibly-parallel loops. © 2013 IEEE.published_or_final_versio

Towards payment-bound analysis in cloud systems with task-prediction errors

Conference Theme: Change we are leadingIn modern cloud systems, how to optimize user service level based on virtual resources customized on demand is a critical issue. In this paper, we comprehensively analyze the payment bound under a cloud model with virtual machines (VMs), by taking into account that task’s workload may be predicted with errors. The analysis is based on an optimized resource allocation algorithm with polynomial time complexity. We theoretically derive the upper bound of task payment based on a particular margin of workload prediction-error. We also extend the payment-minimization algorithm to adapt to the dynamic changes of host availability over time, and perform the evaluation by a real-cluster environment with 56 VMs deployed. Experiments confirm the correctness of our theoretical inference, and show that our payment-minimization solution can keep 95% of user payments below 1.15 times as large as the theoretical values of the ideal payment with hypothetically accurate information. The ratio for the rest user payments can be limited to about 1.5 at the worst case.postprin

Effect of Scopoletin on Apoptosis and Cell Cycle Arrest in Human Prostate Cancer Cells In vitro

Purpose: To investigate the anticancer activity of scopoletin against human prostate cancer.Methods: The anticancer activity of scopoletin was evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2, 5- diphenyltetrazolium bromide (MMT) assay. Flow cytometry using propidium iodide and annexin V-FITC was employed to study apoptosis and cell cycle analysis. Hoechst 33258 staining was used to assess the effect of scopoletin on cell morphology and apoptotic body formation in human prostate carcinoma (LNCaP) cells via Florescence microscopy and finally Western blotting was used to evaluate the effect of scopoletin on cyclin D1 and cyclin B1 expressions.Results: Scopoletin induced a dose-dependent growth inhibition in LNCaP prostate cancer cells. It induced G2/M phase growth arrest and led to an increase in the sub-G0/G1 cell population after treatment with increasing doses compared to control cells, scopoletin treatment resulted in cell shrinkage along with membrane blebbing which are characteristic features of cell apoptosis. Approximately 15.45, 32.6 and 21.71 % of the cells underwent early apoptosis after treatment with 40, 80 and 100 μM of scopoletin respectively. Cyclin D expression diminished in a concentration-dependent manner when LNCaP cells were treated with different concentrations of scopoletin.Conclusion: These results reveal that scopoletin may be used as a natural chemotherapeutic agent against prostate cancer.Keywords: Prostate cancer, Apoptosis, Cell cycle analysis, Scopoletin, Flow cytometry, Fluorescence microscop

VEGFR2 Expression Correlates with Postnatal Development of Brain Arteriovenous Malformations in a Mouse Model of Type I Hereditary Hemorrhagic Telangiectasia

\ua9 2023 by the authors.Brain arteriovenous malformations (BAVMs) are a critical concern in hereditary hemorrhagic telangiectasia (HHT) patients, carrying the risk of life-threatening intracranial hemorrhage. While traditionally seen as congenital, the debate continues due to documented de novo cases. Our primary goal was to identify the precise postnatal window in which deletion of the HHT gene Endoglin (Eng) triggers BAVM development. We employed SclCreER(+);Eng2f/2f mice, enabling timed Eng gene deletion in endothelial cells via tamoxifen. Tamoxifen was given during four postnatal periods: P1–3, P8–10, P15–17, and P22–24. BAVM development was assessed at 2–3 months using latex dye perfusion. We examined the angiogenic activity by assessing vascular endothelial growth factor receptor 2 (VEGFR2) expression via Western blotting and Flk1-LacZ reporter mice. Longitudinal magnetic resonance angiography (MRA) was conducted up to 9 months. BAVMs emerged in 88% (P1–3), 86% (P8–10), and 55% (P15–17) of cases, with varying localization. Notably, the P22–24 group did not develop BAVMs but exhibited skin AVMs. VEGFR2 expression peaked in the initial 2 postnatal weeks, coinciding with BAVM onset. These findings support the “second hit” theory, highlighting the role of early postnatal angiogenesis in initiating BAVM development in HHT type I mice

Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics

International audienceSample preparation is a key step in proteomics workflows. Tube-gel (TG) is a fast and repeatable sample preparation method that consists in the instantaneous trapping of the sample in a polyacrylamide gel matrix. It takes advantage of in-gel sample preparations by allowing the use of high concentrations of sodium-dodecyl sulfate but avoids the time-consuming step of electrophoresis. Therefore, TG limits the sample handling and is thus particularly suitable for high-throughput quantitative proteomics when large sample numbers have to be processed, as it is often the case in biomarker research and clinical proteomics projects

