Distributed-Memory Breadth-First Search on Massive Graphs

This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.Comment: arXiv admin note: text overlap with arXiv:1104.451

Implementing Push-Pull Efficiently in GraphBLAS

We factor Beamer's push-pull, also known as direction-optimized breadth-first-search (DOBFS) into 3 separable optimizations, and analyze them for generalizability, asymptotic speedup, and contribution to overall speedup. We demonstrate that masking is critical for high performance and can be generalized to all graph algorithms where the sparsity pattern of the output is known a priori. We show that these graph algorithm optimizations, which together constitute DOBFS, can be neatly and separably described using linear algebra and can be expressed in the GraphBLAS linear-algebra-based framework. We provide experimental evidence that with these optimizations, a DOBFS expressed in a linear-algebra-based graph framework attains competitive performance with state-of-the-art graph frameworks on the GPU and on a multi-threaded CPU, achieving 101 GTEPS on a Scale 22 RMAT graph.Comment: 11 pages, 7 figures, International Conference on Parallel Processing (ICPP) 201

Efficacy of a Novel Molecular Tool in Silencing Arabidopsis Genes

RNA interference (RNAi), a pathway capable of silencing genes, has until recently only been achievable in the laboratory by the use of one method, expression of inverted repeat sequences of DNA. These constructs generate a double-stranded RNA, which in turn induce post-transcriptional silencing of other genes that bear sequence homology with the transgene. This approach of targeted gene silencing is extremely useful for studying the function of genes and engineering new traits in both plants and animals. It has recently been discovered that a transgene lacking the polyadenylation signal, called a truncated transgene, is also capable of inducing RNAi in plant cells. This technique was used in efficiently silencing two genes of Arabidopsis thaliana, the Phytochrome A (PHYA) and Phytochrome B (PHY B) genes; however, the effectiveness of this method on a broader range of genes is unknown. The purpose of this study is to analyze the effect of truncated-transgene expression on the homologous native genes in the Arabidopsis genome. More specifically, the rate of silencing of three genes, Variegated 2 (VAR2), Brassinosteroid Insensitive 1 (BRI1) and Apetala 1 (AP1) due to the expression of truncated VAR2, BRI1, and AP1 transgenes, respectively, in Arabidopsis thaliana was examined. This experiment provided important data for assessing the efficacy of truncated transgene based gene silencing system for plants

Genetic and biochemical differences in populations bred for extremes in maize grain methionine concentration

Background: Methionine is an important nutrient in animal feed and several approaches have been developed to increase methionine concentration in maize (Zea mays L.) grain. One approach is through traditional breeding using recurrent selection. Using divergent selection, genetically related populations with extreme differences in grain methionine content were produced. In order to better understand the molecular mechanisms controlling grain methionine content, we examined seed proteins, transcript levels of candidate genes, and genotypes of these populations. Results: Two populations were selected for high or low methionine concentration for eight generations and 40 and 56% differences between the high and low populations in grain methionine concentration were observed. Mean values between the high and low methionine populations differed by greater than 1.5 standard deviations in some cycles of selection. Other amino acids and total protein concentration exhibited much smaller changes. In an effort to understand the molecular mechanisms that contribute to these differences, we compared transcript levels of candidate genes encoding high methionine seed storage proteins involved in sulfur assimilation or methionine biosynthesis. In combination, we also explored the genetic mechanisms at the SNP level through implementation of an association analysis. Significant differences in methionine-rich seed storage protein genes were observed in comparisons of high and low methionine populations, while transcripts of seed storage proteins lacking high levels of methionine were unchanged. Seed storage protein levels were consistent with transcript levels. Two genes involved in sulfur assimilation, Cys2 and CgS1 showed substantial differences in allele frequencies when two selected populations were compared to the starting populations. Major genes identified across cycles of selection by a high-stringency association analysis included dzs18, wx, dzs10, and zp27. Conclusions: We hypothesize that transcriptional changes alter sink strength by altering the levels of methionine-rich seed storage proteins. To meet the altered need for sulfur, a cysteine-rich seed storage protein is altered while sulfur assimilation and methionine biosynthesis throughput is changed by selection for certain alleles of Cys2 and CgS1

Permeability evolution during progressive development of deformation bands in porous sandstones

[1] Triaxial deformation experiments were carried out on large (0.1 m) diameter cores of a porous sandstone in order to investigate the evolution of bulk sample permeability as a function of axial strain and effective confining pressure. The log permeability of each sample evolved via three stages: (1) a linear decrease prior to sample failure associated with poroelastic compaction, (2) a transient increase associated with dynamic stress drop, and (3) a systematic quasi-static decrease associated with progressive formation of new deformation bands with increasing inelastic axial strain. A quantitative model for permeability evolution with increasing inelastic axial strain is used to analyze the permeability data in the postfailure stage. The model explicitly accounts for the observed fault zone geometry, allowing the permeability of individual deformation bands to be estimated from measured bulk parameters. In a test of the model for Clashach sandstone, the parameters vary systematically with confining pressure and define a simple constitutive rule for bulk permeability of the sample as a function of inelastic axial strain and effective confining pressure. The parameters may thus be useful in predicting fault permeability and sealing potential as a function of burial depth and faul

