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 stable chemokine gradient controls directional persistence of migrating dendritic cells

Navigation of dendritic cells (DCs) from the site of infection to lymphoid organs is guided by concentration gradients of CCR7 ligands. How cells interpret chemokine gradients and how they couple directional sensing to polarization and persistent chemotaxis has remained largely elusive. Previous experimental systems were limited in the ability to control fast de novo formation of the final gradient slope, long-lasting stability of the gradient and to expose cells to dynamic stimulation. Here, we used a combination of microfluidics and quantitative in vitro live cell imaging to elucidate the chemotactic sensing strategy of DCs. The microfluidic approach allows us to generate soluble gradients with high spatio-temporal precision and to analyze actin dynamics, cell polarization, and persistent directional migration in both static and dynamic environments. We demonstrate that directional persistence of DC migration requires steady-state characteristics of the soluble gradient instead of temporally rising CCL19 concentration, implying that spatial sensing mechanisms control chemotaxis of DCs. Kymograph analysis of actin dynamics revealed that the presence of the CCL19 gradient is essential to stabilize leading edge protrusions in DCs and to determine directionality, since both cytoskeletal polarization and persistent chemotaxis are abrogated in the range of seconds when steady-state gradients are perturbed. In contrast to Dictyostelium amoeba, DCs are unable to decode oscillatory stimulation of soluble chemokine traveling waves into a directional response toward the wave source. These findings are consistent with the notion that DCs do not employ adaptive temporal sensing strategies that discriminate temporally increasing and decreasing chemoattractant concentrations in our setting. Taken together, in our experimental system DCs do not depend on increasing absolute chemokine concentration over time to induce persistent migration and do not integrate oscillatory stimulation. The observed capability of DCs to migrate with high directional persistence in stable gradients but not when subjected to periodic temporal cues, identifies spatial sensing as a key requirement for persistent chemotaxis of DCs

Discovery of a Luminous Quasar in the Nearby Universe

In the course of the Pico dos Dias survey (PDS), we identified the stellar like object PDS456 at coordinates alpha = 17h 28m 19.796s, delta = -14deg 15' 55.87'' (epoch 2000), with a relatively nearby (z = 0.184) and bright (B = 14.69) quasar. Its position at Galactic coordinates l_II = 10.4deg, b_II = +11.2deg, near the bulge of the Galaxy, may explain why it was not detected before. The optical spectrum of PDS456 is typical of a luminous quasar, showing a broad (FWHM ~ 4000 km/s) H_\beta line, very intense FeII lines and a weak [OIII]\lambda5007 line. PDS456 is associated to the infrared source IRAS 17254-1413 with a 60 \mum infrared luminosity L_{60} = 3.8 x 10^{45} erg/s. The relatively flat slopes in the infrared (\alpha(25,60) = -0.33 and \alpha(12,25) = -0.78) and a flat power index in the optical (F_{\nu} \propto \nu^{-0.72}) may indicate a low dust content. A good match between the position of PDS456 and the position of the X-ray source RXS J172819.3-141600 implies an X-ray luminosity L_x = 2.8 x 10^{44} erg/s. The good correlation between the strength of the emission lines in the optical and the X-ray luminosity, as well as the steep optical to X-ray index estimated (\alpha_{ox} = -1.64) suggest that PDS456 is radio quiet. A radio survey previously performed in this region yields an upper limit for radio power at ~ 5 GHz of ~ 2.6 x 10^{30} erg/s/Hz. We estimate the Galactic reddening in this line-of-sight to be A_B \simeq 2.0, implying an absolute magnitude M_B = -26.7 (using H_0 = 75 km s^{-1} Mpc^{-1} and q_0 = 0). In the optical, PDS456 is therefore 1.3 times more luminous than 3C 273 and the most luminous quasar in the nearby (z \leq 0.3) Universe.Comment: 12 pages, LaTeX (aasms4.sty) + 3 figures; accepted for publication in the Astrophysical Journal Letter

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific ‘service provision units’ is introduced together with the factors influencing them and the main underlying assumptions for these ‘value influencing factors’. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared

Atomic transition frequencies, isotope shifts, and sensitivity to variation of the fine structure constant for studies of quasar absorption spectra

Theories unifying gravity with other interactions suggest spatial and temporal variation of fundamental "constants" in the Universe. A change in the fine structure constant, alpha, could be detected via shifts in the frequencies of atomic transitions in quasar absorption systems. Recent studies using 140 absorption systems from the Keck telescope and 153 from the Very Large Telescope, suggest that alpha varies spatially. That is, in one direction on the sky alpha seems to have been smaller at the time of absorption, while in the opposite direction it seems to have been larger. To continue this study we need accurate laboratory measurements of atomic transition frequencies. The aim of this paper is to provide a compilation of transitions of importance to the search for alpha variation. They are E1 transitions to the ground state in several different atoms and ions, with wavelengths ranging from around 900 - 6000 A, and require an accuracy of better than 10^{-4} A. We discuss isotope shift measurements that are needed in order to resolve systematic effects in the study. The coefficients of sensitivity to alpha-variation (q) are also presented.Comment: Includes updated version of the "alpha line" lis

Search for the glueball candidates f0(1500) and fJ(1710) in gamma gamma collisions

Data taken with the ALEPH detector at LEP1 have been used to search for gamma gamma production of the glueball candidates f0(1500) and fJ(1710) via their decay to pi+pi-. No signal is observed and upper limits to the product of gamma gamma width and pi+pi- branching ratio of the f0(1500) and the fJ(1710) have been measured to be Gamma_(gamma gamma -> f0(1500)). BR(f0(1500)->pi+pi-) < 0.31 keV and Gamma_(gamma gamma -> fJ(1710)). BR(fJ(1710)->pi+pi-) < 0.55 keV at 95% confidence level.Comment: 10 pages, 3 figure