Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters

Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were use

A runtime approach to dynamic resource allocation for sparse direct solvers

International audience—To face the advent of multicore processors and the ever increasing complexity of hardware architectures, pro-gramming models based on DAG-of-tasks parallelism regained popularity in the high performance, scientific computing com-munity. In this context, enabling HPC applications to perform efficiently when dealing with graphs of parallel tasks that could potentially run simultaneously is a great challenge. Even if a uniform runtime system is used underneath, scheduling multiple parallel tasks over the same set of hardware resources introduces many issues, such as undesirable cache flushes or memory bus contention. In this paper, we show how runtime system-based scheduling contexts can be used to dynamically enforce locality of parallel tasks on multicore machines. We extend an existing generic sparse direct solver to use our mechanism and introduce a new decomposition method based on proportional mapping that is used to build the scheduling contexts. We propose a runtime-level dynamic context management policy to cope with the very irregular behavior of the application. A detailed performance analysis shows significant performance improvements of the solver over various multicore hardware

Author manuscript, published in "Third International Workshop on Accelerators and Hybrid Exascale Systems (2013)" 1 Composing multiple StarPU applications over heterogeneous machines: a supervised approach

Abstract—Enabling HPC applications to perform efficiently when invoking multiple parallel libraries simultaneously is a great challenge. Even if a single runtime system is used underneath, scheduling tasks or threads coming from different libraries over the same set of hardware resources introduces many issues, such as resource oversubscription, undesirable cache flushes or memory bus contention. This paper presents an extension of StarPU, a runtime system specifically designed for heterogeneous architectures, that allows multiple parallel codes to run concurrently with minimal interference. Such parallel codes run within scheduling contexts that provide confined execution environments which can be used to partition computing resources. Scheduling contexts can be dynamically resized to optimize the allocation of computing resources among concurrently running libraries. We introduce a hypervisor that automatically expands or shrinks contexts using feedback from the runtime system (e.g. resource utilization). We demonstrate the relevance of our approach using benchmarks invoking multiple high performance linear algebra kernels simultaneously on top of heterogeneous multicore machines. We show that our mechanism can dramatically improve the overall application run time (-34%), most notably by reducing the average cache miss ratio (-50%). I

Clinical impact of MUC1 and MUC4 expression in Barrett-associated oesophageal adenocarcinoma

International audienceAims: To study the expression of MUC1 and MUC4 mucins in Barrett-associated oesophageal adenocarcinoma and coexisting lesions of the carcinogenic sequence (normal mucosa, metaplasia, dysplasia) if present, and to investigate their prognostic significance.Methods: The expression profiles of MUC1 and MUC4 were investigated by immunohistochemistry in tissue samples obtained from consecutive patients with primary surgically resected lower third oesophageal adenocarcinoma (OA) between 1997 and 2002. Histopathological parameters, recurrence and long-term survival were correlated with the number of cells stained.Results: All 52 patients exhibited OA, with 25 patients (48.1%) having associated Barrett oesophagus lesions (metaplasia or/and dysplasia). MUC1 and MUC4 were expressed in 52 and 41 of the 52 patients with adenocarcinoma (100% and 78%), respectively. All samples expressed MUC1 strongly. The prevalence of MUC4 staining was significantly decreased in metaplasia compared with normal mucosa (53% versus 92%, p<0.001). No correlation was found between the level of MUC1 or MUC4 expression in OA and histopathological variables, recurrence or survival.Conclusions: MUC1 and MUC4 are strongly expressed in OA. The results do not support a role for these two membrane-bound mucins as either a phenotypic or a prognostic marker for the development of Barrett OA. There are several other membrane-bound mucins that have not yet been evaluated in this situation