DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

PubMed

Jiao, Xiaoli; Sherman, Brad T; Huang, Da Wei; Stephens, Robert; Baseler, Michael W; Lane, H Clifford; Lempicki, Richard A

2012-07-01

The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.

libChEBI: an API for accessing the ChEBI database.

PubMed

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

Affirmative Action Plan. Access, Equity, Opportunity. Fifth Edition.

ERIC Educational Resources Information Center

New York State Education Dept., Albany.

The Affirmative Action Plan of the New York State Education Department is described in this document. First, a policy statement is provided by the New York State Education Department, committing the Department to the development of: (1) programmatic approaches to the elimination of all unjust exclusionary employment practices, policies, and…

Programmatic access to data and information at the IRIS DMC via web services

NASA Astrophysics Data System (ADS)

Weertman, B. R.; Trabant, C.; Karstens, R.; Suleiman, Y. Y.; Ahern, T. K.; Casey, R.; Benson, R. B.

2011-12-01

The IRIS Data Management Center (DMC) has developed a suite of web services that provide access to the DMC's time series holdings, their related metadata and earthquake catalogs. In addition, services are available to perform simple, on-demand time series processing at the DMC prior to being shipped to the user. The primary goal is to provide programmatic access to data and processing services in a manner usable by and useful to the research community. The web services are relatively simple to understand and use and will form the foundation on which future DMC access tools will be built. Based on standard Web technologies they can be accessed programmatically with a wide range of programming languages (e.g. Perl, Python, Java), command line utilities such as wget and curl or with any web browser. We anticipate these services being used for everything from simple command line access, used in shell scripts and higher programming languages to being integrated within complex data processing software. In addition to improving access to our data by the seismological community the web services will also make our data more accessible to other disciplines. The web services available from the DMC include ws-bulkdataselect for the retrieval of large volumes of miniSEED data, ws-timeseries for the retrieval of individual segments of time series data in a variety of formats (miniSEED, SAC, ASCII, audio WAVE, and PNG plots) with optional signal processing, ws-station for station metadata in StationXML format, ws-resp for the retrieval of instrument response in RESP format, ws-sacpz for the retrieval of sensor response in the SAC poles and zeros convention and ws-event for the retrieval of earthquake catalogs. To make the services even easier to use, the DMC is developing a library that allows Java programmers to seamlessly retrieve and integrate DMC information into their own programs. The library will handle all aspects of dealing with the services and will parse the returned data. By using this library a developer will not need to learn the details of the service interfaces or understand the data formats returned. This library will be used to build the software bridge needed to request data and information from within MATLAB°. We also provide several client scripts written in Perl for the retrieval of waveform data, metadata and earthquake catalogs using command line programs. For more information on the DMC's web services please visit http://www.iris.edu/ws/

HDDTOOLS: an R package serving Hydrological Data Discovery Tools

NASA Astrophysics Data System (ADS)

Vitolo, C.; Buytaert, W.

2014-12-01

Many governmental bodies and institutions are currently committed to publish open data as the result of a trend of increasing transparency, based on which a wide variety of information produced at public expense is now becoming open and freely available to improve public involvement in the process of decision and policy making. Discovery, access and retrieval of information is, however, not always a simple task. Especially when programmatic access to data resources is not allowed, downloading metadata catalogue, select the information needed, request datasets, de-compression, conversion, manual filtering and parsing can become rather tedious. The R package "hddtools" is an open source project, designed to make all the above operations more efficient by means of re-usable functions. The package facilitate non programmatic access to various online data sources such as the Global Runoff Data Centre, NASA's TRMM mission, the Data60UK database amongst others. This package complements R's growing functionality in environmental web technologies to bridge the gap between data providers and data consumers and it is designed to be the starting building block of scientific workflows for linking data and models in a seamless fashion.

Criteria for the Evaluation of Student Loan Alternatives.

ERIC Educational Resources Information Center

Dresch, Stephen P.

The objectives of student loan programs and the consequences of specific programmatic determinations are considered. In addition to the primary function of providing access to capital markets for the financing of human capital investment, the student loan system in the United States has been utilized as: (1) a mechanism to subsidize schooling…

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

PubMed Central

Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

2015-01-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

Extending the Common Framework for Earth Observation Data to other Disciplinary Data and Programmatic Access

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Wyborn, L. A.; Druken, K. A.; Richards, C. J.; Trenham, C. E.; Wang, J.

2016-12-01

The Australian National Computational Infrastructure (NCI) manages a large geospatial repository (10+ PBytes) of Earth systems, environmental, water management and geophysics research data, co-located with a petascale supercomputer and an integrated research cloud. NCI has applied the principles of the "Common Framework for Earth-Observation Data" (the Framework) to the organisation of these collections enabling a diverse range of researchers to explore different aspects of the data and, in particular, for seamless programmatic data analysis, both in-situ access and via data services. NCI provides access to the collections through the National Environmental Research Data Interoperability Platform (NERDIP) - a comprehensive and integrated data platform with both common and emerging services designed to enable data accessibility and citability. Applying the Framework across the range of datasets ensures that programmatic access, both in-situ and network methods, work as uniformly as possible for any dataset, using both APIs and data services. NCI has also created a comprehensive quality assurance framework to regularise compliance checks across the data, library APIs and data services, and to establish a comprehensive set of benchmarks to quantify both functionality and performance perspectives for the Framework. The quality assurance includes organisation of datasets through a data management plan, which anchors the data directory structure, version controls and data information services so that they are kept aligned with operational changes over time. Specific attention has been placed on the way data are packed inside the files. Our experience has shown that complying with standards such as CF and ACDD is still not enough to ensure that all data services or software packages correctly read the data. Further, data may not be optimally organised for the different access patterns, which causes poor performance of the CPUs and bandwidth utilisation. We will also discuss some gaps in the Framework that have emerged and our approach to resolving these.

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

PubMed Central

Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang

2012-01-01

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users. PMID:23110173

interPopula: a Python API to access the HapMap Project dataset

PubMed Central

2010-01-01

Background The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. Results interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. Conclusions interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset. PMID:21210977

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

PubMed

Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

2015-07-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ensembl Genomes 2013: scaling up access to genome-wide data.

PubMed

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

The Proteins API: accessing key integrated protein and genome information

PubMed Central

Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

2017-01-01

Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

The Proteins API: accessing key integrated protein and genome information.

PubMed

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

The NASA Commercial Crew Program (CCP) Shared Assurance Model for Safety

NASA Technical Reports Server (NTRS)

Kirkpatrick, Paul D.

2014-01-01

NASA established the Commercial Crew Program in order to provide human access to the International Space Station and low earth orbit via the commercial (nongovernmental) sector. A particular challenge to NASA is how to determine the commercial provider's transportation system complies with Programmatic safety requirements while at the same time allowing the provider the flexibility to demonstrate compliance. This will be accomplished through the use of Shared Assurance and Risk Based Assessment by NASA thus shifting more responsibility to the Provider. This model will be the focus of this presentation.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

Contextualizing immigrant access to health resources.

PubMed

Yang, Joshua S

2010-06-01

A vast majority of our understanding of immigrant health centers around traits of individuals and groups. While useful, current approaches to research on immigrant health decontextualize the experience of immigrants in the United States. This paper uses a historical case study of the Chinese community in San Francisco to develop a contextual framework to understand the levels of influence that impact the availability of health resources in immigrant communities. International, transnational, transcommunity, and enclave contexts have shaped health care access for Chinese immigrants in San Francisco. The conceptual framework provides a basis for future research, programmatic, and policy work that integrates individual and contextual factors in assessing and improving immigrant access to health resources.

Using a programmatic mapping approach to plan for HIV prevention and harm reduction interventions for people who inject drugs in three South African cities.

PubMed

Scheibe, Andrew; Shelly, Shaun; Lambert, Andrew; Schneider, Andrea; Basson, Rudolf; Medeiros, Nelson; Padayachee, Kalvanya; Savva, Helen; Hausler, Harry

2017-06-07

Stigma, criminalisation and a lack of data on drug use contribute to the "invisibility" of people who inject drugs (PWID) and make HIV prevention and treatment service delivery challenging. We aimed to confirm locations where PWID congregate in Cape Town, eThekwini and Tshwane (South Africa) and to estimate PWID population sizes within selected electoral wards in these areas to inform South Africa's first multi-site HIV prevention project for PWID. Field workers (including PWID peers) interviewed community informants to identify suspected injecting locations in selected electoral wards in each city and then visited these locations and interviewed PWID. Interviews were used to gather information about the accessibility of sterile injecting equipment, location coordinates and movement patterns. We used the Delphi method to obtain final population size estimates for the mapped wards based on estimates from wisdom of the crowd methods, the literature and programmatic data. Between January and April 2015, we mapped 45 wards. Tshwane teams interviewed 39 PWID in 12 wards, resulting in an estimated number of accessible PWID ranging from 568 to 1431. In eThekwini, teams interviewed 40 PWID in 15 wards with an estimated number of accessible PWID ranging from 184 to 350. The Cape Town team interviewed 61 PWID in 18 wards with an estimated number of accessible PWID ranging between 398 and 503. Sterile needles were only available at one location. Almost all needles were bought from pharmacies. Between 80 and 86% of PWID frequented more than one location per day. PWID who reported movement visited a median of three locations a day. Programmatic mapping led by PWID peers can be used effectively to identify and reach PWID and build relationships where access to HIV prevention commodities for PWID is limited. PWID reported limited access to sterile injecting equipment, highlighting an important HIV prevention need. Programmatic mapping data show that outreach programmes should be flexible and account for the mobile nature of PWID populations. The PWID population size estimates can be used to develop service delivery targets and as baseline measures.

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

77 FR 40144 - Adoption of the Environmental Impact Statement (EIS) and Participation in the Section 106...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-06

...) obligations related to MTA's request for financing for the East Side Access project through the FRA Railroad... Statement (EIS) and Participation in the Section 106 Programmatic Agreement for the East Side Access Project... adoption and recirculation of the Final Environmental Impact Statement for the East Side Access Project and...

Hybrid Pluggable Processing Pipeline (HyP3): Programmatic Access to Cloud-Based Processing of SAR Data

NASA Astrophysics Data System (ADS)

Weeden, R.; Horn, W. B.; Dimarchi, H.; Arko, S. A.; Hogenson, K.

2017-12-01

A problem often faced by Earth science researchers is the question of how to scale algorithms that were developed against few datasets and take them to regional or global scales. This problem only gets worse as we look to a future with larger and larger datasets becoming available. One significant hurdle can be having the processing and storage resources available for such a task, not to mention the administration of those resources. As a processing environment, the cloud offers nearly unlimited potential for compute and storage, with limited administration required. The goal of the Hybrid Pluggable Processing Pipeline (HyP3) project was to demonstrate the utility of the Amazon cloud to process large amounts of data quickly and cost effectively. Principally built by three undergraduate students at the ASF DAAC, the HyP3 system relies on core Amazon cloud services such as Lambda, Relational Database Service (RDS), Elastic Compute Cloud (EC2), Simple Storage Service (S3), and Elastic Beanstalk. HyP3 provides an Application Programming Interface (API) through which users can programmatically interface with the HyP3 system; allowing them to monitor and control processing jobs running in HyP3, and retrieve the generated HyP3 products when completed. This presentation will focus on the development techniques and enabling technologies that were used in developing the HyP3 system. Data and process flow, from new subscription through to order completion will be shown, highlighting the benefits of the cloud for each step. Because the HyP3 system can be accessed directly from a user's Python scripts, powerful applications leveraging SAR products can be put together fairly easily. This is the true power of HyP3; allowing people to programmatically leverage the power of the cloud.

JASPAR RESTful API: accessing JASPAR data from any programming language.

PubMed

Khan, Aziz; Mathelier, Anthony

2018-05-01

JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no. Supplementary data are available at Bioinformatics online.

Advancements in Data Access at the IRIS Data Management Center to Broaden Data Use

NASA Astrophysics Data System (ADS)

Benson, R. B.; Trabant, C. M.; Ahern, T. K.

2013-12-01

The IRIS Data Management Center (DMC) has been serving digital seismic data for more than 20 years and has offered a variety of access mechanisms that have stood the test of time. However, beginning in 2010, and in response to multiple needs being requested from the IRIS DMC, we have developed web service interfaces to access our primary data repository. These new interfaces have rapidly grown in popularity. In 2013, the third full year of their operation, these services were responsible for half of all the data shipped from the DMC. In the same time period, the amount of data shipped from the other data access mechanisms has also increased. This non-linear growth of data shipments reflects the increased data usage by the research community. We believe that our new web service interfaces are well suited to fit future data access needs and signify a significant evolution in integrating different scientific data sets. Based on standardized web technologies, support for writing access software is ubiquitous. As fundamentally programmatic interfaces, the services are well suited for integration into data processing systems, in particular large-scale data processing systems. Their programmatic nature also makes then well suited for use with brokering systems where, for example, data from multiple disciplines can be integrated. In addition to providing access to raw data, the DMC created web services that apply simple, on-the-fly processing and format conversion. Processing the data (e.g. converting to Earth units) and formatting the result into something generally usable (e.g. ASCII) removes important barriers for users working in other disciplines. The end result is that we are shipping a much larger amount of data in a manner more directly usable by users. Many of these principles will be applied to the DMC's future work in the NSF's EarthCube Web Service Building Blocks project.

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

A Practical Approach to Programmatic Assessment Design

ERIC Educational Resources Information Center

Timmerman, A. A.; Dijkstra, J.

2017-01-01

Assessment of complex tasks integrating several competencies calls for a programmatic design approach. As single instruments do not provide the information required to reach a robust judgment of integral performance, 73 guidelines for programmatic assessment design were developed. When simultaneously applying these interrelated guidelines, it is…

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets

PubMed Central

Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

2016-01-01

Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. PMID:27084938

Implementing a Data Quality Strategy to Simplify Access to Data

NASA Astrophysics Data System (ADS)

Druken, K. A.; Trenham, C. E.; Evans, B. J. K.; Richards, C. J.; Wang, J.; Wyborn, L. A.

2016-12-01

To ensure seamless programmatic access for data analysis (including machine learning), standardization of both data and services is vital. At the Australian National Computational Infrastructure (NCI) we have developed a Data Quality Strategy (DQS) that currently provides processes for: (1) the consistency of data structures in the underlying High Performance Data (HPD) platform; (2) quality control through compliance with recognized community standards; and (3) data quality assurance through demonstrated functionality across common platforms, tools and services. NCI hosts one of Australia's largest repositories (10+ PBytes) of research data collections spanning datasets from climate, coasts, oceans and geophysics through to astronomy, bioinformatics and the social sciences. A key challenge is the application of community-agreed data standards to the broad set of Earth systems and environmental data that are being used. Within these disciplines, data span a wide range of gridded, ungridded (i.e., line surveys, point clouds), and raster image types, as well as diverse coordinate reference projections and resolutions. By implementing our DQS we have seen progressive improvement in the quality of the datasets across the different subject domains, and through this, the ease by which the users can programmatically access the data, either in situ or via web services. As part of its quality control procedures, NCI has developed a compliance checker based upon existing domain standards. The DQS also includes extensive Functionality Testing which include readability by commonly used libraries (e.g., netCDF, HDF, GDAL, etc.); accessibility by data servers (e.g., THREDDS, Hyrax, GeoServer), validation against scientific analysis and programming platforms (e.g., Python, Matlab, QGIS); and visualization tools (e.g., ParaView, NASA Web World Wind). These tests ensure smooth interoperability between products and services as well as exposing unforeseen requirements and dependencies. The results provide an important component of quality control within the DQS as well as clarifying the requirement for any extensions to the relevant standards that help support the uptake of data by broader international communities.

The Ares I Crew Launch Vehicle: Human Space Access for the Moon and Beyond

NASA Technical Reports Server (NTRS)

Cook, Stephen A.

2008-01-01

The National Aeronautics and Space Administration (NASA)'s Constellation Program is depending on the Ares Projects to deliver the crew launch capabilities needed to send human explorers to the Moon and beyond. The Ares Projects continue to make progress toward design, component testing, and early flight testing of the Ares I crew launch vehicle (Figure 1), the United States first new human-rated launch vehicle in over 25 years. Ares I will provide the core space launch capabilities the United States needs to continue providing crew and cargo access to the International Space Station (ISS), maintaining the U.S. pioneering tradition as a spacefaring nation, and enabling cooperative international ventures to the Moon and beyond. This paper will discuss programmatic, design, fabrication, and testing progress toward building this new launch vehicle.

75 FR 4066 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

..., access the index listing of the contents of the docket, and to access those documents in the docket that... of the funding. The information is organized by programmatic goal and desired result, which aligns... organization is assigned a user ID and password. Security measures have been established to protect data that...

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

OpenAQ: A Platform to Aggregate and Freely Share Global Air Quality Data

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.; Flasher, J. C.; Veerman, O.; DeWitt, H. L.

2015-12-01

Thousands of ground-based air quality monitors around the world publicly publish real-time air quality data; however, researchers and the public do not have access to this information in the ways most useful to them. Often, air quality data are posted on obscure websites showing only current values, are programmatically inaccessible, and/or are in inconsistent data formats across sites. Yet, historical and programmatic access to such a global dataset would be transformative to several scientific fields, from epidemiology to low-cost sensor technologies to estimates of ground-level aerosol by satellite retrievals. To increase accessibility and standardize this disparate dataset, we have built OpenAQ, an innovative, open platform created by a group of scientists and open data programmers. The source code for the platform is viewable at github.com/openaq. Currently, we are aggregating, storing, and making publicly available real-time air quality data (PM2.5, PM10, SO2, NO2, and O3) via an Application Program Interface (API). We will present the OpenAQ platform, which currently has the following specific capabilities: A continuous ingest mechanism for some of the most polluted cities, generalizable to more sources An API providing data-querying, including ability to filter by location, measurement type and value and date, as well as custom sort options A generalized, chart-based visualization tool to explore data accessible via the API At this stage, we are seeking wider participation and input from multiple research communities in expanding our data retrieval sites, standardizing our protocols, receiving feedback on quality issues, and creating tools that can be built on top of this open platform.

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

PubMed

Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

2016-01-01

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

New tools and methods for direct programmatic access to the dbSNP relational database.

PubMed

Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

Implementation Plan. Environmental Restoration and Waste Management Programmatic Environmental Impact Statement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-01-01

In accordance with the Department of Energy`s National Environmental Policy Act implementing procedures in Volume 10 of the Code of Federal Regulations, Section 1021,312, the Environmental Restoration and Waste Management Programmatic Environmental Impact Statement Implementation Plan has two primary purposes: to provide guidance for the preparation of the Programmatic Environmental Impact Statement and to record the issues resulting from the scoping and the extended public participation process. The Implementation Plan identifies and discusses the following: background of Environmental Restoration and Waste Management activities, the purpose of the Programmatic Environmental Impact Statement, and the relationship of the Programmatic Environmental Impact Statementmore » to other Departmental initiatives (Chapter 1); need and purposes for action (Chapter 2); scoping process and results of the public participation program in defining the scope of the Programmatic Environmental Impact Statement, including a summary of the comments received and their disposition (Chapter 3); planned scope and content of the Programmatic Environmental Impact Statement (Chapter 4); consultations with other agencies and the role of cooperating agencies (Chapter 5); planned schedule of major Programmatic Environmental Impact Statement milestones (Chapter 6); and responsibilities for preparation of the Programmatic Environmental Impact Statement (Chapter 7).« less

25 CFR 900.65 - What programmatic reports and data shall the Indian tribe or tribal organization provide?

Code of Federal Regulations, 2011 CFR

2011-04-01

... organization shall negotiate with the Secretary the type and frequency of program narrative and program data... 25 Indians 2 2011-04-01 2011-04-01 false What programmatic reports and data shall the Indian tribe... INDIAN SELF-DETERMINATION AND EDUCATION ASSISTANCE ACT Programmatic Reports and Data Requirements § 900...

25 CFR 900.65 - What programmatic reports and data shall the Indian tribe or tribal organization provide?

Code of Federal Regulations, 2012 CFR

2012-04-01

... organization shall negotiate with the Secretary the type and frequency of program narrative and program data... 25 Indians 2 2012-04-01 2012-04-01 false What programmatic reports and data shall the Indian tribe... INDIAN SELF-DETERMINATION AND EDUCATION ASSISTANCE ACT Programmatic Reports and Data Requirements § 900...

25 CFR 900.65 - What programmatic reports and data shall the Indian tribe or tribal organization provide?

Code of Federal Regulations, 2010 CFR

2010-04-01

... organization shall negotiate with the Secretary the type and frequency of program narrative and program data... 25 Indians 2 2010-04-01 2010-04-01 false What programmatic reports and data shall the Indian tribe... INDIAN SELF-DETERMINATION AND EDUCATION ASSISTANCE ACT Programmatic Reports and Data Requirements § 900...

The NASA Commercial Crew Program (CCP) Mission Assurance Process

NASA Technical Reports Server (NTRS)

Canfield, Amy

2016-01-01

In 2010, NASA established the Commercial Crew Program in order to provide human access to the International Space Station and low earth orbit via the commercial (non-governmental) sector. A particular challenge to NASA has been how to determine the commercial providers transportation system complies with Programmatic safety requirements. The process used in this determination is the Safety Technical Review Board which reviews and approves provider submitted Hazard Reports. One significant product of the review is a set of hazard control verifications. In past NASA programs, 100 percent of these safety critical verifications were typically confirmed by NASA. The traditional Safety and Mission Assurance (SMA) model does not support the nature of the Commercial Crew Program. To that end, NASA SMA is implementing a Risk Based Assurance (RBA) process to determine which hazard control verifications require NASA authentication. Additionally, a Shared Assurance Model is also being developed to efficiently use the available resources to execute the verifications. This paper will describe the evolution of the CCP Mission Assurance process from the beginning of the Program to its current incarnation. Topics to be covered include a short history of the CCP; the development of the Programmatic mission assurance requirements; the current safety review process; a description of the RBA process and its products and ending with a description of the Shared Assurance Model.

Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development.

PubMed

McEntire, Robin; Szalkowski, Debbie; Butler, James; Kuo, Michelle S; Chang, Meiping; Chang, Man; Freeman, Darren; McQuay, Sarah; Patel, Jagruti; McGlashen, Michael; Cornell, Wendy D; Xu, Jinghai James

2016-05-01

External content sources such as MEDLINE(®), National Institutes of Health (NIH) grants and conference websites provide access to the latest breaking biomedical information, which can inform pharmaceutical and biotechnology company pipeline decisions. The value of the sites for industry, however, is limited by the use of the public internet, the limited synonyms, the rarity of batch searching capability and the disconnected nature of the sites. Fortunately, many sites now offer their content for download and we have developed an automated internal workflow that uses text mining and tailored ontologies for programmatic search and knowledge extraction. We believe such an efficient and secure approach provides a competitive advantage to companies needing access to the latest information for a range of use cases and complements manually curated commercial sources. Copyright © 2016. Published by Elsevier Ltd.

ChEMBL web services: streamlining access to drug discovery data and utilities

PubMed Central

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P.

2015-01-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. PMID:25883136

7 CFR 3015.113 - Programmatic changes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agriculture Regulations of the Department of Agriculture (Continued) OFFICE OF THE CHIEF FINANCIAL OFFICER... project than was anticipated when the award was made. (d) Transferring work and providing financial... performance of the substantive programmatic work, and for providing any form of financial assistance to...

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.

PubMed

Albrecht, Felipe; List, Markus; Bock, Christoph; Lengauer, Thomas

2016-07-08

Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion.

PubMed

Shen, Lishuang; Attimonelli, Marcella; Bai, Renkui; Lott, Marie T; Wallace, Douglas C; Falk, Marni J; Gai, Xiaowu

2018-06-01

Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 2013). mvTools also provides mtDNA somatic variants annotations. "mvTool API" is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php. © 2018 Wiley Periodicals, Inc.

FY 2016 Grant Announcement: FY 2016 Technical Analysis and Programmatic Evaluation Support to the Chesapeake Bay Program Partnership

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency’s Chesapeake Bay Program Office is announcing a Request for Proposals for applicants to provide the Chesapeake Bay Program partners with a proposal(s) for providing technical analysis and programmatic evaluation

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

The provision of emergency contraception in Kinshasa's private sector pharmacies: experiences of mystery clients.

PubMed

Hernandez, Julie H; Mbadu, Muanda Fidèle; Garcia, Mélissa; Glover, Annie

2018-01-01

Recent programmatic and research efforts on addressing gaps in health systems of low-income countries increasingly see task shifting, i.e. the provision of healthcare by non-medically trained personnel, as a possible solution to increase the availability of specific services and commodities. In Kinshasa, private-sector pharmacies are the primary and preferred provider of family planning (FP) methods, and thus constitute a potential resource for expanding access to specific contraceptives. The objective of this study is to explore selected pharmacies' readiness to serve women seeking emergency contraception (EC). This study used a mystery client (MC) methodology to visit 73 pharmacies in Kinshasa, Democratic Republic of Congo (DRC). Trained interviewers posed as novice EC users and asked specific questions to evaluate the pharmacy staff's technical knowledge of EC and their attitudes towards EC clients. The results of the MC visit were recorded immediately after the MC left the pharmacy. Findings indicate that more than two-thirds of EC providers were knowledgeable about EC dosage, timeframe, and side effects, and 90% were deemed helpful towards novice EC users. Rare but glaring misconceptions about EC timeframe (20% of providers) and long-term side effects (4% of providers), as well as frequent stock-out (22%) and cost issues highlight priorities for programmatic improvements. As new service delivery strategies are explored to complement the uneven network of health structures in DRC, this study suggests that, given proper training and integration in FP programming, private-sector pharmacies have the potential to meet specific contraceptive needs for women living in Kinshasa. Private pharmacies included in study sample in Kinshasa (DRC) have adequate family planning (FP) service skills to provide clients with emergency contraceptive pills. These higher-end outlets constitute an opportunity for expanding access to FP, although, under total market approaches, a more diverse range of drugs shops should be investigated. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

An Integrated Tiered Service Delivery Model (ITSDM) Based on Local CD4 Testing Demands Can Improve Turn-Around Times and Save Costs whilst Ensuring Accessible and Scalable CD4 Services across a National Programme

PubMed Central

Glencross, Deborah K.; Coetzee, Lindi M.; Cassim, Naseem

2014-01-01

Background The South African National Health Laboratory Service (NHLS) responded to HIV treatment initiatives with two-tiered CD4 laboratory services in 2004. Increasing programmatic burden, as more patients access anti-retroviral therapy (ART), has demanded extending CD4 services to meet increasing clinical needs. The aim of this study was to review existing services and develop a service-model that integrated laboratory-based and point-of-care testing (POCT), to extend national coverage, improve local turn-around/(TAT) and contain programmatic costs. Methods NHLS Corporate Data Warehouse CD4 data, from 60–70 laboratories and 4756 referring health facilities was reviewed for referral laboratory workload, respective referring facility volumes and related TAT, from 2009–2012. Results An integrated tiered service delivery model (ITSDM) is proposed. Tier-1/POCT delivers CD4 testing at single health-clinics providing ART in hard-to-reach areas (<5 samples/day). Laboratory-based testing is extended with Tier-2/POC-Hubs (processing ≤30–40 CD4 samples/day), consolidating POCT across 8–10 health-clinics with other HIV-related testing and Tier-3/‘community’ laboratories, serving ≤40 health-clinics, processing ≤150 samples/day. Existing Tier-4/‘regional’ laboratories serve ≤100 facilities and process <350 samples/day; Tier-5 are high-volume ‘metro’/centralized laboratories (>350–1500 tests/day, serving ≥200 health-clinics). Tier-6 provides national support for standardisation, harmonization and quality across the organization. Conclusion The ITSDM offers improved local TAT by extending CD4 services into rural/remote areas with new Tier-3 or Tier-2/POC-Hub services installed in existing community laboratories, most with developed infrastructure. The advantage of lower laboratory CD4 costs and use of existing infrastructure enables subsidization of delivery of more expensive POC services, into hard-to-reach districts without reasonable access to a local CD4 laboratory. Full ITSDM implementation across 5 service tiers (as opposed to widespread implementation of POC testing to extend service) can facilitate sustainable ‘full service coverage’ across South Africa, and save>than R125 million in HIV/AIDS programmatic costs. ITSDM hierarchical parental-support also assures laboratory/POC management, equipment maintenance, quality control and on-going training between tiers. PMID:25490718

Implementation of Programmatic Quality and the Impact on Safety

NASA Astrophysics Data System (ADS)

Huls, Dale T.; Meehan, Kevin M.

2005-12-01

The implementation of an inadequate programmatic quality assurance discipline has the potential to adversely affect safety and mission success. This is best demonstrated in the lessons provided by the Apollo 1 Apollo 13 Challenger, and Columbia accidents; NASA Safety and Mission Assurance (S&MA) benchmarking exchanges; and conclusions reached by the Shuttle Return-to-Flight Task Group established following the Columbia Shuttle accident. Examples from the ISS Program demonstrate continuing issues with programmatic quality. Failure to adequately address programmatic quality assurance issues has a real potential to lead to continued inefficiency, increases in program costs, and additional catastrophic accidents.

How Bioethics is Complementing Human Rights in Realizing Health Access for Clinical Trial Participants: The Case of Formative PrEP Access in South Africa.

PubMed

Singh, Jerome

2015-06-11

Following the demise of apartheid, human rights in South Africa are now constitutionally enshrined.The right to health in South Africa's Constitution has been credited with transforming the lives of millions of people by triggering programmatic reforms in HIV treatment and the prevention of mother to child transmission (MTCT) of HIV.However, a constitutionally enshrined right to health offers no guarantee that clinical trial participants will enjoy post-trial access to beneficial interventions. Using access to HIV pre-exposure prophylaxis (PrEP) in South Africa as an example, this paper argues that adherence to bioethics norms could realize the right to health for trial participants following the end of a clinical trial. Copyright 2015 Singh. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Review of 10 Years of Vasectomy Programming and Research in Low-Resource Settings.

PubMed

Shattuck, Dominick; Perry, Brian; Packer, Catherine; Chin Quee, Dawn

2016-12-23

Vasectomy is a highly effective and safe contraceptive method for couples who want to stop childbearing, but only 2.4% of men around the world use this method. We conducted an extensive review of the vasectomy research literature and programmatic reports, published between April 2005 and April 2015, to synthesize barriers and facilitators to vasectomy adoption. Of the more than 230 documents initially retrieved in our search, we ultimately included 75 documents in our review and synthesized the findings according to the Supply-Enabling Environment-Demand (SEED) Programming Model. Regarding promoting demand for vasectomy services, we found there was a general lack of awareness about the method among both men and women, which often fueled erroneous assumptions about how vasectomy affects men. Several types of programmatic activities directly addressed knowledge gaps and negative misperceptions, including community-based and mass media communications, employer-based promotion, and group counseling. For supply of services, the lack of or inaccurate knowledge about vasectomy was also prevalent among providers, particularly among community-based health workers. Programmatic activities to improve service delivery included the use of evidence-based vasectomy techniques such as no-scalpel vasectomy, whole-site trainings, task shifting, cascade training, and mobile outreach. Finally, programmatic approaches to building a more enabling environment included engagement of governments and other community and religious leaders as well as campaigns with gender transformative messaging that countered common myths and encouraged men's positive engagement in family planning and reproductive health. In summary, a successful vasectomy program is comprised of the mutually reinforcing components of continual demand for services and access to and supply of well-trained providers. In addition, there is an underlying need for enabling policies within the cultural and gender environments that extend beyond vasectomy and include men not just as default partners of female family planning clients but as equal beneficiaries of family planning and reproductive health programs in their own right. Accelerating progress toward meaningful integration of vasectomy into a comprehensive contraceptive method mix is only possible when political and financial will are aligned and support the logistical and promotional activities of a male reproductive health agenda. © Shattuck et al.

A Review of 10 Years of Vasectomy Programming and Research in Low-Resource Settings

PubMed Central

Shattuck, Dominick; Perry, Brian; Packer, Catherine; Chin Quee, Dawn

2016-01-01

ABSTRACT Vasectomy is a highly effective and safe contraceptive method for couples who want to stop childbearing, but only 2.4% of men around the world use this method. We conducted an extensive review of the vasectomy research literature and programmatic reports, published between April 2005 and April 2015, to synthesize barriers and facilitators to vasectomy adoption. Of the more than 230 documents initially retrieved in our search, we ultimately included 75 documents in our review and synthesized the findings according to the Supply–Enabling Environment–Demand (SEED) Programming Model. Regarding promoting demand for vasectomy services, we found there was a general lack of awareness about the method among both men and women, which often fueled erroneous assumptions about how vasectomy affects men. Several types of programmatic activities directly addressed knowledge gaps and negative misperceptions, including community-based and mass media communications, employer-based promotion, and group counseling. For supply of services, the lack of or inaccurate knowledge about vasectomy was also prevalent among providers, particularly among community-based health workers. Programmatic activities to improve service delivery included the use of evidence-based vasectomy techniques such as no-scalpel vasectomy, whole-site trainings, task shifting, cascade training, and mobile outreach. Finally, programmatic approaches to building a more enabling environment included engagement of governments and other community and religious leaders as well as campaigns with gender transformative messaging that countered common myths and encouraged men's positive engagement in family planning and reproductive health. In summary, a successful vasectomy program is comprised of the mutually reinforcing components of continual demand for services and access to and supply of well-trained providers. In addition, there is an underlying need for enabling policies within the cultural and gender environments that extend beyond vasectomy and include men not just as default partners of female family planning clients but as equal beneficiaries of family planning and reproductive health programs in their own right. Accelerating progress toward meaningful integration of vasectomy into a comprehensive contraceptive method mix is only possible when political and financial will are aligned and support the logistical and promotional activities of a male reproductive health agenda. PMID:28031302

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations.

PubMed

Huang, Linda; Fernandes, Helen; Zia, Hamid; Tavassoli, Peyman; Rennert, Hanna; Pisapia, David; Imielinski, Marcin; Sboner, Andrea; Rubin, Mark A; Kluk, Michael; Elemento, Olivier

2017-05-01

This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu ), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB's interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association.

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

PubMed Central

Huang, Linda; Fernandes, Helen; Zia, Hamid; Tavassoli, Peyman; Rennert, Hanna; Pisapia, David; Imielinski, Marcin; Sboner, Andrea; Rubin, Mark A; Kluk, Michael

2017-01-01

Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API. PMID:27789569

New tools and methods for direct programmatic access to the dbSNP relational database

PubMed Central

Saccone, Scott F.; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A.; Rice, John P.

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale. PMID:21037260

Space station data system analysis/architecture study. Task 2: Options development, DR-5. Volume 3: Programmatic options

NASA Technical Reports Server (NTRS)

1985-01-01

Task 2 in the Space Station Data System (SSDS) Analysis/Architecture Study is the development of an information base that will support the conduct of trade studies and provide sufficient data to make design/programmatic decisions. This volume identifies the preferred options in the programmatic category and characterizes these options with respect to performance attributes, constraints, costs, and risks. The programmatic category includes methods used to administrate/manage the development, operation and maintenance of the SSDS. The specific areas discussed include standardization/commonality; systems management; and systems development, including hardware procurement, software development and system integration, test and verification.

44 CFR 13.42 - Retention and access requirements for records.

Code of Federal Regulations, 2014 CFR

2014-10-01

... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND... to all financial and programmatic records, supporting documents, statistical records, and other... computations of the rate at which a particular group of costs is chargeable (such as computer usage chargeback...

44 CFR 13.42 - Retention and access requirements for records.

Code of Federal Regulations, 2011 CFR

2011-10-01

... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND... to all financial and programmatic records, supporting documents, statistical records, and other... computations of the rate at which a particular group of costs is chargeable (such as computer usage chargeback...

44 CFR 13.42 - Retention and access requirements for records.

Code of Federal Regulations, 2013 CFR

2013-10-01

... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND... to all financial and programmatic records, supporting documents, statistical records, and other... computations of the rate at which a particular group of costs is chargeable (such as computer usage chargeback...

44 CFR 13.42 - Retention and access requirements for records.

Code of Federal Regulations, 2010 CFR

2010-10-01

... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND... to all financial and programmatic records, supporting documents, statistical records, and other... computations of the rate at which a particular group of costs is chargeable (such as computer usage chargeback...

44 CFR 13.42 - Retention and access requirements for records.

Code of Federal Regulations, 2012 CFR

2012-10-01

... AGENCY, DEPARTMENT OF HOMELAND SECURITY GENERAL UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND... to all financial and programmatic records, supporting documents, statistical records, and other... computations of the rate at which a particular group of costs is chargeable (such as computer usage chargeback...

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

PubMed

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L; Sherman, Westley A; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-06-15

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.

JPL Innovation Foundry

NASA Technical Reports Server (NTRS)

Sherwood, Brent; McCleese, Daniel J.

2012-01-01

NASA supports the community of mission principal investigators by helping them ideate, mature, and propose concepts for new missions. As NASA's Federally Funded Research and Development Center (FFRDC), JPL is a primary resource for providing this service. The environmental context for the formulation lifecycle evolves continuously. Contemporary trends include: more competitors; more-complex mission ideas; scarcer formulation resources; and higher standards for technical evaluation. Derived requirements for formulation support include: stable, clear, reliable methods tailored for each stage of the formulation lifecycle; on-demand access to standout technical and programmatic subject-matter experts; optimized, outfitted facilities; smart access to learning embodied in a vast oeuvre of prior formulation work; hands-on method coaching. JPL has retooled its provision of integrated formulation lifecycle support to PIs, teams, and program offices in response to this need. This mission formulation enterprise is the JPL Innovation Foundry.

Urban transportation : challenges to widespread deployment of intelligent transportation systems : report to Congressional committees

DOT National Transportation Integrated Search

The federal government can take programmatic and financial actions to : promote the deployment of intelligent transportation systems. The : programmatic actions include providing technical assistance and training : to state and local officials, disse...

The Need for Comprehensive Reform: From Access to Completion

ERIC Educational Resources Information Center

Bailey, Thomas

2016-01-01

This chapter examines why typical reforms at community colleges in recent years have not improved institutional graduation rates. It argues that substantially increasing college completion requires comprehensive institutional reform with a focus on measurable student success, an intentional and cohesive package of programmatic components, and a…

ChEMBL web services: streamlining access to drug discovery data and utilities.

PubMed

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P

2015-07-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Resilience Activation Framework: A conceptual model of how access to social resources promotes adaptation and rapid recovery in post-disaster settings

PubMed Central

Abramson, David M.; Grattan, Lynn M.; Mayer, Brian; Colten, Craig E.; Arosemena, Farah A.; Rung, Ariane; Lichtveld, Maureen

2014-01-01

A number of governmental agencies have called for enhancing citizen’s resilience as a means of preparing populations in advance of disasters, and as a counter-balance to social and individual vulnerabilities. This increasing scholarly, policy and programmatic interest in promoting individual and communal resilience presents a challenge to the research and practice communities: to develop a translational framework that can accommodate multi-disciplinary scientific perspectives into a single, applied model. The Resilience Activation Framework provides a basis for testing how access to social resources, such as formal and informal social support and help, promotes positive adaptation or reduced psychopathology among individuals and communities exposed to the acute collective stressors associated with disasters, whether manmade, natural, or technological in origin. Articulating the mechanisms by which access to social resources activate and sustain resilience capacities for optimal mental health outcomes post-disaster can lead to the development of effective preventive and early intervention programs. PMID:24870399

Programmatic access to logical models in the Cell Collective modeling environment via a REST API.

PubMed

Kowal, Bryan M; Schreier, Travis R; Dauer, Joseph T; Helikar, Tomáš

2016-01-01

Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective (http://thecellcollective.org). thelikar2@unl.edu. Technical user documentation: https://goo.gl/U52GWo. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The resilience activation framework: a conceptual model of how access to social resources promotes adaptation and rapid recovery in post-disaster settings.

PubMed

Abramson, David M; Grattan, Lynn M; Mayer, Brian; Colten, Craig E; Arosemena, Farah A; Bedimo-Rung, Ariane; Lichtveld, Maureen

2015-01-01

A number of governmental agencies have called for enhancing citizens' resilience as a means of preparing populations in advance of disasters, and as a counterbalance to social and individual vulnerabilities. This increasing scholarly, policy, and programmatic interest in promoting individual and communal resilience presents a challenge to the research and practice communities: to develop a translational framework that can accommodate multidisciplinary scientific perspectives into a single, applied model. The Resilience Activation Framework provides a basis for testing how access to social resources, such as formal and informal social support and help, promotes positive adaptation or reduced psychopathology among individuals and communities exposed to the acute collective stressors associated with disasters, whether human-made, natural, or technological in origin. Articulating the mechanisms by which access to social resources activate and sustain resilience capacities for optimal mental health outcomes post-disaster can lead to the development of effective preventive and early intervention programs.

Process mapping as a tool for home health network analysis.

PubMed

Pluto, Delores M; Hirshorn, Barbara A

2003-01-01

Process mapping is a qualitative tool that allows service providers, policy makers, researchers, and other concerned stakeholders to get a "bird's eye view" of a home health care organizational network or a very focused, in-depth view of a component of such a network. It can be used to share knowledge about community resources directed at the older population, identify gaps in resource availability and access, and promote on-going collaborative interactions that encourage systemic policy reassessment and programmatic refinement. This article is a methodological description of process mapping, which explores its utility as a practice and research tool, illustrates its use in describing service-providing networks, and discusses some of the issues that are key to successfully using this methodology.

A practical approach to programmatic assessment design.

PubMed

Timmerman, A A; Dijkstra, J

2017-12-01

Assessment of complex tasks integrating several competencies calls for a programmatic design approach. As single instruments do not provide the information required to reach a robust judgment of integral performance, 73 guidelines for programmatic assessment design were developed. When simultaneously applying these interrelated guidelines, it is challenging to keep a clear overview of all assessment activities. The goal of this study was to provide practical support for applying a programmatic approach to assessment design, not bound to any specific educational paradigm. The guidelines were first applied in a postgraduate medical training setting, and a process analysis was conducted. This resulted in the identification of four steps for programmatic assessment design: evaluation, contextualisation, prioritisation and justification. Firstly, the (re)design process starts with sufficiently detailing the assessment environment and formulating the principal purpose. Key stakeholders with sufficient (assessment) expertise need to be involved in the analysis of strengths and weaknesses and identification of developmental needs. Central governance is essential to balance efforts and stakes with the principal purpose and decide on prioritisation of design decisions and selection of relevant guidelines. Finally, justification of assessment design decisions, quality assurance and external accountability close the loop, to ensure sound underpinning and continuous improvement of the assessment programme.

Programmatic and teaching initiatives for ethnically diverse nursing students: a literature review.

PubMed

Torregosa, Marivic B; Morin, Karen H

2012-06-01

The purpose of this study was to examine the evidence of programmatic and teaching initiatives implemented by nursing faculty to enhance the academic success rates of ethnically diverse students (EDS). A search of the literature in the Cumulative Index to Nursing and Allied Health Literature and MEDLINE databases, wherein primary sources about programmatic and teaching initiative to promote academic success among EDS, was conducted. Using specific the Cumulative Index to Nursing and Allied Health Literature subject headings and Medical Subject Headings, 230 articles were retrieved from both databases. A total of 22 peer-reviewed articles published between 2000 and 2011 were included in the literature review. We found that evidence on the predominant programmatic and teaching initiatives for EDS academic success was inconclusive. The most common programmatic and teaching initiatives implemented by nursing faculty were peer mentoring, faculty-student mentoring, social networking, academic support, and financial support. Although positive student outcomes were reported about programmatic and teaching initiatives for EDS, the evidence remained inconclusive. Recommendations for policy and future research in this area of nursing education research were provided. Copyright © 2012. Published by Elsevier B.V.

76 FR 32238 - Detroit Edison Company, Fermi 2; Exemption

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-03

..., to M. S. Fertel, Nuclear Energy Institute (ADAMS Accession No. ML091410309)). The licensee's request... Programmatic Environmental Assessment and Finding of No Significant Impact (76 FR 187) for the treatment of..., the Commission) now or hereafter in effect. The facility consists of one boiling-water reactor located...

Patient, Program, and System Barriers and Facilitators to Detoxification Services in the U.S. Veterans Health Administration: A Qualitative Study of Provider Perspectives.

PubMed

Schultz, Nicole R; Martinez, Rociel; Cucciare, Michael A; Timko, Christine

2016-08-23

Because substance use disorder (SUD) treatment is expanding, and detoxification (detox) is often the entry point to SUD treatment, it is critical to provide ready access to detox services. The purpose of the current study was to examine patient, program, and system barriers or facilitators to detox access within an integrated health care system with variable rates of detox utilization across facilities. Inpatient and outpatient providers from 31 different U.S. Veterans Health Administration detox programs were interviewed. Qualitative analyses identified six facilitators and 11 barriers to detox access. Facilitators included program staff and program characteristics such as encouragement and immediate access, as well as systemic cooperation and patient circumstances. Barriers to detox included programmatic and systemic problems, including lack of available detox services, program rules or admission requirements, funding shortages, stigma related to a SUD diagnosis or receiving detox services, and a deficiency of education and training. Other major barriers pertained to patients' lack of motivation and competing responsibilities. To improve detox access, health care settings should consider enhancing supportive relationships by emphasizing outreach, engagement, and rapport-building with patients, improving systemic communication and teamwork, educating patients on available detox services and the detox process, and addressing patient centered barriers such as resistance to detox or competing responsibilities. In addition, programs should consider open-door and immediate-admission policies. These approaches may improve detox access, which is important for increasing the likelihood of transitioning patients to SUD treatment, thus improving outcomes and reducing utilization of high-cost services.

Strengthening the role of Community Health Representatives in the Navajo Nation.

PubMed

King, Caroline; Goldman, Alex; Gampa, Vikas; Smith, Casey; Muskett, Olivia; Brown, Christian; Malone, Jamy; Sehn, Hannah; Curley, Cameron; Begay, Mae-Gilene; Nelson, Adrianne Katrina; Shin, Sonya Sunhi

2017-04-21

Strengthening Community Health Worker systems has been recognized to improve access to chronic disease prevention and management efforts in low-resource communities. The Community Outreach and Patient Empowerment (COPE) Program is a Native non-profit organization with formal partnerships with both the Navajo Nation Community Health Representative (CHR) Program and the clinical facilities serving the Navajo Nation. COPE works to better integrate CHRs into the local health care system through training, strengthening care coordination, and a standardized culturally appropriate suite of health promotion materials for CHRs to deliver to high-risk individuals in their homes. The objective of this mixed methods, cross sectional evaluation of a longitudinal cohort study was to explore how the COPE Program has effected CHR teams over the past 6 years. COPE staff surveyed CHRs in concurrent years (2014 and 2015) about their perceptions of and experience working with COPE, including potential effects COPE may have had on communication among patients, CHRs, and hospital-based providers. COPE staff also conducted focus groups with all eight Navajo Nation CHR teams. CHRs and other stakeholders who viewed our results agree that COPE has improved clinic-community linkages, primarily through strengthened collaborations between Public Health Nurses and CHRs, and access to the Electronic Health Records. CHRs perceived that COPE’s programmatic support has strengthened their validity and reputation with providers and clients, and has enhanced their ability to positively effect health outcomes among their clients. CHRs report an improved ability to deliver health coaching to their clients. Survey results show that 80. 2% of CHRs feel strongly positive that COPE trainings are useful, while 44.6% of CHRs felt that communication and teamwork had improved because of COPE. These findings suggest that CHRs have experienced positive benefits from COPE through training. COPE may provide a useful programmatic model on how best to support other Community Health Workers through strengthening clinic-community linkages, standardizing competencies and training support, and structuring home-based interventions for high-risk individuals.

The vital signs of chronic disease management.

PubMed

Harries, Anthony D; Zachariah, Rony; Kapur, Anil; Jahn, Andreas; Enarson, Donald A

2009-06-01

The vital signs of pulse rate, blood pressure, temperature and respiratory rate are the 'nub' of individual patient management. At the programmatic level, vital signs could also be used to monitor the burden and treatment outcome of chronic disease. Case detection and treatment outcome constitute the vital signs of tuberculosis control within the WHO's 'DOTS' framework, and similar vital signs could be adapted and used for management of chronic diseases. The numbers of new patients started on therapy in each month or quarter (new incident cases) are sensitive indicators for programme performance and access to services. Using similar reporting cycles, treatment outcomes for all patients can be assessed, the vital signs being: alive and retained on therapy at the respective facility; died; stopped therapy; lost to follow-up; and transferred out to another facility. Retention on treatment constitutes the prevalent number of cases, the burden of disease, and this provides important strategic information for rational drug forecasting and logistic planning. If case numbers and outcomes of chronic diseases were measured reliably and consistently as part of an integrated programmatic approach, this would strengthen the ability of resource-poor countries to monitor and assess their response to these growing epidemics.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

PubMed Central

Eckes, Annemarie H.; Gubała, Tomasz; Nowakowski, Piotr; Szymczyszyn, Tomasz; Wells, Rachel; Irwin, Judith A.; Horro, Carlos; Hancock, John M.; King, Graham; Dyer, Sarah C.; Jurkowski, Wiktor

2017-01-01

The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository. PMID:28529710

76 FR 29217 - Notice of Availability of the Final Programmatic Environmental Impact Statement for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-20

... Final Programmatic Environmental Impact Statement for the Mechanical and Artificial Creation and... Statement (FPEIS) for the Mechanical and Artificial Creation and Maintenance of Emergent Sandbar Habitat on... provide National Environmental Policy Act (NEPA) coverage for the mechanical and artificial construction...

Fostering Social and Cultural Capital in Urban Youth: A Programmatic Approach to Promoting College Success

ERIC Educational Resources Information Center

Sommerfeld, Amanda K.; Bowen, Paul

2013-01-01

Bachelor's degree attainment has become essential for U.S. labor market participation. However, degree attainment is differentially accessible across racial and economic lines. One explanation of degree disparities is that urban students often lack the social and cultural capital needed to succeed in higher education institutions. This article…

Complexities in Managing the Child Care Industry: An Observation on Challenges and Potentials

ERIC Educational Resources Information Center

Zaman, Ahmed; Amin, Ruhul; Momjian, Ina Eduardovna; Lei, Ting

2012-01-01

The evolution of programmatic childcare since the American Recovery and Reinvestment Act of early 2009, as well as the increasing diversity of childcare recipients, call urgently for novel insight into the morphology of the childcare sector. This paper attempts such elucidation, focusing especially on the structure, accessibility, delivery…

Programmatic, Systematic, Automatic: An Online Course Accessibility Support Model

ERIC Educational Resources Information Center

Bastedo, Kathleen; Sugar, Amy; Swenson, Nancy; Vargas, Jessica

2013-01-01

Over the past few years, there has been a noticeable increase in the number of requests for online course material accommodations at the University of Central Florida (UCF). In response to these requests, UCF's Center for Distributed Learning (CDL) formed new teams, reevaluated its processes, and initiated a partnership with UCF's Student…

When Less Is More: Prioritizing Open Access

ERIC Educational Resources Information Center

Mullin, Christopher M.

2017-01-01

In policy circles, the first question of the year often relates to college enrollment. Most common is the question: "Are you up or down in enrollment?" More often than not, the enrollment question may be answered in terms of full-time equivalent (FTE) enrollment. While the answer does have programmatic implications, the initial interest…

Programmatic Knowledge Management: Technology, Literacy, and Access in 21st-Century Writing Programs

ERIC Educational Resources Information Center

York, Eric James

2015-01-01

Growing out of research in Technical Communication, Composition Studies, and Writing Program Administration, the articles in this dissertation explicitly seek to address changes in the practices and products of writing and writing studies wrought by the so-called "digital revolution" in communication technology, which has been ongoing in…

Challenges for the Urban Community College. AACJC Issues Series No. 4.

ERIC Educational Resources Information Center

Stahl, Frederick E., Ed.

Using as its premise that access and excellence are mutually interdependent goals for urban community colleges, this monograph considers the direction and nature of programmatic responses to the needs of the constituencies of urban two-year colleges and the direction and quality of the research efforts required to measure institutional impact on…

Vulnerabilities in snakebites in Sao Paulo, Brazil.

PubMed

Bertolozzi, Maria Rita; Scatena, Camila Morato da Conceição; França, Francisco Oscar de Siqueira

2015-01-01

To describe elements of vulnerability of victims of snakebite. This qualitative, descriptive, cross-sectional study had, as theoretical framework, the concept of vulnerability in individual, social, and programmatic dimensions. We interviewed 21 patients admitted into a hospital specialized in the care of accidents caused by venomous animals. The interviews were analyzed according to a discourse analysis technique. Patients were mainly young men, living in remote countryside areas, where health services frequently have limited resources. We found social and individual conditions of vulnerability, such as precarious schooling, low professional qualification, housing without access to piped water, no sewage treated, and no regular garbage collection, and lack of knowledge on this health problem. Regarding the programmatic dimension, we found limited accessibility to the health services that could affect the prognosis and the frequency of sequelae and deaths. Considering such vulnerabilities evoke the need to improve the program for control the Accidents by Venomous Animals and the training of health workers, we highlight the potential use of the concept of vulnerability, which may amplify the understanding and the recommendations for the practice and education related to snakebites.

Vulnerabilities in snakebites in Sao Paulo, Brazil

PubMed Central

Bertolozzi, Maria Rita; Scatena, Camila Morato da Conceição; França, Francisco Oscar de Siqueira

2015-01-01

ABSTRACT OBJECTIVE To describe elements of vulnerability of victims of snakebite. METHODS This qualitative, descriptive, cross-sectional study had, as theoretical framework, the concept of vulnerability in individual, social, and programmatic dimensions. We interviewed 21 patients admitted into a hospital specialized in the care of accidents caused by venomous animals. The interviews were analyzed according to a discourse analysis technique. RESULTS Patients were mainly young men, living in remote countryside areas, where health services frequently have limited resources. We found social and individual conditions of vulnerability, such as precarious schooling, low professional qualification, housing without access to piped water, no sewage treated, and no regular garbage collection, and lack of knowledge on this health problem. Regarding the programmatic dimension, we found limited accessibility to the health services that could affect the prognosis and the frequency of sequelae and deaths. CONCLUSIONS Considering such vulnerabilities evoke the need to improve the program for control the Accidents by Venomous Animals and the training of health workers, we highlight the potential use of the concept of vulnerability, which may amplify the understanding and the recommendations for the practice and education related to snakebites. PMID:26603351

Student Retention in Higher Education: Some Conceptual and Programmatic Perspectives.

ERIC Educational Resources Information Center

Lang, Marvel

2002-01-01

Provides a review of conceptual perspectives on the salient issues affecting student retention in higher education generally, and minority student retention in particular, over the past few decades. Also summarizes programmatic strategies implemented at institutions as examples of student retention initiatives that have had significant impacts.…

75 FR 26269 - Draft Programmatic Environmental Assessment for the Integrated Public Alert and Warning Program's...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

...] Draft Programmatic Environmental Assessment for the Integrated Public Alert and Warning Program's... from construction- related actions taken under the Integrated Public Alert and Warning Program (IPAWS... Order 13407, Public Alert and Warning System, by providing robust and survivable power generation, fuel...

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

U.S. Comparative and International Graduate Programs: An Overview of Programmatic Size, Relevance, Philosophy, and Methodology

ERIC Educational Resources Information Center

Drake, Timothy A.

