Specification and Verification of Media Constraints using UPPAAL

We present the formal specification and verification of a multimedia stream. The stream is described in a timed automata notation. We verify that the stream satisfies certain quality of service properties, in particular, throughput and end-to-end latency. The verification tool used is the real-time model checker UPPAAL

Wall Orientation and Shear Stress in the Lattice Boltzmann Model

The wall shear stress is a quantity of profound importance for clinical diagnosis of artery diseases. The lattice Boltzmann is an easily parallelizable numerical method of solving the flow problems, but it suffers from errors of the velocity field near the boundaries which leads to errors in the wall shear stress and normal vectors computed from the velocity. In this work we present a simple formula to calculate the wall shear stress in the lattice Boltzmann model and propose to compute wall normals, which are necessary to compute the wall shear stress, by taking the weighted mean over boundary facets lying in a vicinity of a wall element. We carry out several tests and observe an increase of accuracy of computed normal vectors over other methods in two and three dimensions. Using the scheme we compute the wall shear stress in an inclined and bent channel fluid flow and show a minor influence of the normal on the numerical error, implying that that the main error arises due to a corrupted velocity field near the staircase boundary. Finally, we calculate the wall shear stress in the human abdominal aorta in steady conditions using our method and compare the results with a standard finite volume solver and experimental data available in the literature. Applications of our ideas in a simplified protocol for data preprocessing in medical applications are discussed.Comment: 9 pages, 11 figure

Relational Concurrent Refinement II: Internal Operations and Outputs

Two styles of description arise naturally in formal specification: state-based and behavioural. In state-based notations, a system is characterised by a collection of variables, and their values determine which actions may occur throughout a system history. Behavioural specifications describe the chronologies of actions -- interactions between a system and its environment. The exact nature of such interactions is captured in a variety of semantic models with corresponding notions of refinement; refinement in state based systems is based on the semantics of sequential programs and is modelled relationally. Acknowledging that these viewpoints are complementary, substantial research has gone into combining the paradigms. The purpose of this paper is to do three things. First, we survey recent results linking the relational model of refinement to the process algebraic models. Specifically, we detail how variations in the relational framework lead to relational data refinement being in correspondence with traces-divergences, singleton failures and failures-divergences refinement in a process semantics. Second, we generalise these results by providing a general flexible scheme for incorporating the two main ''erroneous'' concurrent behaviours: deadlock and divergence, into relational refinement. This is shown to subsume previous characterisations. In doing this we derive relational refinement rules for specifications containing both internal operations and outputs that corresponds to failures-divergences refinement. Third, the theory has been formally specified and verified using the interactive theorem prover KIV

Metal Ion-dependent Heavy Chain Transfer Activity of TSG-6 Mediates Assembly of the Cumulus-Oocyte Matrix

The matrix polysaccharide hyaluronan (HA) has a critical role in the expansion of the cumulus cell-oocyte complex (COC), a process that is necessary for ovulation and fertilization in most mammals. Hyaluronan is organized into a cross-linked network by the cooperative action of three proteins, inter-α-inhibitor (IαI), pentraxin-3, and TNF-stimulated gene-6 (TSG-6), driving the expansion of the COC and providing the cumulus matrix with its required viscoelastic properties. Although it is known that matrix stabilization involves the TSG-6-mediated transfer of IαI heavy chains (HCs) onto hyaluronan (to form covalent HC·HA complexes that are cross-linked by pentraxin-3) and that this occurs via the formation of covalent HC·TSG-6 intermediates, the underlying molecular mechanisms are not well understood. Here, we have determined the tertiary structure of the CUB module from human TSG-6, identifying a calcium ion-binding site and chelating glutamic acid residue that mediate the formation of HC·TSG-6. This occurs via an initial metal ion-dependent, non-covalent, interaction between TSG-6 and HCs that also requires the presence of an HC-associated magnesium ion. In addition, we have found that the well characterized hyaluronan-binding site in the TSG-6 Link module is not used for recognition during transfer of HCs onto HA. Analysis of TSG-6 mutants (with impaired transferase and/or hyaluronan-binding functions) revealed that although the TSG-6-mediated formation of HC·HA complexes is essential for the expansion of mouse COCs in vitro, the hyaluronan-binding function of TSG-6 does not play a major role in the stabilization of the murine cumulus matrix

Studying Parton Energy Loss in Heavy-Ion Collisions via Direct-Photon and Charged-Particle Azimuthal Correlations

