Probabilistic abstract interpretation: From trace semantics to DTMC’s and linear regression

In order to perform probabilistic program analysis we need to consider probabilistic languages or languages with a probabilistic semantics, as well as a corresponding framework for the analysis which is able to accommodate probabilistic properties and properties of probabilistic computations. To this purpose we investigate the relationship between three different types of probabilistic semantics for a core imperative language, namely Kozen’s Fixpoint Semantics, our Linear Operator Semantics and probabilistic versions of Maximal Trace Semantics. We also discuss the relationship between Probabilistic Abstract Interpretation (PAI) and statistical or linear regression analysis. While classical Abstract Interpretation, based on Galois connection, allows only for worst-case analyses, the use of the Moore-Penrose pseudo inverse in PAI opens the possibility of exploiting statistical and noisy observations in order to analyse and identify various system properties

An Algorithmic Approach to Quantum Field Theory

The lattice formulation provides a way to regularize, define and compute the Path Integral in a Quantum Field Theory. In this paper we review the theoretical foundations and the most basic algorithms required to implement a typical lattice computation, including the Metropolis, the Gibbs sampling, the Minimal Residual, and the Stabilized Biconjugate inverters. The main emphasis is on gauge theories with fermions such as QCD. We also provide examples of typical results from lattice QCD computations for quantities of phenomenological interest.Comment: 44 pages, to be published in IJMP

Properties of charmonium in lattice QCD with 2+1 flavors of improved staggered sea quarks

We use the dynamical gluon configurations provided by the MILC collaboration in a study of the charmonium spectrum and psi leptonic width. We examine sea quark effects on mass splitting and on the leptonic decay matrix element for light masses as low as m_s/5, while keeping the strange quark mass fixed and the lattice spacing nearly constant.Comment: Lattice2003(heavy

Light hadrons with improved staggered quarks: approaching the continuum limit

We have extended our program of QCD simulations with an improved Kogut-Susskind quark action to a smaller lattice spacing, approximately 0.09 fm. Also, the simulations with a approximately 0.12 fm have been extended to smaller quark masses. In this paper we describe the new simulations and computations of the static quark potential and light hadron spectrum. These results give information about the remaining dependences on the lattice spacing. We examine the dependence of computed quantities on the spatial size of the lattice, on the numerical precision in the computations, and on the step size used in the numerical integrations. We examine the effects of autocorrelations in "simulation time" on the potential and spectrum. We see effects of decays, or coupling to two-meson states, in the 0++, 1+, and 0- meson propagators, and we make a preliminary mass computation for a radially excited 0- meson.Comment: 43 pages, 16 figure

Mode Confinement in Photonic Quasi-Crystal Point-Defect Cavities for Particle Accelerators

In this Letter, we present a study of the confinement properties of point-defect resonators in finite-size photonic-bandgap structures composed of aperiodic arrangements of dielectric rods, with special emphasis on their use for the design of cavities for particle accelerators. Specifically, for representative geometries, we study the properties of the fundamental mode (as a function of the filling fraction, structure size, and losses) via 2-D and 3-D full-wave numerical simulations, as well as microwave measurements at room temperature. Results indicate that, for reduced-size structures, aperiodic geometries exhibit superior confinement properties by comparison with periodic ones.Comment: 4 pages, 4 figures, accepted for publication in Applied Physics Letter

Consanguinity and polygenic diseases: a model for antibody deficiencies

Primary immunodeficiencies represent a heterogeneous group of disorders of the immune system, predisposing to various types of infections. Among them, common variable immunodeficiency is the most common symptomatic antibody deficiency. It includes several different forms characterized by defects in the terminal stage of B lymphocyte differentiation, leading to markedly reduced immunoglobulin serum levels and increased susceptibility to bacterial infections. The clinical phenotype is complex, including autoimmunity, granulomatous inflammation, lymphoproliferative disorders and malignancies. Rare autosomal recessive mutations in a number of single genes have recently been reported. However, the underlying genetic defects remain unknown in the majority of cases. In order to seek new genes responsible for the disease, we studied a consanguineous Italian family through exome sequencing combined with homozygosity mapping. Six missense homozygous variants passed our filtering selection and at least two of them were associated with some aspects of the pathological phenotype. Our data remark the complexity of immune system disorders and emphasize the difficulty to understand the significance of genetic results and their correlation with the disease phenotype

Effects of a natural extract from Mangifera indica L, and its active compound, mangiferin, on energy state and lipid peroxidation of red blood cells

Following oxidative stress, modifications of several biologically important macromolecules have been demonstrated. In this study we investigated the effect of a natural extract from Mangifera indica L (Vimang), its main ingredient mangiferin and epigallocatechin gallate (EGCG) on energy metabolism, energy state and malondialdehyde (MDA) production in a red blood cell system. Analysis of NIDA, high energy phosphates and ascorbate was carried out by high performance liquid chromatography (HPLC). Under the experimental conditions, concentrations of NIDA and ATP catabolites were affected in a dose-dependent way by H2O2. Incubation with Vimang (0.1, 1, 10, 50 and 100 mu g/mL), mangiferin (1, 10, 100 mu g/mL) and EGCG (0.01, 0.1, 1, 10 mu M) significantly enhances erythrocyte resistance to H2O2-induced reactive oxygen species production. In particular, we demonstrate the protective activity of these compounds on ATP, GTP and total nucleotides (NT) depletion after H2O2-induced damage and a reduction of NAD and ADP, which both increase because of the energy consumption following H2O2 addition. Energy charge potential, decreased in H2O2-treated erythrocytes, was also restored in a dose-dependent way by these substances. Their protective effects might be related to the strong free radical scavenging ability described for polyphenols. (c) 2006 Elsevier B.V All rights reserved

Estimating offspring production using capture-mark-recapture and genetic methods in red squirrels.

Reproductive rate is a key demographic parameter of life history and population ecology. In traditional population-ecology studies of small mammals, this and other vital rates are inferred from capture-mark-recapture (CMR) data. However, CMR assumes that immigrants at first capture can be distinguished from unmarked locally born offspring, an assumption not always met. We verified CMR estimates of locally born red squirrel (Sciurus vulgaris) offspring as a measure of reproductive rate, with candidate offspring (CO)\u2013candidate parent (mothers, CPs) assignment by CERVUS, using ten DNA microsatellite loci. Seventytwo of 122 candidate offspring (59%) were assigned to 52 of 125 CPs in six populations. Estimates of mean litter size were 1.5 young (range 1\u20133). The 50 CO (41%) not assigned to a reproducing female in the study site were considered immigrants. Parentage assignment also provided evidence of dispersal between two of our sites. Overall, CMR and CERVUS agreed in 77% of cases. Considering only the 55 juveniles determined as locally born by CMR, 50 (91%) were also assigned as local offspring with CERVUS. The main discrepancy between the two methods was that 22 subadult squirrels classified immigrants by CMR, were assigned by CERVUS to females which had reproduced in our sites. It is concluded that although in our study system agreement between CMR and CERVUS in determining local offspring was high, using genetic parentage assignment helped to correctly classify some subadults, considered immigrants by CMR, as locally born. Hence, in largescale demographic studies, combining CMR with parentage assignment will allow more precise estimates of reproduction and dispersal