2011-01-01

Previous work has concentrated on the epistemological foundation of comparative and international education (CIE) graduate programs. This study focuses on programmatic size, philosophy, methodology, and pedagogy. It begins by reviewing previous studies. It then provides a theoretical framework and describes the size, relevance, content, and…

ACHP | News | ACHP and Department of Energy Streamline Section 106 Process

Science.gov Websites

Energy The ACHP and DOE are providing a prototype Programmatic Agreement for dealing with historic properties as part of Recovery Act projects. Press Release (PDF) Protoype Programmatic Agreement (PDF) When DOE approves the use of an existing state interagency agreement for Section 106 compliance purposes in

PyXNAT: XNAT in Python.

PubMed

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line.

PyXNAT: XNAT in Python

PubMed Central

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S.; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line. PMID:22654752

Responding to Changes in HIV Policy: Updating and Enhancing the "Families Matter!" Curriculum

ERIC Educational Resources Information Center

Miller, Kim S; Winskell, Kate; Berrier, Faith L

2016-01-01

Objectives: The past decade has seen changes in US HIV policy in sub-Saharan Africa in response to a new Administration and far-reaching technical, scientific and programmatic developments. These include dramatically increased access to life-saving anti-retroviral therapy (ART) and related services, the roll-out of voluntary medical male…

Evaluating Admission Practices as Potential Barriers to Creating Equitable Access to Undergraduate Engineering Education

ERIC Educational Resources Information Center

Myers, Beth Ann

2016-01-01

To create a more competitive and creative engineering workforce, breakthroughs in how we attract and educate more diverse engineers are mandated. Despite a programmatic focus on increasing the representation of women and minorities in engineering during the last few decades, no single solution has been identified and is probably not realistic. But…

The three-dimensional Event-Driven Graphics Environment (3D-EDGE)

NASA Technical Reports Server (NTRS)

Freedman, Jeffrey; Hahn, Roger; Schwartz, David M.

1993-01-01

Stanford Telecom developed the Three-Dimensional Event-Driven Graphics Environment (3D-EDGE) for NASA GSFC's (GSFC) Communications Link Analysis and Simulation System (CLASS). 3D-EDGE consists of a library of object-oriented subroutines which allow engineers with little or no computer graphics experience to programmatically manipulate, render, animate, and access complex three-dimensional objects.

The Changing Role of Data Stewardship in Creating Trustworthy, Interdisciplinary High Performance Data Platforms for the Future.

NASA Astrophysics Data System (ADS)

Richards, C. J.; Evans, B. J. K.; Wyborn, L. A.; Wang, J.; Trenham, C. E.; Druken, K. A.

2016-12-01

The Australian National Computational Infrastructure (NCI) has ingested over 10PB of national and international environmental, Earth systems science and geophysics reference data onto a single platform to advance high performance data (HPD) techniques that enable interdisciplinary Data-intensive Science. Improved Data Stewardship is critical to evolve both data and data services that support the increasing need for programmatic usability and that prioritises interoperability rather than just traditional data download or portal access. A data platform designed for programmatic access requires quality checked collections that better utilise interoperable data formats and standards. Achieving this involves strategies to meet both the technical and `social' challenges. Aggregating datasets used by different communities and organisations requires satisfying multiple use cases for the broader research community, whilst addressing existing BAU requirements. For NCI, this requires working with data stewards to manage the process of replicating data to the common platform, community representatives and developers to confirm their requirements, and with international peers to better enable globally integrated data communities. It is particularly important to engage with representatives from each community who can work collaboratively to a common goal, as well as capture their community needs, apply quality assurance, determine any barriers to change and to understand priorities. This is critical when managing the aggregation of data collections from multiple producers with different levels of stewardship maturity, technologies and standards, and where organisational barriers can impact the transformation to interoperable and performant data access. To facilitate the management, development and operation of the HPD platform, NCI coordinates technical and domain committees made up of user representatives, data stewards and informatics experts to provide a forum to discuss, learn and advise NCI's management. This experience has been a useful collaboration and suggests that in the age of interdisciplinary HPD research, Data Stewardship is evolving from a focus on the needs of a single community to one which helps balance priorities and navigates change for multiple communities.

Accessing near real-time Antarctic meteorological data through an OGC Sensor Observation Service (SOS)

NASA Astrophysics Data System (ADS)

Kirsch, Peter; Breen, Paul

2013-04-01

We wish to highlight outputs of a project conceived from a science requirement to improve discovery and access to Antarctic meteorological data in near real-time. Given that the data was distributed in both spatial and temporal domains and is to be accessed across several science disciplines, the creation of an interoperable, OGC compliant web service was deemed the most appropriate approach. We will demonstrate an implementation of the OGC SOS Interface Standard to discover, browse, and access Antarctic meteorological data-sets. A selection of programmatic (R, Perl) and web client interfaces utilizing open technologies ( e.g. jQuery, Flot, openLayers ) will be demonstrated. In addition we will show how high level abstractions can be constructed to allow the users flexible and straightforward access to SOS retrieved data.

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

A Cost Benefit Analysis of Professional Accreditation by ABET for Baccalaureate Engineering Degree Programs

ERIC Educational Resources Information Center

Yuen, Faye Sui Yee

2012-01-01

Tightening fiscal budgets and the growing emphasis on accountability has created a need to assess the value that programmatic accreditation provides. For degrees in engineering, ABET is the only organization recognized in the U.S. responsible for the programmatic accreditation. This research examines the costs and benefits of ABET accreditation to…

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE Office of Scientific and Technical Information (OSTI.GOV)

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

PubMed Central

Mathelier, Anthony; Fornes, Oriol; Arenillas, David J.; Chen, Chih-yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W.; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.

2016-01-01

JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. PMID:26531826

A SOAP Web Service for accessing MODIS land product subsets

DOE Office of Scientific and Technical Information (OSTI.GOV)

SanthanaVannan, Suresh K; Cook, Robert B; Pan, Jerry Yun

2011-01-01

Remote sensing data from satellites have provided valuable information on the state of the earth for several decades. Since March 2000, the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor on board NASA s Terra and Aqua satellites have been providing estimates of several land parameters useful in understanding earth system processes at global, continental, and regional scales. However, the HDF-EOS file format, specialized software needed to process the HDF-EOS files, data volume, and the high spatial and temporal resolution of MODIS data make it difficult for users wanting to extract small but valuable amounts of information from the MODIS record. Tomore » overcome this usability issue, the NASA-funded Distributed Active Archive Center (DAAC) for Biogeochemical Dynamics at Oak Ridge National Laboratory (ORNL) developed a Web service that provides subsets of MODIS land products using Simple Object Access Protocol (SOAP). The ORNL DAAC MODIS subsetting Web service is a unique way of serving satellite data that exploits a fairly established and popular Internet protocol to allow users access to massive amounts of remote sensing data. The Web service provides MODIS land product subsets up to 201 x 201 km in a non-proprietary comma delimited text file format. Users can programmatically query the Web service to extract MODIS land parameters for real time data integration into models, decision support tools or connect to workflow software. Information regarding the MODIS SOAP subsetting Web service is available on the World Wide Web (WWW) at http://daac.ornl.gov/modiswebservice.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolbasin, V. A.; Ivanov, A. I.; Pedash, V. Y.

The two pulse shape discrimination methods were implemented in real-time. The pulse gradient analysis method was implemented programmatically on PC. The method based on artificial neural network was programmatically implemented using CUDA platform. It is shown that both implementations can provide up to 10{sup 6} pulses per second processing performance. The results for pulse shape discrimination using polycrystalline stilbene and LiF detectors were shown. (authors)

Technologies and Methods Used at the Laboratory for Atmospheric and Space Physics (LASP) to Serve Solar Irradiance Data

NASA Technical Reports Server (NTRS)

Pankratz, Chris; Beland, Stephane; Craft, James; Baltzer, Thomas; Wilson, Anne; Lindholm, Doug; Snow, Martin; Woods, Thomas; Woodraska, Don

2018-01-01

The Laboratory for Atmospheric and Space Physics (LASP) at the University of Colorado in Boulder, USA operates the Solar Radiation and Climate Experiment (SORCE) NASA mission, as well as several other NASA spacecraft and instruments. Dozens of Solar Irradiance data sets are produced, managed, and disseminated to the science community. Data are made freely available to the scientific immediately after they are produced using a variety of data access interfaces, including the LASP Interactive Solar Irradiance Datacenter (LISIRD), which provides centralized access to a variety of solar irradiance data sets using both interactive and scriptable/programmatic methods. This poster highlights the key technological elements used for the NASA SORCE mission ground system to produce, manage, and disseminate data to the scientific community and facilitate long-term data stewardship. The poster presentation will convey designs, technological elements, practices and procedures, and software management processes used for SORCE and their relationship to data quality and data management standards, interoperability, NASA data policy, and community expectations.

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

ProbOnto: ontology and knowledge base of probability distributions.

PubMed

Swat, Maciej J; Grenon, Pierre; Wimalaratne, Sarala

2016-09-01

Probability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of probability distributions. Although some resources exist, no suitably detailed and complex ontology exists nor any database allowing programmatic access. ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 80 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. http://probonto.org mjswat@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

PubMed

Kersey, Paul J; Staines, Daniel M; Lawson, Daniel; Kulesha, Eugene; Derwent, Paul; Humphrey, Jay C; Hughes, Daniel S T; Keenan, Stephan; Kerhornou, Arnaud; Koscielny, Gautier; Langridge, Nicholas; McDowall, Mark D; Megy, Karine; Maheswari, Uma; Nuhn, Michael; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Wilson, Derek; Yates, Andrew; Birney, Ewan

2012-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

Contraception for adolescents in low and middle income countries: needs, barriers, and access

PubMed Central

2014-01-01

Substantial numbers of adolescents experience the negative health consequences of early, unprotected sexual activity - unintended pregnancy, unsafe abortions, pregnancy-related mortality and morbidity and Sexually Transmitted Infections including Human Immunodeficiency Virus; as well as its social and economic costs. Improving access to and use of contraceptives – including condoms - needs to be a key component of an overall strategy to preventing these problems. This paper contains a review of research evidence and programmatic experiences on needs, barriers, and approaches to access and use of contraception by adolescents in low and middle income countries (LMIC). Although the sexual activity of adolescents (ages 10–19) varies markedly for boys versus girls and by region, a significant number of adolescents are sexually active; and this increases steadily from mid-to-late adolescence. Sexually active adolescents – both married and unmarried - need contraception. All adolescents in LMIC - especially unmarried ones - face a number of barriers in obtaining contraception and in using them correctly and consistently. Effective interventions to improve access and use of contraception include enacting and implementing laws and policies requiring the provision of sexuality education and contraceptive services for adolescents; building community support for the provision of contraception to adolescents, providing sexuality education within and outside school settings, and increasing the access to and use of contraception by making health services adolescent-friendly, integrating contraceptive services with other health services, and providing contraception through a variety of outlets. Emerging data suggest mobile phones and social media are promising means of increasing contraceptive use among adolescents. PMID:24383405

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

PubMed Central

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L.; Sherman, Westley A.; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-01-01

Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. PMID:22531216

National Utility Rate Database: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, S.; McKeel, R.

2012-08-01

When modeling solar energy technologies and other distributed energy systems, using high-quality expansive electricity rates is essential. The National Renewable Energy Laboratory (NREL) developed a utility rate platform for entering, storing, updating, and accessing a large collection of utility rates from around the United States. This utility rate platform lives on the Open Energy Information (OpenEI) website, OpenEI.org, allowing the data to be programmatically accessed from a web browser, using an application programming interface (API). The semantic-based utility rate platform currently has record of 1,885 utility rates and covers over 85% of the electricity consumption in the United States.

Data federation strategies for ATLAS using XRootD

NASA Astrophysics Data System (ADS)

Gardner, Robert; Campana, Simone; Duckeck, Guenter; Elmsheuser, Johannes; Hanushevsky, Andrew; Hönig, Friedrich G.; Iven, Jan; Legger, Federica; Vukotic, Ilija; Yang, Wei; Atlas Collaboration

2014-06-01

In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the wide area network and staging of remote data files to local disk. To support job-brokering decisions, a time-dependent cost-of-data-access matrix is made taking into account network performance and key site performance factors. The system's response to production-scale physics analysis workloads, either from individual end-users or ATLAS analysis services, is discussed.

Antarctica - Lessons for a Mars exploration program

NASA Technical Reports Server (NTRS)

Mckay, C. P.

1985-01-01

The history of exploration and the international system of control of Antarctica has often been cited as a paradigm for the exploration of space. The small isolated research stations have been used to model the psychological stresses of future space missions. In addition, the programmatic structure of the U.S. Antarctic Research Program provides several possible analogs to future Mars Programs presently under discussion. These are: (1) Continued presence; (2) Civilian, military and private sector involvement; (3) Scientific activities; (4) Risk assessment and logistical support; (5) Accessibility for non-specialists; (6) Political and strategic motivations; (7) International cooperation/competition. Survival in Antarctica is contingent on advanced technology and the active transport of supplies. The scientific exploration of this remote and barren expanse without, of course, the aid and guidance of indigenous people certainly provides one of the closest analogs available to future science activities on the Martian surface.

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

PubMed

Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

2012-07-01

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

BioGPS and MyGene.info: organizing online, gene-centric information.

PubMed

Wu, Chunlei; Macleod, Ian; Su, Andrew I

2013-01-01

Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.

Systems Engineering Programmatic Estimation Using Technology Variance

NASA Technical Reports Server (NTRS)

Mog, Robert A.

2000-01-01

Unique and innovative system programmatic estimation is conducted using the variance of the packaged technologies. Covariance analysis is performed on the subsystems and components comprising the system of interest. Technological "return" and "variation" parameters are estimated. These parameters are combined with the model error to arrive at a measure of system development stability. The resulting estimates provide valuable information concerning the potential cost growth of the system under development.

JEnsembl: a version-aware Java API to Ensembl data systems

PubMed Central

Paterson, Trevor; Law, Andy

2012-01-01

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk PMID:22945789

Gender and care: access to HIV testing, care, and treatment.

PubMed

Remien, Robert H; Chowdhury, Jenifar; Mokhbat, Jacques E; Soliman, Cherif; Adawy, Maha El; El-Sadr, Wafaa

2009-07-01

HIV transmission and occurrence of AIDS in the Middle East and North Africa region (MENA) is increasing, while access to ART in the region lags behind most low to middle-income countries. Like in other parts of the world, there is a growing feminization of the epidemic, and men and women each confront unique barriers to adequate HIV prevention and treatment services, while sharing some common obstacles as well. This paper focuses on important gender dimensions of access to HIV testing, care and treatment in the MENA region, including issues related to stigma, religion and morality, gender power imbalances, work status, and migration. Culturally specific policy and programmatic recommendations for improving HIV prevention and treatment in the MENA region are offered.

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

PubMed

Rattei, Thomas; Tischler, Patrick; Götz, Stefan; Jehl, Marc-André; Hoser, Jonathan; Arnold, Roland; Conesa, Ana; Mewes, Hans-Werner

2010-01-01

The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

PubMed

Mathelier, Anthony; Fornes, Oriol; Arenillas, David J; Chen, Chih-Yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

2016-01-04

JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cyber-Physical Security Assessment (CyPSA) Toolset

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Luis; Patapanchala, Panini; Zonouz, Saman

CyPSA seeks to organize and gain insight into the diverse sets of data that a critical infrastructure provider must manage. Specifically CyPSA inventories, manages, and analyzes assets and relations among those assets. A variety of interfaces are provided. CyPSA inventories assets (both cyber and physical). This may include the cataloging of assets through a common interface. Data sources used to generate a catalogue of assets include PowerWorld, NPView, NMap Scans, and device configurations. Depending upon the role of the person using the tool the types of assets accessed as well as the data sources through which asset information is accessedmore » may vary. CyPSA allows practitioners to catalogue relations among assets and these may either be manually or programmatically generated. For example, some common relations among assets include the following: Topological Network Data: Which devices and assets are connected and how? Data sources for this kind of information include NMap scans, NPView topologies (via Firewall rule analysis). Security Metrics Outputs: The output of various security metrics such as overall exposure. Configure Assets:CyPSA may eventually include the ability to configure assets including relays and switches. For example, a system administrator would be able to configure and alter the state of a relay via the CyPSA interface. Annotate Assets: CyPSA also allows practitioners to manually and programmatically annotate assets. Sources of information with which to annotate assets include provenance metadata regarding the data source from which the asset was loaded, vulnerability information from vulnerability databases, configuration information, and the output of an analysis in general.« less

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

2018-01-01

We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

Chemical Stockpile Disposal Program. Transportation of Chemical Munitions at Reduced Temperature

DTIC Science & Technology

1987-08-01

ADA193346 Chemical Stockpile Disposal Program. Transportation of Chemical Munitions at Reduced Temperature. MITRE CORP MCLEAN VA AUG 1987...NO. ACCESSION NO. Aberdeen Proving Ground, fD 21010-5401 11. TITLE (Include Security Classification) Transportation of Chemical Munitions at Reducfd...Year, Month, Day) S. PAGE COUNT nal FROM TO Au USt 1987 65 16. SUPPLEMENTARY NOTATION Prepared for the Chemical Stockpile D’i sal Program Programmatic

Unipept web services for metaproteomics analysis.

PubMed

Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-06-01

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Unipept@ugent.be Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Primary Care Integration of Psychiatric and Behavioral Health Services: A Primer for Providers and Case Report of Local Implementation.

PubMed

Guerrero, Anthony Ps; Takesue, Cori L; Medeiros, Jared Hn; Duran, Aileen A; Humphry, Joseph W; Lunsford, Ryan M; Shaw, Diana V; Fukuda, Michael H; Hishinuma, Earl S

2017-06-01

Mental health conditions are common, disabling, potentially life-threatening, and costly; however, they are mostly treatable with early detection and intervention. Unfortunately, mental healthcare is in significantly short supply both nationally and locally, and particularly in small, rural, and relatively isolated communities. This article provides physicians and other health practitioners with a primer on the basic rationale and principles of integrating behavioral healthcare - particularly psychiatric specialty care - in primary care settings, including effective use of teleconferencing. Referring to a local-based example, this paper describes the programmatic components (universal screening, telephone availability, mutually educational team rounds, as-needed consultations, etc) that operationalize and facilitate successful primary care integration, and illustrates how these elements are applied to population segments with differing needs for behavioral healthcare involvement. Lastly, the article discusses the potential value of primary care integration in promoting quality, accessibility, and provider retention; discusses how new developments in healthcare financing could enhance the sustainability of primary care integration models; and summarizes lessons learned.

The Evolution of the NASA Commercial Crew Program Mission Assurance Process

NASA Technical Reports Server (NTRS)

Canfield, Amy C.

2016-01-01

In 2010, the National Aeronautics and Space Administration (NASA) established the Commercial Crew Program (CCP) in order to provide human access to the International Space Station and low Earth orbit via the commercial (non-governmental) sector. A particular challenge to NASA has been how to determine that the Commercial Provider's transportation system complies with programmatic safety requirements. The process used in this determination is the Safety Technical Review Board which reviews and approves provider submitted hazard reports. One significant product of the review is a set of hazard control verifications. In past NASA programs, 100% of these safety critical verifications were typically confirmed by NASA. The traditional Safety and Mission Assurance (S&MA) model does not support the nature of the CCP. To that end, NASA S&MA is implementing a Risk Based Assurance process to determine which hazard control verifications require NASA authentication. Additionally, a Shared Assurance Model is also being developed to efficiently use the available resources to execute the verifications.

NASA Technical Interchange Meeting (TIM): Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box

NASA Technical Reports Server (NTRS)

ONeil, D. A.; Craig, D. A.; Christensen, C. B.; Gresham, E. C.

2005-01-01

The objective of this Technical Interchange Meeting was to increase the quantity and quality of technical, cost, and programmatic data used to model the impact of investing in different technologies. The focus of this meeting was the Technology Tool Box (TTB), a database of performance, operations, and programmatic parameters provided by technologists and used by systems engineers. The TTB is the data repository used by a system of models known as the Advanced Technology Lifecycle Analysis System (ATLAS). This report describes the result of the November meeting, and also provides background information on ATLAS and the TTB.

Maintaining health sector collaborations between United States non-governmental organizations and North Korea through innovation and planning.

PubMed

Yim, Eugene S; Choi, Ricky Y; VanRooyen, Michael

2009-01-01

Humanitarian agencies in North Korea operate within a complex sociopolitical environment historically characterized by a baseline of mistrust. As a result of operating within such a heated environment, health sector collaborations between such agencies and the North Korean government have followed unpredictable courses. The factors that have contributed to successful programmatic collaborations, as perceived by United States non-governmental organizations (NGOs) and North Korean officials were investigated. A qualitative, multi-case, comparative, research design using semistructured interviews was used. Expert North Korean informants were interviewed to generate a list of factors contributing to programmatic success, defined as fulfilling mutually established objectives through collaboration. The North Korean informants were asked to identify US NGOs that fulfill these criteria ("mission-compatible NGOs"). Representatives from all of the mission compatible NGOs were interviewed. All informants provided their perspectives on the factors that contributed to successful programmatic collaborations. The interviews were recorded, transcribed, and analyzed for thematic content. North Korean informants identified six mission-compatible US NGOs. The North Korean and US NGO informants provided a number of factors that contributed to successful programs. These factors were grouped into the following themes: (1) responsiveness to North Korean requests; (2) resident status; (3) program monitoring; (4) sincerity (apolitical objectives); (5) information gathering; and (6) interagency collaboration. Some US NGOs have devised innovative measures to work within a unique set of parameters in North Korea. Both US NGOs and North Korean authorities have made significant concessions to maintain their programmatic partnerships. In this manner, seasoned collaborators have employed creative strategies and a form of health diplomacy to facilitate programmatic success in North Korea by building trust within a complex sociopolitical space.

Software aspects of the Geant4 validation repository

NASA Astrophysics Data System (ADS)

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel; Genser, Krzysztof; Yarba, Julia; Carminati, Federico; Folger, Gunter; Konstantinov, Dmitri; Pokorski, Witold; Ribon, Alberto

2017-10-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

The Ensembl REST API: Ensembl Data for Any Language.

PubMed

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R S; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. © The Author 2014. Published by Oxford University Press.

Software Aspects of the Geant4 Validation Repository

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel

2016-01-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientic Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

DoSSiER: Database of scientific simulation and experimental results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wenzel, Hans; Yarba, Julia; Genser, Krzystof

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

DoSSiER: Database of scientific simulation and experimental results

DOE PAGES

Wenzel, Hans; Yarba, Julia; Genser, Krzystof; ...

2016-08-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

In-home firearm access among US adolescents and the role of religious subculture: Results from a nationally representative study.

PubMed

Stroope, Samuel; Tom, Joshua C

2017-09-01

Religious participation is linked to numerous positive safety outcomes for adolescents. Scant attention, however, has been paid to associations between religious participation and safety risks among adolescents. Using data from Add Health (N = 18,449), a nationally representative school-based sample of US adolescents, this study examines the relationship between adolescents' religious affiliation and easy access to firearms at home. Regression analyses adjust for complex sampling design and compare easy firearm access at home among conservative Protestant adolescents to adolescent firearm access in other religious traditions. Conservative Protestant adolescents have a substantially greater likelihood of easy access to a gun at home compared to adolescents of all other major religious traditions in the United States. Recognizing differences in adolescent firearm access between subcultural groups can help public health interventions more effectively identify and address the needs of vulnerable populations. The paper's conclusion considers suggestions for effective policy and programmatic initiatives. Copyright © 2017 Elsevier Inc. All rights reserved.

Satellite Power Systems (SPS) concept definition study, exhibit C. Volume 2, part 2: System engineering, cost and programmatics

NASA Technical Reports Server (NTRS)

Hanley, G. M.

1979-01-01

Volume 2, Part 2, of a seven volume Satellite Power Systems (SPS) report is presented. Part 2 covers cost and programmatics and is divided into four sections. The first section gives illustrations of the SPS reference satellite and rectenna concept, and an overall scenario for SPS space transportation involvement. The second section presents SPS program plans for the implementation of PHASE C/D activities. These plans describe SPS program schedules and networks, critical items of systems evolution/technology development, and the natural resources analysis. The fourth section presents summary comments on the methods and rationale followed in arriving at the results documented. Suggestions are also provided in those areas where further analysis or evaluation will enhance SPS cost and programmatic definitions.

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

PubMed

Li, Chen; Courtot, Mélanie; Le Novère, Nicolas; Laibe, Camille

2010-05-01

Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.

Barriers to free antiretroviral treatment access for female sex workers in Chennai, India.

PubMed

Chakrapani, Venkatesan; Newman, Peter A; Shunmugam, Murali; Kurian, Abraham K; Dubrow, Robert

2009-11-01

India's National AIDS Control Organization (NACO) provides free first-line antiretroviral treatment (ART) at government centers for people living with HIV. To assist in developing policies and programs to ensure equity in ART access, we explored barriers to ART access among female sex workers (FSWs) living with HIV in Chennai. Between August and November 2007, we conducted three focus group discussions and two key informant interviews. Data were explored using framework analysis to identify categories and derive themes. We found interrelated barriers at the family/social, health care system/programmatic, and individual levels. Major barriers included fear of adverse consequences of disclosure of HIV status due to stigma and discrimination associated with HIV and sex work, lack of family support, negative experiences with health care providers, lack of adequate counseling services at government centers and by outreach workers employed by nongovernmental organizations (NGOs), perceived biased treatment of FSWs who are not referred by NGOs, lack of adequate knowledge about ART, and fatalism. Barriers can be addressed by: creating effective measures to reduce stigma associated with HIV/AIDS and sex work at the familial, societal, and health care system levels; incorporating information about ART into targeted interventions among FSWs; training counselors at government hospitals and NGO outreach workers on treatment issues; improving infrastructure and staffing levels at government centers to allow adequate time and privacy for counseling; and implementing government mass media campaigns on ART availability. Finally, it is crucial that NACO begin monitoring ART coverage of FSWs and other marginalized populations to ensure equitable ART access.

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Technical Reports Server (NTRS)

Monell, Donald W.; Piland, William M.

1999-01-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g. manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often lead to the inability of assessing critical programmatic and technical issues (e.g., cost risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across the Agency.

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Technical Reports Server (NTRS)

Monell, Donald W.; Piland, William M.

2000-01-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g., manufacturing and systems operation). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often lead to the inability of assessing critical programmatic and technical issues (e.g., cost, risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographical distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across Agency.

Aerospace Systems Design in NASA's Collaborative Engineering Environment

NASA Astrophysics Data System (ADS)

Monell, Donald W.; Piland, William M.

2000-07-01

Past designs of complex aerospace systems involved an environment consisting of collocated design teams with project managers, technical discipline experts, and other experts (e.g., manufacturing and systems operations). These experts were generally qualified only on the basis of past design experience and typically had access to a limited set of integrated analysis tools. These environments provided less than desirable design fidelity, often led to the inability of assessing critical programmatic and technical issues (e.g., cost, risk, technical impacts), and generally derived a design that was not necessarily optimized across the entire system. The continually changing, modern aerospace industry demands systems design processes that involve the best talent available (no matter where it resides) and access to the best design and analysis tools. A solution to these demands involves a design environment referred to as collaborative engineering. The collaborative engineering environment evolving within the National Aeronautics and Space Administration (NASA) is a capability that enables the Agency's engineering infrastructure to interact and use the best state-of-the-art tools and data across organizational boundaries. Using collaborative engineering, the collocated team is replaced with an interactive team structure where the team members are geographically distributed and the best engineering talent can be applied to the design effort regardless of physical location. In addition, a more efficient, higher quality design product is delivered by bringing together the best engineering talent with more up-to-date design and analysis tools. These tools are focused on interactive, multidisciplinary design and analysis with emphasis on the complete life cycle of the system, and they include nontraditional, integrated tools for life cycle cost estimation and risk assessment. NASA has made substantial progress during the last two years in developing a collaborative engineering environment. NASA is planning to use this collaborative engineering infrastructure to provide better aerospace systems life cycle design and analysis, which includes analytical assessment of the technical and programmatic aspects of a system from "cradle to grave." This paper describes the recent NASA developments in the area of collaborative engineering, the benefits (realized and anticipated) of using the developed capability, and the long-term plans for implementing this capability across the Agency.

caCORE: a common infrastructure for cancer informatics.