Histomorphology of Salivary Glands after Ligature and Reconstruction of Common Carotid Artery in Rabbits

Introduction. In occlusive diseases of carotid arteries may be involved salivary glands which play important role in oral and general homeostasis.Aim of the study. The purpose of this study was histomorphological evaluation of rabbit’s salivary glands after regional reduction af arterial circulation and reconstruction of ligated common carotid arteries comparing with normal histological sight.Materials and methods. The experiments were authorized by the Animal Ethics Committee of the Latvian Food and Veterinary Service. 20 male Californian rabbits weighing approximately 3 kg were used. Under intravenous general anesthesia and local anesthesia the ligature of a. carotis communis dextra was done. After 28 days 10 rabbits were sacrificed and samples were taken from all major salivary glands and histological measured acinar dimensions and acinar epithelial cell.For rest 10 rabbits under the general anesthesia were performed revascularization of a. carotis communis dextra. After 28 days the rabbits were sacrificed with intrapulmonal injection of T61. The acini dimensions and acinar epithelial cell diameter in microns in all glands were measured except buccal glands were measured. Results. In ischemic conditions all glands react with decrease of acinar epithelial cell diameter and also diametr of functional unit of salivary gland.After revascularisation reestablishment of acini and secretory epithelial cells was observed. Conclusions. Rabbit’s salivary glands have potential to recovery in diminished after ligation of ipsilateral common carotid artery size of acini and secretory epithelium after 4 week ischemia if the blood supply is reestabilished.publishersversionPeer reviewe

Benefits of maximum likelihood estimators for fracture attribute analysis: Implications for permeability and up-scaling

The authors thank Andrew Hurst for support during the field work, and also Antonio Grippa, Giuseppe Palladino and Gustavo Zvirtes for help and constructive discussions during the field work. We are particularly grateful to Tom Manzocchi for his important comments that greatly improved the first version of this paper. We acknowledge constructive reviews by Julia Gale and Ken McCaffrey, which have greatly improved our manuscript. This work forms part of a NERC New Investigator award for David Healy (NE/I001743/1), which is gratefully acknowledged. Finally, Roberto Emanuele Rizzo is very appreciative of AFES (Aberdeen Formation Evaluation Society) for funding support during his PhD.Peer reviewedPublisher PD

Positive Result in the Early Passive Phase of the Tilt-table Test: A Predictor of Neurocardiogenic Syncope in Young Men

Background/Aims: This study elucidated the prognostic factors for neurocardiogenic syncope in males in their late teens and early twenties. Methods: Tilt-table testing (TTT) was performed on 665 males (age range, 17 to 27 years) following the Italian protocol. The subjects were tilted head-up at a 70 ° angle on a table for 30 minutes during the passive phase. If the passive phase was negative, the subjects were given sublingual nitroglycerin and tilted to the same angle for 20 minutes during the drugprovocation phase. The subjects with positive results were followed without medication. We analyzed factors related to the recurrence rate of syncope. Results: Of 305 subjects (45.8%) with positive results, 223 (age range, 18 to 26 years) were followed for 12 months. The frequency of previous syncopal episodes ≥ 4 (p = 0.001) and a positive result during the passive phase (p = 0.022) were significantly related to a high recurrence rate. A positive result during the early passive phase ( ≤ 12 minutes) was significantly related to a higher recurrence rate than was that during the late passive phase (> 12 minutes; p = 0.011). Conclusions: A positive result during the early passive phase of TTT and frequent previous syncopal episodes were prognostic factors for neurocardiogenic syncope in men in their late teens and early twenties. Keywords: Syncope, vasovagal; Prognosis; Tilt-table tes

Surveys of rice sold in Canada for aflatoxins, ochratoxin A and fumonisins

Approximately 200 samples of rice (including white, brown, red, black, basmati and jasmine, as well as wild rice) from several different countries, including the United States, Canada, Pakistan, India and Thailand, were analysed for aflatoxins, ochratoxin A (OTA) and fumonisins by separate liquid Chromatographic methods in two different years. The mean concentrations for aflatoxin B1 (AFB1) were 0.19 and 0.17 ng g−1 with respective positive incidences of 56% and 43% (≥ the limit of detection (LOD) of 0.002 ng g−1). Twenty-three samples analysed in the second year also contained aflatoxin B2 (AFB2) at levels ≥LOD of 0.002 ng g−1 The five most contaminated samples in each year contained 1.44–7.14 ng AFB1 g−1 (year 1) and 1.45–3.48 ng AFB1 g−1 (year 2); they were mostly basmati rice from India and Pakistan and black and red rice from Thailand. The average concentrations of ochratoxin A (OTA) were 0.05 and 0.005 ng g−1 in year 1 and year 2, respectively; incidences of samples containing ≥LOD of 0.05 ng g−1 were 43% and 1%, respectively, in the 2 years. All positive OTA results were confirmed by LC-MS/MS. For fumonisins, concentrations of fumonisin B1 (FB1) averaged 4.5 ng g−1 in 15 positive samples (≥0.7 ng g−1) from year 1 (n = 99); fumonisin B2 (FB2) and fumonisin B3 (FB3) were also present (≥1 ng g−1). In the second year there was only one positive sample (14 ng g−1 FB1) out of 100 analysed. All positive FB1 results were confirmed by LC-MS/MS