Toward a Core Design to Distribute an Execution on a Many-Core Processor

International audienceThis paper presents a parallel execution model and a many-core processor design to run C programs in parallel. The model automatically builds parallel sections of machine instructions from the run trace. It parallelizes instructions fetches, renamings, executions and retirements. Predictor based fetch is replaced by a fetch-decode-and-partly-execute stage able to compute in-order most of the control instructions. Tomasulo's register renaming is extended to memory with a technique to match consumer/producer pairs. The Reorder Buffer is adapted to allow parallel retirement. The model is presented on a sum reduction example which is also used to give a short analytical evaluation of the model performance potential

The Comparative Toxicogenomics Database: update 2011

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the interaction of environmental chemicals with gene products, and their effects on human health. Biocurators at CTD manually curate a triad of chemical–gene, chemical–disease and gene–disease relationships from the literature. These core data are then integrated to construct chemical–gene–disease networks and to predict many novel relationships using different types of associated data. Since 2009, we dramatically increased the content of CTD to 1.4 million chemical–gene–disease data points and added many features, statistical analyses and analytical tools, including GeneComps and ChemComps (to find comparable genes and chemicals that share toxicogenomic profiles), enriched Gene Ontology terms associated with chemicals, statistically ranked chemical–disease inferences, Venn diagram tools to discover overlapping and unique attributes of any set of chemicals, genes or disease, and enhanced gene pathway data content, among other features. Together, this wealth of expanded chemical–gene–disease data continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases. CTD is freely available at http://ctd.mdibl.org

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks

The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical–gene interactions, chemical–disease relationships and gene–disease relationships from the literature. This strategy allows data to be integrated to construct chemical–gene–disease networks. CTD is unique in numerous respects: curation focuses on environmental chemicals; interactions are manually curated; interactions are constructed using controlled vocabularies and hierarchies; additional gene attributes (such as Gene Ontology, taxonomy and KEGG pathways) are integrated; data can be viewed from the perspective of a chemical, gene or disease; results and batch queries can be downloaded and saved; and most importantly, CTD acts as both a knowledgebase (by reporting data) and a discovery tool (by generating novel inferences). Over 116 000 interactions between 3900 chemicals and 13 300 genes have been curated from 270 species, and 5900 gene–disease and 2500 chemical–disease direct relationships have been captured. By integrating these data, 350 000 gene–disease relationships and 77 000 chemical–disease relationships can be inferred. This wealth of chemical–gene–disease information yields testable hypotheses for understanding the effects of environmental chemicals on human health. CTD is freely available at http://ctd.mdibl.org

Quantum dots coordinated with conjugated organic ligands: new nanomaterials with novel photophysics

CdSe quantum dots functionalized with oligo-(phenylene vinylene) (OPV) ligands (CdSe-OPV nanostructures) represent a new class of composite nanomaterials with significantly modified photophysics relative to bulk blends or isolated components. Single-molecule spectroscopy on these species have revealed novel photophysics such as enhanced energy transfer, spectral stability, and strongly modified excited state lifetimes and blinking statistics. Here, we review the role of ligands in quantum dot applications and summarize some of our recent efforts probing energy and charge transfer in hybrid CdSe-OPV composite nanostructures