WormBase 2007

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences

Randomized in situ evaluation of surface polishing protocols on the caries-protective effect of resin Infiltrant.

The aim of this placebo-controlled randomized in situ study was to evaluate the effect of different surface polishing protocols on enamel roughness, bacterial adhesion and caries-protective effect of a resin infiltrant. Seventy-five bovine enamel samples having artificial caries lesions were treated with a resinous infiltrant and afterwards randomly dividided into five polishing protocols: aluminum oxide flexible disks (Al2O3-Disks), silicon carbide tips (SIC-Tips), silicon carbide brush (SIC-Brush), silicon carbide polyester strips (SIC-Strips) or no polishing [negative control (NC)]. Average surface roughness (Ra) was assessed by profilometry. Samples were mounted in palatal appliances under a mesh for biofilm accumulation. Fifteen volunteers wore the intraoral appliances (14-days) and cariogenic challenge was triggered by sucrose solutions. Biofilm formed was collected for microbiological analysis of caries-related bacteria (Streptococcus mutans, Lactobacillus acidophilus) and demineralization was assessed by cross-sectional microhardness. Mean Knoop hardness numbers (Kg/mm2) were plotted over lesion depth (µm) and area under the lesion curve was subtracted from sound enamel to determine demineralization (ΔS, Kg/mm2xµm). Data were analyzed by ANOVA and post-hoc comparisons (α = 0.05). NC resulted in significantly higher Ra means than Al2O3-Disks and SIC-Strips. Bacterial counts were not significantly different between the groups (p > 0.05). Regards ΔS means, however none of the groups were significantly different to NC (6983.3 kg/mm2xµm /CI 4246.1-9720.5, p > 0.05). Conclusions: Polishing protocols (Al2O3-Disks, SIC-Strips) significantly decreseased roughness of infiltrated-enamel, however none of the polishing protocols could signicantly decrease bacterial counts nor resulted in significant less demineralization

Near infrared imaging of NGC2316

In the present paper we present JHK photometric results of the young embedded cluster NGC 2316. We construct the cluster radial profile from which we determine a radius of 0.63 pc. We find 189 $\pm$ 29 cluster members in an extinction limited sub-sample of the survey, 22 $\pm$ 19 of which are possibly substellar. An average extinction of 4.5 visual magnitudes is derived using (H-K) colours of control fields. This extinction is due to the presence of residual parental molecular cloud. NGC 2316 presents 16% source fraction of excess emission which is consistent with other results from clusters with an age of 2-3 Myr. This age is consistent with the distribution of sources in the colour-magnitude diagram when compared to theoretical isochrones, and the overall shape of the cluster KLF. The substellar population of the cluster is similar or smaller than that observed for other embedded clusters and the stellar objects dominate the cluster membership.Comment: 4 pages, 5 figures, accepted for publication in Astronomy & Astrophysics Letters. Full resolution images and paper available from http://www-cfa.harvard.edu/~pteixeir/NGC2316

A mechanism for the inhibition of DNA-PK-mediated DNA sensing by a virus

The innate immune system is critical in the response to infection by pathogens and it is activated by pattern recognition receptors (PRRs) binding to pathogen associated molecular patterns (PAMPs). During viral infection, the direct recognition of the viral nucleic acids, such as the genomes of DNA viruses, is very important for activation of innate immunity. Recently, DNA-dependent protein kinase (DNA-PK), a heterotrimeric complex consisting of the Ku70/Ku80 heterodimer and the catalytic subunit DNA-PKcs was identified as a cytoplasmic PRR for DNA that is important for the innate immune response to intracellular DNA and DNA virus infection. Here we show that vaccinia virus (VACV) has evolved to inhibit this function of DNA-PK by expression of a highly conserved protein called C16, which was known to contribute to virulence but by an unknown mechanism. Data presented show that C16 binds directly to the Ku heterodimer and thereby inhibits the innate immune response to DNA in fibroblasts, characterised by the decreased production of cytokines and chemokines. Mechanistically, C16 acts by blocking DNA-PK binding to DNA, which correlates with reduced DNA-PK-dependent DNA sensing. The C-terminal region of C16 is sufficient for binding Ku and this activity is conserved in the variola virus (VARV) orthologue of C16. In contrast, deletion of 5 amino acids in this domain is enough to knockout this function from the attenuated vaccine strain modified vaccinia virus Ankara (MVA). In vivo a VACV mutant lacking C16 induced higher levels of cytokines and chemokines early after infection compared to control viruses, confirming the role of this virulence factor in attenuating the innate immune response. Overall this study describes the inhibition of DNA-PK-dependent DNA sensing by a poxvirus protein, adding to the evidence that DNA-PK is a critical component of innate immunity to DNA viruses

Detection of variable VHE gamma-ray emission from the extra-galactic gamma-ray binary LMC P3

Context. Recently, the high-energy (HE, 0.1-100 GeV) $\gamma$-ray emission from the object LMC P3 in the Large Magellanic Cloud (LMC) has been discovered to be modulated with a 10.3-day period, making it the first extra-galactic $\gamma$-ray binary. Aims. This work aims at the detection of very-high-energy (VHE, >100 GeV) $\gamma$-ray emission and the search for modulation of the VHE signal with the orbital period of the binary system. Methods. LMC P3 has been observed with the High Energy Stereoscopic System (H.E.S.S.); the acceptance-corrected exposure time is 100 h. The data set has been folded with the known orbital period of the system in order to test for variability of the emission. Energy spectra are obtained for the orbit-averaged data set, and for the orbital phase bin around the VHE maximum. Results. VHE $\gamma$-ray emission is detected with a statistical significance of 6.4 $\sigma$. The data clearly show variability which is phase-locked to the orbital period of the system. Periodicity cannot be deduced from the H.E.S.S. data set alone. The orbit-averaged luminosity in the $1-10$ TeV energy range is $(1.4 \pm 0.2) \times 10^{35}$ erg/s. A luminosity of $(5 \pm 1) \times 10^{35}$ erg/s is reached during 20% of the orbit. HE and VHE $\gamma$-ray emissions are anti-correlated. LMC P3 is the most luminous $\gamma$-ray binary known so far.Comment: 5 pages, 3 figures, 1 table, accepted for publication in A&

Detailed spectral and morphological analysis of the shell type SNR RCW 86

Aims: We aim for an understanding of the morphological and spectral properties of the supernova remnant RCW~86 and for insights into the production mechanism leading to the RCW~86 very high-energy gamma-ray emission. Methods: We analyzed High Energy Spectroscopic System data that had increased sensitivity compared to the observations presented in the RCW~86 H.E.S.S. discovery publication. Studies of the morphological correlation between the 0.5-1~keV X-ray band, the 2-5~keV X-ray band, radio, and gamma-ray emissions have been performed as well as broadband modeling of the spectral energy distribution with two different emission models. Results:We present the first conclusive evidence that the TeV gamma-ray emission region is shell-like based on our morphological studies. The comparison with 2-5~keV X-ray data reveals a correlation with the 0.4-50~TeV gamma-ray emission.The spectrum of RCW~86 is best described by a power law with an exponential cutoff at $E_{cut}=(3.5\pm 1.2_{stat})$ TeV and a spectral index of $\Gamma$~$1.6\pm 0.2$. A static leptonic one-zone model adequately describes the measured spectral energy distribution of RCW~86, with the resultant total kinetic energy of the electrons above 1 GeV being equivalent to $\sim$0.1\% of the initial kinetic energy of a Type I a supernova explosion. When using a hadronic model, a magnetic field of $B$~100$\mu$G is needed to represent the measured data. Although this is comparable to formerly published estimates, a standard E$^{-2}$ spectrum for the proton distribution cannot describe the gamma-ray data. Instead, a spectral index of $\Gamma_p$~1.7 would be required, which implies that ~$7\times 10^{49}/n_{cm^{-3}}$erg has been transferred into high-energy protons with the effective density $n_{cm^{-3}}=n/ 1$ cm^-3. This is about 10\% of the kinetic energy of a typical Type Ia supernova under the assumption of a density of 1~cm^-3.Comment: accepted for publication by A&

Characterizing the gamma-ray long-term variability of PKS 2155-304 with H.E.S.S. and Fermi-LAT

