Abnormally high content of free glucosamine residues identified in a preparation of commercially available porcine intestinal heparan sulfate

Heparan sulfate (HS) polysaccharides are ubiquitous in animal tissues as components of proteoglycans, and they participate in many important biological processes. HS carbohydrate chains are complex and can contain rare structural components such as N-unsubstituted glucosamine (GlcN). Commercially available HS preparations have been invaluable in many types of research activities. In the course of preparing microarrays to include probes derived from HS oligosaccharides, we found an unusually high content of GlcN residue in a recently purchased batch of porcine intestinal mucosal HS. Composition and sequence analysis by mass spectrometry of the oligosaccharides obtained after heparin lyase III digestion of the polysaccharide indicated two and three GlcN in the tetrasaccharide and hexasaccharide fractions, respectively. (1)H NMR of the intact polysaccharide showed that this unusual batch differed strikingly from other HS preparations obtained from bovine kidney and porcine intestine. The very high content of GlcN (30%) and low content of GlcNAc (4.2%) determined by disaccharide composition analysis indicated that N-deacetylation and/or N-desulfation may have taken place. HS is widely used by the scientific community to investigate HS structures and activities. Great care has to be taken in drawing conclusions from investigations of structural features of HS and specificities of HS interaction with proteins when commercial HS is used without further analysis. Pending the availability of a validated commercial HS reference preparation, our data may be useful to members of the scientific community who have used the present preparation in their studies

The alpha-dependence of transition frequencies for some ions of Ti, Mn, Na, C, and O, and the search for variation of the fine structure constant

We use the relativistic Hartree-Fock method, many-body perturbation theory and configuration-interaction method to calculate the dependence of atomic transition frequencies on the fine structure constant, alpha. The results of these calculations will be used in the search for variation of the fine structure constant in quasar absorption spectra.Comment: 4 pages, 5 table

An Upper Limit on Omega_matter Using Lensed Arcs

We use current observations on the number statistics of gravitationally lensed optical arcs towards galaxy clusters to derive an upper limit on the cosmological mass density of the Universe. The gravitational lensing statistics due to foreground clusters combine properties of both cluster evolution, which is sensitive to the matter density, and volume change, which is sensitive to the cosmological constant. The uncertainties associated with the predicted number of lensing events, however, currently do not allow one to distinguish between flat and open cosmological models with and without a cosmological constant. Still, after accounting for known errors, and assuming that clusters in general have dark matter core radii of the order ~ 35 h^-1 kpc, we find that the cosmological mass density, Omega_m, is less than 0.56 at the 95% confidence. Such a dark matter core radius is consistent with cluster potentials determined recently by detailed numerical inversions of strong and weak lensing imaging data. If no core radius is present, the upper limit on Omega_m increases to 0.62 (95% confidence level). The estimated upper limit on Omega_m is consistent with various cosmological probes that suggest a low matter density for the Universe.Comment: 6 pages, 3 figures. Accepted version (ApJ in press

Physics Analysis Expert PAX: First Applications

PAX (Physics Analysis Expert) is a novel, C++ based toolkit designed to assist teams in particle physics data analysis issues. The core of PAX are event interpretation containers, holding relevant information about and possible interpretations of a physics event. Providing this new level of abstraction beyond the results of the detector reconstruction programs, PAX facilitates the buildup and use of modern analysis factories. Class structure and user command syntax of PAX are set up to support expert teams as well as newcomers in preparing for the challenges expected to arise in the data analysis at future hadron colliders.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 7 pages, LaTeX, 10 eps figures. PSN THLT00

Dynamic extensions of batch systems with cloud resources

Compute clusters use Portable Batch Systems (PBS) to distribute workload among individual cluster machines. To extend standard batch systems to Cloud infrastructures, a new service monitors the number of queued jobs and keeps track of the price of available resources. This meta-scheduler dynamically adapts the number of Cloud worker nodes according to the requirement profile. Two different worker node topologies are presented and tested on the Amazon EC2 Cloud service

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

Challenges of the LHC Computing Grid by the CMS experiment

This document summarises the status of the existing grid infrastructure and functionality for the high-energy physics experiment CMS and the expertise in operation attained during the so-called ”Computing, Software and Analysis Challenge” performed in 2006 (CSA06). This report is especially focused on the role of the participating computing centres in Germany located at Karlsruhe, Hamburg and Aachen