Visualization of comparative genomic analyses by BLAST score ratio

BACKGROUND: The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis. RESULTS: The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared. CONCLUSIONS: Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at:

Radio Detection of Cosmic Ray Air Showers with Codalema

Studies of the radio detection of Extensive Air Showers is the goal of the demonstrative experiment CODALEMA. Previous analysis have demonstrated that detection around $5.10^{16}$ eV was achieved with this set-up. New results allow for the first time to study the topology of the electric field associated to EAS events on a event by event basis.Comment: 6 pages, 4 figures Proceedings of the Rencontres de Moriond, Very High Energy Phenomena in the Universe, La Thuile, Italy (March 12-19, 2005

Radio Detection of Extensive Air Showers with CODALEMA

The principle and performances of the CODALEMA experimental device, set up to study the possibility of high energy cosmic rays radio detection, are presented. Radio transient signals associated to cosmic rays have been identified, for which arrival directions and shower's electric field topologies have been extracted from the antenna signals. The measured rate, about 1 event per day, corresponds to an energy threshold around 5.10^16 eV. These results allow to determine the perspectives offered by the present experimental design for radiodetection of UHECR at a larger scale.Comment: 4 pages and 3 figures. To appear in the Proceedings of the 29th ICRC, Pune (2005

Radio Detection of Cosmic Ray Extensive Air Showers: present status of the CODALEMA experiment

Data acquisition and analysis for the CODALEMA experiment, in operation for more than one year, has provided improved knowledge of the characteristics of this new device. At the same time, an important effort has been made to develop processing techniques for extracting transient signals from data containing interference.Comment: september 200

Radiodetection of Cosmic Ray Extensive Air Showers

We present the characteristics and performance of a demonstration experiment devoted to the observation of ultra high- energy cosmic ray extensive air showers using a radiodetection technique. In a first step, one antenna narrowed band filtered acting as trigger, with a 4 $\sigma$ threshold above sky background-level, was used to tag any radio transient in coincidence on the antenna array. Recently, the addition of 4 particle detectors has allowed us to observe cosmic ray events in coincidence with antennas

Common iliac aneurysms with short or absent proximal necks: Endoluminal repair with a covered endoprosthesis

AbstractEur J Vasc Endovasc Surg 26, 334-336 (2003

Experimental evidence of thermal fluctuations on the X-ray absorption near-edge structure at the aluminum K-edge

After a review of temperature-dependent experimental x-ray absorption near-edge structure (XANES) and related theoretical developments, we present the Al K-edge XANES spectra of corundum and beryl for temperature ranging from 300K to 930K. These experimental results provide a first evidence of the role of thermal fluctuation in XANES at the Al K-edge especially in the pre-edge region. The study is carried out by polarized XANES measurements of single crystals. For any orientation of the sample with respect to the x-ray beam, the pre-edge peak grows and shifts to lower energy with temperature. In addition temperature induces modifications in the position and intensities of the main XANES features. First-principles DFT calculations are performed for both compounds. They show that the pre-edge peak originates from forbidden 1s to 3s transitions induced by vibrations. Three existing theoretical models are used to take vibrations into account in the absorption cross section calculations: i) an average of the XANES spectra over the thermal displacements of the absorbing atom around its equilibrium position, ii) a method based on the crude Born-Oppenheimer approximation where only the initial state is averaged over thermal displacements, iii) a convolution of the spectra obtained for the atoms at the equilibrium positions with an approximate phonon spectral function. The theoretical spectra so obtained permit to qualitatively understand the origin of the spectral modifications induced by temperature. However the correct treatment of thermal fluctuation in XANES spectroscopy requires more sophisticated theoretical tools