PubMed

Covitz, Peter A; Hartel, Frank; Schaefer, Carl; De Coronado, Sherri; Fragoso, Gilberto; Sahni, Himanso; Gustafson, Scott; Buetow, Kenneth H

2003-12-12

Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).

Household water treatment and the millennium development goals: keeping the focus on health.

PubMed

Clasen, Thomas F

2010-10-01

Waterborne diseases such as diarrhea are a major killer in low-income settings, particularly of young children. For those without access to safe drinking water, household water treatment, such as boiling, chlorinating, and filtering water in the home, when combined with safe storage (HWTS) can significantly improve water quality and prevent disease, thereby contributing to the child survival and other health priorities encompassed within the Millennium Development Goals (MDGs). There is uncertainly, however, about whether HWTS should count toward the MDG water target, which promotes "sustainable access to safe drinking water". This paper reviews the relevant research and concludes that it should not. Although HWTS can significantly improve water quality, it does not improve water quantity and access-key aspects of the MDG water target that are essential for optimal improvements in health and development. A policy that excludes HWTS from the MDG water target will discourage governments from diverting scarce public resources from comprehensive and long-term improvements in water supplies. At the same time, the health-oriented MDGs provide a sufficient case for scaling up effective and appropriate HWTS among target populations. Moreover, a health-based strategy for HWTS will help ensure that promotion of the intervention is driven by measurable improvements in outcomes rather than inputs, thus encouraging advances in both hardware and programmatic delivery that will make HWTS more effective, appropriate, and accessible to vulnerable populations.

Prioritization methodology for chemical replacement

NASA Technical Reports Server (NTRS)

Goldberg, Ben; Cruit, Wendy; Schutzenhofer, Scott

1995-01-01

This methodology serves to define a system for effective prioritization of efforts required to develop replacement technologies mandated by imposed and forecast legislation. The methodology used is a semi quantitative approach derived from quality function deployment techniques (QFD Matrix). QFD is a conceptual map that provides a method of transforming customer wants and needs into quantitative engineering terms. This methodology aims to weight the full environmental, cost, safety, reliability, and programmatic implications of replacement technology development to allow appropriate identification of viable candidates and programmatic alternatives.

The German Long-Term Care Insurance Program: Evolution and Recent Developments.

PubMed

Nadash, Pamela; Doty, Pamela; von Schwanenflügel, Matthias

2018-05-08

Since 1995, Germany has operated one of the longest-running public programs providing universal support for the cost of long term services and supports (LTSS). Its self-funding, social insurance approach provides basic supports to nearly all Germans. We discuss its design and development, including recent reforms expanding the program and ensuring its ongoing sustainability. The study reviews legislative and programmatic changes, using program data, as well as legislative documents and program reports. The program is widely accepted among citizens and has achieved many of its original goals: ensuring access to LTSS and reducing reliance on the locally-funded safety-net social assistance program, which can be used to cover nursing home costs. It also strengthened the LTSS provider infrastructure and expanded access to home care. Recent reforms have addressed some of the program's key issues: the benefit's decreasing value, the eligibility and benefit structure that largely excluded cognitive impairment, and the program's longer-term financial sustainability-particularly its ability to sustain newly expanded benefits, which provide stronger protections to caregivers, index-link benefits, and more systematically incorporate cognitive impairment via a new assessment system. It has addressed financing issues by increasing premiums, introducing subsidies for the purchase of private insurance, and creating a "demographic reserve fund." The reforms constitute a significant strengthening of the program, remarkable in an era of retrenchment. Overall, the program provides evidence for the financial viability of a social insurance model, although longer-term challenges may yet arise.

New Web Services for Broader Access to National Deep Submergence Facility Data Resources Through the Interdisciplinary Earth Data Alliance

NASA Astrophysics Data System (ADS)

Ferrini, V. L.; Grange, B.; Morton, J. J.; Soule, S. A.; Carbotte, S. M.; Lehnert, K.

2016-12-01

The National Deep Submergence Facility (NDSF) operates the Human Occupied Vehicle (HOV) Alvin, the Remotely Operated Vehicle (ROV) Jason, and the Autonomous Underwater Vehicle (AUV) Sentry. These vehicles are deployed throughout the global oceans to acquire sensor data and physical samples for a variety of interdisciplinary science programs. As part of the EarthCube Integrative Activity Alliance Testbed Project (ATP), new web services were developed to improve access to existing online NDSF data and metadata resources. These services make use of tools and infrastructure developed by the Interdisciplinary Earth Data Alliance (IEDA) and enable programmatic access to metadata and data resources as well as the development of new service-driven user interfaces. The Alvin Frame Grabber and Jason Virtual Van enable the exploration of frame-grabbed images derived from video cameras on NDSF dives. Metadata available for each image includes time and vehicle position, data from environmental sensors, and scientist-generated annotations, and data are organized and accessible by cruise and/or dive. A new FrameGrabber web service and service-driven user interface were deployed to offer integrated access to these data resources through a single API and allows users to search across content curated in both systems. In addition, a new NDSF Dive Metadata web service and service-driven user interface was deployed to provide consolidated access to basic information about each NDSF dive (e.g. vehicle name, dive ID, location, etc), which is important for linking distributed data resources curated in different data systems.

Unifying Access to National Hydrologic Data Repositories via Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Jennings, B.; Zaslavsky, I.; Maidment, D. R.

2006-12-01

The CUAHSI hydrologic information system (HIS) is designed to be a live, multiscale web portal system for accessing, querying, visualizing, and publishing distributed hydrologic observation data and models for any location or region in the United States. The HIS design follows the principles of open service oriented architecture, i.e. system components are represented as web services with well defined standard service APIs. WaterOneFlow web services are the main component of the design. The currently available services have been completely re-written compared to the previous version, and provide programmatic access to USGS NWIS. (steam flow, groundwater and water quality repositories), DAYMET daily observations, NASA MODIS, and Unidata NAM streams, with several additional web service wrappers being added (EPA STORET, NCDC and others.). Different repositories of hydrologic data use different vocabularies, and support different types of query access. Resolving semantic and structural heterogeneities across different hydrologic observation archives and distilling a generic set of service signatures is one of the main scalability challenges in this project, and a requirement in our web service design. To accomplish the uniformity of the web services API, data repositories are modeled following the CUAHSI Observation Data Model. The web service responses are document-based, and use an XML schema to express the semantics in a standard format. Access to station metadata is provided via web service methods, GetSites, GetSiteInfo and GetVariableInfo. The methdods form the foundation of CUAHSI HIS discovery interface and may execute over locally-stored metadata or request the information from remote repositories directly. Observation values are retrieved via a generic GetValues method which is executed against national data repositories. The service is implemented in ASP.Net, and other providers are implementing WaterOneFlow services in java. Reference implementation of WaterOneFlow web services is available. More information about the ongoing development of CUAHSI HIS is available from http://www.cuahsi.org/his/.

Falling through the gaps: how should HIV programmes respond to families that persistently deny treatment to children?

PubMed

Busza, Joanna; Strode, Ann; Dauya, Ethel; Ferrand, Rashida A

2016-01-01

Children living with HIV rely on adult caregivers for access to HIV testing and care, including clinical monitoring and adherence to treatment. Yet, many caregivers confront barriers to ensuring children's care, including fear of disclosure of the child's or the parents' HIV status, competing family demands, fluctuating care arrangements and broader structural factors such as entrenched poverty or alternative beliefs about HIV's aetiology and treatment. Thus, many children are "falling through the gaps" because their access to testing and care is mediated by guardians who appear unable or unwilling to facilitate it. These children are likely to suffer treatment failure or death due to their caregivers' recalcitrance. This Commentary presents three cases from paediatric HIV services in Zimbabwe that highlight the complexities facing health care providers in providing HIV testing and care to children, and discusses the implications as a child's rights issue requiring both legal and programmatic responses. The cases provide examples of how disagreements between family members about appropriate care, conflicts between a child and caregiver and religious objections to medical treatment interrupt children's engagement with HIV services. In all three cases, no social or legal mechanisms were in place for health staff to intervene and prevent "loss to follow up." We suggest that conceptualizing this as a child's rights issue may be a useful way to raise the debate and move towards improved treatment access. Our cases reflect policy failure to facilitate access to children's HIV testing and treatment, and are likely to be similar across international settings. We propose sharing experiences and encouraging dialogue between health practitioners and global advocates for children's right to health to raise awareness that children are the bearers of rights even if they lack legal capacity, and that the failure of either the state or their caregiver to facilitate access to care is in fact a rights violation.

Gendered Empowerment and HIV Prevention: Policy and Programmatic Pathways to Success in the MENA Region

PubMed Central

Dworkin, Shari L.; Kambou, Sarah Degnan; Sutherland, Carla; Moalla, Khadija; Kapoor, Archana

2011-01-01

Although HIV in the Middle East and North Africa is currently characterized as a low seroprevalence epidemic, there are numerous factors that are present in the region that could prevent—or exacerbate—the epidemic. The time to invest substantially in prevention—and gender-specific prevention in particular—is now. Given that most policy makers do not make gender-specific plans as epidemics progress, our research team—which draws upon expertise from both within and outside the region—worked together to make programmatic and policy suggestions in the Middle East and North Africa region in 5 key areas: (1) gender-specific and gender transformative HIV prevention interventions; (2) access to quality education and improvements in life skills and sex education; (3) economic empowerment; (4) property rights; and (5) antiviolence. In short, this work builds upon many ongoing efforts in the region and elucidates some of the links between gendered empowerment and health outcomes around the world, particularly HIV and AIDS. PMID:19553778

Gendered empowerment and HIV prevention: policy and programmatic pathways to success in the MENA region.

PubMed

Dworkin, Shari L; Kambou, Sarah Degnan; Sutherland, Carla; Moalla, Khadija; Kapoor, Archana

2009-07-01

Although HIV in the Middle East and North Africa is currently characterized as a low seroprevalence epidemic, there are numerous factors that are present in the region that could prevent-or exacerbate-the epidemic. The time to invest substantially in prevention-and gender-specific prevention in particular-is now. Given that most policy makers do not make gender-specific plans as epidemics progress, our research team-which draws upon expertise from both within and outside the region-worked together to make programmatic and policy suggestions in the Middle East and North Africa region in 5 key areas: (1) gender-specific and gender transformative HIV prevention interventions; (2) access to quality education and improvements in life skills and sex education; (3) economic empowerment; (4) property rights; and (5) antiviolence. In short, this work builds upon many ongoing efforts in the region and elucidates some of the links between gendered empowerment and health outcomes around the world, particularly HIV and AIDS.

Introduction: the realities of antiretroviral therapy rollout: overcoming challenges to successful programmatic implementation.

PubMed

Ojikutu, Bisola

2007-12-01

In 2006, 2 million human immunodeficiency virus (HIV)-infected people living in low- to middle-income countries were receiving antiretroviral therapy (ART). Although this is an improvement over previous years, significant operational challenges have inhibited progress toward universal access to HIV care and treatment. Despite these challenges, the intense efforts focused on addressing the HIV epidemic present an opportunity for overall health systems improvement in developing nations. In October 2006, Harvard University's Centers for AIDS Research, the Nelson Mandela School of Medicine, the Department of Health of KwaZulu-Natal, and the Medical Research Council of South Africa held a conference entitled "The Realities of Antiretroviral Therapy Rollout: Challenges to Successful Programmatic Implementation" in Durban, South Africa. The goal of the meeting was to bring together international and local leadership, including policy makers, health care workers, and funders, to propose an agenda that would address the challenges to more expeditious provision of HIV care and treatment in resource-limited settings.

BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

PubMed

Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

2015-06-02

Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

Telemetry and Communication IP Video Player

NASA Technical Reports Server (NTRS)

OFarrell, Zachary L.

2011-01-01

Aegis Video Player is the name of the video over IP system for the Telemetry and Communications group of the Launch Services Program. Aegis' purpose is to display video streamed over a network connection to be viewed during launches. To accomplish this task, a VLC ActiveX plug-in was used in C# to provide the basic capabilities of video streaming. The program was then customized to be used during launches. The VLC plug-in can be configured programmatically to display a single stream, but for this project multiple streams needed to be accessed. To accomplish this, an easy to use, informative menu system was added to the program to enable users to quickly switch between videos. Other features were added to make the player more useful, such as watching multiple videos and watching a video in full screen.

Programmatic Integration of Cyber into the Institutional Domain of Leader Development

DTIC Science & Technology

2015-06-12

tl·~’! [_;l"t.t\\li.’t’’ clc•;.,.~nl~ (If Lit:."’ (".(lt:tbiru::i nc:~!; tc"l:rt Oil L~\\C lol:"H.lf·l"t\\ h;~:tlt· fi. t·ld \\o:;jtl!:, ~:i..:lulut~·d...its information capabilities. The use of government informat ion systems and access to government networks is a revocable privilege, not a right

[Access barriers to comprehensive care for people affected by tuberculosis and human immunodeficiency virus coinfection in Peru, 2010-2015].

PubMed

García-Fernández, Lisset; Benites, Carlos; Huamán, Byelca

2017-05-25

Identify the programmatic barriers that hinder access to comprehensive care of patients with tuberculosis and human immunodeficiency virus (TB/HIV) coinfection. This is a mixed-method study. Qualitative research was conducted via in-depth interviews with key actors and the quantitative component involved cross-sectional descriptive analysis of programmatic data from 2010-2015 on tuberculosis and HIV programs at health facilities in the cities of Lima and Iquitos. Twenty-two key actors in seven establishments were interviewed. The identified barriers were: little or no coordination between tuberculosis and HIV teams, separate management of tuberculosis and HIV cases at different levels of care, insufficient financing, limited or poorly trained human resources, and lack of an integrated information system. It was found that HIV screening in TB patients increased (from 18.8% in 2011 to 95.2% in 2015), isoniazid coverage of HIV patients declined (from 62% to 9%), and the proportion of deaths among TB/HIV coinfection cases averaged 20%. There is poor coordination between HIV and TB health strategies. Management of TB/HIV coinfection is fragmented into different levels of care, which has an impact on comprehensive patient care. As a result of this research, a technical document was prepared to establish joint procedures that should be implemented to improve comprehensive care of TB/HIV coinfection.

Shared Medical Imaging Repositories.

PubMed

Lebre, Rui; Bastião, Luís; Costa, Carlos

2018-01-01

This article describes the implementation of a solution for the integration of ownership concept and access control over medical imaging resources, making possible the centralization of multiple instances of repositories. The proposed architecture allows the association of permissions to repository resources and delegation of rights to third entities. It includes a programmatic interface for management of proposed services, made available through web services, with the ability to create, read, update and remove all components resulting from the architecture. The resulting work is a role-based access control mechanism that was integrated with Dicoogle Open-Source Project. The solution has several application scenarios like, for instance, collaborative platforms for research and tele-radiology services deployed at Cloud.

ACHP | News | St. Elizabeths Programmatic Agreement Signed

Science.gov Websites

Search skip specific nav links Home arrow News arrow St. Elizabeths Programmatic Agreement Signed St . Elizabeths Programmatic Agreement Signed December 9, 2008-- The General Services Administration (GSA), the ), and the Department of Homeland Security (DHS) executed a Programmatic Agreement (PA) for the

Perspectives in Peer Programs. Volume 28, Number 1, Winter 2018

ERIC Educational Resources Information Center

Tindall, Judith, Ed.; Black, David R., Ed.; Routson, Sue, Ed.

2018-01-01

This issue of "Perspectives in Peer Programs," the official journal of the National Association of Peer Program Professionals (NAPP), includes: (1) Introduction to this Issue on NAPPP Programmatic Standards Checklist, Programmatic Standards, Ethics, and Rubric; (2) NAPPP Programmatic Standards Checklist; (3) NAPPP Programmatic Standards;…

75 FR 78980 - Notice of Availability of the Draft Programmatic Environmental Impact Statement for Solar Energy...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

...] Notice of Availability of the Draft Programmatic Environmental Impact Statement for Solar Energy... Draft Programmatic Environmental Impact Statement (EIS) for Solar Energy Development in Six Southwestern... preferred method of commenting. Mail: Addressed to: Solar Energy Draft Programmatic EIS, Argonne National...

ACHP | News | Nationwide Programmatic Agreement Streamlines 106 Process for

Science.gov Websites

Publications Search skip specific nav links Home arrow News arrow Nationwide Programmatic Agreement Streamlines 106 Process for NPS Nationwide Programmatic Agreement Streamlines 106 Process for NPS Pursuant to Service (NPS) on November 14, 2008, executed a nationwide Programmatic Agreement (PA) with the Advisory

77 FR 36998 - Notice of Availability of a Draft Programmatic Environmental Assessment for Office of Coast...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-20

... Draft Programmatic Environmental Assessment for Office of Coast Survey Hydrographic Survey Projects... Programmatic Environmental Assessment; Request for comments. SUMMARY: NOAA's Office of Coast Survey (OCS) seeks comment on a draft programmatic environmental assessment (PEA) of the hydrographic surveys and related...

75 FR 38822 - Notice of Intent To Prepare Four Programmatic Environmental Impact Statements for the Northern...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-06

... Four Programmatic Environmental Impact Statements for the Northern Border Between the United States and...: Notice of Intent to Prepare Programmatic Environmental Impact Statements; Request for Comments; and... four Programmatic Environmental Impact Statements (PEISs) to identify and assess potential impacts upon...

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

Health-Seeking Challenges Among Homeless Youth

PubMed Central

Hudson, Angela L.; Nyamathi, Adeline; Greengold, Barbara; Slagle, Alexandra; Koniak-Griffin, Deborah; Khalilifard, Farinaz; Getzoff, Daniel

2010-01-01

Background Approximately 1.5 to 2 million homeless young persons live on the streets in the United States. With the current economic situation, research is needed on quality of services geared toward homeless young adults. Objectives The objective of this study was to explore homeless young adults' perspectives on barriers and facilitators of health-care-seeking behavior and their perspectives on improving existing programs for homeless persons. Methods This article is a descriptive qualitative study using focus groups, with a purposeful sample of 24 homeless drug-using young adults. Results Identified themes were failing access to care based on perceived structural barriers (limited clinic sites, limited hours of operation, priority health conditions, and long wait times) and social barriers (perception of discrimination by uncaring professionals, law enforcement, and society in general). Discussion Results provide insight into programmatic and agency resources that facilitate health-seeking behaviors among homeless young adults and include implications for more research with providers of homeless health and social services. PMID:20404776

Identifying components for programmatic latent tuberculosis infection control in the European Union

PubMed Central

Sandgren, Andreas; Vonk Noordegraaf-Schouten, Jannigje M; Oordt-Speets, Anouk M; van Kessel, Gerarda B; de Vlas, Sake J; van der Werf, Marieke J

2016-01-01

Individuals with latent tuberculosis infection (LTBI) are the reservoir of Mycobacterium tuberculosis in a population and as long as this reservoir exists, elimination of tuberculosis (TB) will not be feasible. In 2013, the European Centre for Disease Prevention and Control (ECDC) started an assessment of benefits and risks of introducing programmatic LTBI control, with the aim of providing guidance on how to incorporate LTBI control into national TB strategies in European Union/European Economic Area (EU/EEA) Member States and candidate countries. In a first step, experts from the Member States, candidate countries, and international and national organisations were consulted on the components of programmatic LTBI control that should be considered and evaluated in literature reviews, mathematical models and cost-effectiveness studies. This was done through a questionnaire and two interactive discussion rounds. The main components identified were identification and targeting of risk groups, determinants of LTBI and progression to active TB, optimal diagnostic tests for LTBI, effective preventive treatment regimens, and to explore the potential for combining LTBI control with other health programmes. Political commitment, a solid healthcare infrastructure, and favourable economic situation in specific countries were identified as essential to facilitate the implementation of programmatic LTBI control. PMID:27589214

Opting in and Creating Demand: Why Young People Choose to Teach Mathematics to Each Other

NASA Astrophysics Data System (ADS)

Tucker-Raymond, Eli; Lewis, Naama; Moses, Maisha; Milner, Chad

2016-12-01

Access to science, technology, engineering, and mathematics fields serves as a key entry point to economic mobility and civic enfranchisement. Such access must take seriously the intellectual power of the knowledge and practices of non-dominant youth. In our case, this has meant to shift epistemic authority in mathematics from academic institutions to young people themselves. This article is about why high school-aged students, from underrepresented groups, choose to participate in an out-of-school time program in which they teach younger children in the domains of mathematics and computer science. It argues for programmatic principles based on access, identity engagement, relationship building, and connections to community to support underrepresented youth as learners, teachers, leaders, and organizers in mathematics-related activities using game design as the focus of activity.

76 FR 36097 - Notice of Intent To Prepare a Programmatic Environmental Impact Statement for the U.S. Department...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-21

... DEPARTMENT OF ENERGY Notice of Intent To Prepare a Programmatic Environmental Impact Statement for...: Notice of intent to prepare a programmatic environmental impact statement for the DOE Uranium Leasing Program. SUMMARY: DOE announces its intent to prepare a Programmatic Environmental Impact Statement (PEIS...

DASTCOM5: A Portable and Current Database of Asteroid and Comet Orbit Solutions

NASA Astrophysics Data System (ADS)

Giorgini, Jon D.; Chamberlin, Alan B.

2014-11-01

A portable direct-access database containing all NASA/JPL asteroid and comet orbit solutions, with the software to access it, is available for download (ftp://ssd.jpl.nasa.gov/pub/xfr/dastcom5.zip; unzip -ao dastcom5.zip). DASTCOM5 contains the latest heliocentric IAU76/J2000 ecliptic osculating orbital elements for all known asteroids and comets as determined by a least-squares best-fit to ground-based optical, spacecraft, and radar astrometric measurements. Other physical, dynamical, and covariance parameters are included when known. A total of 142 parameters per object are supported within DASTCOM5. This information is suitable for initializing high-precision numerical integrations, assessing orbit geometry, computing trajectory uncertainties, visual magnitude, and summarizing physical characteristics of the body. The DASTCOM5 distribution is updated as often as hourly to include newly discovered objects or orbit solution updates. It includes an ASCII index of objects that supports look-ups based on name, current or past designation, SPK ID, MPC packed-designations, or record number. DASTCOM5 is the database used by the NASA/JPL Horizons ephemeris system. It is a subset exported from a larger MySQL-based relational Small-Body Database ("SBDB") maintained at JPL. The DASTCOM5 distribution is intended for programmers comfortable with UNIX/LINUX/MacOSX command-line usage who need to develop stand-alone applications. The goal of the implementation is to provide small, fast, portable, and flexibly programmatic access to JPL comet and asteroid orbit solutions. The supplied software library, examples, and application programs have been verified under gfortran, Lahey, Intel, and Sun 32/64-bit Linux/UNIX FORTRAN compilers. A command-line tool ("dxlook") is provided to enable database access from shell or script environments.

77 FR 10803 - Intent of Preparation of a Programmatic Environmental Assessment, To Open a Public Scoping Period...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-23

... Preparation of a Programmatic Environmental Assessment, To Open a Public Scoping Period, and To Conduct Public... Intent of Preparation of a Programmatic Environmental Assessment, to Open a Public Scoping Period, and to...), of the U.S. Department of Transportation (U.S. DOT), will prepare a Programmatic Environmental...

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

PubMed

Smelter, Andrey; Moseley, Hunter N B

2018-01-01

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific 'mwTab' flat file format. In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in 'mwTab' formatted files, we implemented a Python library and package. This Python package, named 'mwtab', is a parser for the domain-specific 'mwTab' flat file format, which provides facilities for reading, accessing, and writing 'mwTab' formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given 'mwTab' formatted file. In order to develop the 'mwtab' package we used the official 'mwTab' format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator. The 'mwtab' package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating 'mwTab' formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, 'pythonic' access and manipulation of data and metadata. Also, the package provides facilities to convert 'mwTab' files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The 'mwtab' package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between 'mwTab' and JSONized formats in raw text and a variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

Validation of Structures in the Protein Data Bank.

PubMed

Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M S; Gutmanas, Aleksandras; Westbrook, John D; Yang, Huanwang; Feng, Zukang; Baskaran, Kumaran; Berrisford, John M; Hudson, Brian P; Ikegawa, Yasuyo; Kobayashi, Naohiro; Lawson, Catherine L; Mading, Steve; Mak, Lora; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Peisach, Ezra; Sahni, Gaurav; Sekharan, Monica R; Sen, Sanchayita; Shao, Chenghua; Smart, Oliver S; Ulrich, Eldon L; Yamashita, Reiko; Quesada, Martha; Young, Jasmine Y; Nakamura, Haruki; Markley, John L; Berman, Helen M; Burley, Stephen K; Velankar, Sameer; Kleywegt, Gerard J

2017-12-05

The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The maximum contraceptive prevalence ‘demand curve’: guiding discussions on programmatic investments

PubMed Central

Weinberger, Michelle; Sonneveldt, Emily; Stover, John

2017-01-01

Most frameworks for family planning include both access and demand interventions. Understanding how these two are linked and when each should be prioritized is difficult. The maximum contraceptive prevalence ‘demand curve’ was created based on a relationship between the modern contraceptive prevalence rate (mCPR) and mean ideal number of children to allow for a quantitative assessment of the balance between access and demand interventions. The curve represents the maximum mCPR that is likely to be seen given fertility intentions and related norms and constructs that influence contraceptive use. The gap between a country’s mCPR and this maximum is referred to as the ‘potential use gap.’ This concept can be used by countries to prioritize access investments where the gap is large, and discuss implications for future contraceptive use where the gap is small. It is also used within the FP Goals model to ensure mCPR growth from access interventions does not exceed available demand. PMID:29355228

The Ensembl REST API: Ensembl Data for Any Language

PubMed Central

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R. S.; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. Availability and implementation: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. Contact: ayates@ebi.ac.uk or flicek@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25236461

Linking Sexual and Reproductive Health and Rights and HIV Services for Young People: The Link Up Project.

PubMed

Stackpool-Moore, Lucy; Bajpai, Divya; Caswell, Georgina; Crone, Tyler; Dewar, Fleur; Gray, Greg; Kyendikuwa, Allen; Mellin, Julie; Miller, Andrew; Morgan, Felicity; Orza, Luisa; Stevenson, Jacqui; Westerhof, Nienke; Wong, Felicia; Yam, Eileen; Zieman, Brady

2017-02-01

Sexual health and access to services are a pressing need for young people. This article introduces Link Up, a 3-year project in three African and two Asian countries, to enable and scale up access to integrated HIV services and sexual and reproductive health and rights for marginalized young people. The young people we worked with in this project included young men who have sex with men, young sex workers, young people who use drugs, young transgender people, young homeless people, and other vulnerable young people. The research and programmatic activities of Link Up, as illustrated in this Supplement, have highlighted the importance of recognizing and engaging with diversity among young people to improve access to services and outcomes protecting their health and human rights. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Barriers to Modern Contraceptive Use in Kinshasa, DRC.

PubMed

Muanda, Mbadu; Gahungu Ndongo, Parfait; Taub, Leah D; Bertrand, Jane T

2016-01-01

Recent research from Kinshasa, DRC, has shown that only one in five married women uses modern contraception; over one quarter have an unmet need for family planning; and almost 400 health facilities across Kinshasa report that they provide modern contraception. This study addresses the question: with reasonable physical access and relatively high unmet need, why is modern contraceptive prevalence so low? To this end, the research team conducted 6 focus groups of women (non-users of any method, users of traditional methods, and users of modern methods) and 4 of husbands (of users of traditional methods and in non-user unions) in health zones with relatively strong physical access to FP services. Five key barriers emerged from the focus group discussions: fear of side effects (especially sterility), costs of the method, sociocultural norms (especially the dominant position of the male in family decision-making), pressure from family members to avoid modern contraception, and lack of information/misinformation. These findings are very similar to those from 12 other studies of sociocultural barriers to family planning in sub-Saharan Africa. Moreover, they have strong programmatic implications for the training of FP workers to counsel future clients and for the content of behavior change communication interventions.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

Chemical Transformation System: Cloud Based ...

