Application of avalanche photodiodes as a readout for scintillator tile-fiber systems

The application of reach-through avalanche photodiodes (R'APD) as a photodetector for scintillator tiles has been investigated. The light collected by WLS fibers (0.84mm and 1mm diameter) embedded in the scintillator has been transmited to the 0.5mm2 active surface of APD by clear optical fibers and optical connectors. A low noise charge sensitive preamplifier (approximately 400 electrons equivalent noise charge) has been used to gain the photodiode signal. Various configurations of tile-fibre systems, suitable for CMS and LHCb experiments at LHC have been studied using cosmic muons and muon beam at SPS at CERN. In order to optimize the performance of APD, measurments in the temperature range from -10C to +25C have been done. The MIP detection efficiency and electron/MIP separation have been estimated in order to determine applicability of the readout for LHCb preshower.Comment: 20 pages,13 figure

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm

Neighborhood Resources for Physical Activity and Healthy Foods and Their Association with Insulin Resistance

OBJECTIVE:: Little is known about the influence of the built environment, and in particular neighborhood resources, on health. We hypothesized that neighborhood resources for physical activity and healthy foods are associated with insulin resistance. METHODS:: Person-level data (n = 2026) came from 3 sites of The Multi-Ethnic Study of Atherosclerosis, a study of adults aged 45-84 years. Area-level data were derived from a population-based residential survey. The homeostasis model assessment index was used as an insulin resistance measure among persons not treated for diabetes. We used linear regression to estimate associations between area features and insulin resistance. RESULTS:: Greater neighborhood physical activity resources consistently were associated with lower insulin resistance. Adjusted for age, sex, family history of diabetes, race/ethnicity, income and education, insulin resistance was reduced by 17% (95% confidence interval = -31% to -1%) for an increase from the 10th to 90th percentiles of resources. Greater healthy food resources were also inversely related to insulin resistance, although the association was not robust to adjustment for race/ethnicity. Analyses including diet, physical activity, and body mass index suggested that these variables partly mediated observed associations. Results were similar when impaired fasting glucose/diabetes was considered as the outcome variable. CONCLUSION:: Diabetes prevention efforts may need to consider features of residential environment.http://deepblue.lib.umich.edu/bitstream/2027.42/57885/1/Neighborhood Resources for Physical Activity and Healthy Foods and Their Association With Insulin Resistance.pd

Filling the gaps: spatial interpolation of residential survey data in the estimation of neighborhood characteristics

The measurement of area-level attributes remains a major challenge in studies of neighborhood health effects. Even when neighborhood survey data are collected, they necessarily have incomplete spatial coverage. We investigated whether interpolation of neighborhood survey data was aided by information on spatial dependencies and supplementary data. Neighborhood "availability of healthy foods" was measured in a population-based survey of 5186 persons in Baltimore, New York, and Forsyth County (North Carolina). The following supplementary data were compiled from Census 2000 and InfoUSA, Inc.: distance to supermarkets, density of supermarkets and fruit and vegetable stores, housing density, distance to a high-income area, and percent of households that do not own a vehicle. We compared 4 interpolation models (ordinary least squares, residual kriging, spatial error regression, and thin-plate splines) using error statistics and Pearson correlation coefficients (r) from repeated replications of cross-validations. There was positive spatial autocorrelation in neighborhood availability of healthy foods (by site, Moran coefficient range = 0.10-0.28; all P < 0.0001). Prediction performances were generally similar for the evaluated models (r [almost equal to] 0.35 for Baltimore and Forsyth; r [almost equal to] 0.54 for New York). Supplementary data accounted for much of the spatial autocorrelation and, thus, spatial modeling was only advantageous when spatial correlation was at least moderate. A variety of interpolation techniques will likely need to be utilized in order to increase the data available for examining health effects of residential environments. The most appropriate method will vary depending on the construct of interest, availability of relevant supplementary data, and types of observed spatial patterns.http://deepblue.lib.umich.edu/bitstream/2027.42/57780/1/Filling the gaps Spatail Interpolation of Residental Survey Data in the Estimation of Neighborhood Characteristics.pd

Neutrino Interactions In Oscillation Experiments

We calculate neutrino induced cross-sections relevant for oscillation experiments, including the $\tau$-lepton threshold for quasi-elastic, resonance and deep inelastic scattering. In addition to threshold effects, we include nuclear corrections for heavy targets which are moderate for quasi-elastic and large for single pion production. Nuclear effects for deep inelastic reactions are small. We present cross sections together with their nuclear corrections for various channels which are useful for interpreting the experimental results and for determining parameters of the neutrino sector..Comment: 24 pages, 18 figure

A measurement of alphas(Q2)alpha_s(Q^2) from the Gross-Llewellyn Smith Sum Rule

We extract a set of values for the Gross-Llewellyn Smith sum rule at different values of 4-momentum transfer squared ($Q^{2}$), by combining revised CCFR neutrino data with data from other neutrino deep-inelastic scattering experiments for $1 < Q^2 < 15 GeV^2/c^2$. A comparison with the order $\alpha^{3}_{s}$ theoretical predictions yields a determination of $\alpha_{s}$ at the scale of the Z-boson mass of $0.114 \pm^{.009}_{.012}$. This measurement provides a new and useful test of perturbative QCD at low $Q^2$, because of the low uncertainties in the higher order calculations.Comment: 4 pages, 4 figure

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap)

A Precise Measurement of the Weak Mixing Angle in Neutrino-Nucleon Scattering

We report a precise measurement of the weak mixing angle from the ratio of neutral current to charged current inclusive cross-sections in deep-inelastic neutrino-nucleon scattering. The data were gathered at the CCFR neutrino detector in the Fermilab quadrupole-triplet neutrino beam, with neutrino energies up to 600 GeV. Using the on-shell definition, ${\rm sin ^2\theta_W} \equiv 1 - \frac{{\rm M_W} ^2}{{\rm M_Z} ^2}$, we obtain ${\rm sin ^2\theta_W} = 0.2218 \pm 0.0025 ({\rm stat.}) \pm 0.0036 ({\rm exp.\: syst.}) \pm 0.0040 ({\rm model})$.Comment: 10 pages, Nevis Preprint #1498 (Submitted to Phys. Rev. Lett.