An Overview of the Use of Neural Networks for Data Mining Tasks

In the recent years the area of data mining has experienced a considerable demand for technologies that extract knowledge from large and complex data sources. There is a substantial commercial interest as well as research investigations in the area that aim to develop new and improved approaches for extracting information, relationships, and patterns from datasets. Artificial Neural Networks (NN) are popular biologically inspired intelligent methodologies, whose classification, prediction and pattern recognition capabilities have been utilised successfully in many areas, including science, engineering, medicine, business, banking, telecommunication, and many other fields. This paper highlights from a data mining perspective the implementation of NN, using supervised and unsupervised learning, for pattern recognition, classification, prediction and cluster analysis, and focuses the discussion on their usage in bioinformatics and financial data analysis tasks

Review on the acute Daphnia magna

Executive summary : One of the most internationally used bioassays for toxicity screening of chemicals and for toxicity monitoring of effluents and contaminated waters is the acute toxicity test with daphnid crustaceans, and in particular that performed with Daphnia magna. Standard methods have been developed for this assay that were gradually endorsed by national and international organisations dealing with toxicity testing procedures, in view of its application within a regulatory framework. As for all toxicity tests, the organisms used for the acute D. magna assay have to be obtained from live stocks which are cultured in the laboratory on live food (micro-algae). Unsurprisingly the various standard protocols of this particular assay differ – at least to a certain extent – with regard to the test organism culturing conditions. In addition, some technical aspects of the toxicity test such as the effect criterion (mortality of immobility), the exposure time, the type of dilution water, etc., also vary from one standard to another. Although this particular assay is currently used in many countries, the technical and biological problems inherent in year-round culturing and availability of the biological material and the culturing/maintenance costs of live stocks restrict its application to a limited number of highly specialised laboratories. This fundamental bottleneck in toxicity testing triggered investigations which brought forward the concept of “microbiotests” or “small-scale” toxicity tests. “Culture/maintenance free” aquatic microbiotests with species of different phylogenetic groups were developed in the early 1990s at the Laboratory for Environmental Toxicology and Aquatic Ecology at the Ghent University in Belgium. These assays which were given the generic name “Toxkits”, are unique in that they employ dormant stages (“cryptobiotic eggs”) of the test species, which can be stored for long periods of time and “hatched” at the time of performance of the assays. One of these microbiotests is the Daphtoxkit F magna, which is currently used in many laboratories worldwide for research as well as for toxicity monitoring purposes. The microbiotest technology has several advantages in comparison to the “traditional” tests based on laboratory cultures, especially its independence of the stock culturing burden. However, the acceptance (or possible non-acceptance) of performing assays with test organisms obtained from “dormant eggs” should be clearly dictated by the “sensitivity” and “precision” criteria of the former assays in comparison to the latter. The first part of this review therefore thoroughly reviews the scientific literature and of data obtained from various laboratories for assays performed with either D. magna test organisms obtained from lab cultures or hatched from dormant eggs. Attention has focused on data of quality control tests performed on reference chemicals, and in particular on potassium dichromate (K2Cr2O7) for which an acceptability range of 0.6–2.1 mg·L–1 has been set in ISO standard 6341 for the 24 h EC50 of the acute D. magna assay. Mean EC50s, standard deviations and variation coefficients were calculated from the collected data, all of which are presented in tables and figures and discussed in detail. The major conclusions drawn from the analysis of the large number of quality control (QC) data on the acute D. magna toxicity test are that : (1) Virtually all results from assays performed with Daphnias taken from lab cultures or with Daphnia microbiotests are within the acceptability range set by ISO standard 6341 for the reference chemical potassium dichromate. (2) The mean 24 h EC50s of the Daphnia microbiotests performed in different laboratories are within the range of the mean EC50s of the assays based on lab cultures, and the variation coefficients (20 to 30%) are similar. (3) The precision – in terms of the long term in house variability – of the quality control Daphnia microbiotests is as good as that of the QC tests based on lab cultures. The review further reports on intra-laboratory sensitivity comparison studies performed during the last 15 years on pure chemicals and on natural samples, with both laboratory cultured organisms and Daphnias hatched from dormant eggs. These studies carried out in different laboratories showed EC50 correlation coefficients of 0.86 to 0.98, corroborating a similar sensitivity of the two types of test organisms. The third part of the review reports and analyses data on proficiency ringtests on the acute D. magna assay which have been organised in different countries since 2002 with either reference chemicals or with natural samples, and in which part of the laboratories performed their assays with Daphnia microbiotests and others with lab cultured Daphnias. The conclusions drawn from all the ringtests indicate that the sensitivity of Daphnia neonates hatched from dormant eggs is similar to that of test organisms taken from lab cultures and that in most cases the precision of the Daphnia microbiotest is superior to that of the assays based on lab cultures. The review finally addresses the issue of possible sensitivity differences of Daphnias hatched from dormant eggs which are produced by different D. magna strains. From these investigations it appeared that the EC50s from assays performed with Daphnias hatched from dormant eggs of different strains did not differ significantly from those from assays undertaken with daphnids from lab cultures. The obvious advantages of Daphnia microbiotests over tests with Daphnias stemming from lab cultures have led to the worldwide use of these culture/maintenance free and low cost small-scale assays in both research and toxicity monitoring. The Daphnia microbiotest is in current use in several countries for toxicity testing in a regulatory framework, and recent calculations indicate that about 10 000 acute D. magna assays are now performed annually with neonates hatched from dormant eggs. The use of dormant eggs to obtain test organisms independently of stock culturing has recently also been accepted in international standards for toxicity testing. ISO standard 20665 (2008) related to the determination of chronic toxicity with Ceriodaphnia dubia, and ISO standard 20666 (2008) for the determination of the chronic toxicity with Brachionus calyciflorus in 48 h, both indicate that the assays can be conducted with organisms hatched from dormant eggs. On the basis of the extensive scientific evidence provided in this review that is justifiably supported by the two ISO methods mentioned above, the authors therefore recommend that the use of Daphnias hatched from dormant eggs should also be incorporated in national and international standards, as an alternative to the use of Daphnias taken from laboratory cultures

Beyond the culture effect on credibility perception on microblogs

We investigated the credibility perception of tweet readers from the USA and by readers from eight Arabic countries; our aim was to understand if credibility was affected by country and/or by culture. Results from a crowd-sourcing experiment, showed a wide variety of factors affected credibility perception, including a tweet author's gender, profile image, username style, location, and social network overlap with the reader. We found that culture determines readers' credibility perception, but country has no effect. We discuss the implications of our findings for user interface design and social media systems

Graphene for spintronics: giant Rashba splitting due to hybridization with Au

Graphene in spintronics has so far primarily meant spin current leads of high performance because the intrinsic spin-orbit coupling of its pi-electrons is very weak. If a large spin-orbit coupling could be created by a proximity effect, the material could also form active elements of a spintronic device such as the Das-Datta spin field-effect transistor, however, metal interfaces often compromise the band dispersion of massless Dirac fermions. Our measurements show that Au intercalation at the graphene-Ni interface creates a giant spin-orbit splitting (~100 meV) in the graphene Dirac cone up to the Fermi energy. Photoelectron spectroscopy reveals hybridization with Au-5d states as the source for the giant spin-orbit splitting. An ab initio model of the system shows a Rashba-split dispersion with the analytically predicted gapless band topology around the Dirac point of graphene and indicates that a sharp graphene-Au interface at equilibrium distance will account for only ~10 meV spin-orbit splitting. The ab initio calculations suggest an enhancement due to Au atoms that get closer to the graphene and do not violate the sublattice symmetry.Comment: 16 pages (3 figures) + supplementary information 16 pages (14 figures

How the other half lives: CRISPR-Cas's influence on bacteriophages

CRISPR-Cas is a genetic adaptive immune system unique to prokaryotic cells used to combat phage and plasmid threats. The host cell adapts by incorporating DNA sequences from invading phages or plasmids into its CRISPR locus as spacers. These spacers are expressed as mobile surveillance RNAs that direct CRISPR-associated (Cas) proteins to protect against subsequent attack by the same phages or plasmids. The threat from mobile genetic elements inevitably shapes the CRISPR loci of archaea and bacteria, and simultaneously the CRISPR-Cas immune system drives evolution of these invaders. Here we highlight our recent work, as well as that of others, that seeks to understand phage mechanisms of CRISPR-Cas evasion and conditions for population coexistence of phages with CRISPR-protected prokaryotes.Comment: 24 pages, 8 figure