The Urban Built Environment and Mobility in Older Adults: A Comprehensive Review

Mobility restrictions in older adults are common and increase the likelihood of negative health outcomes and premature mortality. The effect of built environment on mobility in older populations, among whom environmental effects may be strongest, is the focus of a growing body of the literature. We reviewed recent research (1990–2010) that examined associations of objective measures of the built environment with mobility and disability in adults aged 60 years or older. Seventeen empirical articles were identified. The existing literature suggests that mobility is associated with higher street connectivity leading to shorter pedestrian distances, street and traffic conditions such as safety measures, and proximity to destinations such as retail establishments, parks, and green spaces. Existing research is limited by differences in exposure and outcome assessments and use of cross-sectional study designs. This research could lead to policy interventions that allow older adults to live more healthy and active lives in their communities

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

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

Community College Instructors’ Perceptions of Constraints and Affordances Related to Teaching Quantitative Biology Skills and Concepts

Quantitative skills are an important competency for undergraduate biology students and should be incorporated early and frequently in an undergraduate&rsquo;s career. Community colleges (CCs) are responsible for teaching introductory biology to a large proportion of biology and prehealth students, and quantitative skills are critical for their careers. However, we know little about the challenges and affordances that CC instructors encounter when incorporating quantitative skills into their courses. To explore this, we interviewed CC biology instructors ( n = 20) about incorporating quantitative biology (QB) instruction into their classes. We used a purposeful sampling approach to recruit instructors who were likely to have tried evidence-based pedagogies and were likely aware of the importance of QB instruction. We used open coding to identify themes related to the affordances to and constraints on teaching QB. Overall, our study participants met with challenges typical of incorporating new material or techniques into any college-level class, including perceptions of student deficits, tension between time to teach quantitative skills and cover biology content, and gaps in teacher professional knowledge (e.g., content and pedagogical content knowledge). We analyze these challenges and offer potential solutions and recommendations for professional development to support QB instruction at CCs.</p

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

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

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

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)