EPA Pesticide Factsheets

Integrated Environmental Modeling (IEM) systems that account for the fate/transport of organics frequently require physicochemical properties as well as transformation products. A myriad of chemical property databases exist but these can be difficult to access and often do not contain the proprietary chemicals that environmental regulators must consider. We are building the Chemical Transformation System (CTS) to facilitate model parameterization and analysis. CTS integrates a number of physicochemical property calculators into the system including EPI Suite, SPARC, TEST and ChemAxon. The calculators are heterogeneous in their scientific methodologies, technology implementations and deployment stacks. CTS also includes a chemical transformation processing engine that has been loaded with reaction libraries for human biotransformation, abiotic reduction and abiotic hydrolysis. CTS implements a common interface for the disparate calculators accepting molecular identifiers (SMILES, IUPAC, CAS#, user-drawn molecule) before submission for processing. To make the system as accessible as possible and provide a consistent programmatic interface, we wrapped the calculators in a standardized RESTful Application Programming Interface (API) which makes it capable of servicing a much broader spectrum of clients without constraints to interoperability such as operating system or programming language. CTS is hosted in a shared cloud environment, the Quantitative Environmental

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of RESTful services and map-based user interface tools for access and delivery of data and metadata from the Marine-Geo Digital Library

NASA Astrophysics Data System (ADS)

Morton, J. J.; Ferrini, V. L.

2015-12-01

The Marine Geoscience Data System (MGDS, www.marine-geo.org) operates an interactive digital data repository and metadata catalog that provides access to a variety of marine geology and geophysical data from throughout the global oceans. Its Marine-Geo Digital Library includes common marine geophysical data types and supporting data and metadata, as well as complementary long-tail data. The Digital Library also includes community data collections and custom data portals for the GeoPRISMS, MARGINS and Ridge2000 programs, for active source reflection data (Academic Seismic Portal), and for marine data acquired by the US Antarctic Program (Antarctic and Southern Ocean Data Portal). Ensuring that these data are discoverable not only through our own interfaces but also through standards-compliant web services is critical for enabling investigators to find data of interest.Over the past two years, MGDS has developed several new RESTful web services that enable programmatic access to metadata and data holdings. These web services are compliant with the EarthCube GeoWS Building Blocks specifications and are currently used to drive our own user interfaces. New web applications have also been deployed to provide a more intuitive user experience for searching, accessing and browsing metadata and data. Our new map-based search interface combines components of the Google Maps API with our web services for dynamic searching and exploration of geospatially constrained data sets. Direct introspection of nearly all data formats for hundreds of thousands of data files curated in the Marine-Geo Digital Library has allowed for precise geographic bounds, which allow geographic searches to an extent not previously possible. All MGDS map interfaces utilize the web services of the Global Multi-Resolution Topography (GMRT) synthesis for displaying global basemap imagery and for dynamically provide depth values at the cursor location.

TMFoldWeb: a web server for predicting transmembrane protein fold class.

PubMed

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

Design and Execution of make-like, distributed Analyses based on Spotify’s Pipelining Package Luigi

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, B.; Fischer, R.; Rieger, M.

2017-10-01

In high-energy particle physics, workflow management systems are primarily used as tailored solutions in dedicated areas such as Monte Carlo production. However, physicists performing data analyses are usually required to steer their individual workflows manually which is time-consuming and often leads to undocumented relations between particular workloads. We present a generic analysis design pattern that copes with the sophisticated demands of end-to-end HEP analyses and provides a make-like execution system. It is based on the open-source pipelining package Luigi which was developed at Spotify and enables the definition of arbitrary workloads, so-called Tasks, and the dependencies between them in a lightweight and scalable structure. Further features are multi-user support, automated dependency resolution and error handling, central scheduling, and status visualization in the web. In addition to already built-in features for remote jobs and file systems like Hadoop and HDFS, we added support for WLCG infrastructure such as LSF and CREAM job submission, as well as remote file access through the Grid File Access Library. Furthermore, we implemented automated resubmission functionality, software sandboxing, and a command line interface with auto-completion for a convenient working environment. For the implementation of a t \\overline{{{t}}} H cross section measurement, we created a generic Python interface that provides programmatic access to all external information such as datasets, physics processes, statistical models, and additional files and values. In summary, the setup enables the execution of the entire analysis in a parallelized and distributed fashion with a single command.

The Future of Opioid Agonist Therapies in Ukraine: a Qualitative Assessment of Multilevel Barriers and Ways Forward to Promote Retention in Treatment

PubMed Central

Bojko, Martha J.; Mazhnaya, Alyona; Marcus, Ruthanne; Makarenko, Iuliia; Islam, Zahedul; Filippovych, Sergey; Dvoriak, Sergii; Altice, Frederick L.

2016-01-01

Opioid agonist therapies (OAT) to treat opioid addiction in people who inject drugs (PWID) began in Ukraine in 2004. Scale-up of OAT, however, has been hampered by both low enrollment and high attrition. To better understand the factors influencing OAT retention among PWID in Ukraine, qualitative data from 199 PWIDs were collected during 25 focus groups conducted in five Ukrainian cities from February-April 2013. The experiences of PWID who were currently or previously on OAT or currently trying to access OAT were analyzed to identify entry and retention barriers encountered. Transcribed data were analyzed using a grounded theory approach. Individual beliefs about OAT, particularly misaligned treatment goals between clients and providers, influenced PWID's treatment seeking behaviors. Multiple programmatic and structural issues, including inconvenient hours and treatment site locations, complicated dosing regimens, inflexible medication dispensing guidelines, and mistreatment by clinic and medical staff also strongly influenced OAT retention. Findings suggest the need for both programmatic and policy-level structural changes such as revising legal regulations covering OAT dispensing, formalizing prescription dosing policies and making OAT more available through other sites, including primary care settings as a way to improve treatment retention. Quality improvement interventions that target treatment settings could also be deployed to overcome healthcare delivery barriers. Additional patient education and medical professional development around establishing realistic treatment goals as well as community awareness campaigns that address the myths and fears associated with OAT can be leveraged to overcome individual, family and community-level barriers. PMID:27211995

The Future of Opioid Agonist Therapies in Ukraine: A Qualitative Assessment of Multilevel Barriers and Ways Forward to Promote Retention in Treatment.

PubMed

Bojko, Martha J; Mazhnaya, Alyona; Marcus, Ruthanne; Makarenko, Iuliia; Islam, Zahedul; Filippovych, Sergey; Dvoriak, Sergii; Altice, Frederick L

2016-07-01

Opioid agonist therapies (OAT) to treat opioid addiction in people who inject drugs (PWID) began in Ukraine in 2004. Scale-up of OAT, however, has been hampered by both low enrollment and high attrition. To better understand the factors influencing OAT retention among PWID in Ukraine, qualitative data from 199 PWIDs were collected during 25 focus groups conducted in five Ukrainian cities from February to April 2013. The experiences of PWID who were currently or previously on OAT or currently trying to access OAT were analyzed to identify entry and retention barriers encountered. Transcribed data were analyzed using a grounded theory approach. Individual beliefs about OAT, particularly misaligned treatment goals between clients and providers, influenced PWID's treatment seeking behaviors. Multiple programmatic and structural issues, including inconvenient hours and treatment site locations, complicated dosing regimens, inflexible medication dispensing guidelines, and mistreatment by clinic and medical staff also strongly influenced OAT retention. Findings suggest the need for both programmatic and policy-level structural changes such as revising legal regulations covering OAT dispensing, formalizing prescription dosing policies and making OAT more available through other sites, including primary care settings as a way to improve treatment retention. Quality improvement interventions that target treatment settings could also be deployed to overcome healthcare delivery barriers. Additional patient education and medical professional development around establishing realistic treatment goals as well as community awareness campaigns that address the myths and fears associated with OAT can be leveraged to overcome individual, family and community-level barriers. Copyright © 2016 Elsevier Inc. All rights reserved.

AOP Wiki Version 2.0

EPA Science Inventory

Version 2.0 of the AOP-Wiki was released on December 4, 2016. This was a major upgrade and should provide a better user experience. It fixes a number of bugs with the previous version, provides a more streamlined user interface, and sets the stage for providing more programmatic...

76 FR 50744 - Notice To Announce the Award of an Urgent Single-Source Grant to Survivors of Torture...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-16

... United States. SOTI is well positioned to provide medical, psychological, social, and legal services to... network of pro bono service providers and possesses the clinical and programmatic expertise to serve...

76 FR 61295 - Programmatic Environmental Assessment

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-04

...-1608] Programmatic Environmental Assessment AGENCY: Federal Communications Commission. ACTION: Proposed... time to file comments in response to a draft programmatic environmental assessment (PEA) of the Antenna Structure Registration (ASR) program. The purpose of the PEA is to evaluate the potential environmental...

Geographic Access Modeling of Emergency Obstetric and Neonatal Care in Kigoma Region, Tanzania: Transportation Schemes and Programmatic Implications.

PubMed

Chen, Yi No; Schmitz, Michelle M; Serbanescu, Florina; Dynes, Michelle M; Maro, Godson; Kramer, Michael R

2017-09-27

Access to transportation is vital to reducing the travel time to emergency obstetric and neonatal care (EmONC) for managing complications and preventing adverse maternal and neonatal outcomes. This study examines the distribution of travel times to EmONC in Kigoma Region, Tanzania, using various transportation schemes, to estimate the proportion of live births (a proxy indicator of women needing delivery care) with poor geographic access to EmONC services. The 2014 Reproductive Health Survey of Kigoma Region identified 4 primary means of transportation used to travel to health facilities: walking, cycling, motorcycle, and 4-wheeled motor vehicle. A raster-based travel time model was used to map the 2-hour travel time catchment for each mode of transportation. Live birth density distributions were aggregated by travel time catchments, and by administrative council, to estimate the proportion of births with poor access. Of all live births in Kigoma Region, 13% occurred in areas where women can reach EmONC facilities within 2 hours on foot, 33% in areas that can be reached within 2 hours only by motorized vehicles, and 32% where it is impossible to reach EmONC facilities within 2 hours. Over 50% of births in 3 of the 8 administrative councils had poor estimated access. In half the councils, births with poor access could be reduced to no higher than 12% if all female residents had access to motorized vehicles. Significant differences in geographic access to EmONC in Kigoma Region, Tanzania, were observed both by location and by primary transportation type. As most of the population may only have good EmONC access when using mechanized or motorized vehicles, bicycles and motorcycles should be incorporated into the health transportation strategy. Collaboration between private transportation sectors and obstetric service providers could improve access to EmONC services among most populations. In areas where residents may not access EmONC facilities within 2 hours regardless of the type of transportation used, upgrading EmONC capacity among nearby non-EmONC facilities may be required to improve accessibility. © Chen Y, Schmitz, et al.

Geographic Access Modeling of Emergency Obstetric and Neonatal Care in Kigoma Region, Tanzania: Transportation Schemes and Programmatic Implications

PubMed Central

Chen, Yi No; Schmitz, Michelle M; Serbanescu, Florina; Dynes, Michelle M; Maro, Godson; Kramer, Michael R

2017-01-01

ABSTRACT Background: Access to transportation is vital to reducing the travel time to emergency obstetric and neonatal care (EmONC) for managing complications and preventing adverse maternal and neonatal outcomes. This study examines the distribution of travel times to EmONC in Kigoma Region, Tanzania, using various transportation schemes, to estimate the proportion of live births (a proxy indicator of women needing delivery care) with poor geographic access to EmONC services. Methods: The 2014 Reproductive Health Survey of Kigoma Region identified 4 primary means of transportation used to travel to health facilities: walking, cycling, motorcycle, and 4-wheeled motor vehicle. A raster-based travel time model was used to map the 2-hour travel time catchment for each mode of transportation. Live birth density distributions were aggregated by travel time catchments, and by administrative council, to estimate the proportion of births with poor access. Results: Of all live births in Kigoma Region, 13% occurred in areas where women can reach EmONC facilities within 2 hours on foot, 33% in areas that can be reached within 2 hours only by motorized vehicles, and 32% where it is impossible to reach EmONC facilities within 2 hours. Over 50% of births in 3 of the 8 administrative councils had poor estimated access. In half the councils, births with poor access could be reduced to no higher than 12% if all female residents had access to motorized vehicles. Conclusion: Significant differences in geographic access to EmONC in Kigoma Region, Tanzania, were observed both by location and by primary transportation type. As most of the population may only have good EmONC access when using mechanized or motorized vehicles, bicycles and motorcycles should be incorporated into the health transportation strategy. Collaboration between private transportation sectors and obstetric service providers could improve access to EmONC services among most populations. In areas where residents may not access EmONC facilities within 2 hours regardless of the type of transportation used, upgrading EmONC capacity among nearby non-EmONC facilities may be required to improve accessibility. PMID:28839113

Summary of Session Activities: Coordination of Environmental Education Projects

NASA Technical Reports Server (NTRS)

Keeler, Michael; Mahootian, Farzad

1995-01-01

In this session, we address four fundamental questions related to environmental fields with emphasis on education. These are: What are the goals, objectives, and practical opportunities for coordinating our projects? How can we improve awareness of, interest in, access to, and support the products of our work? How can we build relationships between projects for scientific, educational, technical, and programmatic benefit? How can we evaluate the effectiveness of coordination efforts. In this working session, we produced answers to these questions and proposed a structure for future collaboration.

NRCS Prototype Programmatic Agreement FAQ

Science.gov Websites

Search Frequently Asked Questions regarding the Natural Resources Conservation Service Prototype Programmatic Agreement The Advisory Council on Historic Preservation (ACHP) recently designated a prototype programmatic agreement (PPA) for the United States Department of Agriculture, Natural Resources Conservation

Programmatic Instructional Development.

ERIC Educational Resources Information Center

Schutz, Richard E.

Programmatic instructional development refers to sequenced and coordinated efforts to produce effective instructional programs which cumulate over time and which attain outcomes that would be impossible under non-programmatic projects. As practiced at the Southwest Regional Laboratory (SWRL), it involves the combined efforts of specialists from…

Validated environmental and physiological data from the CELSS Breadboard Projects Biomass Production Chamber. BWT931 (Wheat cv. Yecora Rojo)

NASA Technical Reports Server (NTRS)

Stutte, G. W.; Mackowiak, C. L.; Markwell, G. A.; Wheeler, R. M.; Sager, J. C.

1993-01-01

This KSC database is being made available to the scientific research community to facilitate the development of crop development models, to test monitoring and control strategies, and to identify environmental limitations in crop production systems. The KSC validated dataset consists of 17 parameters necessary to maintain bioregenerative life support functions: water purification, CO2 removal, O2 production, and biomass production. The data are available on disk as either a DATABASE SUBSET (one week of 5-minute data) or DATABASE SUMMARY (daily averages of parameters). Online access to the VALIDATED DATABASE will be made available to institutions with specific programmatic requirements. Availability and access to the KSC validated database are subject to approval and limitations implicit in KSC computer security policies.

WIWS: a protein structure bioinformatics Web service collection.

PubMed

Hekkelman, M L; Te Beek, T A H; Pettifer, S R; Thorne, D; Attwood, T K; Vriend, G

2010-07-01

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

BioModels Database: a repository of mathematical models of biological processes.

PubMed

Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

2013-01-01

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

The CMS DBS query language

NASA Astrophysics Data System (ADS)

Kuznetsov, Valentin; Riley, Daniel; Afaq, Anzar; Sekhri, Vijay; Guo, Yuyi; Lueking, Lee

2010-04-01

The CMS experiment has implemented a flexible and powerful system enabling users to find data within the CMS physics data catalog. The Dataset Bookkeeping Service (DBS) comprises a database and the services used to store and access metadata related to CMS physics data. To this, we have added a generalized query system in addition to the existing web and programmatic interfaces to the DBS. This query system is based on a query language that hides the complexity of the underlying database structure by discovering the join conditions between database tables. This provides a way of querying the system that is simple and straightforward for CMS data managers and physicists to use without requiring knowledge of the database tables or keys. The DBS Query Language uses the ANTLR tool to build the input query parser and tokenizer, followed by a query builder that uses a graph representation of the DBS schema to construct the SQL query sent to underlying database. We will describe the design of the query system, provide details of the language components and overview of how this component fits into the overall data discovery system architecture.

Systems Engineering Design Via Experimental Operation Research: Complex Organizational Metric for Programmatic Risk Environments (COMPRE)

NASA Technical Reports Server (NTRS)

Mog, Robert A.

1999-01-01

Unique and innovative graph theory, neural network, organizational modeling, and genetic algorithms are applied to the design and evolution of programmatic and organizational architectures. Graph theory representations of programs and organizations increase modeling capabilities and flexibility, while illuminating preferable programmatic/organizational design features. Treating programs and organizations as neural networks results in better system synthesis, and more robust data modeling. Organizational modeling using covariance structures enhances the determination of organizational risk factors. Genetic algorithms improve programmatic evolution characteristics, while shedding light on rulebase requirements for achieving specified technological readiness levels, given budget and schedule resources. This program of research improves the robustness and verifiability of systems synthesis tools, including the Complex Organizational Metric for Programmatic Risk Environments (COMPRE).

7 CFR 3570.85 - Programmatic changes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 15 2010-01-01 2010-01-01 false Programmatic changes. 3570.85 Section 3570.85... AGRICULTURE COMMUNITY PROGRAMS Community Facilities Grant Program § 3570.85 Programmatic changes. The grantee shall obtain prior Agency approval for any change to the objectives of the approved project. (For...

75 FR 21650 - Coral Reef Restoration Plan, Draft Programmatic Environmental Impact Statement, Biscayne National...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

... DEPARTMENT OF THE INTERIOR National Park Service Coral Reef Restoration Plan, Draft Programmatic... Coral Reef Restoration Plan, Biscayne National Park. SUMMARY: Pursuant to the National Environmental... availability of a Draft Programmatic Environmental Impact Statement (DEIS) for the Coral Reef Restoration Plan...

78 FR 5403 - Fisheries of the Caribbean, Gulf, and South Atlantic; Aquaculture

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-25

...: Supplemental Notice of Intent (NOI) to prepare a supplement to the final programmatic environmental impact... programmatic environmental impact statement (PEIS) was published on September 12, 2008. On June 26, 2009, a... includes a final programmatic environmental impact statement (FPEIS), an initial regulatory flexibility...

7 CFR 25.623 - Programmatic changes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 1 2012-01-01 2012-01-01 false Programmatic changes. 25.623 Section 25.623 Agriculture Office of the Secretary of Agriculture RURAL EMPOWERMENT ZONES AND ENTERPRISE COMMUNITIES Round II and Round IIS Grants § 25.623 Programmatic changes. Prior approval from USDA is required for all...

7 CFR 25.623 - Programmatic changes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 1 2014-01-01 2014-01-01 false Programmatic changes. 25.623 Section 25.623 Agriculture Office of the Secretary of Agriculture RURAL EMPOWERMENT ZONES AND ENTERPRISE COMMUNITIES Round II and Round IIS Grants § 25.623 Programmatic changes. Prior approval from USDA is required for all...

7 CFR 25.623 - Programmatic changes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 1 2013-01-01 2013-01-01 false Programmatic changes. 25.623 Section 25.623 Agriculture Office of the Secretary of Agriculture RURAL EMPOWERMENT ZONES AND ENTERPRISE COMMUNITIES Round II and Round IIS Grants § 25.623 Programmatic changes. Prior approval from USDA is required for all...

7 CFR 25.623 - Programmatic changes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 1 2010-01-01 2010-01-01 false Programmatic changes. 25.623 Section 25.623 Agriculture Office of the Secretary of Agriculture RURAL EMPOWERMENT ZONES AND ENTERPRISE COMMUNITIES Round II and Round IIS Grants § 25.623 Programmatic changes. Prior approval from USDA is required for all...

7 CFR 25.623 - Programmatic changes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 1 2011-01-01 2011-01-01 false Programmatic changes. 25.623 Section 25.623 Agriculture Office of the Secretary of Agriculture RURAL EMPOWERMENT ZONES AND ENTERPRISE COMMUNITIES Round II and Round IIS Grants § 25.623 Programmatic changes. Prior approval from USDA is required for all...

Structural barriers to comprehensive, coordinated HIV care: geographic accessibility in the US South.

PubMed

Kimmel, April D; Masiano, Steven P; Bono, Rose S; Martin, Erika G; Belgrave, Faye Z; Adimora, Adaora A; Dahman, Bassam; Galadima, Hadiza; Sabik, Lindsay M

2018-05-30

Structural barriers to HIV care are particularly challenging in the US South, which has higher HIV diagnosis rates, poverty, uninsurance, HIV stigma, and rurality, and fewer comprehensive public health programs versus other US regions. Focusing on one structural barrier, we examined geographic accessibility to comprehensive, coordinated HIV care (HIVCCC) in the US South. We integrated publicly available data to study travel time to HIVCCC in 16 Southern states and District of Columbia. We geocoded HIVCCC service locations and estimated drive time between the population-weighted county centroid and closest HIVCCC facility. We evaluated drive time in aggregate, and by county-level HIV prevalence quintile, urbanicity, and race/ethnicity. Optimal drive time was ≤30 min, a common primary care accessibility threshold. We identified 228 service locations providing HIVCCC across 1422 Southern counties, with median drive time to care of 70 min (IQR 64 min). For 368 counties in the top HIV prevalence quintile, median drive time is 50 min (IQR 61 min), exceeding 60 min in over one-third of these counties. Among counties in the top HIV prevalence quintile, drive time to care is six-folder higher for rural versus super-urban counties. Counties in the top HIV prevalence quintiles for non-Hispanic Blacks and for Hispanics have >50% longer drive time to care versus for non-Hispanic Whites. Including another potential care source-publicly-funded health centers serving low-income populations-could double the number of high-HIV burden counties with drive time ≤30 min, representing nearly 35,000 additional people living with HIV with accessible HIVCCC. Geographic accessibility to HIVCCC is inadequate in the US South, even in high HIV burden areas, and geographic and racial/ethnic disparities exist. Structural factors, such as geographic accessibility to care, may drive disparities in health outcomes. Further research on programmatic policies, and evidence-based alternative HIV care delivery models improving access to care, is critical.

The TDR: A Repository for Long Term Storage of Geophysical Data and Metadata

NASA Astrophysics Data System (ADS)

Wilson, A.; Baltzer, T.; Caron, J.

2006-12-01

For many years Unidata has provided easy, low cost data access to universities and research labs. Historically Unidata technology provided access to data in near real time. In recent years Unidata has additionally turned to providing middleware to serve longer term data and associated metadata via its THREDDS technology, the most recent offering being the THREDDS Data Server (TDS). The TDS provides middleware for metadata access and management, OPeNDAP data access, and integration with the Unidata Integrated Data Viewer (IDV), among other benefits. The TDS was designed to support rolling archives of data, that is, data that exist only for a relatively short, predefined time window. Now we are creating an addition to the TDS, called the THREDDS Data Repository (TDR), which allows users to store and retrieve data and other objects for an arbitrarily long time period. Data in the TDR can also be served by the TDS. The TDR performs important functions of locating storage for the data, moving the data to and from the repository, assigning unique identifiers, and generating metadata. The TDR framework supports pluggable components that allow tailoring an implementation for a particular application. The Linked Environments for Atmospheric Discovery (LEAD) project provides an excellent use case for the TDR. LEAD is a multi-institutional Large Information Technology Research project funded by the National Science Foundation (NSF). The goal of LEAD is to create a framework based on Grid and Web Services to support mesoscale meteorology research and education. This includes capabilities such as launching forecast models, mining data for meteorological phenomena, and dynamic workflows that are automatically reconfigurable in response to changing weather. LEAD presents unique challenges in managing and storing large data volumes from real-time observational systems as well as data that are dynamically created during the execution of adaptive workflows. For example, in order to support storage of many large data products, the LEAD implementation of the TDR will provide a variety of data movement options, including gridftp. It will have a web service interface and will be callable programmatically as well as via interactive user requests. Future plans include the use of a mass storage device to provide robust long term storage. This talk will present the current state of the TDR effort.

Getting the Most out of PubChem for Virtual Screening

PubMed Central

Kim, Sunghwan

2016-01-01

Introduction With the emergence of the “big data” era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge. Areas covered This article provides an overview of how PubChem’s data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery. Expert opinion PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area. PMID:27454129

Cost of providing injectable contraceptives through a community-based social marketing program in Tigray, Ethiopia.

PubMed

Prata, Ndola; Downing, Janelle; Bell, Suzanne; Weidert, Karen; Godefay, Hagos; Gessessew, Amanuel

2016-06-01

To provide a cost analysis of an injectable contraceptive program combining community-based distribution and social marketing in Tigray, Ethiopia. We conducted a cost analysis, modeling the costs and programmatic outcomes of the program's initial implementation in 3 districts of Tigray, Ethiopia. Costs were estimated from a review of program expense records, invoices, and interviews with health workers. Programmatic outcomes include number of injections and couple-year of protection (CYP) provided. We performed a sensitivity analysis on the average number of injections provided per month by community health workers (CHWs), the cost of the commodity, and the number of CHWs trained. The average programmatic CYP was US $17.91 for all districts with a substantial range from US $15.48-38.09 per CYP across districts. Direct service cost was estimated at US $2.96 per CYP. The cost per CYP was slightly sensitive to the commodity cost of the injectable contraceptives and the number of CHWs. The capacity of each CHW, measured by the number of injections sold, was a key input that drove the cost per CYP of this model. With a direct service cost of US $2.96 per CYP, this study demonstrates the potential cost of community-based social marketing programs of injectable contraceptives. The findings suggest that the cost of social marketing of contraceptives in rural communities is comparable to other delivery mechanisms with regards to CYP, but further research is needed to determine the full impact and cost-effectiveness for women and communities beyond what is measured in CYP. Copyright © 2016 Elsevier Inc. All rights reserved.

Socioeconomic and programmatic determinants of renewal of membership in a voluntary micro health insurance scheme: evidence from Chakaria, Bangladesh.

PubMed

Iqbal, Mohammad; Chowdhury, Asiful Haidar; Mahmood, Shehrin Shaila; Mia, Mohammad Nahid; Hanifi, S M A; Bhuiya, Abbas

2017-01-01

Out-of-pocket (OOP) healthcare expenditure is a major obstacle for achieving universal health coverage in low-income countries including Bangladesh. Sixty-three percent of the USD 27 annual per-capita healthcare expenditure in Bangladesh comes from individuals' pockets. Although health insurance is a financial tool for reducing OOP, use of such tools in Bangladesh has been limited to some small-scale voluntary micro health insurance (MHI) schemes run by non-governmental organizations (NGO). The MHI, however, can orient people on health insurance concept and provide learning for product development, implementation, barriers to enrolment, membership renewal, and other operational challenges and solutions. Keeping this in mind, icddr,b in 2012 initiated a pilot MHI, Amader Shasthya, in Chakaria, Bangladesh. This paper explores the determinants of membership renewal in this scheme, which is a perpetual challenge for MHI. Identify socioeconomic and programmatic determinants and their effects on membership renewal in a voluntary MHI scheme. Data came from the online management information system of the scheme and Health and Demographic Surveillance System of Chakaria, covering the period February 2012-May 2015. Association between renewal and independent variables was examined using cross-tabular and logistic regression analyses. Nearly 20% of households in the catchment area ever enroled in the scheme, and 38% renewed membership over the initial 3 years of operation. Frequency of consultation with healthcare providers, benefits received, proximity of member's residence to health facility, socioeconomic status, educational level, and age of the household head showed significant positive association with renewal of membership. Villagers' enrolment in the scheme indicated that even in poor economic and literacy conditions people can be motivated to enrol in insurance schemes. Degree of service utilization and benefits received can greatly enhance the probability of membership renewal, which can be ensured with good quality of services and ease of access.

