A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Four dimensional "old minimal" N=2 supersymmetrization of R^4

We write in superspace the lagrangian containing the fourth power of the Weyl tensor in the "old minimal" d=4, N=2 supergravity, without local SO(2) symmetry. Using gauge completion, we analyze the lagrangian in components. We find out that the auxiliary fields which belong to the Weyl and compensating vector multiplets have derivative terms and therefore cannot be eliminated on-shell. Only the auxiliary fields which belong to the compensating nonlinear multiplet do not get derivatives and could still be eliminated; we check that this is possible in the leading terms of the lagrangian. We compare this result to the similar one of "old minimal" N=1 supergravity and we comment on possible generalizations to other versions of N=1,2 supergravity.Comment: 31 pages, no figures. Minor corrections. Details of the full calculation included as an appendix. Reference adde

Classification of Invariant Star Products up to Equivariant Morita Equivalence on Symplectic Manifolds

In this paper we investigate equivariant Morita theory for algebras with momentum maps and compute the equivariant Picard groupoid in terms of the Picard groupoid explicitly. We consider three types of Morita theory: ring-theoretic equivalence, *-equivalence and strong equivalence. Then we apply these general considerations to star product algebras over symplectic manifolds with a Lie algebra symmetry. We obtain the full classification up to equivariant Morita equivalence.Comment: 28 pages. Minor update, fixed typos

ECIU position paper on living labs and experimentation spaces:Recommendations and insights about the potential of Living Labs as innovation and learning platforms in the ECIU University

To accelerate transformations towards just and sustainable future cities across Europe, local and regional projects need to scale up and share sustainability pathways and planning efforts. In this context, Living Labs, and innovation and experimentation spaces in general, have demonstrated great potential in serving as platforms for connecting universities with societal stakeholder, facilitating transdisciplinary collaboration in the innovation process but also as tools for cross-case learning and upscaling innovative solutions. At the same time there is an ever increasing emergence and diversification of these spaces, even within ECIU, that can often create a certain confusion and at the same time reluctance to engage and make use of them or explore their full potential

Sex differences in neurodevelopmental and common mental disorders examined from three epidemiological perspectives.

Sex differences in neurodevelopmental and common mental disorders are a ubiquitous, well-known, though poorly understood phenomenon. This study examined the issue from three epidemiological perspectives: congruence in age of onset, distribution of sex-ratios with respect to age of onset and similarity of comorbidity and risk factor patterns. The analysis was based on data from the population-based PsyCoLaus study (N = 4874, age 35-82 y). Congruence in age of onset and distribution of sex-ratios were examined with the Mann-Whitney test and cluster analysis. The similarity of comorbidity and risk factor patterns, which were represented by 35 variables, was assessed with the Jaccard coefficient and, after factor analysis, with Tucker's congruence coefficient. While age of onset parameters differed little by sex, the sex ratio varied markedly both in early and in late onset disorders. Moreover, the Jaccard coefficients for most disorders indicated that the similarity of comorbidity and further association patterns was low. Similarly, Tucker's congruence coefficient remained below the range of fair similarity in all factor combinations. In sum, sex differences in common mental disorders were impressively reflected by diverging sex ratios and comorbidity / risk factor patterns. This outcome supports the notion that most mental disorders need a sex-specific etiopathogenetic understanding

Optimal prediction for moment models: Crescendo diffusion and reordered equations

A direct numerical solution of the radiative transfer equation or any kinetic equation is typically expensive, since the radiative intensity depends on time, space and direction. An expansion in the direction variables yields an equivalent system of infinitely many moments. A fundamental problem is how to truncate the system. Various closures have been presented in the literature. We want to study moment closure generally within the framework of optimal prediction, a strategy to approximate the mean solution of a large system by a smaller system, for radiation moment systems. We apply this strategy to radiative transfer and show that several closures can be re-derived within this framework, e.g. $P_N$, diffusion, and diffusion correction closures. In addition, the formalism gives rise to new parabolic systems, the reordered $P_N$ equations, that are similar to the simplified $P_N$ equations. Furthermore, we propose a modification to existing closures. Although simple and with no extra cost, this newly derived crescendo diffusion yields better approximations in numerical tests.Comment: Revised version: 17 pages, 6 figures, presented at Workshop on Moment Methods in Kinetic Gas Theory, ETH Zurich, 2008 2 figures added, minor correction

Gupta–Bleuler Quantization of the Maxwell Field in Globally Hyperbolic Space-Times

