IPD - the Immuno Polymorphism Database

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute

The effect of minihaloes on cosmic reionization

One of the most debated issues in the theoretical modeling of cosmic reionization is the impact of small-mass gravitationally-bound structures. We carry out the first numerical investigation of the role of such sterile `minihaloes', which serve as self-shielding screens of ionizing photons. Minihaloes are too small to be properly resolved in current large-scale cosmological simulations, and thus we estimate their effects using a sub-grid model, considering two cases that bracket their effect within this framework. In the `extreme suppression' case in which minihalo formation ceases once a region is partially ionized, their effect on cosmic reionization is modest, reducing the volume-averaged ionization fraction by an overall factor of less than 15%. In the other extreme, in which minihalo formation is never suppressed, they delay complete reionization as much as Delta z~2, in rough agreement with the results from a previous semi-analytical study by the authors. Thus, depending on the details of the minihalo formation process, their effect on the overall progress of reionization can range from modest to significant, but the minihalo photon consumption is by itself insufficient to force an extended reionization epoch.Comment: 9 pages, 2 figures, accepted for pubblication in MNRA

The Hubble Legacy Archive ACS Grism Data

A public release of slitless spectra, obtained with ACS/WFC and the G800L grism, is presented. Spectra were automatically extracted in a uniform way from 153 archival fields (or "associations") distributed across the two Galactic caps, covering all observations to 2008. The ACS G800L grism provides a wavelength range of 0.55-1.00 \mu$m, with a dispersion of$40 \ \AA / pixel$and a resolution of$\sim 80\ \AA$for point-like sources. The ACS G800L images and matched direct images were reduced with an automatic pipeline that handles all steps from archive retrieval, alignment and astrometric calibration, direct image combination, catalogue generation, spectral extraction and collection of metadata. The large number of extracted spectra (73,581) demanded automatic methods for quality control and an automated classification algorithm was trained on the visual inspection of several thousand spectra. The final sample of quality controlled spectra includes 47,919 datasets (65of extracted spectra) for$32,149$unique objects, with a median$i_{\rm AB}$-band magnitude of 23.7, reaching 26.5 AB for the faintest objects. Each released dataset contains science-ready 1D and 2D spectra, as well as multi-band image cutouts of corresponding sources and a useful preview page summarising the direct and slitless data, astrometric and photometric parameters. In order to characterize the slitless spectra, emission-line flux and equivalent width sensitivity of the ACS data were compared with public ground-based spectra in the GOODS-South field. An example list of emission line galaxies with two or more identified lines is also included, covering the redshift range$0.2-4.6$.Comment: Accepted for publication in Astronomy and Astrophysics; 29 pages, 16 Figures, 4 Tables in text and 3Tables in Appendi

The impact of the dark matter-gas interaction on the collapse behaviour of spherical symmetric systems

If the gas in the evolving cosmic halos is dissipating energy (cooling) then due to the variation of the gravitational potential the dark matter halo also undergoes a compactification. This is well-known as Adiabatic contraction (AC). Complementary to the AC we investigate the resulting dynamical behaviour of the whole system if the backreaction of the AC of DM onto the gas is taken into account. In order to achieve sufficient high resolution also within the central halo region, we use a crude fluid approximation for the DM obeying the adiabatic contraction behaviour. Further, we restrict ourself to spherical symmetry and vanishing angular momentum of the studied matter configurations. The computations are done using a first-order Godunov type scheme. Our results show that the dynamical interaction between gas and DM may lead to significant shorter collapse times. If the gas cools the dynamical behaviour of the whole system depends strongly on the shape of the initial density profile. Our findings indicate that for a certain mass range of halo configurations the dynamical interaction between gas and DM might be important for the halo evolution and must be taken into account.Comment: 9 pages, 13 figures, accepted for publication in A&A, added reference

Are Great Disks Defined by Satellite Galaxies in Milky-Way Type Halos Rare in Λ\LambdaCDM model?

We study the spatial distribution of satellite galaxies by assuming that they follow the dark matter distribution. This assumption is supported by semi-analytical studies based on high-resolution numerical simulations. We find that for a Milky-Way type halo, if only a dozen satellite galaxies are observed, then they can lie on a ``great'' disk with an rms height of about 40 kpc. The normal to the plane is roughly isotropic on the sky. These results are consistent with the observed properties of the satellite galaxies in the Milky Way. If, however, the satellite galaxies follow the distribution of substructure selected by present mass, then great disks similar to the one in the Milky Way are rare and difficult to reproduce, in agreement with the conclusion reached by Kroupa et al. (2004).Comment: Major revised, new figure and text added, to appear in A&

SOAP-based services provided by the European Bioinformatics Institute

SOAP (Simple Object Access Protocol) () based Web Services technology () has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3–9]. These services are available free to all users from

GTP and Ca2+ Modulate the Inositol 1,4,5-Trisphosphate-Dependent Ca2+ Release in Streptolysin O-Permeabilized Bovine Adrenal Chromaffin Cells

The inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ release was studied using streptolysin O-permeabilized bovine adrenal chromaffin cells. The IP3-induced Ca2+ release was followed by Ca2+ reuptake into intracellular compartments. The IP3-induced Ca2+ release diminished after sequential applications of the same amount of IP3. Addition of 20 μM GTP fully restored the sensitivity to IP3. Guanosine 5'-O-(3-thio)triphosphate (GTPγS) could not replace GTP but prevented the action of GTP. The effects of GTP and GTPγS were reversible. Neither GTP nor GTPγS induced release of Ca2+ in the absence of IP3. The amount of Ca2+ whose release was induced by IP3 depended on the free Ca2+ concentration of the medium. At 0.3 μM free Ca2+, a half-maximal Ca2+ release was elicited with ∼0.1 μM IP3. At 1 μM free Ca2+, no Ca2+ release was observed with 0.1 μM IP3; at this Ca2+ concentration, higher concentrations of IP3 (0.25 μM) were required to evoke Ca2+ release. At 8 μM free Ca2+, even 0.25 μM IP3 failed to induce release of Ca2+ from the store. The IP3-induced Ca2+ release at constant low (0.2 μM) free Ca2+ concentrations correlated directly with the amount of stored Ca2+. Depending on the filling state of the intracellular compartment, 1 mol of IP3 induced release of between 5 and 30 mol of Ca2+

Component-wise approximate Bayesian computation via Gibbs-like step

Approximate Bayesian computation methods are useful for generative models with intractable likelihoods. These methods are however sensitive to the dimension of the parameter space, requiring exponentially increasing resources as this dimension grows. To tackle this difficulty, we explore a Gibbs version of the Approximate Bayesian computation approach that runs component-wise approximate Bayesian computation steps aimed at the corresponding conditional posterior distributions, and based on summary statistics of reduced dimensions. While lacking the standard justifications for the Gibbs sampler, the resulting Markov chain is shown to converge in distribution under some partial independence conditions.The associated stationary distribution can further be shown to be close to the true posterior distribution and some hierarchical versions of the proposed mechanism enjoy a closed form limiting distribution. Experiments also demonstrate the gain in efficiency brought by the Gibbs version over the standard solution

Vasopressinergic modulation of stress responses in the central amygdala of the Roman high-avoidance and low-avoidance rat

The central nucleus of the amygdala (CEA) is selectively involved in the passive component of the behavioral (immobility) and the accompanying parasympathetic response during conditioned, stressful environmental challenges. Vasopressinergic mechanisms in the brain seem to play a role in these stress responses. The effects of the neuropeptides arginine-8-vasopressin (AVP) and oxytocin (OXT) on modulating CEA activity during conditioned stress of inescapable footshock were studied in male Roman high-avoidance (RHA/Verh) and low-avoidance (RLA/Verh) rats, psychogenetically selected on the basis of shuttle-box acquisition behavior. In RLA/Verh rats, the cardiac and behavioral responses to the conditioned emotional stressor were bradycardia and immobility, suggesting an important role for the CEA in these rats. The RHA/Verh rats, however, failed to show any change in heart rate or immobility in response to a conditioned stress situation. The low dose of AVP (20 pg) in the CEA of conscious RLA/Verh rats caused an enhancement of the stress-induced bradycardiac and immobility response. However, the high dose of AVP (2 ng) and OXT (200 pg) attenuated the bradycardiac and immobility responses in the RLA/Verh rats. Infusion of AVP and OXT in the RHA/Verh rats failed to induce any change in heart rate nr immobility. Binding studies revealed that the AVP receptor selectively binds AVP with high affinity. In contrast, the OXT receptor recognizes both AVP and OXT with a similar (but lower) affinity. This suggests that the behavioral and autonomic responses of the high dose of AVP may be caused by OXT receptor stimulation. In conclusion, on the basis of the present results one may hypothesize that CEA differences in AVP and OXT innervation and/or receptor densities may contribute to the differences in coping strategy found in these animals.