78 FR 4135 - Programmatic Environmental Impact Statement for the Training Mission and Mission Support...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-18

... DEPARTMENT OF DEFENSE Department of the Army Programmatic Environmental Impact Statement for the... Programmatic Environmental Impact Statement (PEIS) to evaluate the impacts of current and future training and... (NEPA) to evaluate the environmental impacts of proposed alternatives for implementing the training and...

32 CFR 651.27 - Programmatic NEPA analyses.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 4 2010-07-01 2010-07-01 true Programmatic NEPA analyses. 651.27 Section 651.27 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) ENVIRONMENTAL QUALITY ENVIRONMENTAL ANALYSIS OF ARMY ACTIONS (AR 200-2) Records and Documents § 651.27 Programmatic NEPA analyses...

76 FR 61120 - Notice of Intent To Prepare a Programmatic Environmental Assessment for Proposed Network...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-03

... POSTAL SERVICE Notice of Intent To Prepare a Programmatic Environmental Assessment for Proposed... of intent to prepare a Programmatic Environmental Assessment; Notice of Public Scoping Period. SUMMARY: To comply with the requirements of the National Environmental Policy Act (NEPA), the Postal...

78 FR 23926 - Extension of the Public Comment Period for the Draft Uranium Leasing Program Programmatic...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-23

... DEPARTMENT OF ENERGY Extension of the Public Comment Period for the Draft Uranium Leasing Program Programmatic Environmental Impact Statement AGENCY: Department of Energy. ACTION: Extension of the public... the Draft Uranium Leasing Program Programmatic Environmental Impact Statement (Draft ULP PEIS, DOE/EIS...

76 FR 77244 - Renewal of Information Collection; OMB Control Number 1040-0001, DOI Programmatic Clearance for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-12

... Number 1040-0001, DOI Programmatic Clearance for Customer Satisfaction Surveys AGENCY: Department of [email protected] . Reference ``DOI Programmatic Clearance for Customer Satisfaction Surveys'' in your email... public accountability by promoting a new focus on results, service quality, and customer satisfaction...

40 CFR 35.102 - Definitions of terms.

Code of Federal Regulations, 2010 CFR

2010-07-01

... that is related to an environmental or programmatic goal or objective. Outcomes must be quantitative... will be produced or provided over a period of time or by a specified date. Outputs may be quantitative...

40 CFR 35.102 - Definitions of terms.

Code of Federal Regulations, 2012 CFR

2012-07-01

... that is related to an environmental or programmatic goal or objective. Outcomes must be quantitative... will be produced or provided over a period of time or by a specified date. Outputs may be quantitative...

40 CFR 35.102 - Definitions of terms.

Code of Federal Regulations, 2014 CFR

2014-07-01

... that is related to an environmental or programmatic goal or objective. Outcomes must be quantitative... will be produced or provided over a period of time or by a specified date. Outputs may be quantitative...

40 CFR 35.102 - Definitions of terms.

Code of Federal Regulations, 2011 CFR

2011-07-01

... that is related to an environmental or programmatic goal or objective. Outcomes must be quantitative... will be produced or provided over a period of time or by a specified date. Outputs may be quantitative...

40 CFR 35.102 - Definitions of terms.

Code of Federal Regulations, 2013 CFR

2013-07-01

... that is related to an environmental or programmatic goal or objective. Outcomes must be quantitative... will be produced or provided over a period of time or by a specified date. Outputs may be quantitative...

Managing Challenges in a Multi Contractor Project

NASA Technical Reports Server (NTRS)

King, Ron

2011-01-01

The presentation provides a project description, describes the integrated product team, and review project challenges. The challenges include programmatic, technical, basic drop tests, heavy drop tests, C-17 envelope expansion, and Ares I-X.

Empowering communities and strengthening systems to improve transgender health: outcomes from the Pehchan programme in India

PubMed Central

Shaikh, Simran; Mburu, Gitau; Arumugam, Viswanathan; Mattipalli, Naveen; Aher, Abhina; Mehta, Sonal; Robertson, James

2016-01-01

Introduction Transgender populations face inequalities in access to HIV, health and social services. In addition, there is limited documentation of models for providing appropriately tailored services and social support for transgender populations in low- and middle-income countries. This paper presents outcomes of the Global Fund-supported Pehchan programme, which aimed to strengthen community systems and provide HIV, health, legal and social services to transgender communities across 18 Indian states through a rights-based empowerment approach. Methods We used a pre- and post-intervention cross-sectional survey design with retrospective analysis of programmatic data. Using stratified sampling, we identified 268 transgender participants in six Indian states from a total of 48,280 transgender people served by Pehchan through 186 community-based organizations. We quantified the impact of interventions by comparing baseline and end line indicators of accessed health social and legal services. We also assessed end line self-efficacy and collective action with regard to social support networks. Results There were significant increases in community-based demand and use of tailored health, legal, social and psychological services over the time of the Pehchan programme. We report significant increases in access to condoms (12.5%, p<0.001) and condom use at last anal sex with both regular (18.1%, p<0.001) and casual (8.1%, p<0.001) male partners. Access to HIV outreach education and testing and counselling services significantly increased (20.10%, p<0.001; 33.7%, p<0.001). In addition, significant increases in access to emergency crisis response (19.7%, p<0.001), legal support (26.8%, p<0.001) and mental health services (33.0%, p<0.001) were identified. Finally, we note that the Pehchan programme successfully provided a platform for the formation, collectivization and visibility of peer support groups. Conclusions The Pehchan programme's community involvement, rights-based collectivization and gender-affirming approaches significantly improved both demand and access to tailored HIV, health and social services for transgender individuals across India. Furthermore, the Pehchan programme successfully fostered both self-efficacy and collective identity and served as a model for addressing the unique health needs of transgender communities. Continued strengthening of health, social and community systems to better respond to the unique needs of transgender communities is needed in order to sustain these gains. PMID:27431474

Empowering communities and strengthening systems to improve transgender health: outcomes from the Pehchan programme in India.

PubMed

Shaikh, Simran; Mburu, Gitau; Arumugam, Viswanathan; Mattipalli, Naveen; Aher, Abhina; Mehta, Sonal; Robertson, James

2016-01-01

Transgender populations face inequalities in access to HIV, health and social services. In addition, there is limited documentation of models for providing appropriately tailored services and social support for transgender populations in low- and middle-income countries. This paper presents outcomes of the Global Fund-supported Pehchan programme, which aimed to strengthen community systems and provide HIV, health, legal and social services to transgender communities across 18 Indian states through a rights-based empowerment approach. We used a pre- and post-intervention cross-sectional survey design with retrospective analysis of programmatic data. Using stratified sampling, we identified 268 transgender participants in six Indian states from a total of 48,280 transgender people served by Pehchan through 186 community-based organizations. We quantified the impact of interventions by comparing baseline and end line indicators of accessed health social and legal services. We also assessed end line self-efficacy and collective action with regard to social support networks. There were significant increases in community-based demand and use of tailored health, legal, social and psychological services over the time of the Pehchan programme. We report significant increases in access to condoms (12.5%, p<0.001) and condom use at last anal sex with both regular (18.1%, p<0.001) and casual (8.1%, p<0.001) male partners. Access to HIV outreach education and testing and counselling services significantly increased (20.10%, p<0.001; 33.7%, p<0.001). In addition, significant increases in access to emergency crisis response (19.7%, p<0.001), legal support (26.8%, p<0.001) and mental health services (33.0%, p<0.001) were identified. Finally, we note that the Pehchan programme successfully provided a platform for the formation, collectivization and visibility of peer support groups. The Pehchan programme's community involvement, rights-based collectivization and gender-affirming approaches significantly improved both demand and access to tailored HIV, health and social services for transgender individuals across India. Furthermore, the Pehchan programme successfully fostered both self-efficacy and collective identity and served as a model for addressing the unique health needs of transgender communities. Continued strengthening of health, social and community systems to better respond to the unique needs of transgender communities is needed in order to sustain these gains.

32 CFR 37.900 - May I tell a participant that information in financial and programmatic reports will not be...

Code of Federal Regulations, 2010 CFR

2010-07-01

... financial and programmatic reports will not be publicly disclosed? 37.900 Section 37.900 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DoD GRANT AND AGREEMENT REGULATIONS TECHNOLOGY INVESTMENT AGREEMENTS Award Terms Related to Other Administrative Matters Financial and Programmatic...

10 CFR 1021.330 - Programmatic (including site-wide) NEPA documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... prepare a programmatic EIS or EA (40 CFR 1502.4). DOE may also prepare a programmatic EIS or EA at any... Analysis, DOE shall determine whether the existing EIS remains adequate or whether to prepare a new site-wide EIS or supplement the existing EIS, as appropriate. The determination and supporting analysis...

75 FR 22589 - Cordova Electric Cooperative, Inc.; Notice of Proposed Restricted Service List for a Programmatic...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-29

... a Programmatic Agreement for Managing Properties Included in or Eligible for Inclusion in the... a programmatic agreement for managing properties included in, or eligible for inclusion in, the... person on the official service list for the above-captioned proceeding may request inclusion on the...

78 FR 11632 - Notice of Availability for the Draft Finding of No Significant Impact and Final Programmatic...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-19

... Significant Impact and Final Programmatic Environmental Assessment for Army 2020 Force Structure Realignment... Significant Impact (FNSI) and final Programmatic Environmental Assessment (PEA) for Army 2020 force structure realignments that may occur from Fiscal Years (FYs) 2013-2020. The Army published the Notice of Availability of...

Spacelab Level 4 programmatic Implementation Assessment Study. Volume 3: Optimization and programmatics

NASA Technical Reports Server (NTRS)

1978-01-01

Alternate level 4 integration approaches were synthesized and evaluated to establish the most cost effective experiment integration approach. Program baseline system trade studies are described, as well as Spacelab equipment utilization. Programmatic analysis of the baseline program was evaluated; the 2/3 and 1/3 traffic models were also considered.

78 FR 33090 - Re-Opening of the Public Comment Period for the Draft Uranium Leasing Program Programmatic...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-03

... DEPARTMENT OF ENERGY Re-Opening of the Public Comment Period for the Draft Uranium Leasing Program Programmatic Environmental Impact Statement AGENCY: Department of Energy. ACTION: Re-opening of the public... the Draft Uranium Leasing Program Programmatic Environmental Impact Statement (Draft ULP PEIS, DOE/EIS...

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

PubMed

Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

2017-10-01

The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Achieving human and machine accessibility of cited data in scholarly publications

PubMed Central

Starr, Joan; Castro, Eleni; Crosas, Mercè; Dumontier, Michel; Downs, Robert R.; Duerr, Ruth; Haak, Laurel L.; Haendel, Melissa; Herman, Ivan; Hodson, Simon; Hourclé, Joe; Kratz, John Ernest; Lin, Jennifer; Nielsen, Lars Holm; Nurnberger, Amy; Proell, Stefan; Rauber, Andreas; Sacchi, Simone; Smith, Arthur; Taylor, Mike; Clark, Tim

2015-01-01

Reproducibility and reusability of research results is an important concern in scientific communication and science policy. A foundational element of reproducibility and reusability is the open and persistently available presentation of research data. However, many common approaches for primary data publication in use today do not achieve sufficient long-term robustness, openness, accessibility or uniformity. Nor do they permit comprehensive exploitation by modern Web technologies. This has led to several authoritative studies recommending uniform direct citation of data archived in persistent repositories. Data are to be considered as first-class scholarly objects, and treated similarly in many ways to cited and archived scientific and scholarly literature. Here we briefly review the most current and widely agreed set of principle-based recommendations for scholarly data citation, the Joint Declaration of Data Citation Principles (JDDCP). We then present a framework for operationalizing the JDDCP; and a set of initial recommendations on identifier schemes, identifier resolution behavior, required metadata elements, and best practices for realizing programmatic machine actionability of cited data. The main target audience for the common implementation guidelines in this article consists of publishers, scholarly organizations, and persistent data repositories, including technical staff members in these organizations. But ordinary researchers can also benefit from these recommendations. The guidance provided here is intended to help achieve widespread, uniform human and machine accessibility of deposited data, in support of significantly improved verification, validation, reproducibility and re-use of scholarly/scientific data. PMID:26167542

Achieving human and machine accessibility of cited data in scholarly publications.

PubMed

Starr, Joan; Castro, Eleni; Crosas, Mercè; Dumontier, Michel; Downs, Robert R; Duerr, Ruth; Haak, Laurel L; Haendel, Melissa; Herman, Ivan; Hodson, Simon; Hourclé, Joe; Kratz, John Ernest; Lin, Jennifer; Nielsen, Lars Holm; Nurnberger, Amy; Proell, Stefan; Rauber, Andreas; Sacchi, Simone; Smith, Arthur; Taylor, Mike; Clark, Tim

Reproducibility and reusability of research results is an important concern in scientific communication and science policy. A foundational element of reproducibility and reusability is the open and persistently available presentation of research data. However, many common approaches for primary data publication in use today do not achieve sufficient long-term robustness, openness, accessibility or uniformity. Nor do they permit comprehensive exploitation by modern Web technologies. This has led to several authoritative studies recommending uniform direct citation of data archived in persistent repositories. Data are to be considered as first-class scholarly objects, and treated similarly in many ways to cited and archived scientific and scholarly literature. Here we briefly review the most current and widely agreed set of principle-based recommendations for scholarly data citation, the Joint Declaration of Data Citation Principles (JDDCP). We then present a framework for operationalizing the JDDCP; and a set of initial recommendations on identifier schemes, identifier resolution behavior, required metadata elements, and best practices for realizing programmatic machine actionability of cited data. The main target audience for the common implementation guidelines in this article consists of publishers, scholarly organizations, and persistent data repositories, including technical staff members in these organizations. But ordinary researchers can also benefit from these recommendations. The guidance provided here is intended to help achieve widespread, uniform human and machine accessibility of deposited data, in support of significantly improved verification, validation, reproducibility and re-use of scholarly/scientific data.

Promotor(a)s, the organizations in which they work, and an emerging paradox: how organizational structure and scope impact promotor(a)s' work.

PubMed

May, Marlynn L; Contreras, Ricardo B

2007-07-01

To analyze how organizational structures and scope (geographic and programmatic) generate dissonance between the organization and its workers, creating a paradox with policy implications for access to health care in hard-to-reach populations. The workers are lay community health workers called promotor(a)s. The organizations are community based organizations in which the promotor(a)s work, either as volunteers, part-time or as full-time wage staff. Ethnographic study of 12 organizations and their promotor(a)s. Data gathering included interviews with organization directors, promotor(a)s, service providers working with the organizations, and community residents served by the organizations and workers. In addition, promotor(a)s were observed in the course of their work. Sampling was a non-probability, snowball procedure for identifying the organizations and the workers within them. A paradox is emerging between (a) promotor(a)s who perceive their work to be locally focused and tightly integrated with the communities they serve and live in, and (b) the employing organizations that are expanding in geographical and programmatic scope because the work promotor(a)s do is in increasing demand by agencies and funding sources external to the communities served. The paradox potentially threatens to undermine and transform the work and working environment of the promotor(a)s. The challenge is to find a balance that will sustain a workable and working relationship among the organization, the workers, and the communities served. Care is needed in setting out policies that translate the paradox into greater congruence among organization, workers and communities. Policy needs discussed focus on (a) worker training, (b) worker employment and deployment, and (c) funding source recognition of the paradox.

Development and use of the generic WHO/CDC logic model for vitamin and mineral interventions in public health programmes

PubMed Central

De-Regil, Luz Maria; Peña-Rosas, Juan Pablo; Flores-Ayala, Rafael; del Socorro Jefferds, Maria Elena

2015-01-01

Objective Nutrition interventions are critical to achieve the Millennium Development Goals; among them, micronutrient interventions are considered cost-effective and programmatically feasible to scale up, but there are limited tools to communicate the programme components and their relationships. The WHO/CDC (Centers for Disease Control and Prevention) logic model for micronutrient interventions in public health programmes is a useful resource for planning, implementation, monitoring and evaluation of these interventions, which depicts the programme theory and expected relationships between inputs and expected Millennium Development Goals. Design The model was developed by applying principles of programme evaluation, public health nutrition theory and programmatic expertise. The multifaceted and iterative structure validation included feedback from potential users and adaptation by national stakeholders involved in public health programmes' design and implementation. Results In addition to the inputs, main activity domains identified as essential for programme development, implementation and performance include: (i) policy; (ii) products and supply; (iii) delivery systems; (iv) quality control; and (v) behaviour change communication. Outputs encompass the access to and coverage of interventions. Outcomes include knowledge and appropriate use of the intervention, as well as effects on micronutrient intake, nutritional status and health of target populations, for ultimate achievement of the Millennium Development Goals. Conclusions The WHO/CDC logic model simplifies the process of developing a logic model by providing a tool that has identified high-priority areas and concepts that apply to virtually all public health micronutrient interventions. Countries can adapt it to their context in order to support programme design, implementation, monitoring and evaluation for the successful scale-up of nutrition interventions in public health. PMID:23507463

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

Developing the community empowered research training program: building research capacity for community-initiated and community-driven research.

PubMed

Kwon, Simona; Rideout, Catlin; Tseng, Winston; Islam, Nadia; Cook, Won Kim; Ro, Marguerite; Trinh-Shevrin, Chau

2012-01-01

Health promotion practice research conducted by or in partnership with community-based organizations (CBOs) serving Asian Americans, Native Hawaiians, and Pacific Islanders (AA and NHPI) can address health disparities. Few CBOs have the tools to integrate or initiate research into their programmatic agenda. The New York University (NYU) Center for the Study of Asian American Health (CSAAH) and the Asian & Pacific Islander American Health Forum (APIAHF) created a partnership with the goal to support CBO research infrastructure development by creating the Community Empowered Research Training (CERT) program. A survey was conducted and discussions held with CBO leaders representing AA and NHPI communities to inform the development of the CERT program. The majority of participants are engaged in service-related research and reported interest in building their research capacity. CBOs may require help reframing how data can be collected and used to better inform programmatic activities and to address health disparities facing AA and NHPI communities. CBOs possess both an interest in and access to local knowledge that can inform health priorities. Findings have been applied to the CERT program to build capacity to support community-initiated/driven research to address health disparities affecting AAs and NHPIs.

The Neotoma Paleoecology Database

NASA Astrophysics Data System (ADS)

Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

2015-12-01

The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community. Research is supported by NSF EAR-0622349.

Zero-gravity atmospheric Cloud Physics Experiment Laboratory; Programmatics report

NASA Technical Reports Server (NTRS)

1974-01-01

The programmatics effort included comprehensive analyses in four major areas: (1) work breakdown structure, (2) schedules, (3) costs, and (4) supporting research and technology. These analyses are discussed in detail in the following sections which identify and define the laboratory project development schedule, cost estimates, funding distributions and supporting research and technology requirements. All programmatics analyses are correlated among themselves and with the technical analyses by means of the work breakdown structure which serves as a common framework for program definition. In addition, the programmatic analyses reflect the results of analyses and plans for reliability, safety, test, and maintenance and refurbishment.

The post Challenger era Get Away Special program January 1992

NASA Technical Reports Server (NTRS)

Prouty, Clarke

1992-01-01

The Get Away Special (GAS) program is described in terms of the changes that have taken place in both NASA and the GAS itself. Attention is given to the relationships developed between NASA and GAS customers in the context of programmatic and technical issues. The background of the GAS program is outlined with reference given to policy publications, the design of the Flight Verification Payload, and the first GAS payload launched. A review process is described that facilitates the management of the payloads through flight certification. The GAS Bridge was developed to carry up to 12 payloads simultaneously, and the recent period of GAS inactivity is explained. A price increase is introduced for future GAS payloads with negotiable access to optional services, and the ease and accessibility of the GAS programs for private experiments is emphasized.

Creating the Southern Region 4-H Volunteer Advisory Group

ERIC Educational Resources Information Center

Culp, Ken, III; Edwards, Harriett C.; Jordan, Jenny W.

2014-01-01

The SR4-HVAG combines the efforts of states to provide quality educational programming for volunteers and Extension professionals using an advisory group system. An advisory group rather than a council was created because the group provides programmatic input rather than sets policy. The purposes of the SR4-HVAG are to: provide a mechanism for…

Using multi-disciplinary strategic master facilities planning for organizations experiencing programmatic re-direction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heubach, J.G.; Weimer, W.C.; Bruce, W.A.

Facility master planning is critical to the future productivity of a laboratory and the quality of worklife for the laboratory staff. For organizations undergoing programmatic re-direction, a master facility planning approach linked to the organization`s strategic planning process is even more important. Major changes in an organization such as programmatic re-direction can significantly impact a broad range of variables which exceed the expertise of traditional planning teams, e.g., capacity variability, work team organization, organizational culture, and work process simplification. By expanding the diversity of the participants of the planning team, there is a greater likelihood that a research organization`s scientific,more » organizational, economic, and employees` needs can be meshed in the strategic plan and facility plan. Recent recommendations from facility planners suggest drawing from diverse fields in building multi-disciplinary planning teams: Architecture, engineering, natural science, social psychology, and strategic planning (Gibson,1993). For organizations undergoing significant operational or culture change, the master facility planning team should also include members with expertise in organizational effectiveness, industrial engineering, human resources, and environmental psychology. A recent planning and design project provides an example which illustrates the use of an expanded multi-disciplinary team engaged in planning laboratory renovations for a research organization undergoing programmatic re-direction. The purpose of the proposed poster session is to present a multi-disciplinary master facility planning process linked to an organization`s strategic planning process or organizational strategies.« less

Improved Functionality and Curation Support in the ADS

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto; Kurtz, Michael J.; Henneken, Edwin A.; Grant, Carolyn S.; Thompson, Donna; Chyla, Roman; Holachek, Alexandra; Sudilovsky, Vladimir; Murray, Stephen S.

2015-01-01

In this poster we describe the developments of the new ADS platform over the past year, focusing on the functionality which improves its discovery and curation capabilities.The ADS Application Programming Interface (API) is being updated to support authenticated access to the entire suite of ADS services, in addition to the search functionality itself. This allows programmatic access to resources which are specific to a user or class of users.A new interface, built directly on top of the API, now provides a more intuitive search experience and takes into account the best practices in web usability and responsive design. The interface now incorporates in-line views of graphics from the AAS Astroexplorer and the ADS All-Sky Survey image collections.The ADS Private Libraries, first introduced over 10 years ago, are now being enhanced to allow the bookmarking, tagging and annotation of records of interest. In addition, libraries can be shared with one or more ADS users, providing an easy way to collaborate in the curation of lists of papers. A library can also be explicitly made public and shared at large via the publishing of its URL.In collaboration with the AAS, the ADS plans to support the adoption of ORCID identifiers by implementing a plugin which will simplify the import of papers in ORCID via a query to the ADS API. Deeper integration between the two systems will depend on available resources and feedback from the community.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

GIANT API: an application programming interface for functional genomics

PubMed Central

Roberts, Andrew M.; Wong, Aaron K.; Fisk, Ian; Troyanskaya, Olga G.

2016-01-01

GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

Advanced protein crystal growth programmatic sensitivity study

NASA Technical Reports Server (NTRS)

1992-01-01

The purpose of this study is to define the costs of various APCG (Advanced Protein Crystal Growth) program options and to determine the parameters which, if changed, impact the costs and goals of the programs and to what extent. This was accomplished by developing and evaluating several alternate programmatic scenarios for the microgravity Advanced Protein Crystal Growth program transitioning from the present shuttle activity to the man tended Space Station to the permanently manned Space Station. These scenarios include selected variations in such sensitivity parameters as development and operational costs, schedules, technology issues, and crystal growth methods. This final report provides information that will aid in planning the Advanced Protein Crystal Growth Program.

Overview of NASA's Pulsed Plasma Thruster Development Program

NASA Technical Reports Server (NTRS)

Pencil, Eric J.; Kamhawi, Hani; Arrington, Lynn A.

2004-01-01

NASA's Pulsed Plasma Thruster Program consists of flight demonstration experiments, base research, and development efforts being conducted through a combination of in-house work, contracts, and collaborative programs. The program receives sponsorship from Energetics Project, the New Millennium Program, and the Small Business Innovative Research Program. The Energetics Project sponsors basic and fundamental research to increase thruster life, improve thruster performance, and reduce system mass. The New Millennium Program sponsors the in-orbit operation of the Pulsed Plasma Thruster experiment on the Earth Observing 1 spacecraft. The Small Business Innovative Research Program sponsors the development of innovative diamond-film capacitors, piezoelectric ignitors, and advanced fuels. Programmatic background, recent technical accomplishments, and future activities for each programmatic element are provided.

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

PubMed

Jupp, Simon; Burdett, Tony; Welter, Danielle; Sarntivijai, Sirarat; Parkinson, Helen; Malone, James

2016-01-01

Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such experts. As requests for new terms are made, the need for expert ontologists represents a bottleneck in the development process. Furthermore, the ability to rigorously enforce ontology design patterns in large, collaboratively developed ontologies is difficult with existing ontology authoring software. We present Webulous, an application suite for supporting ontology creation by design patterns. Webulous provides infrastructure to specify templates for populating ontology design patterns that get transformed into OWL assertions in a target ontology. Webulous provides programmatic access to the template server and a client application has been developed for Google Sheets that allows templates to be loaded, populated and resubmitted to the Webulous server for processing. The development and delivery of ontologies to the community requires software support that goes beyond the ontology editor. Building ontologies by design patterns and providing simple mechanisms for the addition of new content helps reduce the overall cost and effort required to develop an ontology. The Webulous system provides support for this process and is used as part of the development of several ontologies at the European Bioinformatics Institute.

Community-based field implementation scenarios of a short message service reporting tool for lymphatic filariasis case estimates in Africa and Asia.

PubMed

Mableson, Hayley E; Martindale, Sarah; Stanton, Michelle C; Mackenzie, Charles; Kelly-Hope, Louise A

2017-01-01

Lymphatic filariasis (LF) is a neglected tropical disease (NTD) targeted for global elimination by 2020. Currently there is considerable international effort to scale-up morbidity management activities in endemic countries, however there remains a need for rapid, cost-effective methods and adaptable tools for obtaining estimates of people presenting with clinical manifestations of LF, namely lymphoedema and hydrocele. The mHealth tool ' MeasureSMS-Morbidity ' allows health workers in endemic areas to use their own mobile phones to send clinical information in a simple format using short message service (SMS). The experience gained through programmatic use of the tool in five endemic countries across a diversity of settings in Africa and Asia is used here to present implementation scenarios that are suitable for adapting the tool for use in a range of different programmatic, endemic, demographic and health system settings. A checklist of five key factors and sub-questions was used to determine and define specific community-based field implementation scenarios for using the MeasureSMS-Morbidity tool in a range of settings. These factors included: (I) tool feasibility (acceptability; community access and ownership); (II) LF endemicity (high; low prevalence); (III) population demography (urban; rural); (IV) health system structure (human resources; community access); and (V) integration with other diseases (co-endemicity). Based on experiences in Bangladesh, Ethiopia, Malawi, Nepal and Tanzania, four implementation scenarios were identified as suitable for using the MeasureSMS-Morbidity tool for searching and reporting LF clinical case data across a range of programmatic, endemic, demographic and health system settings. These include: (I) urban, high endemic setting with two-tier reporting; (II) rural, high endemic setting with one-tier reporting; (III) rural, high endemic setting with two-tier reporting; and (IV) low-endemic, urban and rural setting with one-tier reporting. A decision-making framework built from the key factors and questions, and the resulting four implementation scenarios is proposed as a means of using the MeasureSMS-Morbidity tool. This framework will help national LF programmes consider appropriate methods to implement a survey using this tool to improve estimates of the clinical burden of LF. Obtaining LF case estimates is a vital step towards the elimination of LF as a public health problem in endemic countries.

