Expressed sequence tags from the oomycete fish pathogen Saprolegnia parasitica reveal putative virulence factors

Peer reviewedPublisher PD

HepForge: A lightweight development environment for HEP software

Setting up the infrastructure to manage a software project can become a task as significant writing the software itself. A variety of useful open source tools are available, such as Web-based viewers for version control systems, "wikis" for collaborative discussions and bug-tracking systems, but their use in high-energy physics, outside large collaborations, is insubstantial. Understandably, physicists would rather do physics than configure project management tools. We introduce the CEDAR HepForge system, which provides a lightweight development environment for HEP software. Services available as part of HepForge include the above-mentioned tools as well as mailing lists, shell accounts, archiving of releases and low-maintenance Web space. HepForge also exists to promote best-practice software development methods and to provide a central repository for re-usable HEP software and phenomenology codes.Comment: 3 pages, 0 figures. To be published in proceedings of CHEP06. Refers to the HepForge facility at http://hepforge.cedar.ac.u

HepData and JetWeb: HEP data archiving and model validation

The CEDAR collaboration is extending and combining the JetWeb and HepData systems to provide a single service for tuning and validating models of high-energy physics processes. The centrepiece of this activity is the fitting by JetWeb of observables computed from Monte Carlo event generator events against their experimentally determined distributions, as stored in HepData. Caching the results of the JetWeb simulation and comparison stages provides a single cumulative database of event generator tunings, fitted against a wide range of experimental quantities. An important feature of this integration is a family of XML data formats, called HepML.Comment: 4 pages, 0 figures. To be published in proceedings of CHEP0

KtJet: A C++ implementation of the Kt clustering algorithm

A C++ implementation of the Kt jet algorithm for high energy particle collisions is presented. The time performance of this implementation is comparable to the widely used Fortran implementation. Identical algorithmic functionality is provided, with a clean and intuitive user interface and additional recombination schemes. A short description of the algorithm and examples of its use are given

Low Temperature Physics

Contains research objectives and reports on one research project

Bath generated work extraction and inversion-free gain in two-level systems

The spin-boson model, often used in NMR and ESR physics, quantum optics and spintronics, is considered in a solvable limit to model a spin one-half particle interacting with a bosonic thermal bath. By applying external pulses to a non-equilibrium initial state of the spin, work can be extracted from the thermalized bath. It occurs on the timescale \T_2 inherent to transversal (`quantum') fluctuations. The work (partly) arises from heat given off by the surrounding bath, while the spin entropy remains constant during a pulse. This presents a violation of the Clausius inequality and the Thomson formulation of the second law (cycles cost work) for the two-level system. Starting from a fully disordered state, coherence can be induced by employing the bath. Due to this, a gain from a positive-temperature (inversion-free) two-level system is shown to be possible.Comment: 4 pages revte

Consistent thermodynamics for spin echoes

Spin-echo experiments are often said to constitute an instant of anti-thermodynamic behavior in a concrete physical system that violates the second law of thermodynamics. We argue that a proper thermodynamic treatment of the effect should take into account the correlations between the spin and translational degrees of freedom of the molecules. To this end, we construct an entropy functional using Boltzmann macrostates that incorporates both spin and translational degrees of freedom. With this definition there is nothing special in the thermodynamics of spin echoes: dephasing corresponds to Hamiltonian evolution and leaves the entropy unchanged; dissipation increases the entropy. In particular, there is no phase of entropy decrease in the echo. We also discuss the definition of macrostates from the underlying quantum theory and we show that the decay of net magnetization provides a faithful measure of entropy change.Comment: 15 pages, 2 figs. Changed figures, version to appear in PR

Individual differences in toddlers' social understanding and prosocial behavior: Disposition or socialization?

We examined how individual differences in social understanding contribute to variability in early-appearing prosocial behavior. Moreover, potential sources of variability in social understanding were explored and examined as additional possible predictors of prosocial behavior. Using a multi-method approach with both observed and parent-report measures, 325 children aged 18-30 months were administered measures of social understanding (e.g., use of emotion words; self-understanding), prosocial behavior (in separate tasks measuring instrumental helping, empathic helping, and sharing, as well as parent-reported prosociality at home), temperament (fearfulness, shyness, and social fear), and parental socialization of prosocial behavior in the family. Individual differences in social understanding predicted variability in empathic helping and parent-reported prosociality, but not instrumental helping or sharing. Parental socialization of prosocial behavior was positively associated with toddlers' social understanding, prosocial behavior at home, and instrumental helping in the lab, and negatively associated with sharing (possibly reflecting parents' increased efforts to encourage children who were less likely to share). Further, socialization moderated the association between social understanding and prosocial behavior, such that social understanding was less predictive of prosocial behavior among children whose parents took a more active role in socializing their prosociality. None of the dimensions of temperament was associated with either social understanding or prosocial behavior. Parental socialization of prosocial behavior is thus an important source of variability in children's early prosociality, acting in concert with early differences in social understanding, with different patterns of influence for different subtypes of prosocial behavior

Force balance and membrane shedding at the Red Blood Cell surface

During the aging of the red-blood cell, or under conditions of extreme echinocytosis, membrane is shed from the cell plasma membrane in the form of nano-vesicles. We propose that this process is the result of the self-adaptation of the membrane surface area to the elastic stress imposed by the spectrin cytoskeleton, via the local buckling of membrane under increasing cytoskeleton stiffness. This model introduces the concept of force balance as a regulatory process at the cell membrane, and quantitatively reproduces the rate of area loss in aging red-blood cells.Comment: 4 pages, 3 figure