cuIBM -- A GPU-accelerated Immersed Boundary Method

A projection-based immersed boundary method is dominated by sparse linear algebra routines. Using the open-source Cusp library, we observe a speedup (with respect to a single CPU core) which reflects the constraints of a bandwidth-dominated problem on the GPU. Nevertheless, GPUs offer the capacity to solve large problems on commodity hardware. This work includes validation and a convergence study of the GPU-accelerated IBM, and various optimizations.Comment: Extended paper post-conference, presented at the 23rd International Conference on Parallel Computational Fluid Dynamics (http://www.parcfd.org), ParCFD 2011, Barcelona (unpublished

Reproducible Research for Computing in Science & Engineering

The editors of the new track for reproducible research outline the parameters for future peer review, submission, and access, highlighting the magazine’s previous work in this field and some of the challenges still to come

A Tuned and Scalable Fast Multipole Method as a Preeminent Algorithm for Exascale Systems

Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the order of billions of unknowns. That work led to an extremely parallel FMM, scaling to thousands of GPUs or tens of thousands of CPUs. This paper reports on a a campaign of performance tuning and scalability studies using multi-core CPUs, on the Kraken supercomputer. All kernels in the FMM were parallelized using OpenMP, and a test using 10^7 particles randomly distributed in a cube showed 78% efficiency on 8 threads. Tuning of the particle-to-particle kernel using SIMD instructions resulted in 4x speed-up of the overall algorithm on single-core tests with 10^3 - 10^7 particles. Parallel scalability was studied in both strong and weak scaling. The strong scaling test used 10^8 particles and resulted in 93% parallel efficiency on 2048 processes for the non-SIMD code and 54% for the SIMD-optimized code (which was still 2x faster). The weak scaling test used 10^6 particles per process, and resulted in 72% efficiency on 32,768 processes, with the largest calculation taking about 40 seconds to evaluate more than 32 billion unknowns. This work builds up evidence for our view that FMM is poised to play a leading role in exascale computing, and we end the paper with a discussion of the features that make it a particularly favorable algorithm for the emerging heterogeneous and massively parallel architectural landscape

Redefining the performing arts archive

This paper investigates representations of performance and the role of the archive. Notions of record and archive are critically investigated, raising questions about applying traditional archival definitions to the performing arts. Defining the nature of performances is at the root of all difficulties regarding their representation. Performances are live events, so for many people the idea of recording them for posterity is inappropriate. The challenge of creating and curating representations of an ephemeral art form are explored and performance-specific concepts of record and archive are posited. An open model of archives, encouraging multiple representations and allowing for creative reuse and reinterpretation to keep the spirit of the performance alive, is envisaged as the future of the performing arts archive

Application of chemometrics to assess the influence of ultrasound frequency, Lactobacillus sakei culture and drying on beef jerky manufacture: Impact on amino acid profile, organic acids, texture and colour

The effects of ultrasound (US) frequency, addition of Lactobacillus sakei culture and drying time on key nutritional (protein, amino acids, and organic acids) and physicochemical properties (texture and colour) of cultured and uncultured beef jerky were evaluated. Cultured and uncultured jerky samples were subjected to US frequencies of 25 kHz, 33 kHz and 45 kHz for 30 min prior to marination and drying. Principal component analysis demonstrated a significant effect of beef jerky processing conditions on physicochemical properties. Taurine content of jerky samples was found to increase with an increase in ultrasonic frequencies for cultured samples. No significant changes in colour values were observed for ultrasound pre-treated and control samples. Interactive effects of culture treatment, drying and ultrasonic frequency were observed. This study demonstrates that the nutritional profile of beef jerky can be improved through the incorporation of L. sakei

Klebsiella pneumoniae carbapenamases in Escherichia coli isolated from humans and livestock in rural South-Western Uganda

