Computing Execution Times with eXecution Decision Diagrams in the Presence of Out-Of-Order Resources

Worst-Case Execution Time (WCET) is a key component for the verification of critical real-time applications. Yet, even the simplest microprocessors implement pipelines with concurrently-accessed resources, such as the memory bus shared by fetch and memory stages. Although their in-order pipelines are, by nature, very deterministic, the bus can cause out-of-order accesses to the memory and, therefore, timing anomalies: local timing effects that can have global effects but that cannot be easily composed to estimate the global WCET. To cope with this situation, WCET analyses have to generate important over-estimations in order to preserve safety of the computed times or have to explicitly track all possible executions. In the latter case, the presence of out-of-order behavior leads to a combinatorial blowup of the number of pipeline states for which efficient state abstractions are difficult to design. This paper proposes instead a compact and exact representation of the timings in the pipeline, using eXecution Decision Diagram (XDD) [1]. We show how XDD can be used to model pipeline states all along the execution paths by leveraging the algebraic properties of XDD. This computational model allows to compute the exact temporal behavior at control flow graph level and is amenable to efficiently and precisely support WCET calculation in presence of out-of-order bus accesses. This model is finally experimented on the TACLe benchmark suite and we observe good performance making this approach appropriate for industrial applications

Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Microarray profiling has the potential to illuminate the molecular processes that govern the phenotypic characteristics of porcine skeletal muscles, such as hypertrophy or atrophy, and the expression of specific fibre types. This information is not only important for understanding basic muscle biology but also provides underpinning knowledge for enhancing the efficiency of livestock production. Results We report on the de novo development of a composite skeletal muscle cDNA microarray, comprising 5500 clones from two developmentally distinct cDNA libraries (longissimus dorsi of a 50-day porcine foetus and the gastrocnemius of a 3-day-old pig). Clones selected for the microarray assembly were of low to moderate abundance, as indicated by colony hybridisation. We profiled the differential expression of genes between the psoas (red muscle) and the longissimus dorsi (white muscle), by co-hybridisation of Cy3 and Cy5 labelled cDNA derived from these two muscles. Results from seven microarray slides (replicates) correctly identified genes that were expected to be differentially expressed, as well as a number of novel candidate regulatory genes. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray. Conclusion We have developed a porcine skeletal muscle cDNA microarray and have identified a number of candidate genes that could be involved in muscle phenotype determination, including several members of the casein kinase 2 signalling pathway.Peer Reviewe

Transportation Logistics and Economics of the Processed Meat and Related Industries in Southwest Kansas

Kansas is one of the nation’s leaders in meat production. Specifically, in the southwest Kansas region, there are more than three hundred feed yards and four meat processing plants. Traditionally, processed meat, some of the meat byproducts, grain, and other industry-related products are transported using large trucks (tractor-trailers). In addition to the highway system, there are two Class I railroad carriers and four Class III railroad carriers in the southwest Kansas region. Because there is a rich railroad network in the southwest Kansas region, it is necessary to study whether there is a need to utilize other transportation modes, such as railroad and intermodal, to transport goods and products for the processed meat and related industries. The objectives of this research are to study the transportation modes, their utilizations for the processed meat and related industries in southwest Kansas, and their impacts on local economic development. To achieve the objectives, the research team conducted a literature review, collected data through site visits, interviews, and web-sites, estimated vehicle miles of travel (VMT) by truck using TransCAD software, and projected future growth of processed meat and related industries as well as emerging industry development in the region. The research results demonstrate that there is heavy usage of trucks in the southwest Kansas region which need to be diversified to other transportation modes such as railroad and intermodal. To utilize railroad and intermodal transportation for the processed meat and related industries, there is a need to build required infrastructure near or within the feed yards and meat processing plants to support these transportation modes. In addition, to use the railroad for transporting feed grains, the system infrastructure of short line railroads needs to be improved. During this project, the research team also found that two new industries, dairy and ethanol, are emerging in southwest Kansas. With the development of new businesses, the demand on railroad service (both Class I and Class III) has been increasing recently. Thus, it is important to have adequate investment in railroad infrastructure, particularly, to keep short line railroads running rather than being abandoned

NIPA Defines an SCF-Type Mammalian E3 Ligase that Regulates Mitotic Entry

SummaryThe regulated oscillation of protein expression is an essential mechanism of cell cycle control. The SCF class of E3 ubiquitin ligases is involved in this process by targeting cell cycle regulatory proteins for degradation by the proteasome, with the F-box subunit of the SCF specifically recruiting a given substrate to the SCF core. Here we identify NIPA (nuclear interaction partner of ALK) as a human F-box-containing protein that defines an SCF-type E3 ligase (SCFNIPA) controlling mitotic entry. Assembly of this SCF complex is regulated by cell-cycle-dependent phosphorylation of NIPA, which restricts substrate ubiquitination activity to interphase. We show nuclear cyclin B1 to be a substrate of SCFNIPA. Inactivation of NIPA by RNAi results in nuclear accumulation of cyclin B1 in interphase, activation of cyclin B1-Cdk1 kinase activity, and premature mitotic entry. Thus, SCFNIPA-based ubiquitination may regulate S-phase completion and mitotic entry in the mammalian cell cycle

