SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

<p>Abstract</p> <p>Background</p> <p>Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data.</p> <p>Results</p> <p>We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads.</p> <p>Conclusion</p> <p>The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.</p

Rural America At A Glance, 2007 Edition

Rural America At A Glance, 2007 highlights the most recent indicators of social and economic conditions in rural areas for use in developing policies and programs to assist rural areas. The brochure provides information on key rural conditions and trends for use by public and private decisionmakers and others involved in efforts to enhance the economic opportunities and quality of life for rural people and their communities.rural indicators, population growth, employment, rural unemployment, rural economy, nonmetro, metro, creative occupations, rural America, natural amenities, census data, educational attainment, college education, poverty, domestic migration, ERS, USDA, Agricultural and Food Policy, Community/Rural/Urban Development,

The two Ultraluminous X-ray sources in the galaxy NGC 925

NGC 925 ULX-1 and ULX-2 are two ultraluminous X-ray sources in the galaxy NGC 925, at a distance of 8.5 Mpc. For the first time, we analyzed high quality, simultaneous XMM-Newton and NuSTAR data of both sources. Although at a first glance ULX-1 resembles an intermediate mass black hole candidate (IMBH) because of its high X-ray luminosity ($(2$$-$$4)\times10^{40}$ erg s$^{-1}$) and its spectral/temporal features, a closer inspection shows that its properties are more similar to those of a typical super-Eddington accreting stellar black hole and we classify it as a `broadened disc' ultraluminous X-ray source. Based on the physical interpretation of this spectral state, we suggest that ULX-1 is seen at small inclination angles, possibly through the evacuated cone of a powerful wind originating in the accretion disc. The spectral classification of ULX-2 is less certain, but we disfavour an IMBH accreting at sub-Eddington rates as none of its spectral/temporal properties can be associated to either the soft or hard state of Galactic accreting black hole binaries.Comment: Accepted on MNRAS with very minor comments, 7 pages, 5 figures, 1 tabl

Rural Hispanics At A Glance

Rural Hispanics at a Glance provides the latest information from the 2000 Census and other Federal data sources about Hispanics living in nonmetro counties. This six-page brochure highlights growth and geographic dispersion, demographic characteristics, and the most recent indicators of social and economic conditions for this population. It emphasizes rapid Hispanic population growth, particularly in new rural destinations of the Midwest and Southeast, and it illustrates differences in age structure between Hispanics and non-Hispanic Whites. The report also provides data on important demographic, labor market, income, poverty, and social service indicators for nonmetro Hispanics. Using a visually interesting format that incorporates text bullets with charts and maps, it quickly provides information on key indicators of the rural Hispanic population to assist public officials, community organizations, private decision makers and others in their efforts to enhance the economic opportunities and quality of life for this rapidly growing population.Farm Structure, Employment and Wages, Agribusiness, Food processing, Rural Policy Food and Nutrition, Poverty and Economy, Rural America, Rural Income, Rural Welfare, Labor and Education, Rural Population, and Rural Migration, ERS, USDA, Agribusiness, Agricultural and Food Policy, Food Consumption/Nutrition/Food Safety,

Comparing Shape-Constrained Regression Algorithms for Data Validation

Industrial and scientific applications handle large volumes of data that render manual validation by humans infeasible. Therefore, we require automated data validation approaches that are able to consider the prior knowledge of domain experts to produce dependable, trustworthy assessments of data quality. Prior knowledge is often available as rules that describe interactions of inputs with regard to the target e.g. the target must be monotonically decreasing and convex over increasing input values. Domain experts are able to validate multiple such interactions at a glance. However, existing rule-based data validation approaches are unable to consider these constraints. In this work, we compare different shape-constrained regression algorithms for the purpose of data validation based on their classification accuracy and runtime performance.Comment: 9 pages, Submitted manuscript to be published in Computer Aided System Theory - EUROCAST 2022, Las Palmas de Gran Canaria, February 202

Lives of Women & Girls Report in Monterey County

The Lives of Women & Girls in Monterey County is the next step in a process that began in 2004. At that time, the Women's Fund of Monterey County and Tellus/ Díganos Center for Community Research published First Glance: Quality of Life of Women and Girls report on the status of local women and girls. In 2011, local researchers refreshed the data, convened focus groups and conducted key interviews as the basis for this updated report. Input from dozens of local girls, adult and elder women, representatives of service agencies and public officials helped to provide focus and context for the findings. The full report is not intended to be a comprehensive assessment of the quality of life of women and girls, but a snapshot of the critical issues that currently impact the women of our community and a call to action to address trends of concern

The importance, challenges and prospects of taking work practices into account for healthcare quality improvement

Purpose – The purpose of this paper is to underline the importance of taking work practices into account for quality improvement (QI) purposes, highlight some of the challenges of doing so, and suggest strategies for future research and practice. Patient status at a glance, a Lean-inspired QI intervention designed to alleviate nurses of their knowledge mobilisation function, is deployed as an illustrative case. Design/methodology/approach – Ethnographic data and practice-based theories are utilised to describe nurses’ knowledge mobilisation work. The assumptions about knowledge sharing embedded in patient status at a glance white boards (PSAGWBs) are analysed drawing on actor network theory. Findings – There is a disparity between nurses’ knowledge mobilisation practices and the scripts that inform the design of PSAGWBs. PSAGWBs are designed to be intermediaries and to transport meaning without transformation. When nurses circulate knowledge for patient management purposes, they operate as mediators, translating diverse information sources and modifying meaning for different audiences. PSAGWBs are unlikely to relieve nurses of their knowledge mobilisation function and may actually add to the burdens of this work. Despite this nurses have readily embraced this QI intervention. Research limitations/implications – The study is limited by its focus on a single case and by the inferential (rather than the empirical) nature of its conclusions. Originality/value – This paper illustrates the importance of taking practice into account in healthcare QI, points to some of the challenges of doing so and highlights the potential of practice-based approaches in supporting progress in this field

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD