Tanaka-Tagoshi Parametrization of post-1PN Spin-Free Gravitational Wave Chirps: Equispaced and Cardinal Interpolated Lattices For First Generation Interferometric Antennas

The spin-free binary-inspiral parameter-space introduced by Tanaka and Tagoshi to construct a uniformly-spaced lattice of templates at (and possibly beyond) $2.5PN$ order is shown to work for all first generation interferometric gravitational wave antennas. This allows to extend the minimum-redundant cardinal interpolation techniques of the correlator bank developed by the Authors to the highest available order PN templates. The total number of 2PN templates to be computed for a minimal match $\Gamma=0.97$ is reduced by a factor 4, as in the 1PN case.Comment: 9 pages, 8 figures, 3 tables, accepted for publication in Phys. Rev.

Spatial variation of reef fishes and the relative influence of biotic and abiotic habitat traits

Patterns of distribution of reef fishes were examined across three spatial scales and related to habitat traits along 25 km of the northern Portuguese coast. Response variables included the multivariate assemblage structure, the total number of taxa and individuals, and the abundance of single groups categorized according to their preference for the benthic, proximo-benthic or pelagic environment, feeding and reproductive behaviour. Habitat traits included topographic elements (small and large ‘drops’ like cracks and crevices) and the extent of dominant morpho-functional types of macroalgae (kelp, large foliose, small erect, turf-forming filamentous, and encrusting). All fish responses were characterized by the largest variance at the smallest scale (among transects tens m apart), followed by that among reefs (hundreds m to 1 km apart) and almost null variance among sites (some km apart). Small and large ‘drops’ of the substratum explained, respectively, considerable variation of assemblage structure and the total abundance of individuals, while the extent of bare rock influenced the richness of taxa and that of benthic fishes, fishes feeding on sessile invertebrates and fishes laying benthic eggs or having nesting behaviour. Combinations of abiotic and biotic structural attributes of reefs influenced proximo-benthic fishes, the predators of mobile animals and fishes releasing pelagic eggs. The here reported associations between patterns of distribution of reef fishes and habitat traits have implications for the design of future protection schemes suitable to guarantee the conservation of reef fish communities and of the processes responsible for their variation. Within the SLOSS (single-large vs. several-small) debate in the design of marine reserves, for example, effective protection to the studied reef fishes would be provided by a set of small reserves, rather than a single large which might be appropriate for fishes having wider home ranges

Probing BH mass and accretion through X-ray variability in the CDFS

Recent work on nearby AGNs has shown that X-ray variability is correlated with the mass and accretion rate onto the central SMBH. Here we present the application of the variability-luminosity relation to high redshift AGNs in the CDFS, making use of XMM-Newton observations. We use Monte Carlo simulations in order to properly account for bias and uncertainties introduced by the sparse sampling and the very low statistics. Our preliminary results indicate that BH masses span over the range from 10^5 to 10^9 solar mass while accretion rates range from 10^-3 up to values greater than 1, in unit of Eddington accretion rate.Comment: 2 pages, 2 figures,in press in the X-ray 2009 Conference Proceedings (Bologna, 7-11 September 2009

Highlighting metabolic strategies using network analysis over strain optimization results

The field of Metabolic Engineering has been growing, sup- ported by the increase in the number of annotated genomes and genome- scale metabolic models. In silico strain optimization methods allow to create mutant strains able to overproduce certain metabolites of interest in Biotechnology. Thus, it is possible to reach (near-) optimal solutions, i.e. strains that provide the desired phenotype in computational pheno- type simulations. However, the validation of the results involves under- standing the strategies followed by these mutant strains to achieve the desired phenotype, studying the different use of reactions/ pathways by the mutants. This is quite complex given the size of the networks and the interactions between (sometimes distant) components. The manual verification and comparison of phenotypes is typically impossible. Here, automatic methods are proposed to analyse large sets of mutant strains, by taking the phenotypes of a large number of possible solutions and identifying shared patterns, using methods from network topology analysis. The topological comparison between the networks provided by the wild type and mutant strains highlights the major changes that lead to successful mutants. The methods are applied to a case study consider- ing E. coli and aiming at the production of succinate, optimizing the set of gene knockouts to apply to the wild type. Solutions provided by the use of Simulated Annealing and Evolutionary Algorithms are analyzed. The results show that these methods can help in the identification of the strategies leading to the overproduction of succinate.This work is supported by project PTDC/EIA-EIA/115176/2009, funded by Portuguese FCT and Programa COMPETE.José Pedro Pinto work is funded by a PhD grant from the Portuguese FCT (ref. SFRH/BD/41763/2007)

Reconstruction of a genome-scale metabolic network for Streptococcus pneumoniae R6

The gram-positive, lancet-shaped bacteria Streptococcus pneumoniae thrives in almost any environment. Under certain conditions this pathogen can cause several infections such as meningitis, otitis media, endocarditis or pneumonia. Genome-scale metabolic networks (GSMs) are commonly used to study phenotype-genotype relationships using biochemical, physiological and genomic information. These relationships might shed some light on identification of targets for metabolic engineering or, in the case of S. pneumoniae, determine if the bacteria´s increased invasiveness and virulence is dependent on specific genomic regions or determined by environmental conditions. In order to obtain a robust and reliable metabolic model, a proper, up-to-date genome annotation must be performed. In our work we aimed to re-annotate the genome of Streptococcus pneumoniae strain R6 and which would be used to reconstruct a metabolic network at a genomic level. For these tasks merlin was used, a software tool capable of performing automatic annotation of the genome using the amino acid sequences as well as reconstruction of the metabolic network. For validation purposes, another in-house tool (Optflux) capable of performing simulations and optimization tasks was used. Re-annotation of the genome was performed in accordance to an in-house generated pipeline which established rules for gene identification acceptance (and attribution of confidence levels) or rejection. Out of the 2043 genes present in S. pneumoniae´s genome, an initial 822 were identified as metabolic, representing an increase of almost 9 and 15% when compared to those of KEGG and Uniprot. An extended comparison revealed that a large number of genes (359 and 271 when compared to Uniprot and KEGG, respectively) were only present in our re-annotation. Although a significant amount of genes (113) were identified as only being present in KEGG and not in our study, this can be explained by the dismissal of genes associated to DNA and RNA processes from the statistical analysis. The metabolic network is comprised of 795 genes, 776 that only encode enzymes and 19 that only encode transporters. The biomass equation was adapted from close-related organisms such as B. subtilis and L. lactis cross-referenced with the biomass equation determined by ModelSEED for S. pneumoniae R6. Despite the considerable amount of essential genes in our model (83), only 38 were in accordance to literature regarding gene essentiality although it identified others (45) which have not been studied to date. The mismatch between results might be related to strain metabolic specificities, regulatory phenomena or even the dismissal of genes that affect DNA and RNA processes and capsule synthesis which should be addressed in future work. In order to validate the accuracy of the model, simulations were performed using experimental data retrieved from literature. The results obtained were very similar to the ones described in in vitro studies elevating the confidence level of the reconstructed model