A Study of an Acrylic Cerenkov Radiation Detector

An experiment investigating the angle of Cerenkov light emitted by 3-MeV electrons traversing an acrylic detector has been developed for use in the advanced physics laboratory course at the University of Rochester. In addition to exploring the experimental phenomena of Cerenkov radiation and total internal reflection, the experiment introduces students to several experimental techniques used in actual high energy and nuclear physics experiments, as well as to analysis techniques involving Poisson statistics. [to be published in Am. J. Phys. 67 (Oct/Nov 1999).

Simulations from a new neutrino event generator

We construct a new Monte Carlo generator of events for neutrino interactions. The dynamical models for quasi-elastic reactions, $\Delta$ excitation and more inelastic events described by the DIS formalism with the PDFs modified according to recent JLab data are used. We describe in detail single pion production channels, which combine the $\Delta$ excitation and DIS contribution. Many comparisons of the outcome of simulations with experimental data are presented.Comment: To appear in the proceedings of 4th International Workshop on Neutrino Nucleus Interactions in the Few GeV Region (NuInt05), Okayama, Japan, 26-29 September, 200

An Actor-Based Model of Social Network Influence on Adolescent Body Size, Screen Time, and Playing Sports

Recent studies suggest that obesity may be “contagious” between individuals in social networks. Social contagion (influence), however, may not be identifiable using traditional statistical approaches because they cannot distinguish contagion from homophily (the propensity for individuals to select friends who are similar to themselves) or from shared environmental influences. In this paper, we apply the stochastic actor-based model (SABM) framework developed by Snijders and colleagues to data on adolescent body mass index (BMI), screen time, and playing active sports. Our primary hypothesis was that social influences on adolescent body size and related behaviors are independent of friend selection. Employing the SABM, we simultaneously modeled network dynamics (friendship selection based on homophily and structural characteristics of the network) and social influence. We focused on the 2 largest schools in the National Longitudinal Study of Adolescent Health (Add Health) and held the school environment constant by examining the 2 school networks separately (N = 624 and 1151). Results show support in both schools for homophily on BMI, but also for social influence on BMI. There was no evidence of homophily on screen time in either school, while only one of the schools showed homophily on playing active sports. There was, however, evidence of social influence on screen time in one of the schools, and playing active sports in both schools. These results suggest that both homophily and social influence are important in understanding patterns of adolescent obesity. Intervention efforts should take into consideration peers’ influence on one another, rather than treating “high risk” adolescents in isolation

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

Epidemics on contact networks: a general stochastic approach

Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our systematic framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible (SIS) and susceptible-infectious-removed (SIR) dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.Comment: Main document: 16 pages, 7 figures. Electronic Supplementary Material (included): 6 pages, 1 tabl

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 algorith

HAMAP in 2013, new developments in 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 classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profile

Nuclear Structure Functions in the Large x Large Q^2 Kinematic Region in Neutrino Deep Inelastic Scattering

Data from the CCFR E770 Neutrino Deep Inelastic Scattering (DIS) experiment at Fermilab contain events with large Bjorken x (x>0.7) and high momentum transfer (Q^2>50 (GeV/c)^2). A comparison of the data with a model based on no nuclear effects at large x, shows a significant excess of events in the data. Addition of Fermi gas motion of the nucleons in the nucleus to the model does not explain the excess. Adding a higher momentum tail due to the formation of ``quasi-deuterons'' makes some improvement. An exponentially falling F_2 \propto e^-s(x-x_0) at large x, predicted by ``multi-quark clusters'' and ``few-nucleon correlations'', can describe the data. A value of s=8.3 \pm 0.7(stat.)\pm 0.7(sys.) yields the best agreement with the data.Comment: 4 pages, 4 figures, 1 table. Sibmitted to PR

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

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