Improving the scalability of parallel N-body applications with an event driven constraint based execution model

The scalability and efficiency of graph applications are significantly constrained by conventional systems and their supporting programming models. Technology trends like multicore, manycore, and heterogeneous system architectures are introducing further challenges and possibilities for emerging application domains such as graph applications. This paper explores the space of effective parallel execution of ephemeral graphs that are dynamically generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The workloads are expressed using the semantics of an Exascale computing execution model called ParalleX. For comparison, results using conventional execution model semantics are also presented. We find improved load balancing during runtime and automatic parallelism discovery improving efficiency using the advanced semantics for Exascale computing.Comment: 11 figure

Manual Whisker Annotator (MWA): A Modular Open-Source Tool

Rodents are key to generating translational data for healthcare research. Behavioural analyses, in particular, are integral to the non-invasive monitoring of rodent health and welfare. Finding quantitative behavioural measures mitigates stress, allowing for the animal behave freely while also enabling the same animal to be studied over the time-course of its life. Locomotion and whisking are both such quantitative behavioural measures, and have been found to be significantly impacted in rodent models of neurodegenerative disease. While automatic trackers of whiskers and locomotion exist, a manual tracker is required to validate these approaches, and also to annotate complex videos where these automatic versions fail. Manually annotating whiskers for research purposes is a long and tedious task and current software does little to provide an intuitive and simple interface to carry out this task. This led to the creation of the Manual Whisker Annotator (MWA). MWA is an open source, portable whisker annotation tool developed for the Windows platform. Not only does MWA make the process much quicker, it also provides added statistical tools to analyse the data. MWA was developed in C# and WPF using the .NET framework, and could be used in any situation where annotating or tracking multiple targets is desired

Marine bioinvasion management: structural framework

Significant global change has occurred through the accidental and intentional human mediated introductions of species in regions outside of their evolutionary origins can no longer be disputed (e.g., Lubchenco et al. 1991; Carlton 2001; Pimentel 2002). This change is well documented in a variety of terrestrial and freshwater ecosystems (e.g., Drake and Mooney 1989) and is becoming increasingly apparent in marine and estuarine habitats in all of the world’s oceans (e.g., Carlton 2001; Chap. 2, Carlton). Documenting the scale and rates of marine introductions and the subsequent changes to invaded systems has captured much of the marine invasion ecology effort during the last 25 years (e.g., Grosholz et al. 2000; Carlton and Ruiz 2004). While the lessons that can be learned about evolution, ecosystem function, community dynamics, and species biology and ecology from the study of biological introductions are fascinating (e.g., Harper 1965; Carlton and Ruiz 2004), the challenge “what should we and/or what can we do?” remains. The options appear to be simple, however the details of implementation are difficult: we can choose to do nothing or we can choose to act

Assessing spatial and temporal variability of acid-extractable organics in oil sands process-affected waters

The acid-extractable organic compounds (AEOs), including naphthenic acids (NAs), present within oil sands process-affected water (OSPW) receive great attention due to their known toxicity. While recent progress in advanced separation and analytical methodologies for AEOs has improved our understanding of the composition of these mixtures, little is known regarding any variability (i.e., spatial, temporal) inherent within, or between, tailings ponds. In this study, 5 samples were collected from the same location of one tailings pond over a 2-week period. In addition, 5 samples were collected simultaneously from different locations within a tailings pond from a different mine site, as well as its associated recycling pond. In both cases, the AEOs were analyzed using SFS, ESI-MS, HRMS, GC×GC-ToF/MS, and GC- & LC-QToF/MS (GC analyses following conversion to methyl esters). Principal component analysis of HRMS data was able to distinguish the ponds from each other, while data from GC×GC-ToF/MS, and LC- and GC-QToF/MS were used to differentiate samples from within the temporal and spatial sample sets, with the greater variability associated with the latter. Spatial differences could be attributed to pond dynamics, including differences in inputs of tailings and surface run-off. Application of novel chemometric data analyses of unknown compounds detected by LC- and GC-QToF/MS allowed further differentiation of samples both within and between data sets, providing an innovative approach for future fingerprinting studies

Structure and function of a spectrin-like regulator of bacterial cytokinesis

© 2014 Macmillan Publishers Limited. All rights reserved. Bacterial cell division is facilitated by a molecular machine - the divisome - that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60-kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family

Use of the distributions of adamantane acids to profile short-term temporal and pond-scale spatial variations in the composition of oil sands process-affected waters

© The Royal Society of Chemistry. Oil industry produced waters, such as the oils sands process-affected waters (OSPW) of Alberta, Canada, represent a challenge in terms of risk assessment and reclamation due to their extreme complexity, particularly of the organic chemical constituents, including the naphthenic acids (NA). The identification of numerous NA in single samples has raised promise for the use of NA distributions for profiling OSPW. However, monitoring of the success of containment is still difficult, due to the lack of knowledge of the homogeneity (or otherwise) of OSPW composition within, and between, different industry containments. Here we used GC×GC-MS to compare the NA of five OSPW samples from each of two different industries. Short-term temporal and pond-scale spatial variations in the distributions of known adamantane acids and diacids and other unknown tricyclic acids were examined and a statistical appraisal of the replicate data made. The presence/absence of individual acids easily distinguished the OSPW NA of one industry from those of the other. The proportions of tricyclic acids with different carbon numbers also varied significantly between the OSPW of the two industries. The pond-scale spatial variation in NA in OSPW samples was higher than the short-term (2 weeks) temporal variations. An OSPW sample from an aged pond was exceptionally high in the proportion of C<inf>15,16,17</inf> compounds, possibly due to increased biotransformation. Such techniques could possibly also help to distinguish different sources of NA in the environment

Advances in Distinguishing Groundwater Influenced by Oil Sands Process-Affected Water (OSPW) from Natural Bitumen-Influenced Groundwaters.

The objective of this study was to advance analytical methods for detecting oil sands process-affected water (OSPW) seepage from mining containments and discriminating any such seepage from the natural bitumen background in groundwaters influenced by the Alberta McMurray formation. Improved sampling methods and quantitative analyses of two groups of monoaromatic acids were employed to analyze OSPW and bitumen-affected natural background groundwaters for source discrimination. Both groups of monoaromatic acids showed significant enrichment in OSPW, while ratios of O2/O4 containing heteroatomic ion classes of acid extractable organics (AEOs) did not exhibit diagnostic differences. Evaluating the monoaromatic acids to track a known plume of OSPW-affected groundwater confirmed their diagnostic abilities. A secondary objective was to assess anthropogenically derived artificial sweeteners and per- and polyfluoroalkyl substances (PFAS) as potential tracers for OSPW. Despite the discovery of acesulfame and PFAS in most OSPW samples, trace levels in groundwaters influenced by general anthropogenic activities preclude them as individual robust tracers. However, their inclusion with the other metrics employed in this study served to augment the tiered, weight of evidence methodology developed. This methodology was then used to confirm earlier findings of OSPW migrations into groundwater reaching the Athabasca River system adjacent to the reclaimed pond at Tar Island Dyke

Prioritising surveillance for alien organisms transported as stowaways on ships travelling to South Africa

The global shipping network facilitates the transportation and introduction of marine and terrestrial organisms to regions where they are not native, and some of these organisms become invasive. South Africa was used as a case study to evaluate the potential for shipping to contribute to the introduction and establishment of marine and terrestrial alien species (i.e. establishment debt) and to assess how this varies across shipping routes and seasons. As a proxy for the number of species introduced (i.e. 'colonisation pressure') shipping movement data were used to determine, for each season, the number of ships that visited South African ports from foreign ports and the number of days travelled between ports. Seasonal marine and terrestrial environmental similarity between South African and foreign ports was then used to estimate the likelihood that introduced species would establish. These data were used to determine the seasonal relative contribution of shipping routes to South Africa's marine and terrestrial establishment debt. Additionally, distribution data were used to identify marine and terrestrial species that are known to be invasive elsewhere and which might be introduced to each South African port through shipping routes that have a high relative contribution to establishment debt. Shipping routes from Asian ports, especially Singapore, have a particularly high relative contribution to South Africa's establishment debt, while among South African ports, Durban has the highest risk of being invaded. There was seasonal variation in the shipping routes that have a high relative contribution to the establishment debt of the South African ports. The presented method provides a simple way to prioritise surveillance effort and our results indicate that, for South Africa, port-specific prevention strategies should be developed, a large portion of the available resources should be allocated to Durban, and seasonal variations and their consequences for prevention strategies should be explored further. (Résumé d'auteur

The lncRNA HOTAIR transcription is controlled by HNF4α-induced chromatin topology modulation

The expression of the long noncoding RNA HOTAIR (HOX Transcript Antisense Intergenic RNA) is largely deregulated in epithelial cancers and positively correlates with poor prognosis and progression of hepatocellular carcinoma and gastrointestinal cancers. Furthermore, functional studies revealed a pivotal role for HOTAIR in the epithelial-to-mesenchymal transition, as this RNA is causal for the repressive activity of the master factor SNAIL on epithelial genes. Despite the proven oncogenic role of HOTAIR, its transcriptional regulation is still poorly understood. Here hepatocyte nuclear factor 4-α (HNF4α), as inducer of epithelial differentiation, was demonstrated to directly repress HOTAIR transcription in the mesenchymal-to epithelial transition. Mechanistically, HNF4α was found to cause the release of a chromatin loop on HOTAIR regulatory elements thus exerting an enhancer-blocking activity