The Tips, Tricks, and Challenges of Teaching Undergraduate Kinesiology Students Research Methodology through a Programmatic Lens

ERIC Educational Resources Information Center

Beller, Jennifer M.

2013-01-01

This article describes a programmatic approach to undergraduate research (UGR) at Washington State University. In a programmatic approach, UGR is woven throughout the curriculum, with the expressed intent of producing undergraduate students who have at least a moderate ability to read, use, conduct, and present research. Washington State…

77 FR 5833 - Notice of Availability of the Draft Programmatic Environmental Impact Statement for Allocation of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... of the Draft Programmatic Environmental Impact Statement for Allocation of Oil Shale and Tar Sands... of Oil Shale and Tar Sands Resources on Lands Administered by the BLM in Colorado, Utah, and Wyoming... preferred method of commenting. Mail: Addressed to: Oil Shale and Tar Sands Resources Draft Programmatic EIS...

Fourth Generation Undersea Warfare: Getting C2 for Undersea Connectivity Right

DTIC Science & Technology

2013-06-01

information dominance (ID) will not be realized unless undersea connectivity issues are given the same priority as the vehicles and sensors themselves. Said another way, failure to establish an effective C2 architecture in this degraded and austere environment will be a de facto surrender to the adversary’s attempts to deny access. One way in which the U.S. Navy has moved forward to address this issue is by changing the programmatic organization that supports this vehicle and sensor integration. As Executive Agent for the Navy’s undersea connectivity efforts,

The transcription factor encyclopedia.

PubMed

Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A; Zhang, Xiao Yu Cindy; Dickman, Christopher T D; Fulton, Debra L; Lim, Jonathan S; Schnabl, Jake M; Ramos, Oscar H P; Vasseur-Cognet, Mireille; de Leeuw, Charles N; Simpson, Elizabeth M; Ryffel, Gerhart U; Lam, Eric W-F; Kist, Ralf; Wilson, Miranda S C; Marco-Ferreres, Raquel; Brosens, Jan J; Beccari, Leonardo L; Bovolenta, Paola; Benayoun, Bérénice A; Monteiro, Lara J; Schwenen, Helma D C; Grontved, Lars; Wederell, Elizabeth; Mandrup, Susanne; Veitia, Reiner A; Chakravarthy, Harini; Hoodless, Pamela A; Mancarelli, M Michela; Torbett, Bruce E; Banham, Alison H; Reddy, Sekhar P; Cullum, Rebecca L; Liedtke, Michaela; Tschan, Mario P; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J; Eijkelenboom, Astrid; Brown, Philip J; Laperrière, David; Leprince, Dominique; de Cristofaro, Tiziana; Prince, Kelly L; Putker, Marrit; del Peso, Luis; Camenisch, Gieri; Wenger, Roland H; Mikula, Michal; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J; Van Rechem, Capucine; Boulay, Gaylor; Olechnowicz, Sam W Z; Breslin, Mary B; Lan, Michael S; Nanan, Kyster K; Wegner, Michael; Hou, Juan; Mullen, Rachel D; Colvin, Stephanie C; Noy, Peter John; Webb, Carol F; Witek, Matthew E; Ferrell, Scott; Daniel, Juliet M; Park, Jason; Waldman, Scott A; Peet, Daniel J; Taggart, Michael; Jayaraman, Padma-Sheela; Karrich, Julien J; Blom, Bianca; Vesuna, Farhad; O'Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M; Woodcroft, Mark W; Hough, Margaret R; Chen, Edwin; Europe-Finner, G Nicholas; Karolczak-Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; LeBrun, David P; Biswal, Shyam; Harvey, Christopher J; DeBruyne, Jason P; Hogenesch, John B; Hevner, Robert F; Héligon, Christophe; Luo, Xin M; Blank, Marissa Cathleen; Millen, Kathleen Joyce; Sharlin, David S; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Elodie; Sladek, Frances M; Bradley, Philip H; Wasserman, Wyeth W

2012-01-01

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

COMS Day as a Communication Senior Capstone Team Project

ERIC Educational Resources Information Center

Ozley, Raymond R.; Wang, Tiffany R.; Ford, Sherry Greenwood; Hardig, Sally Bennett

2017-01-01

Courses: Senior Seminar. Objectives: (1) To provide graduating students a semester-long capstone experience where they can apply communication theories/skills in a professional context. (2) To create a capstone project that contributes to programmatic assessment.

76 FR 23613 - Draft Programmatic Environmental Assessment for Hazard Mitigation Safe Room Construction

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-27

... Emergency Management Agency (FEMA) may provide funding to eligible applicants for eligible, feasible, and... from hazards and their effects. One such activity is the construction and installation of safe rooms to...

Region 9 Tribal Clean Water Act Programs and Grants

EPA Pesticide Factsheets

EPA's Tribal Water Office in Region 9 manages all grants related to the Clean Water Act for over 100 federally recognized tribes and provides programmatic and technical assistance for water quality standards and CWA grant programs.

Biomass Feedstock and Conversion Supply System Design and Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobson, Jacob J.; Roni, Mohammad S.; Lamers, Patrick

Idaho National Laboratory (INL) supports the U.S. Department of Energy’s bioenergy research program. As part of the research program INL investigates the feedstock logistics economics and sustainability of these fuels. A series of reports were published between 2000 and 2013 to demonstrate the feedstock logistics cost. Those reports were tailored to specific feedstock and conversion process. Although those reports are different in terms of conversion, some of the process in the feedstock logistic are same for each conversion process. As a result, each report has similar information. A single report can be designed that could bring all commonality occurred inmore » the feedstock logistics process while discussing the feedstock logistics cost for different conversion process. Therefore, this report is designed in such a way that it can capture different feedstock logistics cost while eliminating the need of writing a conversion specific design report. Previous work established the current costs based on conventional equipment and processes. The 2012 programmatic target was to demonstrate a delivered biomass logistics cost of $55/dry ton for woody biomass delivered to fast pyrolysis conversion facility. The goal was achieved by applying field and process demonstration unit-scale data from harvest, collection, storage, preprocessing, handling, and transportation operations into INL’s biomass logistics model. The goal of the 2017 Design Case is to enable expansion of biofuels production beyond highly productive resource areas by breaking the reliance of cost-competitive biofuel production on a single, low-cost feedstock. The 2017 programmatic target is to supply feedstock to the conversion facility that meets the in-feed conversion process quality specifications at a total logistics cost of $80/dry T. The $80/dry T. target encompasses total delivered feedstock cost, including both grower payment and logistics costs, while meeting all conversion in-feed quality targets. The 2012 $55/dry T. programmatic target included only logistics costs with a limited focus on biomass quantity, quality and did not include a grower payment. The 2017 Design Case explores two approaches to addressing the logistics challenge: one is an agronomic solution based on blending and integrated landscape management and the second is a logistics solution based on distributed biomass preprocessing depots. The concept behind blended feedstocks and integrated landscape management is to gain access to more regional feedstock at lower access fees (i.e., grower payment) and to reduce preprocessing costs by blending high quality feedstocks with marginal quality feedstocks. Blending has been used in the grain industry for a long time; however, the concept of blended feedstocks in the biofuel industry is a relatively new concept. The blended feedstock strategy relies on the availability of multiple feedstock sources that are blended using a least-cost formulation within an economical supply radius, which, in turn, decreases the grower payment by reducing the amount of any single biomass. This report will introduce the concepts of blending and integrated landscape management and justify their importance in meeting the 2017 programmatic goals.« less

Space Station needs, attributes and architectural options, volume 2, book 3: Cost and programmatics

NASA Technical Reports Server (NTRS)

1983-01-01

The cost and programmatic considerations which integrate mission requirements and architectural options into a cohesive system for exploitation of space opportunities within affordable limits are discussed. The mission requirements, baseline architecture, a top level baseline schedule, and acquisition costs are summarized. The work breakdown structure (WBS) used to structure the program, and the WBS dictionary are included. The costing approach used, including the operation of the primary costing tool, the SPACE cost model are described. The rationale for the choice of cost estimating relationships is given and costs at the module level are shown. Detailed costs at the subsystem level are shown. The baseline schedule and annual funding profiles are provided. Alternate schedules are developed to provide different funding profiles. Alternate funding sources are discussed and foreign and contractor participation is outlined. The results of the benefit analysis are given and the accrued benefits deriving from an implemented space station program are outlined.

The patient perspective: utilizing focus groups to inform care coordination for high-risk medicaid populations.

PubMed

Sheff, Alex; Park, Elyse R; Neagle, Mary; Oreskovic, Nicolas M

2017-07-25

Care coordination programs for high-risk, high-cost patients are a critical component of population health management. These programs aim to improve outcomes and reduce costs and have proliferated over the last decade. Some programs, originally designed for Medicare patients, are now transitioning to also serve Medicaid populations. However, there are still gaps in the understanding of what barriers to care Medicaid patients experience, and what supports will be most effective for providing them care coordination. We conducted two focus groups (n = 13) and thematic analyses to assess the outcomes drivers and programmatic preferences of Medicaid patients enrolled in a high-risk care coordination program at a major academic medical center in Boston, MA. Two focus groups identified areas where care coordination efforts were having a positive impact, as well as areas of unmet needs among the Medicaid population. Six themes emerged from the focus groups that clustered in three groupings: In the first group (1) enrollment in an existing medical care coordination programs, and (2) provider communication largely presented as positive accounts of assistance, and good relationships with providers, though participants also pointed to areas where these efforts fell short. In the second group (3) trauma histories, (4) mental health challenges, and (5) executive function difficulties all presented challenges faced by high-risk Medicaid patients that would likely require redress through additional programmatic supports. Finally, in the third group, (6) peer-to-peer support tendencies among patients suggested an untapped resource for care coordination programs. Programs aimed at high-risk Medicaid patients will want to consider programmatic adjustments to attend to patient needs in five areas: (1) provider connection/care coordination, (2) trauma, (3) mental health, (4) executive function/paperwork and coaching support, and (5) peer-to-peer support.

Infrastructure for the life sciences: design and implementation of the UniProt website.

PubMed

Jain, Eric; Bairoch, Amos; Duvaud, Severine; Phan, Isabelle; Redaschi, Nicole; Suzek, Baris E; Martin, Maria J; McGarvey, Peter; Gasteiger, Elisabeth

2009-05-08

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website http://www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008. The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org. The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users.

The Open Data Repositorys Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

2015-01-01

Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

Research and Development Program Plan for the Center for Engineering Systems Advanced Research (CESAR)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weisbin, C.R.; Barhen, J.; Hamel, W.R.

1987-01-01

A general framework is provided for more detailed planning on an annual basis, both for DOE and for other sponsoring organizations. The charter for the overall intelligent machine research effort is presented along with programmatic and technological goals. A research implementation plan is provided through the FY 1989 horizon.

From Crayons to Perfume: Getting beyond Contrived Collegiality

ERIC Educational Resources Information Center

Beatty, Brenda

2011-01-01

Based on reflections from over a decade of research, scholarship, and programmatic applications, this article provides evidence of impact from the work of Professor Andy Hargreaves with a specific focus on his concept of contrived collegiality. Explorations into matters of emotion provided an entry point through which the author has addressed the…

History of Space Shuttle Rendezvous

NASA Technical Reports Server (NTRS)

Goodman, John L.

2011-01-01

This technical history is intended to provide a technical audience with an introduction to the rendezvous and proximity operations history of the Space Shuttle Program. It details the programmatic constraints and technical challenges encountered during shuttle development in the 1970s and over thirty years of shuttle missions. An overview of rendezvous and proximity operations on many shuttle missions is provided, as well as how some shuttle rendezvous and proximity operations systems and flight techniques evolved to meet new programmatic objectives. This revised edition provides additional information on Mercury, Gemini, Apollo, Skylab, and Apollo/Soyuz. Some chapters on the Space Shuttle have been updated and expanded. Four special focus chapters have been added to provide more detailed information on shuttle rendezvous. A chapter on the STS-39 mission of April/May 1991 describes the most complex deploy/retrieve mission flown by the shuttle. Another chapter focuses on the Hubble Space Telescope servicing missions. A third chapter gives the reader a detailed look at the February 2010 STS-130 mission to the International Space Station. The fourth chapter answers the question why rendezvous was not completely automated on the Gemini, Apollo, and Space Shuttle vehicles.

A successful programmatic structure and strategies to attract and educate students in earth and environmental sciences: an example from the University of Delaware, USA

NASA Astrophysics Data System (ADS)

Levia, Delphis

2013-04-01

The achievement of sustainable use of our natural world is one of the major issues confronting humankind today. Environmental issues are inherently complex and difficult to resolve. Successful resolution of our most pressing environmental problems, such as climate change and ocean acidification, will require well-trained earth and environmental scientists that think critically in a multi-dimensional framework at variable spatial and temporal scales. This begs the question as to how we can both attract and successfully educate students in such a way that will permit them to tackle the multitude of environmental problems currently facing society. This poster details one way to successfully attract and train students in an interdisciplinary environmental education framework by sharing: (1) some of the successful strategies and programmatic structure of the University of Delaware's undergraduate environmental programs that have grown over 60% in two years after a major programmatic revision; and (2) the current round of programmatic revisions that will complete the strategic planning process.* The interdisciplinary environmental education program at the University of Delaware has a strong programmatic core that provides students with the requisite quantitative training and field experience to solve complicated environmental issues. At the same time, the environmental program includes the social, political, and economic contexts of environmental issues. Together, these two parts of the core best equip students to mitigate environmental problems. Following a strategic planning effort, the University of Delaware is building upon past successes in training environmental scientists and managers by further reformulating its environmental programs to leverage the power of theme-based learning which complements the programmatic core in such a way to teach problem-solving skills. This poster details the multidimensional nature of the University of Delaware's environmental programs and the revised program structure that seeks to strike a balance between quantitative science, adaptive management, and solutions oriented thinking. ------------------------ *Please note that the planning process for the environmental programs was and is the collective effort of many dedicated people. Current members of the advisory Environmental Council include Drs. Delphis Levia (Program Director), Nancy Targett (Dean and Council Chair), Frank Newton, Tracy Deliberty, Tom Sims, John Madsen, Paul Imhoff, Jan Johnson, Jerry Kauffman, Murray Johnston.

Final Programmatic Environment Impact Statement for Commercial Reentry Vehicles

DOT National Transportation Integrated Search

1992-05-28

To ensure that space launch services provided by private enterprises are : consistent with national security and foreign policy interests of the U.S., : and do not jeopardize public safety and safety of property, the Department of : Transportation (D...

A Case Study: Service Delivery and Parents with Disabilities.

ERIC Educational Resources Information Center

Pomerantz, Phyllis; And Others

1990-01-01

Describes a home-based intervention program that provided time-intensive, supervised, paraprofessional services to a family in which parents and infant had serious disabilities. Programmatic needs and delivery of services to disabled parents and families are discussed. (NH)

FY2014 National Clean Diesel Funding Assistance (Diesel Emissions Reduction Act) Programmatic Terms and Conditions

EPA Pesticide Factsheets

EPA will provide substantial involvement in the form of technical assistance, development ofoutputs, and oversight. EPA and the recipient in program content, review of project progress, and quantification and reporting of results.

Space construction system analysis. Part 2: Cost and programmatics

NASA Technical Reports Server (NTRS)

Vonflue, F. W.; Cooper, W.

1980-01-01

Cost and programmatic elements of the space construction systems analysis study are discussed. The programmatic aspects of the ETVP program define a comprehensive plan for the development of a space platform, the construction system, and the space shuttle operations/logistics requirements. The cost analysis identified significant items of cost on ETVP development, ground, and flight segments, and detailed the items of space construction equipment and operations.

Spoiled breast milk and bad water; local understandings of diarrhea causes and prevention in rural Sierra Leone.

PubMed

McMahon, Shannon A; George, Asha S; Yumkella, Fatu; Diaz, Theresa

2013-12-13

Globally, diarrhea remains a leading killer of young children. In Sierra Leone, one in seven children die before their fifth birthday and diarrhea is a leading cause. Studies that emphasize the demand-side of health interventions -- how caregivers understand causation and prevention of diarrhea -- have been neglected in research and programming. We undertook applied qualitative research including 68 in-depth interviews and 36 focus group discussions with mothers, fathers and older female caretakers to examine the causes and prevention of childhood diarrhea in villages near and far from health facilities across four rural districts. Verbal consent was obtained. Respondents reported multiple, co-existing descriptions of causation including: contaminated water and difficulties accessing clean water; exposure to an unclean environment and poor food hygiene; contaminated breast milk due to sexual intercourse, overheated breast milk or bodily maternal conditions such as menstruation or pregnancy; and dietary imbalances and curses. Respondents rarely discussed the role of open defecation or the importance of handwashing with soap in preventing diarrhea. Categorizing behaviors as beneficial, harmful, non-existent or benign enables tailored programmatic recommendations. For example, respondents recognized the value of clean water and we correspondingly recommend interventions that reinforce consumption of and access to clean water. Second, respondents report denying "contaminated" breast milk to breastfeeding children. This is a harmful practice that merits attention. Third, the role of open defecation and poor hygiene in causing diarrhea is less understood and warrants introduction or clarification. Finally, the role of exposed feet or curses in causing diarrhea is relatively benign and does not necessitate programmatic attention. Further research supportive of communication and social mobilization strategies building on these findings is required to ensure that improved understanding regarding diarrhea causation translates into improved diarrhea prevention.

Spoiled breast milk and bad water; local understandings of diarrhea causes and prevention in rural Sierra Leone

PubMed Central

2013-01-01

Background Globally, diarrhea remains a leading killer of young children. In Sierra Leone, one in seven children die before their fifth birthday and diarrhea is a leading cause. Studies that emphasize the demand-side of health interventions -- how caregivers understand causation and prevention of diarrhea -- have been neglected in research and programming. Methods We undertook applied qualitative research including 68 in-depth interviews and 36 focus group discussions with mothers, fathers and older female caretakers to examine the causes and prevention of childhood diarrhea in villages near and far from health facilities across four rural districts. Verbal consent was obtained. Results Respondents reported multiple, co-existing descriptions of causation including: contaminated water and difficulties accessing clean water; exposure to an unclean environment and poor food hygiene; contaminated breast milk due to sexual intercourse, overheated breast milk or bodily maternal conditions such as menstruation or pregnancy; and dietary imbalances and curses. Respondents rarely discussed the role of open defecation or the importance of handwashing with soap in preventing diarrhea. Conclusions Categorizing behaviors as beneficial, harmful, non-existent or benign enables tailored programmatic recommendations. For example, respondents recognized the value of clean water and we correspondingly recommend interventions that reinforce consumption of and access to clean water. Second, respondents report denying “contaminated” breast milk to breastfeeding children. This is a harmful practice that merits attention. Third, the role of open defecation and poor hygiene in causing diarrhea is less understood and warrants introduction or clarification. Finally, the role of exposed feet or curses in causing diarrhea is relatively benign and does not necessitate programmatic attention. Further research supportive of communication and social mobilization strategies building on these findings is required to ensure that improved understanding regarding diarrhea causation translates into improved diarrhea prevention. PMID:24330586

Iskuulpa Watershed Management Plan : A Five-Year Plan for Protecting and Enhancing Fish and Wildlife Habitats in the Iskuulpa Watershed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Confederated Tribes of the Umatilla Indian Reservation Wildlife Program

The Confederated Tribes of the Umatilla Indian Reservation (CTUIR) propose to protect, enhance, and mitigate wildlife and wildlife habitat and watershed resources in the Iskuulpa Watershed. The Iskuulpa Watershed Project was approved as a Columbia River Basin Wildlife Fish and Mitigation Project by the Bonneville Power Administration (BPA) and Northwest Power Planning Council (NWPPC) in 1998. Iskuulpa will contribute towards meeting BPA's obligation to compensate for wildlife habitat losses resulting from the construction of the John Day and McNary Hydroelectric facilities on the Columbia River. By funding the enhancement and operation and maintenance of the Iskuulpa Watershed, BPA will receivemore » credit towards their mitigation debt. The purpose of the Iskuulpa Watershed management plan update is to provide programmatic and site-specific standards and guidelines on how the Iskuulpa Watershed will be managed over the next three years. This plan provides overall guidance on both short and long term activities that will move the area towards the goals, objectives, and desired future conditions for the planning area. The plan will incorporate managed and protected wildlife and wildlife habitat, including operations and maintenance, enhancements, and access and travel management.« less

MISTIC2: comprehensive server to study coevolution in protein families.

PubMed

Colell, Eloy A; Iserte, Javier A; Simonetti, Franco L; Marino-Buslje, Cristina

2018-06-14

Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for structurally or functionally important sites. MISTIC is a server designed to assist users to calculate covariation in protein families and provide them with an interactive tool to visualize the results. Here, we present MISTIC2, an update to the previous server, that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA). The results visualization framework has been reworked for improved performance, compatibility and user experience. It includes a circos representation of the information contained in the alignment, an interactive covariation network, a 3D structure viewer and a sequence logo. Others components provide additional information such as residue annotations, a roc curve for assessing contact prediction, data tables and different ways of filtering the data and exporting figures. Comparison of different methods is easily done and scores combination is also possible. A newly implemented web service allows users to access MISTIC2 programmatically using an API to calculate covariation and retrieve results. MISTIC2 is available at: https://mistic2.leloir.org.ar.

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

33 CFR 385.39 - Evaluating progress towards other water-related needs of the region provided for in the Plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS... other. (3) The Department of the Army shall include these interim targets in appropriate Corps of... provided for in the Plan. These interim targets shall reflect the incremental accomplishment of the...

33 CFR 385.39 - Evaluating progress towards other water-related needs of the region provided for in the Plan.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS... other. (3) The Department of the Army shall include these interim targets in appropriate Corps of... provided for in the Plan. These interim targets shall reflect the incremental accomplishment of the...

33 CFR 385.39 - Evaluating progress towards other water-related needs of the region provided for in the Plan.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS... other. (3) The Department of the Army shall include these interim targets in appropriate Corps of... provided for in the Plan. These interim targets shall reflect the incremental accomplishment of the...

33 CFR 385.39 - Evaluating progress towards other water-related needs of the region provided for in the Plan.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS... other. (3) The Department of the Army shall include these interim targets in appropriate Corps of... provided for in the Plan. These interim targets shall reflect the incremental accomplishment of the...

33 CFR 385.39 - Evaluating progress towards other water-related needs of the region provided for in the Plan.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS... other. (3) The Department of the Army shall include these interim targets in appropriate Corps of... provided for in the Plan. These interim targets shall reflect the incremental accomplishment of the...

Programmatic approaches to assessing and improving animal welfare in zoos and aquariums.

PubMed

Barber, Joseph C E

2009-11-01

There continues to be intense public, professional, and scientific focus on the welfare of animals in zoos and aquariums, but implementing welfare assessment tools consistently throughout this community remains challenging. Indirect measures can be used to assess "welfare potential"-the potential that animals will experience good welfare based on the care that they are provided with. Zoos and aquariums focus on welfare potential with their continued commitment to develop animal care guidelines (e.g. Animal Care Manuals) that can play a role within institutional accreditation or certification. The Association of Zoos and Aquariums Animal Welfare Committee has been pursuing approaches to maximize welfare potential by developing the concept of an integrated welfare approach or framework-an attempt to identify recommended animal care programs (e.g. enrichment, nutrition, veterinary care, research, and animal training programs) and their programmatic components. Objectively assessing the influence that animal care recommendations have on the welfare of individual animals is important to determine the efficacy of programmatic approaches. The future of welfare assessment within zoos and aquariums will include population-level evaluations-tracking emerging trends in health and behavior that come from both formal and informal institutional animal reports. Sharing this information, and performing meta-analyses of the data using epidemiological approaches, will become easier with advances in technology and database management software. Identifying welfare "red/green flags" throughout captive populations will provide direction for more focused assessments that will ultimately inform the design of more effective animal care programs.

The 3D Elevation Program—Flood risk management

USGS Publications Warehouse

Carswell, William J.; Lukas, Vicki

2018-01-25

Flood-damage reduction in the United States has been a longstanding but elusive societal goal. The national strategy for reducing flood damage has shifted over recent decades from a focus on construction of flood-control dams and levee systems to a three-pronged strategy to (1) improve the design and operation of such structures, (2) provide more accurate and accessible flood forecasting, and (3) shift the Federal Emergency Management Agency (FEMA) National Flood Insurance Program to a more balanced, less costly flood-insurance paradigm. Expanding the availability and use of high-quality, three-dimensional (3D) elevation information derived from modern light detection and ranging (lidar) technologies to provide essential terrain data poses a singular opportunity to dramatically enhance the effectiveness of all three components of this strategy. Additionally, FEMA, the National Weather Service, and the U.S. Geological Survey (USGS) have developed tools and joint program activities to support the national strategy.The USGS 3D Elevation Program (3DEP) has the programmatic infrastructure to produce and provide essential terrain data. This infrastructure includes (1) data acquisition partnerships that leverage funding and reduce duplicative efforts, (2) contracts with experienced private mapping firms that ensure acquisition of consistent, low-cost 3D elevation data, and (3) the technical expertise, standards, and specifications required for consistent, edge-to-edge utility across multiple collection platforms and public access unfettered by individual database designs and limitations.High-quality elevation data, like that collected through 3DEP, are invaluable for assessing and documenting flood risk and communicating detailed information to both responders and planners alike. Multiple flood-mapping programs make use of USGS streamflow and 3DEP data. Flood insurance rate maps, flood documentation studies, and flood-inundation map libraries are products of these programs.

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics

PubMed Central

Ramirez-Gonzalez, Ricardo H.; Leggett, Richard M.; Waite, Darren; Thanki, Anil; Drou, Nizar; Caccamo, Mario; Davey, Robert

2014-01-01

Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages. PMID:24627795

Piloting an email-based resource package for job seekers with multiple sclerosis.

PubMed

Dorstyn, Diana; Roberts, Rachel; Murphy, Gregory; Kneebone, Ian; Migliorini, Christine; Craig, Ashley; Hutchinson, Claire; Field, Deborah

2017-05-01

Media-based rehabilitation provides a powerful opportunity to examine vocational behaviors in the disability sector. However, this research is preliminary at best. This paper reports pilot data. Eighteen adults with multiple sclerosis (MS) accessed an email-delivered, resource-based package, Work and MS. Pre- and post-access vocational self-efficacy and identity (Job-Procurement Self Efficacy Scale, My Vocational Situation Scale- primary outcomes), life orientation and depressed mood (Life Orientation Test - revised and Patient Health Questionnaire-9 - secondary outcomes) were assessed. Pre- and post-change scores were examined with Wilcoxon signed ranks tests and Hedges g effect sizes with associated 95% confidence intervals. Reliable change analyses were additionally calculated to determine the clinical significance of individual change scores. Significant and positive effects were reported for vocational self-efficacy, identity, and optimism. Reliable change scores in one or more of these key outcomes were reported by 30% of the sample. Satisfaction with the content and delivery of the email-based intervention was also noted. Preliminary evidence suggests that Work and MS can help to promote vocational goals, interests and strengths among job seekers with a disability by providing a set of tools, information and linkages relating to vocational pursuits and career development. Replication with a randomized control design is indicated. Implications for Rehabilitation Research indicates a high unemployment rate among working-age adults with MS. A combination of disease-specific, psychological, programmatic and societal variables contribute to employment instability in this group. This pilot study demonstrates that an e-mail-based resource package, Work and MS, provides an innovative and feasible option for promoting consumer engagement with vocational services and, potentially, improving vocational outcomes. Work and MS has potential applicability to other disability groups.

The importance of addressing gender inequality in efforts to end vertical transmission of HIV.

