The Matanuska-Susitna Borough Community Survey, 2012 and Trends 2008–2012: A Sourcebook of Community Attitudes

The Matanuska-Susitna Borough Community Survey (Mat-Su Survey), conducted annually since 2006, is a cooperative research effort between the Justice Center at University of Alaska Anchorage (UAA) and the Matanuska-Susitna Borough. The survey asks Mat-Su Borough residents to evaluate the quality of Borough services, provide opinions about Borough decision-making, and sum up their perceptions about a range of issues relevant to the present and future of the Mat-Su community. The 2012 survey was distributed to 1,965 adult heads-of-household in the Mat-Su Borough in the late summer and fall of 2012; a total of 845 surveys were returned, for a response rate of 43.0%. This sourcebook presents both the results from the 2012 Mat-Su Survey and trends from 2008–2012 in five major areas: (1) evaluation of current borough services; (2) use of borough facilities; (3) life in Mat-Su neighborhoods; (4) local government access, policies, and practices; and (5) respondent background information. Additionally, findings from a derived importance-performance analysis of the survey data are presented, as is a compilation of respondent comments.Introduction / Organization of Sourcebook / Methods / Executive Summary / 2012 RESULTS AND 2008–2012 TRENDS / Part I. Evaluation of Current Borough Services / Part II. Use of Borough Facilities / Part III. Life in Matanuska-Susitna Borough Neighborhoods / Part IV. Local Government: Access, Policies and Practices / Part V. Sample Characteristics / Part VI. Derived Importance-Performance Analysis / Part VII. Respondents’ Comments / Appendix: Survey Instrumen

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition

Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers

Development of the interRAI Pressure Ulcer Risk Scale (PURS) for use in long-term care and home care settings

<p>Abstract</p> <p>Background</p> <p>In long-term care (LTC) homes in the province of Ontario, implementation of the Minimum Data Set (MDS) assessment and The Braden Scale for predicting pressure ulcer risk were occurring simultaneously. The purpose of this study was, using available data sources, to develop a bedside MDS-based scale to identify individuals under care at various levels of risk for developing pressure ulcers in order to facilitate targeting risk factors for prevention.</p> <p>Methods</p> <p>Data for developing the interRAI Pressure Ulcer Risk Scale (interRAI PURS) were available from 2 Ontario sources: three LTC homes with 257 residents assessed during the same time frame with the MDS and Braden Scale for Predicting Pressure Sore Risk, and eighty-nine Ontario LTC homes with 12,896 residents with baseline/reassessment MDS data (median time 91 days), between 2005-2007. All assessments were done by trained clinical staff, and baseline assessments were restricted to those with no recorded pressure ulcer. MDS baseline/reassessment samples used in further testing included 13,062 patients of Ontario Complex Continuing Care Hospitals (CCC) and 73,183 Ontario long-stay home care (HC) clients.</p> <p>Results</p> <p>A data-informed Braden Scale cross-walk scale using MDS items was devised from the 3-facility dataset, and tested in the larger longitudinal LTC homes data for its association with a future new pressure ulcer, giving a c-statistic of 0.676. Informed by this, LTC homes data along with evidence from the clinical literature was used to create an alternate-form 7-item additive scale, the interRAI PURS, with good distributional characteristics and c-statistic of 0.708. Testing of the scale in CCC and HC longitudinal data showed strong association with development of a new pressure ulcer.</p> <p>Conclusions</p> <p>interRAI PURS differentiates risk of developing pressure ulcers among facility-based residents and home care recipients. As an output from an MDS assessment, it eliminates duplicated effort required for separate pressure ulcer risk scoring. Moreover, it can be done manually at the bedside during critical early days in an admission when the full MDS has yet to be completed. It can be calculated with established MDS instruments as well as with the newer interRAI suite instruments designed to follow persons across various care settings (interRAI Long-Term Care Facilities, interRAI Home Care, interRAI Palliative Care).</p

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

The Matanuska-Susitna Borough Community Survey, 2011 and Trends 2007–2011: A Sourcebook of Community Attitudes

The Matanuska-Susitna Borough Community Survey (Mat-Su Survey), conducted annually since 2006, is a cooperative research effort between the Justice Center at University of Alaska Anchorage (UAA) and the Matanuska-Susitna Borough. The survey asks Mat-Su Borough residents to evaluate the quality of Borough services, provide opinions about Borough decision-making, and sum up their perceptions about a range of issues relevant to the present and future of the Mat-Su community. The 2011 survey was distributed to 2,577 adult heads-of-household in the Mat-Su Borough in the late summer and fall of 2011; a total of 1,159 surveys were returned, for a response rate of 45.0%. This sourcebook presents both the results from the 2011 Mat-Su Survey and trends from 2006–2011 in five major areas: (1) evaluation of current borough services; (2) use of borough facilities; (3) life in Mat-Su neighborhoods; (4) local government access, policies, and practices; and (5) respondent background information. Additionally, findings from a derived importance-performance analysis of the survey data are presented, as is a compilation of respondent comments.Introduction / Organization of Sourcebook / Methods / Executive Summary / 2011 RESULTS AND 2007–2011 TRENDS / Part I. Evaluation of Current Borough Services / Part II. Use of Borough Facilities / Part III. Life in Matanuska-Susitna Borough Neighborhoods / Part IV. Local Government: Access, Policies and Practices / Part V. Sample Characteristics / Part VI. Respondents’ Comments / Part VII. Derived Importance-Performance Analysis / Appendix: Survey Instrumen

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Although no clear sequence motif emerged, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a preferred nucleosomal landscape for ORC association. Open chromatin appears to be the underlying feature that is deterministic for ORC binding. ORC-associated sequences are enriched for the histone variant, H3.3, often at transcription start sites, and depleted for bulk nucleosomes. The density of ORC binding along the chromosome is reflected in the time at which a sequence replicates, with early replicating sequences having a high density of ORC binding. Finally, we found a high concordance between sites of ORC binding and cohesin loading, suggesting that, in addition to DNA replication, ORC may be required for the loading of cohesin on DNA in Drosophila

Coordination of replication and transcription along a Drosophila chromosome

The mechanisms by which metazoan origins of DNA replication are defined, regulated, and influenced by chromosomal events remain poorly understood. To gain insights into these mechanisms, we developed a systematic approach using a Drosophila high-resolution genomic microarray to determine replication timing, identify replication origins, and map protein-binding sites along a chromosome arm. We identify a defined temporal pattern of replication that correlates with the density of active transcription. These data indicate that the influence of transcription status on replication timing is exerted over large domains (>100 kb) rather than at the level of individual genes. We identify 62 early activating replication origins across the chromosome by mapping sites of nucleotide incorporation during hydroxyurea arrest. Using genome-wide location analysis, we demonstrate that the origin recognition complex (ORC) is localized to specific chromosomal sites, many of which coincide with early activating origins. The molecular attributes of ORC-binding sites include increased AT-content and association with a subset of RNA Pol II-binding sites. Based on these findings, we suggest that the distribution of transcription along the chromosome acts locally to influence origin selection and globally to regulate origin activation