The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports

Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed

High-Energy Cosmology: gamma rays and neutrinos from beyond the galaxy

Our knowledge of the high-energy universe is undergoing a period of rapid change as new astronomical detectors of high-energy radiation start to operate at their design sensitivities. Now is a boomtime for high-energy astrophysics, with new discoveries from Swift and HESS, results from MAGIC and VERITAS starting to be reported, the upcoming launches of the gamma-ray space telescopes GLAST and AGILE, and anticipated data releases from IceCube and Auger. A formalism for calculating statistical properties of cosmological gamma-ray sources is presented. Application is made to model calculations of the statistical distributions of gamma-ray and neutrino emission from (i) beamed sources, specifically, long-duration GRBs, blazars, and extagalactic microquasars, and (ii) unbeamed sources, including normal galaxies, starburst galaxies and clusters. Expressions for the integrated intensities of faint beamed and unbeamed high-energy radiation sources are also derived. A toy model for the background intensity of radiation from dark-matter annihilation taking place in the early universe is constructed. Estimates for the gamma-ray fluxes of local group galaxies, starburst, and infrared luminous galaxies are briefly reviewed. Because the brightest extragalactic gamma-ray sources are flaring sources, and these are the best targets for sources of PeV -- EeV neutrinos and ultra-high energy cosmic rays, rapidly slewing all-sky telescopes like MAGIC and an all-sky gamma-ray observatory beyond Milagro will be crucial for optimal science return in the multi-messenger age.Comment: 10 pages, 3 figs, accepted for publication in the Barcelona Conference on Multimessenger Astronomy; corrected eq. 27, revised Fig. 3, added 2 ref

Unidentified EGRET Sources and the Extragalactic Gamma-Ray Background

The large majority of EGRET point sources remain to this day without an identified low-energy counterpart. Whatever the nature of the EGRET unidentified sources, faint unresolved objects of the same class must have a contribution to the diffuse gamma-ray background: if most unidentified objects are extragalactic, faint unresolved sources of the same class contribute to the background, as a distinct extragalactic population; on the other hand, if most unidentified sources are Galactic, their counterparts in external galaxies will contribute to the unresolved emission from these systems. Understanding this component of the gamma-ray background, along with other guaranteed contributions from known sources, is essential in any attempt to use gamma-ray observations to constrain exotic high-energy physics. Here, we follow an empirical approach to estimate whether a potential contribution of unidentified sources to the extragalactic gamma-ray background is likely to be important, and we find that it is. Additionally, we comment on how the anticipated GLAST measurement of the diffuse gamma-ray background will change, depending on the nature of the majority of these sources.Comment: 6 pages, 3 figures, to appear in proceedings of "The Multi-Messenger Approach to High Energy Gamma-Ray Sources", Barcelona, 4-7 July 2006; comments welcom

Slightly Non-Minimal Dark Matter in PAMELA and ATIC

We present a simple model in which dark matter couples to the standard model through a light scalar intermediary that is itself unstable. We find this model has several notable features, and allows a natural explanation for a surplus of positrons, but no surplus of anti-protons, as has been suggested by early data from PAMELA and ATIC. Moreover, this model yields a very small nucleon coupling, well below the direct detection limits. In this paper we explore the effect of this model in both the early universe and in the galaxy.Comment: 7 pages, 6 figures, v3: updated for new data, added discussion of Ferm

The obscured gamma-ray and UHECR universe

Auger results on clustering of > 60 EeV ultra-high energy cosmic ray (UHECR) ions and the interpretation of the gamma-ray spectra of TeV blazars are connected by effects from the extragalactic background light (EBL). The EBL acts as an obscuring medium for gamma rays and a reprocessing medium for UHECR ions and protons, causing the GZK cutoff. The study of the physics underlying the coincidence between the GZK energy and the clustering energy of UHECR ions favors a composition of > 60 EeV UHECRs in CNO group nucleons. This has interesting implications for the sources of UHECRs. We also comment on the Auger analysis.Comment: 11 pages, 10 figures, in the International Conference on Topics in Astroparticle and Underground Physics (TAUP) 2007, Sendai, Japan, September 11-15, 200

Influence of the Earth on the background and the sensitivity of the GRM and ECLAIRs instruments aboard the Chinese-French mission SVOM

SVOM (Space-based multi-band astronomical Variable Object Monitor) is a future Chinese-French satellite mission which is dedicated to Gamma-Ray Burst (GRB) studies. Its anti-solar pointing strategy makes the Earth cross the field of view of its payload every orbit. In this paper, we present the variations of the gamma-ray background of the two high energy instruments aboard SVOM, the Gamma-Ray Monitor (GRM) and ECLAIRs, as a function of the Earth position. We conclude with an estimate of the Earth influence on their sensitivity and their GRB detection capability.Comment: 24 pages, 15 figures, accepted for publication in Experimental Astronom

Quantitative CT: Associations between Emphysema, Airway Wall Thickness and Body Composition in COPD

The objective of the present study was to determine the association between CT phenotypes—emphysema by low attenuation area and bronchitis by airway wall thickness—and body composition parameters in a large cohort of subjects with and without COPD. In 452 COPD subjects and 459 subjects without COPD, CT scans were performed to determine emphysema (%LAA), airway wall thickness (AWT-Pi10), and lung mass. Muscle wasting based on FFMI was assessed by bioelectrical impedance. In both the men and women with COPD, FFMI was negatively associated with %LAA. FMI was positively associated with AWT-Pi10 in both subjects with and without COPD. Among the subjects with muscle wasting, the percentage emphysema was high, but the predictive value was moderate. In conclusion, the present study strengthens the hypothesis that the subgroup of COPD cases with muscle wasting have emphysema. Airway wall thickness is positively associated with fat mass index in both subjects with and without COPD

Broadband Spectral Analysis of PKS 0528+134: A Report on Six Years of EGRET Observations

The multiwavelength spectra of PKS 0528+134 during six years of observations by EGRET have been analyzed using synchrotron self-Compton (SSC) and external radiation Compton (ERC) models. We find that a two-component model, in which the target photons are produced externally to the gamma-ray emitting region, but also including an SSC component, is required to suitably reproduce the spectral energy distributions of the source. Our analysis indicates that there is a trend in the observed properties of PKS 0528+134, as the source goes from a gamma-ray low state to a flaring state. We observe that during the higher gamma-ray states, the bulk Lorentz factor of the jet increases and the ERC component dominates the high-energy emission. Our model calculations indicate the trend that the energies of the electrons giving rise to the synchrotron peak decreases, and the power-ratio of the gamma-ray and low energy spectral components increases, as the source goes from a low to a high gamma-ray state.Comment: 36 pages, 13 figures, final version accepted for publication in ApJ; includes minor modification