Studying the temporal variability of BL Lac objects at the highest energies provides unique insights into the extreme physical processes occurring in relativistic jets and in the vicinity of super-massive black holes. To this end, the long-term variability of the BL Lac object PKS 2155-304 is analyzed in the high (HE, 100 MeV 200 GeV) gamma-ray domain. Over the course of ~9 yr of H.E.S.S observations the VHE light curve in the quiescent state is consistent with a log-normal behavior. The VHE variability in this state is well described by flicker noise (power-spectral-density index {\ss}_VHE = 1.10 +0.10 -0.13) on time scales larger than one day. An analysis of 5.5 yr of HE Fermi LAT data gives consistent results ({\ss}_HE = 1.20 +0.21 -0.23, on time scales larger than 10 days) compatible with the VHE findings. The HE and VHE power spectral densities show a scale invariance across the probed time ranges. A direct linear correlation between the VHE and HE fluxes could neither be excluded nor firmly established. These long-term-variability properties are discussed and compared to the red noise behavior ({\ss} ~ 2) seen on shorter time scales during VHE-flaring states. The difference in power spectral noise behavior at VHE energies during quiescent and flaring states provides evidence that these states are influenced by different physical processes, while the compatibility of the HE and VHE long-term results is suggestive of a common physical link as it might be introduced by an underlying jet-disk connection.Comment: 11 pages, 16 figure

Integration of DFDs into a UML - based model-driven engineering approach

The main aim of this article is to discuss how the functional and the object-oriented views can be inter-played to represent the various modeling perspectives of embedded systems.We discuss whether the object-oriented modeling paradigm, the predominant one to develop software at the present time, is also adequate for modeling embedded software and how it can be used with the functional paradigm.More specifically, we present how the main modeling tool of the traditional structured methods, data flow diagrams, can be integrated in an object-oriented development strategy based on the unified modeling language. The rationale behind the approach is that both views are important for modeling purposes in embedded systems environments, and thus a combined and integrated model is not only useful, but also fundamental for developing complex systems. The approach was integrated in amodel-driven engineering process, where tool support for the models used was provided. In addition, model transformations have been specified and implemented to automate the process.We exemplify the approach with an IPv6 router case study.FEDER -Fundação para a Ciência e a Tecnologia(HH-02-383

Emerging roles and competencies of district and sub-district pharmacists: a case study from Cape Town

District and sub-district pharmacist positions were created during health sector reform in South Africa. High prevalence of HIV/AIDS, tuberculosis and increasing chronic non-communicable diseases have drawn attention to their pivotal roles in improving accessibility and appropriate use of medicines at the primary level. This research describes new roles and related competencies of district and sub-district pharmacists in Cape Town. Between 2008 and 2011, the author (HB) conducted participatory action research in Cape Town Metro District, an urban district in the Western Cape Province of South Africa, partnering with pharmacists and managers of the two government primary health care (PHC) providers. The two providers function independently delivering complementary PHC services across the entire geographic area, with one provider employing district pharmacists and the other sub-district pharmacists. After an initiation phase, the research evolved into a series of iterative cycles of action and reflection, each providing increasing understanding of district and sub-district pharmacists’ roles and competencies. Data was generated through workshops, semi-structured interviews and focus groups with pharmacists and managers which were recorded and transcribed. Thematic analysis was carried out iteratively during the 4-year engagement and triangulated with document reviews and published literature. Five main roles for district and sub-district pharmacists were identified: district/sub-district management; planning, co-ordination and monitoring of pharmaceuticals; information and advice; quality assurance and clinical governance; and research (district pharmacists)/dispensing at clinics (sub-district pharmacists). Although the roles looked similar, there were important differences, reflecting the differing governance and leadership models and services of each provider. Five competency clusters were identified: professional pharmacy practice; health system and public health; management; leadership; and personal, interpersonal and cognitive competencies. Whilst professional pharmacy competencies were important, generic management and leadership competencies were considered critical for pharmacists working in these positions. Similar roles and competencies for district and sub-district pharmacists were identified in the two PHC providers in Cape Town, although contextual factors influenced precise specifications. These insights are important for pharmacists and managers from other districts and sub-districts in South Africa and inform health workforce planning and capacity development initiatives in countries with similar health systems.Web of Scienc