A Development Environment for Visual Physics Analysis

The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The project provides an extendable plug-in mechanism and includes plug-ins for designing the analysis flow, for running the analysis on batch systems, and for browsing the data content. The corresponding plug-ins are based on an object-oriented toolkit for modular data analysis. We introduce the main concepts of the project, describe the technical realization and demonstrate the functionality in example applications

Automated Reconstruction of Particle Cascades in High Energy Physics Experiments

We present a procedure for reconstructing particle cascades from event data measured in a high energy physics experiment. For evaluating the hypothesis of a specific physics process causing the observed data, all possible reconstruction versions of the scattering process are constructed from the final state objects. We describe the procedure as well as examples of physics processes of different complexity studied at hadron-hadron colliders. We estimate the performance by 20 microseconds per reconstructed decay vertex, and 0.6 kByte per reconstructed particle in the decay trees.Comment: 8 pages, 2 figures. Submitted to Computational Science & Discover

Noise-Induced Transition from Translational to Rotational Motion of Swarms

We consider a model of active Brownian agents interacting via a harmonic attractive potential in a two-dimensional system in the presence of noise. By numerical simulations, we show that this model possesses a noise-induced transition characterized by the breakdown of translational motion and the onset of swarm rotation as the noise intensity is increased. Statistical properties of swarm dynamics in the weak noise limit are further analytically investigated.Comment: 7 pages, 7 figure

Tripartite phase separation of two signal effectors with vesicles priming B cell responsiveness.

Antibody-mediated immune responses rely on antigen recognition by the B cell antigen receptor (BCR) and the proper engagement of its intracellular signal effector proteins. Src homology (SH) 2 domain-containing leukocyte protein of 65 kDa (SLP65) is the key scaffold protein mediating BCR signaling. In resting B cells, SLP65 colocalizes with Cbl-interacting protein of 85 kDa (CIN85) in cytoplasmic granules whose formation is not fully understood. Here we show that effective B cell activation requires tripartite phase separation of SLP65, CIN85, and lipid vesicles into droplets via vesicle binding of SLP65 and promiscuous interactions between nine SH3 domains of the trimeric CIN85 and the proline-rich motifs (PRMs) of SLP65. Vesicles are clustered and the dynamical structure of SLP65 persists in the droplet phase in vitro. Our results demonstrate that phase separation driven by concerted transient interactions between scaffold proteins and vesicles is a cellular mechanism to concentrate and organize signal transducers

Concepts, Developments and Advanced Applications of the PAX Toolkit

The Physics Analysis eXpert (PAX) is an open source toolkit for high energy physics analysis. The C++ class collection provided by PAX is deployed in a number of analyses with complex event topologies at Tevatron and LHC. In this article, we summarize basic concepts and class structure of the PAX kernel. We report about the most recent developments of the kernel and introduce two new PAX accessories. The PaxFactory, that provides a class collection to facilitate event hypothesis evolution, and VisualPax, a Graphical User Interface for PAX objects

A New Technique for Escherichia coli Testing of Beef and Pork Carcasses

A novel technique has been developed to monitor Escherichia coli contamination on carcasses using membrane filtration and m-ColiBlue24 (mCB). mCB is a membrane filtration medium that simultaneously detects total coliforms and E. coli (EC) in a period of 24 +/- 4 h. A study was conducted, using a sponge method to obtain samples from pork carcasses and the excision technique to remove samples from beef carcasses, that compared mCB to standard methods. On pork carcasses (n = 77), the mean values for mCB and violet red bile agar were 7.4 CFU/15 cm2 and 6.1 CFU/15 cm2, respectively. The paired t test (P \u3e 0.05) indicated no significant difference between the two methods (t = 0.5; P = 0.6). Samples from beef carcasses (n = 57) were used to compare mCB to both coliform count and EC Petrifilm. Of these samples, 27 were artificially inoculated with cattle manure. The mean total coliform count was 4.2 log CFU/cm2 and 4.0 log CFU/cm2 on mCB and coliform count Petrifilm, respectively. The mean EC count on mCB was 4.0 log CFU/cm2 and 3.5 log CFU/cm2 on EC Petrifilm. When comparing mCB to both coliform count (t = 2.4; P = 0.02) and EC (t = 3.5; P \u3c 0.01) Petrifilm, paired t tests (P \u3c or = 0.05) indicated significant differences

Adenosine triphosphatases of thermophilic archaeal double-stranded DNA viruses

Peer reviewe

On the attractors of two-dimensional Rayleigh oscillators including noise

We study sustained oscillations in two-dimensional oscillator systems driven by Rayleigh-type negative friction. In particular we investigate the influence of mismatch of the two frequencies. Further we study the influence of external noise and nonlinearity of the conservative forces. Our consideration is restricted to the case that the driving is rather weak and that the forces show only weak deviations from radial symmetry. For this case we provide results for the attractors and the bifurcations of the system. We show that for rational relations of the frequencies the system develops several rotational excitations with right/left symmetry, corresponding to limit cycles in the four-dimensional phase space. The corresponding noisy distributions have the form of hoops or tires in the four-dimensional space. For irrational frequency relations, as well as for increasing strength of driving or noise the periodic excitations are replaced by chaotic oscillations.Comment: 9 pages, 5 figure

HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses.

Antiretroviral therapy, antibody and CD8+ T cell-mediated responses targeting human immunodeficiency virus-1 (HIV-1) exert selection pressure on the virus necessitating escape; however, the ability of CD4+ T cells to exert selective pressure remains unclear. Using a computational approach on HIV gag/pol/nef sequences and HLA-II allelic data, we identified 29 HLA-II associated HIV sequence polymorphisms or adaptations (HLA-AP) in an African cohort of chronically HIV-infected individuals. Epitopes encompassing the predicted adaptation (AE) or its non-adapted (NAE) version were evaluated for immunogenicity. Using a CD8-depleted IFN-γ ELISpot assay, we determined that the magnitude of CD4+ T cell responses to the predicted epitopes in controllers was higher compared to non-controllers (p<0.0001). However, regardless of the group, the magnitude of responses to AE was lower as compared to NAE (p<0.0001). CD4+ T cell responses in patients with acute HIV infection (AHI) demonstrated poor immunogenicity towards AE as compared to NAE encoded by their transmitted founder virus. Longitudinal data in AHI off antiretroviral therapy demonstrated sequence changes that were biologically confirmed to represent CD4+ escape mutations. These data demonstrate an innovative application of HLA-associated polymorphisms to identify biologically relevant CD4+ epitopes and suggests CD4+ T cells are active participants in driving HIV evolution