Chandra Observations of the Optically Dark GRB030528

The X-ray-rich GRB030528 was detected by the HETE satellite and its localization was rapidly disseminated. However, early optical observations failed to detect a counterpart source. In a 2-epoch ToO observation with Chandra, we discovered a fading X-ray source likely counterpart to GRB030528. The source brightness was typical of X-ray afterglows observed at similar epochs. Other observers detected an IR source at a location consistent with the X-ray source. The X-ray spectrum is not consistent with a large absorbing column.Comment: 4 pages, 1 figures, to appear in Santa Fe GRB Conference Proceedings, 200

Previously Claimed(/Unclaimed) X-ray Emission Lines in High Resolution Afterglow Spectra

We review the significance determination for emission lines in the Chandra HETGS spectrum for GRB020813, and we report on a search for additional lines in high resolution Chandra spectra. No previously unclaimed features are found. We also discuss the significance of lines sets reportedly discovered using XMM data for GRB011211 and GRB030227. We find that these features are likely of modest, though not negligible, significance.Comment: 4 pages, 1 figures, to appear in Santa Fe GRB Conference Proceedings, 200

Optical and X-ray Observations of the Afterglow to XRF030723

The X-ray-flash XRF030723 was detected by the HETE satellite and rapidly disseminated, allowing for an optical transient to be detected ~1 day after the burst. We discuss observations in the optical with Magellan, which confirmed the fade of the optical transient. In a 2-epoch ToO observation with Chandra, we discovered a fading X-ray source spatially coincident with the optical transient. We present spectral fits to the X-ray data. We also discuss the possibility that the source underwent a rebrightening in the X-rays, as was observed in the optical. We find that the significance of a possible rebrightening is very low (~1 sigma).Comment: 4 pages, 2 figures, to appear in Santa Fe GRB Conference Proceedings, 200

Fold-specific sequence scoring improves protein sequence matching

Background Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, and also for discriminating between unimportant and disease mutants. At present the functions of a large fraction of genes are unknown; improvements in sequence matching will improve gene annotations. Universal amino acid substitution matrices such as Blosum62 are used to measure sequence similarities and to identify distant homologues, regardless of the structure class. However, such single matrices do not take into account important structural information evident within the different topologies of proteins and treats substitutions within all protein folds identically. Others have suggested that the use of structural information can lead to significant improvements in sequence matching but this has not yet been very effective. Here we develop novel substitution matrices that include not only general sequence information but also have a topology specific component that is unique for each CATH topology. This novel feature of using a combination of sequence and structure information for each protein topology significantly improves the sequence matching scores for the sequence pairs tested. We have used a novel multi-structure alignment method for each homology level of CATH in order to extract topological information. Results We obtain statistically significant improved sequence matching scores for 73 % of the alpha helical test cases. On average, 61 % of the test cases showed improvements in homology detection when structure information was incorporated into the substitution matrices. On average z-scores for homology detection are improved by more than 54 % for all cases, and some individual cases have z-scores more than twice those obtained using generic matrices. Our topology specific similarity matrices also outperform other traditional similarity matrices and single matrix based structure methods. When default amino acid substitution matrix in the Psi-blast algorithm is replaced by our structure-based matrices, the structure matching is significantly improved over conventional Psi-blast. It also outperforms results obtained for the corresponding HMM profiles generated for each topology. Conclusions We show that by incorporating topology-specific structure information in addition to sequence information into specific amino acid substitution matrices, the sequence matching scores and homology detection are significantly improved. Our topology specific similarity matrices outperform other traditional similarity matrices, single matrix based structure methods, also show improvement over conventional Psi-blast and HMM profile based methods in sequence matching. The results support the discriminatory ability of the new amino acid similarity matrices to distinguish between distant homologs and structurally dissimilar pairs

Analyses of the Konus catalogue of gamma-ray bursts with the thermal synchrotron model

Approximately 150 reported gamma bursts of the Konus catalogue using the thermal synchrotron model are analyzed. An overwhelming majority of these spectra can be satsifactorily fitted by theoretical thermal synchrotron spectra of mildly relativistic electrons in strong magnetic fields, making the strong-field neutron star picture at least self-consistent. Valuable additional information is also extracted from various spectral features contained in many of the events

Structural compliance: A new metric for protein flexibility

Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynamics and then compared to the experimental B-factors. However, proteins do not move in a vacuum and their motions are modulated by solvent that can impose forces on the structure. In this paper, we introduce a new structural concept, which has been called the structural compliance, for the evaluation of the global and local deformability of the protein structure in response to intramolecular and solvent forces. Based on the application of pairwise pulling forces to a protein elastic network, this structural quantity has been computed and sometimes is even found to yield an improved correlation with the experimental B-factors, meaning that it may serve as a better metric for protein flexibility. The inverse of structural compliance, namely the structural stiffness, has also been defined, which shows a clear anticorrelation with the experimental data. Although the present applications are made to proteins, this approach can also be applied to other biomolecular structures such as RNA. This present study considers only elastic network models, but the approach could be applied further to conventional atomic molecular dynamics. Compliance is found to have a slightly better agreement with the experimental B-factors, perhaps reflecting its bias toward the effects of local perturbations, in contrast to mean square fluctuations. The code for calculating protein compliance and stiffness is freely accessible at https://jerniganlab.github.io/Software/PACKMAN/Tutorials/compliance

Can brewer-sponsored ‘drink responsibly’ warning message be effective without alcohol policies in Nigeria?

Alcohol availability, use and misuse and their related problems are rising in many parts of the African continent and this has been attributed to many factors such as non-existent or ineffective regulatory measures. In contemporary Nigeria, while a culture of intoxication is growing, there are no regulatory measures in the form of alcohol policies to reduce it. What exists is brewer-sponsored self-regulation. This paper therefore, critically analyses this self-imposed 'drink responsibly' warning message, arguing that because responsible drinking messages are strategically designed to serve the interest of alcohol industries, it cannot be effective. The paper further argues that because there are no definitions of standard drinks and where alcohol by volume (ABV) is scarcely inscribed on product labels of alcoholic beverages, such message will remain ineffective. Therefore, it recommends that an urgent step should be taken by the government to formulate and implement comprehensive evidence-based alcohol policies in Nigeria

Final Report of B548129: Spectral Analysis of Soft X-Ray Data from NSTX

We present a summary of work performed under subcontract B548129 'Spectral Analysis of Soft X-Ray Data from NSTX'. This summary is comprised of papers and poster presentations prepared under this subcontract. The X-ray and Extreme Ultraviolet Spectrometer (XEUS) has been used to monitor the line emission from various impurity ions on NSTX, in particular the K-shell emission of helium-like and hydrogen-like B, C, N, and O. While C VI typically dominates the spectrum, unusually strong emission from N VII has been observed in multiple discharges during the past run campaign. In this case, the nitrogen concentration can exceed that of carbon by an order of magnitude. Time-dependent measurements show that the nitrogen concentration builds up over the course of the discharge and coincides with a build up of boron. In a few cases we observed several unknown lines. These are clearly lines from heavy impurities, possibly molybdenum. Some of these lines can be explained by the emission from Ti XIII