We give a complete framework for the Gupta–Bleuler quantization of the free electromagnetic field on globally hyperbolic space-times. We describe one-particle structures that give rise to states satisfying the microlocal spectrum condition. The field algebras in the so-called Gupta–Bleuler representations satisfy the time-slice axiom, and the corresponding vacuum states satisfy the microlocal spectrum condition. We also give an explicit construction of ground states on ultrastatic space-times. Unlike previous constructions, our method does not require a spectral gap or the absence of zero modes. The only requirement, the absence of zero-resonance states, is shown to be stable under compact perturbations of topology and metric. Usual deformation arguments based on the time-slice axiom then lead to a construction of Gupta–Bleuler representations on a large class of globally hyperbolic space-times. As usual, the field algebra is represented on an indefinite inner product space, in which the physical states form a positive semi-definite subspace. Gauge transformations are incorporated in such a way that the field can be coupled perturbatively to a Dirac field. Our approach does not require any topological restrictions on the underlying space-time

Infectious, atopic and inflammatory diseases, childhood adversities and familial aggregation are independently associated with the risk for mental disorders: Results from a large Swiss epidemiological study.

To examine the associations between mental disorders and infectious, atopic, inflammatory diseases while adjusting for other risk factors. We used data from PsyCoLaus, a large Swiss Population Cohort Study (n = 3720; age range 35-66). Lifetime diagnoses of mental disorders were grouped into the following categories: Neurodevelopmental, anxiety (early and late onset), mood and substance disorders. They were regressed on infectious, atopic and other inflammatory diseases adjusting for sex, educational level, familial aggregation, childhood adversities and traumatic experiences in childhood. A multivariate logistic regression was applied to each group of disorders. In a complementary analysis interactions with sex were introduced via nested effects. Associations with infectious, atopic and other chronic inflammatory diseases were observable together with consistent effects of childhood adversities and familial aggregation, and less consistent effects of trauma in each group of mental disorders. Streptococcal infections were associated with neurodevelopmental disorders (men), and measles/mumps/rubella-infections with early and late anxiety disorders (women). Gastric inflammatory diseases took effect in mood disorders (both sexes) and in early disorders (men). Similarly, irritable bowel syndrome was prominent in a sex-specific way in mood disorders in women, and, moreover, was associated with early and late anxiety disorders. Atopic diseases were associated with late anxiety disorders. Acne (associations with mood disorders in men) and psoriasis (associations with early anxiety disorders in men and mood disorders in women) contributed sex-specific results. Urinary tract infections were associated with mood disorders and, in addition, in a sex-specific way with late anxiety disorders (men), and neurodevelopmental and early anxiety disorders (women). Infectious, atopic and inflammatory diseases are important risk factors for all groups of mental disorders. The sexual dimorphism of the associations is pronounced

Superconformal operators in N=4 super-Yang-Mills theory

We construct, in the framework of the N=4 SYM theory, a supermultiplet of twist-two conformal operators and study their renormalization properties. The components of the supermultiplet have the same anomalous dimension and enter as building blocks into multi-particle quasipartonic operators. The latter are determined by the condition that their twist equals the number of elementary constituent fields from which they are built. A unique feature of the N=4 SYM is that all quasipartonic operators with different SU(4) quantum numbers fall into a single supermultiplet. Among them there is a subsector of the operators of maximal helicity, which has been known to be integrable in the multi-color limit in QCD, independent of the presence of supersymmetry. In the N=4 SYM theory, this symmetry is extended to the whole supermultiplet of quasipartonic operators and the one-loop dilatation operator coincides with a Hamiltonian of integrable SL(2|4) Heisenberg spin chain.Comment: 45 pages, Latex, 4 figure

Launch of the Space experiment PAMELA

PAMELA is a satellite borne experiment designed to study with great accuracy cosmic rays of galactic, solar, and trapped nature in a wide energy range protons: 80 MeV-700 GeV, electrons 50 MeV-400 GeV). Main objective is the study of the antimatter component: antiprotons (80 MeV-190 GeV), positrons (50 MeV-270 GeV) and search for antimatter with a precision of the order of 10^-8). The experiment, housed on board the Russian Resurs-DK1 satellite, was launched on June, 15, 2006 in a 350*600 km orbit with an inclination of 70 degrees. The detector is composed of a series of scintillator counters arranged at the extremities of a permanent magnet spectrometer to provide charge, Time-of-Flight and rigidity information. Lepton/hadron identification is performed by a Silicon-Tungsten calorimeter and a Neutron detector placed at the bottom of the device. An Anticounter system is used offline to reject false triggers coming from the satellite. In self-trigger mode the Calorimeter, the neutron detector and a shower tail catcher are capable of an independent measure of the lepton component up to 2 TeV. In this work we describe the experiment, its scientific objectives and the performance in the first months after launch.Comment: Accepted for publication on Advances in Space Researc