Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation

Background Outer membrane proteins (OMPs) of Pasteurella multocida have various functions related to virulence and pathogenesis and represent important targets for vaccine development. Various bioinformatic algorithms can predict outer membrane localization and discriminate OMPs by structure or function. The designation of a confident prediction framework by integrating different predictors followed by consensus prediction, results integration and manual confirmation will improve the prediction of the outer membrane proteome. Results In the present study, we used 10 different predictors classified into three groups (subcellular localization, transmembrane β-barrel protein and lipoprotein predictors) to identify putative OMPs from two available P. multocida genomes: those of avian strain Pm70 and porcine non-toxigenic strain 3480. Predicted proteins in each group were filtered by optimized criteria for consensus prediction: at least two positive predictions for the subcellular localization predictors, three for the transmembrane β-barrel protein predictors and one for the lipoprotein predictors. The consensus predicted proteins were integrated from each group into a single list of proteins. We further incorporated a manual confirmation step including a public database search against PubMed and sequence analyses, e.g. sequence and structural homology, conserved motifs/domains, functional prediction, and protein-protein interactions to enhance the confidence of prediction. As a result, we were able to confidently predict 98 putative OMPs from the avian strain genome and 107 OMPs from the porcine strain genome with 83% overlap between the two genomes. Conclusions The bioinformatic framework developed in this study has increased the number of putative OMPs identified in P. multocida and allowed these OMPs to be identified with a higher degree of confidence. Our approach can be applied to investigate the outer membrane proteomes of other Gram-negative bacteria

Non-Weyl asymptotics for quantum graphs with general coupling conditions

Inspired by a recent result of Davies and Pushnitski, we study resonance asymptotics of quantum graphs with general coupling conditions at the vertices. We derive a criterion for the asymptotics to be of a non-Weyl character. We show that for balanced vertices with permutation-invariant couplings the asymptotics is non-Weyl only in case of Kirchhoff or anti-Kirchhoff conditions, while for graphs without permutation numerous examples of non-Weyl behaviour can be constructed. Furthermore, we present an insight helping to understand what makes the Kirchhoff/anti-Kirchhoff coupling particular from the resonance point of view. Finally, we demonstrate a generalization to quantum graphs with nonequal edge weights.Comment: minor changes, to appear in Pierre Duclos memorial issue of J. Phys. A: Math. Theo

Influence of organic films on the evaporation and condensation of water in aerosol

Uncertainties in quantifying the kinetics of evaporation and condensation of water from atmospheric aerosol are a significant contributor to the uncertainty in predicting cloud droplet number and the indirect effect of aerosols on climate. The influence of aerosol particle surface composition, particularly the impact of surface active organic films, on the condensation and evaporation coefficients remains ambiguous. Here, we report measurements of the influence of organic films on the evaporation and condensation of water from aerosol particles. Significant reductions in the evaporation coefficient are shown to result when condensed films are formed by monolayers of long-chain alcohols [C(n)H((2n+1))OH], with the value decreasing from 2.4 × 10(−3) to 1.7 × 10(−5) as n increases from 12 to 17. Temperature-dependent measurements confirm that a condensed film of long-range order must be formed to suppress the evaporation coefficient below 0.05. The condensation of water on a droplet coated in a condensed film is shown to be fast, with strong coherence of the long-chain alcohol molecules leading to islanding as the water droplet grows, opening up broad areas of uncoated surface on which water can condense rapidly. We conclude that multicomponent composition of organic films on the surface of atmospheric aerosol particles is likely to preclude the formation of condensed films and that the kinetics of water condensation during the activation of aerosol to form cloud droplets is likely to remain rapid

Measurements continuous in time and a posteriori states in quantum

Measurements continuous in time were consistently introduced in quantum mechanics and applications worked out, mainly in quantum optics. In this context a quantum filtering theory has been developed giving the reduced state after the measurement when a certain trajectory of the measured observables is registered (the a posteriori states). In this paper a new derivation of filtering equations is presented, in the cases of counting processes and of measurement processes of diffusive type. It is also shown that the equation for the a posteriori dynamics in the diffusive case can be obtained, by a suitable limit, from that one in the counting case. Moreover, the paper is intended to clarify the meaning of the various concepts involved and to discuss the connections among them. As an illustration of the theory, simple models are worked out.Comment: 31 page. See also related papers at http://www.maths.nott.ac.uk/personal/vpb/research/mes_fou.html and http://www.maths.nott.ac.uk/personal/vpb/research/fil_con.htm

Convex probability domain of generalized quantum measurements

Generalized quantum measurements with N distinct outcomes are used for determining the density matrix, of order d, of an ensemble of quantum systems. The resulting probabilities are represented by a point in an N-dimensional space. It is shown that this point lies in a convex domain having at most d^2-1 dimensions.Comment: 7 pages LaTeX, one PostScript figure on separate pag

Non-disturbing quantum measurements

We consider pairs of quantum observables (POVMs) and analyze the relation between the notions of non-disturbance, joint measurability and commutativity. We specify conditions under which these properties coincide or differ---depending for instance on the interplay between the number of outcomes and the Hilbert space dimension or on algebraic properties of the effect operators. We also show that (non-)disturbance is in general not a symmetric relation and that it can be decided and quantified by means of a semidefinite program.Comment: Minor corrections in v

Diffusion Approximation of Stochastic Master Equations with Jumps

In the presence of quantum measurements with direct photon detection the evolution of open quantum systems is usually described by stochastic master equations with jumps. Heuristically, from these equations one can obtain diffusion models as approximation. A necessary condition for a general diffusion approximation for jump master equations is presented. This approximation is rigorously proved by using techniques for Markov process which are based upon the convergence of Markov generators and martingale problems. This result is illustrated by rigorously obtaining the diffusion approximation for homodyne and heterodyne detection.Comment: 15 page

PRICE RELATIONSHIPS FOR MEXICAN FRESH TOMATOES IN U.S. AND MEXICAN TERMINAL MARKETS

Tomato trade between the U.S. and Mexico has grown significantly during the past decade, with significant implications for markets in both countries. This work examines how terminal market prices for Mexican fresh tomatoes are being affected by price dynamics in distant, integrated markets by analyzing reaction patterns to various innovation shocks. We conclude that a high interdependence in the price formation process between Mexican markets and Los Angeles, as well as among Mexican markets, exists.Crop Production/Industries, Demand and Price Analysis,