Charged-particle spectra associated with direct photon ($\gamma_{dir}$) and $\pi^0$ are measured in $p$+$p$ and Au+Au collisions at center-of-mass energy $\sqrt{s_{_{NN}}}=200$ GeV with the STAR detector at RHIC. A hower-shape analysis is used to partially discriminate between $\gamma_{dir}$ and $\pi^0$. Assuming no associated charged particles in the $\gamma_{dir}$ direction (near side) and small contribution from fragmentation photons ($\gamma_{frag}$), the associated charged-particle yields opposite to $\gamma_{dir}$ (away side) are extracted. At mid-rapidity ($|\eta|<0.9$) in central Au+Au collisions, charged-particle yields associated with $\gamma_{dir}$ and $\pi^0$ at high transverse momentum ($8< p_{T}^{trig}<16$ GeV/$c$) are suppressed by a factor of 3-5 compared with $p$ + $p$ collisions. The observed suppression of the associated charged particles, in the kinematic range $|\eta|<1$ and $3< p_{T}^{assoc} < 16$ GeV/$c$, is similar for $\gamma_{dir}$ and $\pi^0$, and independent of the $\gamma_{dir}$ energy within uncertainties. These measurements indicate that the parton energy loss, in the covered kinematic range, is insensitive to the parton path length.Comment: submitted to Phys. Rev. Lett, 6 pages, 4 figure

Exclusive Leptoproduction of rho^0 Mesons from Hydrogen at Intermediate Virtual Photon Energies

Measurements of the cross section for exclusive virtual-photoproduction of rho^0 mesons from hydrogen are reported. The data were collected by the HERMES experiment using 27.5 GeV positrons incident on a hydrogen gas target in the HERA storage ring. The invariant mass W of the photon-nucleon system ranges from 4.0 to 6.0 GeV, while the negative squared four-momentum Q^2 of the virtual photon varies from 0.7 to 5.0 GeV^2. The present data together with most of the previous data at W > 4 GeV are well described by a model that infers the W-dependence of the cross section from the dependence on the Bjorken scaling variable x of the unpolarized structure function for deep-inelastic scattering. In addition, a model calculation based on Off-Forward Parton Distributions gives a fairly good account of the longitudinal component of the rho^0 production cross section for Q^2 > 2 GeV^2.Comment: 10 pages, 6 embedded figures, LaTeX for SVJour(epj) document class. Revisions: curves added to Fig. 1, several clarifications added to tex

DNA microarray revealed and RNAi plants confirmed key genes conferring low Cd accumulation in barley grains

List of genes down-regulated in both W6nk2 and Zhenong8 after 15 days exposure to 5 ΟM Cd. (DOC 130 kb

Growth of Long Range Forward-Backward Multiplicity Correlations with Centrality in Au+Au Collisions at sNN\sqrt{s_{NN}} = 200 GeV

Forward-backward multiplicity correlation strengths have been measured with the STAR detector for Au+Au and $\textit{p+p}$ collisions at $\sqrt{s_{NN}}$ = 200 GeV. Strong short and long range correlations (LRC) are seen in central Au+Au collisions. The magnitude of these correlations decrease with decreasing centrality until only short range correlations are observed in peripheral Au+Au collisions. Both the Dual Parton Model (DPM) and the Color Glass Condensate (CGC) predict the existence of the long range correlations. In the DPM the fluctuation in the number of elementary (parton) inelastic collisions produces the LRC. In the CGC longitudinal color flux tubes generate the LRC. The data is in qualitative agreement with the predictions from the DPM and indicates the presence of multiple parton interactions.Comment: 6 pages, 3 figures The abstract has been slightly modifie

K/pi Fluctuations at Relativistic Energies

We report results for $K/\pi$ fluctuations from Au+Au collisions at $\sqrt{s_{NN}}$ = 19.6, 62.4, 130, and 200 GeV using the STAR detector at the Relativistic Heavy Ion Collider. Our results for $K/\pi$ fluctuations in central collisions show little dependence on the incident energies studied and are on the same order as results observed by NA49 at the Super Proton Synchrotron in central Pb+Pb collisions at $\sqrt{s_{NN}}$ = 12.3 and 17.3 GeV. We also report results for the collision centrality dependence of $K/\pi$ fluctuations as well as results for $K^{+}/\pi^{+}$, $K^{-}/\pi^{-}$, $K^{+}/\pi^{-}$, and $K^{-}/\pi^{+}$ fluctuations. We observe that the $K/\pi$ fluctuations scale with the multiplicity density, $dN/d\eta$, rather than the number of participating nucleons.Comment: 6 pages, 4 figure

The case for strategic international alliances to harness nutritional genomics for public and personal health

Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene-nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient-genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countrie