Funding: This work was supported by; The "Holistic Approach to Unravel Antibacterial Resistance in East Africa” project which was a 3-year Global Context Consortia Award (MR/S004785/1) funded by the National Institute for Health Research, Medical Research Council and the Department of Health and Social Care, UK.Background The accumulation of resistance genes in Escherichia coli (E. coli) strains imposes limitations in the therapeutic options available for the treatment of infections caused by E.coli. Production of Klebsiella pneumoniae carbapenemase (KPC) by E. coli renders it resistant to broad-spectrum β-lactam antibiotics. Globally there is existing evidence of spread of carbapenem-resistant E. coli in both humans and livestock driven by acquisition of the several other carbapenemase genes. Overall, there is little information regarding the extent of KPC gene distribution in E. coli. We set out to determine the prevalence, and evaluate the phenotypic and genotypic patterns of KPC in E. coli isolated from humans and their livestock in rural south western Uganda. Methods A laboratory-based, descriptive cross-sectional study was conducted involving 96 human and 96 livestock isolates collected from agro-pastoralist communities in Mbarara district in south western Uganda. Phenotypic and molecular methods (PCR) were used for presence and identification of KPC genes in the E. coli isolates. A chi-square test of independence was used to evaluate the differences in resistant patterns between carbapenems and isolates. Results The overall prevalence of carbapenem resistance by disk diffusion susceptibility testing (DST) for both humans and livestock isolates were 41.7% (80/192). DST-based resistance was identical in both human and livestock isolates (41.7%). The prevalence of carbapenem resistance based on Modified Hodge Test (MHT) was 5% (2/40) and 10% (4/40) for humans and livestock isolates respectively. Both human and livestock isolates, 48.7% (95/192) had the KPC gene, higher than phenotypic expression; 41.7% (80/192). blaKPC gene prevalence was overall similar in human isolates (51%; 49/96) vs livestock isolates (47.9%; 46/96). Approximately, 19% (15/80) of the isolates were phenotypically resistant to carbapenems and over 70% (79/112) of the phenotypically sensitive strains harbored the blaKPC gene. Conclusion Our results suggest that both human and livestock isolates of E. coli in our setting carry the blaKPC gene with a high percentage of strains not actively expressing the blaKPC gene. The finding of fewer isolates carrying the KPC gene than those phenotypically resistant to carbapenems suggests that other mechanisms are playing a role in this phenomenon, calling for further researcher into this phenomenon.Publisher PDFPeer reviewe

Inhibition of Piezo1 attenuates demyelination in the central nervous system

Piezo1 is a mechanosensitive ion channel that facilitates the translation of extracellular mechanical cues to intracellular molecular signaling cascades through a process termed, mechanotransduction. In the central nervous system (CNS), mechanically gated ion channels are important regulators of neurodevelopmental processes such as axon guidance, neural stem cell differentiation, and myelination of axons by oligodendrocytes. Here, we present evidence that pharmacologically mediated overactivation of Piezo1 channels negatively regulates CNS myelination. Moreover, we found that the peptide GsMTx4, an antagonist of mechanosensitive cation channels such as Piezo1, is neuroprotective and prevents chemically induced demyelination. In contrast, the positive modulator of Piezo1 channel opening, Yoda‐1, induces demyelination and neuronal damage. Using an ex vivo murine‐derived organotypic cerebellar slice culture model, we demonstrate that GsMTx4 attenuates demyelination induced by the cytotoxic lipid, psychosine. Importantly, we confirmed the potential therapeutic effects of GsMTx4 peptide in vivo by co‐administering it with lysophosphatidylcholine (LPC), via stereotactic injection, into the cerebral cortex of adult mice. GsMTx4 prevented both demyelination and neuronal damage usually caused by the intracortical injection of LPC in vivo; a well‐characterized model of focal demyelination. GsMTx4 also attenuated both LPC‐induced astrocyte toxicity and microglial reactivity within the lesion core. Overall, our data suggest that pharmacological activation of Piezo1 channels induces demyelination and that inhibition of mechanosensitive channels, using GsMTx4, may alleviate the secondary progressive neurodegeneration often present in the latter stages of demyelinating diseases

Clinical Processes - The Killer Application for Constraint-Based Process Interactions?

For more than a decade, the interest in aligning information systems in a process-oriented way has been increasing. To enable operational support for business processes, the latter are usually specified in an imperative way. The resulting process models, however, tend to be too rigid to meet the flexibility demands of the actors involved. Declarative process modeling languages, in turn, provide a promising alternative in scenarios in which a high level of flexibility is demanded. In the scientific literature, declarative languages have been used for modeling rather simple processes or synthetic examples. However, to the best of our knowledge, they have not been used to model complex, real-world scenarios that comprise constraints going beyond control-flow. In this paper, we propose the use of a declarative language for modeling a sophisticated healthcare process scenario from the real world. The scenario is subject to complex temporal constraints and entails the need for coordinating the constraint-based interactions among the processes related to a patient treatment process. As demonstrated in this work, the selected real process scenario can be suitably modeled through a declarative approach.Ministerio de Economía y Competitividad TIN2016-76956-C3-2-RMinisterio de Economía y Competitividad TIN2015-71938-RED