Timing verification of dynamically reconfigurable logic for Xilinx Virtex FPGA series

This paper reports on a method for extending existing VHDL design and verification software available for the Xilinx Virtex series of FPGAs. It allows the designer to apply standard hardware design and verification tools to the design of dynamically reconfigurable logic (DRL). The technique involves the conversion of a dynamic design into multiple static designs, suitable for input to standard synthesis and APR tools. For timing and functional verification after APR, the sections of the design can then be recombined into a single dynamic system. The technique has been automated by extending an existing DRL design tool named DCSTech, which is part of the Dynamic Circuit Switching (DCS) CAD framework. The principles behind the tools are generic and should be readily extensible to other architectures and CAD toolsets. Implementation of the dynamic system involves the production of partial configuration bitstreams to load sections of circuitry. The process of creating such bitstreams, the final stage of our design flow, is summarized

Localization of the human dihydrolipoamide dehydrogenase gene (DLD) to 7q31→q32

The gene for human dihydrolipoamide dehydrogenase (DLD) has been localized to the long arm of chromosome 7, within bands q31→q32, by gel-blot hybridization analysis with DNA from a panel of somatic cell hybrids containing various portions of human chromosome 7.published_or_final_versio

Localization of the human gene encoding the 13.3-kDa subunit of mitochondrial complex III (UQCRB) to 8q22 by in situ hybridization

We have localized the human gene encoding the 13.3-kDa subunit of mitochondrial complex III (UQCRB) to chromosome 8 using both radioactive in situ hybridization and fluorescence in situ hybridization. The additional peak obtained with the former method is attributed to the higher sensitivity of this technique, which results in hybridization of the probe to the less conserved pseudogene. We therefore conclude that the functional gene is most likely located at 8q22.published_or_final_versio

Genome-Wide Association Analysis Identifies a Mutation in the Thiamine Transporter 2 (SLC19A3) Gene Associated with Alaskan Husky Encephalopathy

Alaskan Husky Encephalopathy (AHE) has been previously proposed as a mitochondrial encephalopathy based on neuropathological similarities with human Leigh Syndrome (LS). We studied 11 Alaskan Husky dogs with AHE, but found no abnormalities in respiratory chain enzyme activities in muscle and liver, or mutations in mitochondrial or nuclear genes that cause LS in people. A genome wide association study was performed using eight of the affected dogs and 20 related but unaffected control AHs using the Illumina canine HD array. SLC19A3 was identified as a positional candidate gene. This gene controls the uptake of thiamine in the CNS via expression of the thiamine transporter protein THTR2. Dogs have two copies of this gene located within the candidate interval (SLC19A3.2 – 43.36–43.38 Mb and SLC19A3.1 – 43.411–43.419 Mb) on chromosome 25. Expression analysis in a normal dog revealed that one of the paralogs, SLC19A3.1, was expressed in the brain and spinal cord while the other was not. Subsequent exon sequencing of SLC19A3.1 revealed a 4bp insertion and SNP in the second exon that is predicted to result in a functional protein truncation of 279 amino acids (c.624 insTTGC, c.625 C>A). All dogs with AHE were homozygous for this mutation, 15/41 healthy AH control dogs were heterozygous carriers while 26/41 normal healthy AH dogs were wild type. Furthermore, this mutation was not detected in another 187 dogs of different breeds. These results suggest that this mutation in SLC19A3.1, encoding a thiamine transporter protein, plays a critical role in the pathogenesis of AHE.University of California, Davis. School of Veterinary Medicine. Center for Companion Animal Healt

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Synthesis of an ordered mesoporous carbon with graphitic characteristics and its application for dye adsorption

An ordered mesoporous carbon (OMC) was prepared by a chemical vapor deposition technique using liquid petroleum gas (LPG) as the carbon source. During synthesis, LPG was effectively adsorbed in the ordered mesopores of SBA-15 silica and converted to a graphitic carbon at 800 °C. X-ray diffraction and nitrogen adsorption/desorption data and high-resolution transmission electron microscopy (HRTEM) of the OMC confirmed its ordered mesoporous structure. The OMC was utilized as an adsorbent in the removal of dyes from aqueous solution. A commercial powder activated carbon (AC) was also investigated to obtain comparative data. The efficiency of the OMC for dye adsorption was tested using acidic dye acid orange 8 (AO8) and basic dyes methylene blue (MB) and rhodamine B (RB). The results show that adsorption was affected by the molecular size of the dye, the textural properties of carbon adsorbent and surface-dye interactions. The adsorption capacities of the OMC for acid orange 8 (AO8), methylene blue (MB) and rhodamine B (RB) were determined to be 222, 833, and 233 mg/g, respectively. The adsorption capacities of the AC for AO8, MB, and RB were determined to be 141, 313, and 185 mg/ g, respectively. The OMC demonstrated to be an excellent adsorbent for the removal of MB from wastewater.Web of Scienc

Individual rules for trail pattern formation in Argentine ants (Linepithema humile)

We studied the formation of trail patterns by Argentine ants exploring an empty arena. Using a novel imaging and analysis technique we estimated pheromone concentrations at all spatial positions in the experimental arena and at different times. Then we derived the response function of individual ants to pheromone concentrations by looking at correlations between concentrations and changes in speed or direction of the ants. Ants were found to turn in response to local pheromone concentrations, while their speed was largely unaffected by these concentrations. Ants did not integrate pheromone concentrations over time, with the concentration of pheromone in a 1 cm radius in front of the ant determining the turning angle. The response to pheromone was found to follow a Weber's Law, such that the difference between quantities of pheromone on the two sides of the ant divided by their sum determines the magnitude of the turning angle. This proportional response is in apparent contradiction with the well-established non-linear choice function used in the literature to model the results of binary bridge experiments in ant colonies (Deneubourg et al. 1990). However, agent based simulations implementing the Weber's Law response function led to the formation of trails and reproduced results reported in the literature. We show analytically that a sigmoidal response, analogous to that in the classical Deneubourg model for collective decision making, can be derived from the individual Weber-type response to pheromone concentrations that we have established in our experiments when directional noise around the preferred direction of movement of the ants is assumed.Comment: final version, 9 figures, submitted to Plos Computational Biology (accepted

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal