First Stellar Abundances in the Dwarf Irregular Galaxy Sextans A

We present the abundance analyses of three isolated A-type supergiant stars in the dwarf irregular galaxy Sextans A from high-resolution spectra the UVES spectrograph at the VLT. Detailed model atmosphere analyses have been used to determine the stellar atmospheric parameters and the elemental abundances of the stars. The mean iron group abundance was determined from these three stars to be [(FeII,CrII)/H]=-0.99+/-0.04+/-0.06. This is the first determination of the present-day iron group abundances in Sextans A. These three stars now represent the most metal-poor massive stars for which detailed abundance analyses have been carried out. The mean stellar alpha element abundance was determined from the alpha element magnesium as [alpha(MgI)/H]=-1.09+/-0.02+/-0.19. This is in excellent agreement with the nebular alpha element abundances as determined from oxygen in the H II regions. These results are consistent from star-to-star with no significant spatial variations over a length of 0.8 kpc in Sextans A. This supports the nebular abundance studies of dwarf irregular galaxies, where homogeneous oxygen abundances are found throughout, and argues against in situ enrichment. The alpha/Fe abundance ratio is [alpha(MgI)/FeII,CrII]=-0.11+/-0.02+/-0.10, which is consistent with the solar ratio. This is consistent with the results from A-supergiant analyses in other Local Group dwarf irregular galaxies but in stark contrast with the high [alpha/Fe] results from metal-poor stars in the Galaxy, and is most clearly seen from these three stars in Sextans A because of their lower metallicities. The low [alpha/Fe] ratios are consistent with the slow chemical evolution expected for dwarf galaxies from analyses of their stellar populations.Comment: 40 pages, 8 figures, accepted for publication in A

Sub-electron Charge Relaxation via 2D Hopping Conductors

We have extended Monte Carlo simulations of hopping transport in completely disordered 2D conductors to the process of external charge relaxation. In this situation, a conductor of area $L \times W$ shunts an external capacitor $C$ with initial charge $Q_i$. At low temperatures, the charge relaxation process stops at some "residual" charge value corresponding to the effective threshold of the Coulomb blockade of hopping. We have calculated the r.m.s$.$ value $Q_R$ of the residual charge for a statistical ensemble of capacitor-shunting conductors with random distribution of localized sites in space and energy and random $Q_i$, as a function of macroscopic parameters of the system. Rather unexpectedly, $Q_{R}$ has turned out to depend only on some parameter combination: $X_0 \equiv L W \nu_0 e^2/C$ for negligible Coulomb interaction and $X_{\chi} \equiv LW \kappa^2/C^{2}$ for substantial interaction. (Here $\nu_0$ is the seed density of localized states, while $\kappa$ is the dielectric constant.) For sufficiently large conductors, both functions $Q_{R}/e =F(X)$ follow the power law $F(X)=DX^{-\beta}$, but with different exponents: $\beta = 0.41 \pm 0.01$ for negligible and $\beta = 0.28 \pm 0.01$ for significant Coulomb interaction. We have been able to derive this law analytically for the former (most practical) case, and also explain the scaling (but not the exact value of the exponent) for the latter case. In conclusion, we discuss possible applications of the sub-electron charge transfer for "grounding" random background charge in single-electron devices.Comment: 12 pages, 5 figures. In addition to fixing minor typos and updating references, the discussion has been changed and expande

Electronic correlation effects and the Coulomb gap at finite temperature

We have investigated the effect of the long-range Coulomb interaction on the one-particle excitation spectrum of n-type Germanium, using tunneling spectroscopy on mechanically controllable break junctions. The tunnel conductance was measured as a function of energy and temperature. At low temperatures, the spectra reveal a minimum at zero bias voltage due to the Coulomb gap. In the temperature range above 1 K the Coulomb gap is filled by thermal excitations. This behavior is reflected in the temperature dependence of the variable-range hopping resitivity measured on the same samples: Up to a few degrees Kelvin the Efros-Shkovskii ln$R \propto T^{-1/2}$ law is obeyed, whereas at higher temperatures deviations from this law are observed, indicating a cross-over to Mott's ln$R \propto T^{-1/4}$ law. The mechanism of this cross-over is different from that considered previously in the literature.Comment: 3 pages, 3 figure

A Numerical Study of Transport and Shot Noise at 2D Hopping

We have used modern supercomputer facilities to carry out extensive Monte Carlo simulations of 2D hopping (at negligible Coulomb interaction) in conductors with the completely random distribution of localized sites in both space and energy, within a broad range of the applied electric field $E$ and temperature $T$, both within and beyond the variable-range hopping region. The calculated properties include not only dc current and statistics of localized site occupation and hop lengths, but also the current fluctuation spectrum. Within the calculation accuracy, the model does not exhibit $1/f$ noise, so that the low-frequency noise at low temperatures may be characterized by the Fano factor $F$. For sufficiently large samples, $F$ scales with conductor length $L$ as $(L_c/L)^{\alpha}$, where $\alpha=0.76\pm 0.08 < 1$, and parameter $L_c$ is interpreted as the average percolation cluster length. At relatively low $E$, the electric field dependence of parameter $L_c$ is compatible with the law $L_c\propto E^{-0.911}$ which follows from directed percolation theory arguments.Comment: 17 pages, 8 figures; Fixed minor typos and updated reference

