Modeling the Scalability of the EuroExa Reconfigurable Accelerators - Preliminary Results

Current technology and application trends push for both performance and power efficiency. EuroEXA is a project that tries to achieve these goals and push its performance to exascale performance. Towards this objective, EuroEXA node integrate reconfigurable (FPGA) accelerators to offload computational intensive workloads. To fully utilize the FPGA’s resource pool, multiple accelerators must be instantiated. System design and dimensioning requires an early performance estimation to evaluate different design options, including using larger FPGA devices, instantiating larger number of accelerator instances, etc. In this paper, we present the preliminary results of modeling the scalability of EuroEXA reconfigurable accelerators in the FPGA fabric. We start by using simple equations to bound the total number of kernels that can work in parallel depending on the available memory channels and reconfigurable resources. Then, we use a 2nd degree polynomial model to predict the performance benefits of instantiating multiple replicated kernels in a FPGA. The model suggests whether the switching to another larger FPGA is advantageous choice in terms of performance. We verify our results using micro-benchmarks on two state-of-the-art FPGAs; AlveoU50 and AlveoU280

Accurate microRNA target prediction correlates with protein repression levels

MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and diseas

Pseudomonas viridiflava, a Multi Host Plant Pathogen with Significant Genetic Variation at the Molecular Level

The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan), as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR) and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB), and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species

Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots

Comparative genomics of closely related pathogens that differ in host range can provide insights into mechanisms of host-pathogen interactions and host adaptation. Furthermore, sequencing of multiple strains with the same host range reveals information concerning pathogen diversity and the molecular basis of virulence. Here we present a comparative analysis of draft genome sequences for four strains of Pseudomonas cannabina pathovar alisalensis (Pcal), which is pathogenic on a range of monocotyledonous and dicotyledonous plants. These draft genome sequences provide a foundation for understanding host range evolution across the monocot-dicot divide. Like other phytopathogenic pseudomonads, Pcal strains harboured a hrp/hrc gene cluster that codes for a type III secretion system. Phylogenetic analysis based on the hrp/hrc cluster genes/proteins, suggests localized recombination and functional divergence within the hrp/hrc cluster. Despite significant conservation of overall genetic content across Pcal genomes, comparison of type III effector repertoires reinforced previous molecular data suggesting the existence of two distinct lineages within this pathovar. Furthermore, all Pcal strains analyzed harbored two distinct genomic islands predicted to code for type VI secretion systems (T6SSs). While one of these systems was orthologous to known P. syringae T6SSs, the other more closely resembled a T6SS found within P. aeruginosa. In summary, our study provides a foundation to unravel Pcal adaptation to both monocot and dicot hosts and provides genetic insights into the mechanisms underlying pathogenicity

Feature-based SpMV Performance Analysis on Contemporary Devices

The SpMV kernel is characterized by high performance variation per input matrix and computing platform. While GPUs were considered State-of-the-Art for SpMV, with the emergence of advanced multicore CPUs and low-power FPGA accelerators, we need to revisit its performance and energy efficiency. This paper provides a high-level SpMV performance analysis based on structural features of matrices related to common bottlenecks of memory-bandwidth intensity, low ILP, load imbalance and memory latency overheads. Towards this, we create a wide artificial matrix dataset that spans these features and study the performance of different storage formats in nine modern HPC platforms; five CPUs, three GPUs and an FPGA. After validating our proposed methodology using real-world matrices, we analyze our extensive experimental results and draw key insights on the competitiveness of different target architectures for SpMV and the impact of each feature/bottleneck on its performance

Cancer patients with large defects. Reconstructional options: a case study

Referimo-nos ao caso de um paciente masculino de setenta e cinco anos de idade, com um carcinoma espinocelular (SCC), que se originou na parte exterior da orelha direita há quatro anos. Sofreu uma remoção cirúrgica da parte lesionada combinada com dissecção modificada do pescoço e reconstrução com o uso de retalho peitoral maior. Além disso, teve radioterapia com 6000 rads na região temporal direita. Há dois meses o paciente mostrou urna recorrência expansiva no que diz respeito ao músculo temporal e ao osso, o osso litóide, os músculos masseter e os músculos pterigóideos, a parte direita da mandíbula, a glândula da parótida com o nervo facial, e o bulbo superior da veia jugular interna. Sofreu uma remoção cirúrgica da lesão afetada até as extremidades saudáveis e reconstrução estética e funcional com a utilização combinada de uma prótese de metal fixa do côndilo e da mandíbula direita e o uso de músculo-cutâneo trapezious flap. Apresentamos o relato de um caso sobre as opções de reconstrução que nós temos em nossos dias para proporcionar qualidade de vida a doentes que sofrem de cancro.We report a case of a seventy-five years old male patient with a squamous cell carcinoma (SCC) originated from the right external ear four years ago. He was undergone surgical removal of the lesion with a combination of modified neck dissection and reconstruction with the use of pectoralis major flap. Furthermore, he had radiotherapy with 6000 rads of the right temporal region. Two months ago the patient showed an extended recurrence concerning the temporal muscle and bone, the lithoid bone, the maseter and the pterygoids muscles, the right part of the mandible, the parotid gland with the facial nerve, and the superior bulb of the internal jugular vein. He had a surgical removal of the lesion in extended healthy margins and functional and esthetic reconstruction of the defect with a combination of metal fixed prosthesis of the condyle and the right mandible and the use of myocutaneous trapezious flap. This is a case report of the reconstruction options we have nowadays to provide quality of life in cancer patients

LOPAT tests of eighteen local (Crete, Greece) <i>P. viridiflava</i> isolates along with <i>P. viridiflava</i> reference strain NCPPB1249 and other pseudomonads.

<p>LOPAT tests of eighteen local (Crete, Greece) <i>P. viridiflava</i> isolates along with <i>P. viridiflava</i> reference strain NCPPB1249 and other pseudomonads.</p

<i>P. viridiflava</i> phylogenetic trees, utilizing <i>rpoB</i> sequences along with sequences obtained from GenBank.

<p>The evolutionary history was inferred using the Neighbor-Joining method. Tree construction and evolutionary distances were carried out as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036090#pone-0036090-g002" target="_blank">Figure 2</a> legend. The analysis involved 27 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 741 positions in the final dataset. The methodology used for the evolutionary analysis, tree construction and other details are described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036090#pone-0036090-g003" target="_blank">Figure 3</a> legend.</p

<i>P. viridiflava</i> phylogenetic trees, utilizing <i>rpoD</i> sequences along with sequences obtained from GenBank.

<p>The evolutionary history was inferred using the Neighbor-Joining method. Tree construction and evolutionary distances were carried out as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036090#pone-0036090-g002" target="_blank">Figure 2</a> legend. The analysis involved 32 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. The methodology used for the evolutionary analysis, tree construction and other details are described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036090#pone-0036090-g003" target="_blank">Figure 3</a> legend.</p