Novel algorithms for improved detection and analysis of fluorescent signal fluctuations

Fluorescent dyes and genetically encoded fuorescence indicators (GEFI) are common tools for visualizing concentration changes of specifc ions and messenger molecules during intra- as well as intercellular communication. Using advanced imaging technologies, fuorescence indicators are a prerequisite for the analysis of physiological molecular signaling. Automated detection and analysis of fuorescence signals require to overcome several challenges, including correct estimation of fuorescence fuctuations at basal concentrations of messenger molecules, detection, and extraction of events themselves as well as proper segmentation of neighboring events. Moreover, event detection algorithms need to be sensitive enough to accurately capture localized and low amplitude events exhibiting a limited spatial extent. Here, we present two algorithms (PBasE and CoRoDe) for accurate baseline estimation and automated detection and segmentation of fuorescence fuctuations

Sex-specific hippocampal metabolic signatures at the onset of systemic inflammation with lipopolysaccharide in the APPswe/PS1dE9 mouse model of Alzheimer's disease

Systemic inflammation enhances the risk and progression of Alzheimer's disease (AD). Lipopolysaccharide (LPS), a potent pro-inflammatory endotoxin produced by the gut, is found in excess levels in AD where it associates with neurological hallmarks of pathology. Sex differences in susceptibility to inflammation and AD progression have been reported, but how this impacts on LPS responses remains under investigated. We previously reported in an APP/PS1 model of AD that systemic LPS administration rapidly altered hippocampal metabolism in males. Here, we used untargeted metabolomics to comprehensively identify hippocampal metabolic processes occurring at onset of systemic inflammation with LPS (100µg/kg, i.v.) in APP/PS1 mice, at an early pathological stage, and investigated the sexual dimorphism in this response. Four hours after LPS administration, both pro-and anti-inflammatory pathways were simultaneously recruited in the hippocampi of 4.5-month-old mice with a more pronounced anti-inflammatory component in females despite their pro-inflammatory metabolic signature in the absence of immune stimulation. LPS induced comparable behavioural sickness responses in male and female wild-type and APP/PS1 mice and comparable activation of both the serotonin and kynurenine pathways of tryptophan metabolism in their hippocampi. Males also exhibited a greater temperature response to LPS associated with a pro-inflammatory-like downregulation of pyruvate metabolism, exacerbated in APP/PS1 males, and methionine metabolism whereas females showed a greater cytokine response and anti-inflammatory-like downregulation of hippocampal methylglyoxal and methionine metabolism. Metabolic changes were not associated with morphological markers of immune cell activation suggesting that they constitute an early event in the development of LPS-induced neuroinflammation and AD exacerbation. These data suggest that the female hippocampus is more tolerant to acute systemic inflammation

A Facile and General Method for the Encapsulation of Different Types of Imaging Contrast Agents Within Micrometer-Sized Polymer Beads

Polystyrene (PS) hollow beads with holes on the surfaces are employed as containers for quick loading and encapsulation of a variety of contrast enhancement agents: saline solutions for thermoacoustic tomography, iodinated organic compounds for micro-computed tomography, and perfluorooctane for magnetic resonance. Because of the hole on the surface of the PS hollow bead, the contrast agent to be encapsulated could quickly enter the hollow interior via direct flow rather than slow diffusion through the wall. After loading, the hole on the surface is conveniently sealed by annealing the sample at a temperature (e.g., 95 °C) slightly above the glass-transition temperature of PS. In vitro methods are also used to investigate the effectiveness of encapsulation by quantifying the contrast enhancement enabled by the contrast agents

Parental transfer of the antimicrobial protein LBP/BPI protects Biomphalaria glabrata eggs against oomycete infections

Copyright: © 2013 Baron et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by ANR (ANR-07-BLAN-0214 and ANR-12-EMMA-00O7-01), CNRS and INRA. PvW was financially supported by the BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Impact Assessment Modeling of Low-Water Management Policy

International audienceWe briefly present the main steps involved in designing and developing a platform for the numerical simulation of environmental and social impacts of the implementation of new environmental norms related to low-water management in France (MAELIA Project: multi-agents for environmental norms impact assessment). Some results are highlighted concerning in particular the structure of the underlying low-water management model and the process and agents' activity modeling