A Numerical Study of Coulomb Interaction Effects on 2D Hopping Transport

We have extended our supercomputer-enabled Monte Carlo simulations of hopping transport in completely disordered 2D conductors to the case of substantial electron-electron Coulomb interaction. Such interaction may not only suppress the average value of hopping current, but also affect its fluctuations rather substantially. In particular, the spectral density $S_I (f)$ of current fluctuations exhibits, at sufficiently low frequencies, a $1/f$-like increase which approximately follows the Hooge scaling, even at vanishing temperature. At higher $f$, there is a crossover to a broad range of frequencies in which $S_I (f)$ is nearly constant, hence allowing characterization of the current noise by the effective Fano factor F\equiv S_I(f)/2e \left. For sufficiently large conductor samples and low temperatures, the Fano factor is suppressed below the Schottky value (F=1), scaling with the length $L$ of the conductor as $F = (L_c / L)^{\alpha}$. The exponent $\alpha$ is significantly affected by the Coulomb interaction effects, changing from $\alpha = 0.76 \pm 0.08$ when such effects are negligible to virtually unity when they are substantial. The scaling parameter $L_c$, interpreted as the average percolation cluster length along the electric field direction, scales as $L_c \propto E^{-(0.98 \pm 0.08)}$ when Coulomb interaction effects are negligible and $L_c \propto E^{-(1.26 \pm 0.15)}$ when such effects are substantial, in good agreement with estimates based on the theory of directed percolation.Comment: 19 pages, 7 figures. Fixed minor typos and updated reference

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework

The solar-like CoRoT target HD 170987: spectroscopic and seismic observations

The CoRoT mission is in its third year of observation and the data from the second long run in the galactic centre direction are being analysed. The solar-like oscillating stars that have been observed up to now have given some interesting results, specially concerning the amplitudes that are lower than predicted. We present here the results from the analysis of the star HD 170987.The goal of this research work is to characterise the global parameters of HD 170987. We look for global seismic parameters such as the mean large separation, maximum amplitude of the modes, and surface rotation because the signal-to-noise ratio in the observations do not allow us to measure individual modes. We also want to retrieve the stellar parameters of the star and its chemical composition.We have studied the chemical composition of the star using ground-based observations performed with the NARVAL spectrograph. We have used several methods to calculate the global parameters from the acoustic oscillations based on CoRoT data. The light curve of the star has been interpolated using inpainting algorithms to reduce the effect of data gaps. We find power excess related to p modes in the range [400 - 1200]muHz with a mean large separation of 55.2+-0.8muHz with a probability above 95% that increases to 55.9 +-0.2muHz in a higher frequency range [500 - 1250] muHz and a rejection level of 1%. A hint of the variation of this quantity with frequency is also found. The rotation period of the star is estimated to be around 4.3 days with an inclination axis of i=50 deg +20/-13. We measure a bolometric amplitude per radial mode in a range [2.4 - 2.9] ppm around 1000 muHz. Finally, using a grid of models, we estimate the stellar mass, M=1.43+-0.05 Msun, the radius, R=1.96+-0.046 Rsun, and the age ~2.4 Gyr.Comment: 12 pages, 15 figures, accepted for publication in A&

A remote secondary binding pocket promotes heteromultivalent targeting of DC-SIGN

Dendritic cells (DC) are antigen-presenting cells coordinating the interplay of the innate and the adaptive immune response. The endocytic C-type lectin receptors DC-SIGN and Langerin display expression profiles restricted to distinct DC subtypes and have emerged as prime targets for next-generation immunotherapies and anti-infectives. Using heteromultivalent liposomes copresenting mannosides bearing aromatic aglycones with natural glycan ligands, we serendipitously discovered striking cooperativity effects for DC-SIGN+ but not for Langerin+ cell lines. Mechanistic investigations combining NMR spectroscopy with molecular docking and molecular dynamics simulations led to the identification of a secondary binding pocket for the glycomimetics. This pocket, located remotely of DC-SIGN’s carbohydrate bindings site, can be leveraged by heteromultivalent avidity enhancement. We further present preliminary evidence that the aglycone allosterically activates glycan recognition and thereby contributes to DC-SIGN-specific cell targeting. Our findings have important implications for both translational and basic glycoscience, showcasing heteromultivalent targeting of DCs to improve specificity and supporting potential allosteric regulation of DC-SIGN and CLRs in general

Genome-wide association study identifies loci associated with liability to alcohol and drug dependence that is associated with variability in reward-related ventral striatum activity in African- and European-Americans.

Genetic influences on alcohol and drug dependence partially overlap, however, specific loci underlying this overlap remain unclear. We conducted a genome-wide association study (GWAS) of a phenotype representing alcohol or illicit drug dependence (ANYDEP) among 7291 European-Americans (EA; 2927 cases) and 3132 African-Americans (AA: 1315 cases) participating in the family-based Collaborative Study on the Genetics of Alcoholism. ANYDEP was heritable (h 2 in EA = 0.60, AA = 0.37). The AA GWAS identified three regions with genome-wide significant (GWS; P &lt; 5E-08) single nucleotide polymorphisms (SNPs) on chromosomes 3 (rs34066662, rs58801820) and 13 (rs75168521, rs78886294), and an insertion-deletion on chromosome 5 (chr5:141988181). No polymorphisms reached GWS in the EA. One GWS region (chromosome 1: rs1890881) emerged from a trans-ancestral meta-analysis (EA + AA) of ANYDEP, and was attributable to alcohol dependence in both samples. Four genes (AA: CRKL, DZIP3, SBK3; EA: P2RX6) and four sets of genes were significantly enriched within biological pathways for hemostasis and signal transduction. GWS signals did not replicate in two independent samples but there was weak evidence for association between rs1890881 and alcohol intake in the UK Biobank. Among 118 AA and 481 EA individuals from the Duke Neurogenetics Study, rs75168521 and rs1890881 genotypes were associated with variability in reward-related ventral striatum activation. This study identified novel loci for substance dependence and provides preliminary evidence that these variants are also associated with individual differences in neural reward reactivity. Gene discovery efforts in non-European samples with distinct patterns of substance use may lead to the identification of novel ancestry-specific genetic markers of risk