PubMed

Ghanotakis, Elena; Peacock, Dean; Wilcher, Rose

2012-07-11

The recently launched "Global Plan towards the Elimination of New HIV Infections among Children by 2015 and Keeping their Mothers Alive" sets forth ambitious targets that will require more widespread implementation of comprehensive prevention of vertical HIV transmission (PMTCT) programmes. As PMTCT policymakers and implementers work toward these new goals, increased attention must be paid to the role that gender inequality plays in limiting PMTCT programmatic progress. A growing body of evidence suggests that gender inequality, including gender-based violence, is a key obstacle to better outcomes related to all four components of a comprehensive PMTCT programme. Gender inequality affects the ability of women and girls to protect themselves from HIV, prevent unintended pregnancies and access and continue to use HIV prevention, care and treatment services. In light of this evidence, global health donors and international bodies increasingly recognize that it is critical to address the gender disparities that put women and children at increased risk of HIV and impede their access to care. The current policy environment provides unprecedented opportunities for PMTCT implementers to integrate efforts to address gender inequality with efforts to expand access to clinical interventions for preventing vertical HIV transmission. Effective community- and facility-based strategies to transform harmful gender norms and mitigate the impacts of gender inequality on HIV-related outcomes are emerging. PMTCT programmes must embrace these strategies and expand beyond the traditional focus of delivering ARV prophylaxis to pregnant women living with HIV. Without greater implementation of comprehensive, gender transformative PMTCT programmes, elimination of vertical transmission of HIV will remain elusive.

The importance of addressing gender inequality in efforts to end vertical transmission of HIV

PubMed Central

Ghanotakis, Elena; Peacock, Dean; Wilcher, Rose

2012-01-01

Issues The recently launched “Global Plan towards the Elimination of New HIV Infections among Children by 2015 and Keeping their Mothers Alive” sets forth ambitious targets that will require more widespread implementation of comprehensive prevention of vertical HIV transmission (PMTCT) programmes. As PMTCT policymakers and implementers work toward these new goals, increased attention must be paid to the role that gender inequality plays in limiting PMTCT programmatic progress. Description A growing body of evidence suggests that gender inequality, including gender-based violence, is a key obstacle to better outcomes related to all four components of a comprehensive PMTCT programme. Gender inequality affects the ability of women and girls to protect themselves from HIV, prevent unintended pregnancies and access and continue to use HIV prevention, care and treatment services. Lessons Learned In light of this evidence, global health donors and international bodies increasingly recognize that it is critical to address the gender disparities that put women and children at increased risk of HIV and impede their access to care. The current policy environment provides unprecedented opportunities for PMTCT implementers to integrate efforts to address gender inequality with efforts to expand access to clinical interventions for preventing vertical HIV transmission. Effective community- and facility-based strategies to transform harmful gender norms and mitigate the impacts of gender inequality on HIV-related outcomes are emerging. PMTCT programmes must embrace these strategies and expand beyond the traditional focus of delivering ARV prophylaxis to pregnant women living with HIV. Without greater implementation of comprehensive, gender transformative PMTCT programmes, elimination of vertical transmission of HIV will remain elusive. PMID:22789642

Let's Talk About B: Barriers to Hepatitis B Screening and Vaccination Among Asian and South Asian Immigrants in British Columbia.

PubMed

Zibrik, Lindsay; Huang, Alan; Wong, Vivian; Novak Lauscher, Helen; Choo, Queenie; Yoshida, Eric M; Ho, Kendall

2018-03-19

Chronic hepatitis B (HBV) is prevalent among Asian immigrants in Canada with high morbidity and mortality rates. While some studies have identified barriers to health care and information access, few have studied the impact of culturally relevant information and addressed challenges with recommendations for effective public education and outreach programs. Culturally tailored HBV education workshops were delivered over a 12-month period to Chinese, Filipino, Korean and Punjabi immigrants in Lower Mainland, British Columbia (BC). Data from pre- and post-workshop surveys and 2-week and 1-month follow-up interviews were collected and analyzed to evaluate knowledge gaps and challenges around HBV prevention and screening. Barriers, health care service gaps and facilitators identified in the interviews were coded and analyzed. Data were collected from 827 workshop participants. Our results show that targeted immigrants in Lower Mainland, BC face many barriers to accessing HBV screening and vaccination. Limited knowledge and awareness of HBV vaccination/prevention/treatment, limited English proficiency and eLiteracy skills, system and provider level barriers to accessing HBV care, and immigration related barriers are among the reported challenges. More than half of participants who took part in the HBV education workshops engaged in actions related to HBV prevention or management. Study findings support the need for culturally tailored HBV public education and outreach programs to further advance HBV immunization and awareness in BC. Addressing barriers and developing targeted programmatic strategies identified in this study will promote more effective HBV education programming and improve uptake of HBV screening and vaccination in BC's immigrant populations.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

PubMed

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

2007-12-11

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Algorithms and semantic infrastructure for mutation impact extraction and grounding.

PubMed

Laurila, Jonas B; Naderi, Nona; Witte, René; Riazanov, Alexandre; Kouznetsov, Alexandre; Baker, Christopher J O

2010-12-02

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases. We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework. We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

An Internship Model for Culturally Relevant Success for Native American High School Students

NASA Astrophysics Data System (ADS)

Nall, J.; Graham, E. M.

2004-12-01

Culturally relevant educational practices can be challenging to implement in the workplace. In an effort to support equity in access to undergraduate internship opportunities for Native American students, NASA Jet Propulsion Laboratory's (JPL) Education Office, Minority Education Initiatives offers a unique approach to supporting students from Native American reservation high schools in Washington State to participate in eight-week technical (Science, Technology, Engineering and Mathematics related) summer internships. This talk will address the Alliance for Learning and Vision for Americans (ALVA) program's twelve years of success based on four programmatic principals, annual review and the critical support of scientists and engineers.

The Transcription Factor Encyclopedia

PubMed Central

2012-01-01

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe. PMID:22458515

Choosing the optimal method in programmatic colorectal cancer screening: current evidence and controversies

PubMed Central

2015-01-01

Colorectal cancer (CRC) is an important health problem all over the world, being the third most common cancer and the second leading cause of cancer-related death in Western countries. The most important strategy for CRC prevention is screening (i.e. secondary prevention). Since it is widely accepted that adenomas and serrated polyps are the precursors of the vast majority of CRC, early detection and removal of these lesions is associated with a reduction of CRC incidence and, consequently, mortality. Moreover, cancers detected by screening are usually diagnosed at early stages and, therefore, curable by endoscopic or surgical procedures. This review will be address CRC screening strategies in average-risk population, which is defined by those individuals, men and women, 50 years of age or older, without any additional personal or familial predisposing risk factor. In order to maximize the impact of screening and ensure high coverage and equity of access, only organized screening programs (i.e. programmatic screening) should be implemented, as opposed to case-finding or opportunistic screening. For that reason and considering that the optimal approach for colorectal screening may differ depending on the scenario, this review will be focused on the advantages and limitations of each screening strategy in an organized setting. PMID:26136839

Phase 1 Space Fission Propulsion System Design Considerations

NASA Technical Reports Server (NTRS)

Houts, Mike; VanDyke, Melissa; Godfroy, Tom; Pedersen, Kevin; Martin, James; Carter, Robert; Dickens, Ricky; Salvail, Pat; Hrbud, Ivana; Rodgers, Stephen L. (Technical Monitor)

2001-01-01

Fission technology can enable rapid, affordable access to any point in the solar system. If fission propulsion systems are to be developed to their full potential; however, near-term customers must be identified and initial fission systems successfully developed, launched, and operated. Studies conducted in fiscal year 2001 (IISTP, 2001) show that fission electric propulsion (FEP) systems operating at 80 kWe or above could enhance or enable numerous robotic outer solar system missions of interest. At these power levels it is possible to develop safe, affordable systems that meet mission performance requirements. In selecting the system design to pursue, seven evaluation criteria were identified: safety, reliability, testability, specific mass, cost, schedule, and programmatic risk. A top-level comparison of three potential concepts was performed: an SP-100 based pumped liquid lithium system, a direct gas cooled system, and a heatpipe cooled system. For power levels up to at least 500 kWt (enabling electric power levels of 125-175 kWe, given 25-35% power conversion efficiency) the heatpipe system has advantages related to several criteria and is competitive with respect to all. Hardware-based research and development has further increased confidence in the heatpipe approach. Successful development and utilization of a "Phase 1" fission electric propulsion system will enable advanced Phase 2 and Phase 3 systems capable of providing rapid, affordable access to any point in the solar system.

Phase 1 space fission propulsion system design considerations

NASA Astrophysics Data System (ADS)

Houts, Mike; van Dyke, Melissa; Godfroy, Tom; Pedersen, Kevin; Martin, James; Dickens, Ricky; Salvail, Pat; Hrbud, Ivana; Carter, Robert

2002-01-01

Fission technology can enable rapid, affordable access to any point in the solar system. If fission propulsion systems are to be developed to their full potential; however, near-term customers must be identified and initial fission systems successfully developed, launched, and operated. Studies conducted in fiscal year 2001 (IISTP, 2001) show that fission electric propulsion (FEP) systems operating at 80 kWe or above could enhance or enable numerous robotic outer solar system missions of interest. At these power levels it is possible to develop safe, affordable systems that meet mission performance requirements. In selecting the system design to pursue, seven evaluation criteria were identified: safety, reliability, testability, specific mass, cost, schedule, and programmatic risk. A top-level comparison of three potential concepts was performed: an SP-100 based pumped liquid lithium system, a direct gas cooled system, and a heatpipe cooled system. For power levels up to at least 500 kWt (enabling electric power levels of 125-175 kWe, given 25-35% power conversion efficiency) the heatpipe system has advantages related to several criteria and is competitive with respect to all. Hardware-based research and development has further increased confidence in the heatpipe approach. Successful development and utilization of a ``Phase 1'' fission electric propulsion system will enable advanced Phase 2 and Phase 3 systems capable of providing rapid, affordable access to any point in the solar system. .

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

PubMed

Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul

2017-01-01

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). http://www.ensembl.org. © The Author(s) 2017. Published by Oxford University Press.

Data Democratization - Promoting Real-Time Data Sharing and Use throughout the Americas

NASA Astrophysics Data System (ADS)

Yoksas, T. C.

2006-05-01

The Unidata Program Center (Unidata) of the University Corporation of Atmospheric Research (UCAR) is actively involved in international collaborations whose goals are real-time sharing of hydro-meteorological data by institutions of higher education throughout the Americas; in the distribution of analysis and visualization tools for those data; and in the establishment of server sites that provide easy-to-use, programmatic remote- access to a wide variety of datasets. Data sharing capabilities are being provided by Unidata's Internet Data Distribution (IDD) system, a community-based effort that has been the primary source of real-time meteorological data for approximately 150 US universities for over a decade. A collaboration among Unidata, Brazil's Centro de PreviSão de Tempo e Estudos Climáticos (CPTEC), the Universidad Federal do Rio de Janeiro (UFRJ), and the Universidade de São Paulo (USP) has resulted in the creation of a Brazilian peer of the North American IDD, the IDD-Brasil. Collaboration among Unidata, the Universidad de Costa Rica (UCR), and the University of Puerto Rico at Mayaguez (UPRM) seeks to extend IDD data sharing throughout Central America and the Caribbean in an IDD-Caribe. Collaboration between Unidata and the Caribbean Institute for Meteorology and Hydrology (CIMH), a World Meteorological Organization (WMO) Regional Meteorological Training Center (RMTC) based in Barbados, has been launched to investigate the possibility of expansion of IDD data sharing throughout Caribbean RMTC member countries. Most recently, efforts aimed at creating a data sharing network for researchers on the Antarctic continent have resulted in the establishment of the Antarctic-IDD. Data analysis and visualization capabilities are being provided by Unidata through a suite of freely-available applications: the National Centers for Environmental Prediction (NCEP) GEneral Meteorology PAcKage (GEMPAK); the Unidata Integrated Data Viewer (IDV); and University of Wisconsin, Space Science and Engineering Center (SSEC) Man-computer Interactive Data Access System (McIDAS). Remote data access capabilities are provided by Unidata's Thematic Realtime Environmental Data Services (THREDDS) servers (which incorporate Open-source Project for a Network Data Access (OPeNDAP) data services), and the Abstract Data Distribution Environment (ADDE) of McIDAS. It is envisioned that the data sharing capabilities available in the IDD, IDD-Brasil, and IDD-Caribe, remote data access capabilities available in THREDDS and ADDE, and analysis capabilities available in GEMPAK, the IDV, and McIDAS will help foster new collaborations among prominent university educators and researchers, national meteorological agencies, and WMO Regional Meteorological Training Centers throughout North, Central, and South America.

Has Chiranjeevi Yojana changed the geographic availability of free comprehensive emergency obstetric care services in Gujarat, India?

PubMed Central

Vora, Kranti Suresh; Yasobant, Sandul; Patel, Amit; Upadhyay, Ashish; Mavalankar, Dileep V.

2015-01-01

Background The high rate of maternal mortality in India is of grave concern. Poor rural Indian women are most vulnerable to preventable maternal deaths primarily because they have limited availability of affordable emergency obstetric care (EmOC) within reasonable geographic proximity. Scarcity of obstetricians in the public sector combined with financial barriers to accessing private sector obstetrician services preclude this underserved population from availing lifesaving functions of comprehensive EmOC such as C-section. In order to overcome this limitation, Government of Gujarat initiated a unique public–private partnership program called Chiranjeevi Yojana (CY) in 2005. The program envisaged leveraging private sector providers to increase availability and thereby accessibility of EmOC care for vulnerable sections of society. Under CY, private sector providers render obstetric care services to poor women at no cost to patients. This paper examines the CY's effectiveness in improving availability of CEmOC services between 2006 and 2012 in three districts of Gujarat, India. Methods Primary data on facility locations, EmOC functionality, and obstetric bed availability were collected in the years 2012 and 2013 in three study districts. Secondary data from Census 2001 and 2011 were used along with required geographic information from Topo sheets and Google Earth maps. ArcGIS version 10 was used to analyze the availability of services using two-step floating catchment area (2SFCA) method. Results Our analysis suggests that the availability of CEmOC services within reasonable travel distance has greatly improved in all three study districts as a result of CY. We also show that the declining participation of the private sector did not result in an increase in distance to the nearest facility, but the extent of availability of providers for several villages was reduced. Spatial and temporal analyses in this paper provide a comprehensive understanding of trends in the availability of EmOC services within reasonable travel distance. Conclusions This paper demonstrates how GIS could be useful for evaluating programs especially those focusing on improving availability and geographic accessibility. The study also shows usefulness of GIS for programmatic planning, particularly for optimizing resource allocation. PMID:26446287

Has Chiranjeevi Yojana changed the geographic availability of free comprehensive emergency obstetric care services in Gujarat, India?

PubMed

Vora, Kranti Suresh; Yasobant, Sandul; Patel, Amit; Upadhyay, Ashish; Mavalankar, Dileep V

2015-01-01

The high rate of maternal mortality in India is of grave concern. Poor rural Indian women are most vulnerable to preventable maternal deaths primarily because they have limited availability of affordable emergency obstetric care (EmOC) within reasonable geographic proximity. Scarcity of obstetricians in the public sector combined with financial barriers to accessing private sector obstetrician services preclude this underserved population from availing lifesaving functions of comprehensive EmOC such as C-section. In order to overcome this limitation, Government of Gujarat initiated a unique public-private partnership program called Chiranjeevi Yojana (CY) in 2005. The program envisaged leveraging private sector providers to increase availability and thereby accessibility of EmOC care for vulnerable sections of society. Under CY, private sector providers render obstetric care services to poor women at no cost to patients. This paper examines the CY's effectiveness in improving availability of CEmOC services between 2006 and 2012 in three districts of Gujarat, India. Primary data on facility locations, EmOC functionality, and obstetric bed availability were collected in the years 2012 and 2013 in three study districts. Secondary data from Census 2001 and 2011 were used along with required geographic information from Topo sheets and Google Earth maps. ArcGIS version 10 was used to analyze the availability of services using two-step floating catchment area (2SFCA) method. Our analysis suggests that the availability of CEmOC services within reasonable travel distance has greatly improved in all three study districts as a result of CY. We also show that the declining participation of the private sector did not result in an increase in distance to the nearest facility, but the extent of availability of providers for several villages was reduced. Spatial and temporal analyses in this paper provide a comprehensive understanding of trends in the availability of EmOC services within reasonable travel distance. This paper demonstrates how GIS could be useful for evaluating programs especially those focusing on improving availability and geographic accessibility. The study also shows usefulness of GIS for programmatic planning, particularly for optimizing resource allocation.

Space station accommodations for life sciences research facilities: Phase A conceptual design and programmatics studies for Missions SAAX0307, SAAX0302 and the transition from SAAX0307 to SAAX0302. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1986-01-01

The conceptual designs and programmatics for a Space Station Nonhuman Life Sciences Research Facility (LSRF) are highlighted. Conceptual designs and programmatics encompass an Initial Orbital Capability (IOC) LSRF, a growth or Follow-on Orbital Capability (FOC), and the transitional process required to modify the IOC LSRF to the FOC LSRF.

75 FR 78722 - Intent To Prepare Programmatic Environmental Assessment Statement for the Nationwide...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... sensor network and provide extended sensor network and components to fill critical situational awareness... different agencies), and share resources. The IOCs will improve tactical decision-making, situational awareness, operations monitoring/ interoperability, rules-based processing, and joint planning in a...

75 FR 78995 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

... fellowship applicants and alumni in one integrated database. FMS provides an efficient and effective way for processing application data, selecting qualified candidates, maintaining a current alumni database...; submission of academic transcripts and letters of recommendation; a review by selected programmatic staff and...

Tank waste remediation system tank waste retrieval risk management plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klimper, S.C.

1997-11-07

This Risk Management Plan defines the approach to be taken to manage programmatic risks in the TWRS Tank Waste Retrieval program. It provides specific instructions applicable to TWR, and is used to supplement the guidance given by the TWRS Risk Management procedure.

Evolutionary space platform concept study. Volume 3: Programmatics for manned space platform concepts

NASA Technical Reports Server (NTRS)

1982-01-01

The programmatic data for the reference concept of the Manned Space Platform is presented. Details regarding work breakdown structure (WBS) and dictionary, the facilities and equipment required to produce the modules, the project schedule and logic diagram, a preliminary assessment of environmental impacts and details regarding the estimated costs for the reference concept are included. The proposed WBS which was developed to provide summary and system level segregation of the nonrecurring and recurring portions of the Manned Space Platform project is also included. The accompanying dictionary outlines the function and activities contained within each WBS element. The facility and equipment required to produce the various modules is discussed. Generally, required equipment is within the existing state of the art although the size of some of the items to be manufactured is a consideration. A preliminary manufacturing flow was also provided. The project schedules presented consist of the Master Project Summary Schedule, the Master Project Phasing Chart and the Logic Network.

Designing an HIV counseling and testing program for bathhouses: the Seattle experience with strategies to improve acceptability.

PubMed

Spielberg, Freya; Branson, Bernard M; Goldbaum, Gary M; Kurth, Ann; Wood, Robert W

2003-01-01

Bathhouses are important venues for providing HIV counseling and testing to high-risk men who have sex with men (MSM), yet relatively few bathhouses routinely provide this service, and few data are available to guide program design. We examine numerous logistic considerations that had been identified in the HIV Alternative Testing Strategies study and that influenced the initiation, effectiveness, and maintenance of HIV testing programs in bathhouses for MSM. Key programmatic considerations in the design of a bathhouse HIV counseling and testing program included building alliances with community agencies, hiring and training staff, developing techniques for offering testing, and providing options for counseling, testing, and disclosure of results. The design included ways to provide client support and follow-up for partner notification and treatment counseling and to maintain relationships with bathhouse management for support of prevention activities. Early detection of HIV infection and HIV prevention can be achieved for some high-risk MSM through an accessible and acceptable HIV counseling and testing program in bathhouses. Keys to success include establishing community prevention collaborations between bathhouse personnel and testing agencies, ensuring that testing staff are supported in their work, and offering anonymous rapid HIV testing. Use of FDA approved, new rapid tests that do not require venipuncture, centrifugation, or laboratory oversight will further decrease barriers to testing and facilitate implementation of bathhouse testing programs in other communities.

Programmatic Impact of 5 Years of Mortality Surveillance of New York City Homeless Populations

PubMed Central

Marder, Dova; Begier, Elizabeth; Gutkovich, Alexander; Mos, Robert; Griffin, Angela; Zimmerman, Regina; Madsen, Ann

2013-01-01

A homeless mortality surveillance system identifies emerging trends in the health of the homeless population and provides this information to key stakeholders in a timely and ongoing manner to effect evidence-based, programmatic change. We describe the first 5 years of the New York City homeless mortality surveillance system and, for the first time in peer-reviewed literature, illustrate the impact of key elements of sustained surveillance (i.e., timely dissemination of aggregate mortality data and real-time sharing of information on individual homeless decedents) on the programs of New York City’s Department of Homeless Services. These key elements had a positive impact on the department’s programs that target sleep-related infant deaths and hypothermia, drug overdose, and alcohol-related deaths among homeless persons. PMID:24148068

Intellectual Capital: For 20 Years, American Indian College Fund Has Been Investing

ERIC Educational Resources Information Center

Horwedel, Dina M.

2009-01-01

For 20 years, the American Indian College Fund (the Fund) has been helping students to afford a higher education. In addition to providing more than 4,000 scholarships for American Indian students last year, it also provides tribal colleges with funding and programmatic support. The Fund was created in 1989 by the tribal colleges and universities…

Analysis of microgravity space experiments Space Shuttle programmatic safety requirements

NASA Technical Reports Server (NTRS)

Terlep, Judith A.

1996-01-01

This report documents the results of an analysis of microgravity space experiments space shuttle programmatic safety requirements and recommends the creation of a Safety Compliance Data Package (SCDP) Template for both flight and ground processes. These templates detail the programmatic requirements necessary to produce a complete SCDP. The templates were developed from various NASA centers' requirement documents, previously written guidelines on safety data packages, and from personal experiences. The templates are included in the back as part of this report.

Commercially Hosted Government Payloads: Lessons from Recent Programs

NASA Technical Reports Server (NTRS)

Andraschko, Mark A.; Antol, Jeffrey; Horan, Stephen; Neil, Doreen

2011-01-01

In a commercially hosted operational mode, a scientific instrument or operational device is attached to a spacecraft but operates independently from the spacecraft s primary mission. Despite the expected benefits of this arrangement, there are few examples of hosted payload programs actually being executed by government organizations. The lack of hosted payload programs is largely driven by programmatic challenges, both real and perceived, rather than by technical challenges. Partly for these reasons, NASA has not sponsored a hosted payload program, in spite of the benefits and visible community interest in doing so. In the interest of increasing the use of hosted payloads across the space community, this paper seeks to alleviate concerns about hosted payloads by identifying these programmatic challenges and presenting ways in which they can be avoided or mitigated. Despite the challenges, several recent hosted payload programs have been successfully completed or are currently in progress. This paper presents an assessment of these programs, with a focus on acquisition, costs, schedules, risks, and other programmatic aspects. The hosted payloads included in this study are the Federal Aviation Administration's Wide Area Augmentation System (WAAS) payloads, United States Coast Guard's Automatic Identification System (AIS) demonstration payload, Department of Defense's IP Router In Space (IRIS) demonstration payload, the United States Air Force's Commercially Hosted Infrared Payload (CHIRP), and the Australian Defence Force's Ultra High Frequency (UHF) payload. General descriptions of each of these programs are presented along with issues that have been encountered and lessons learned from those experiences. A set of recommended approaches for future hosted payload programs is presented, with a focus on addressing risks or potential problem areas through smart and flexible contracting up front. This set of lessons and recommendations is broadly applicable to future hosted payload programs, whether they are technology demonstrations, communications systems, or operational sensors. Additionally, we present a basic cost model for commercial access to space for hosted payloads as a function of payload mass

Mobile-Based Nutrition and Child Health Monitoring to Inform Program Development: An Experience From Liberia.

PubMed

Guyon, Agnes; Bock, Ariella; Buback, Laura; Knittel, Barbara

2016-12-23

Implementing complex nutrition and other public health projects and tracking nutrition interventions, such as women's diet and supplementation and infant and young child feeding practices, requires reliable routine data to identify potential program gaps and to monitor trends in behaviors in real time. However, current monitoring and evaluation practices generally do not create an environment for this real-time tracking. This article describes the development and application of a mobile-based nutrition and health monitoring system, which collected monitoring data on project activities, women's nutrition, and infant and young child feeding practices in real time. The Liberia Agricultural Upgrading Nutrition and Child Health (LAUNCH) project implemented a nutrition and health monitoring system between April 2012 and June 2014. The LAUNCH project analyzed project monitoring and outcome data from the system and shared selected behavioral and programmatic indicators with program managers through a short report, which later evolved into a visual data dashboard, during program-update meetings. The project designed protocols to ensure representativeness of program participants. LAUNCH made programmatic adjustments in response to findings from the monitoring system; these changes were then reflected in subsequent quarterly trends, indicating that the availability of timely data allowed for the project to react quickly to issues and adapt the program appropriately. Such issues included lack of participation in community groups and insufficient numbers of food distribution points. Likewise, the system captured trends in key outcome indicators such as breastfeeding and complementary feeding practices, linking them to project activities and external factors including seasonal changes and national health campaigns. Digital data collection platforms can play a vital role in improving routine programmatic functions. Fixed gathering locations such as food distribution points represent an opportunity to easily access program participants and enable managers to identify strengths and weaknesses in project implementation. For programs that track individuals over time, a mobile tool combined with a strong database can greatly improve efficiency and data visibility and reduce resource leakages. © Guyon et al.

Are "New Building" Learning Gains Sustainable?

ERIC Educational Resources Information Center

Walczak, Mary M.; Van Wylen, David G. L.

2015-01-01

New science facilities have become a reality on many college campuses in the last few decades. Large time investments in creating shared programmatic vision and designing flexible spaces, partnered with large fiscal investments, have created a new generation of science building. Unfortunately, few studies provide evidence about whether the…

Evidence-Based Diagnosis and Treatment for Specific Learning Disabilities Involving Impairments in Written and/or Oral Language

ERIC Educational Resources Information Center

Berninger, Virginia W.; May, Maggie O'Malley

2011-01-01

Programmatic, multidisciplinary research provided converging brain, genetic, and developmental support for evidence-based diagnoses of three specific learning disabilities based on hallmark phenotypes (behavioral expression of underlying genotypes) with treatment relevance: dysgraphia (impaired legible automatic letter writing, orthographic…

78 FR 57587 - Environmental Impact and Related Procedures-Programmatic Agreements and Additional Categorical...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... administrative and NEPA processing by encouraging grant applicants to design proposed projects so that... geotechnical and other investigations to provide information for preliminary design and for environmental... information for preliminary design and for environmental analyses and permitting purposes and is found...

UNESCO-UNEVOC in Action: Biennial Report 2012-2013

ERIC Educational Resources Information Center

UNESCO-UNEVOC International Centre for Technical and Vocational Education and Training, 2014

2014-01-01

This biennial report provides a comprehensive overview of UNESCO-UNEVOC's activities in technical and vocational education and training in 2012-2013. It illustrates UNESCO-UNEVOC's contributions to the UNESCO 36 C/5 sectoral priorities and programmatic objectives. Specifically, UNESCO-UNEVOC contributed to the biennial sectoral priority in…

Transform: UNESCO-UNEVOC in Action. Biennial Report 2014-2015

ERIC Educational Resources Information Center

UNESCO-UNEVOC International Centre for Technical and Vocational Education and Training, 2016

2016-01-01

The Biennial Report presents a selection of UNESCO-UNEVOC's activities during 2014 and 2015. The activities contributed to UNESCO's sectoral priorities and programmatic objectives and assisted Member States to provide equitable, inclusive and quality education and promote lifelong learning for sustainable development. Importantly, the selected…

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.

PubMed

Bolser, Dan M; Staines, Daniel M; Perry, Emily; Kersey, Paul J

2017-01-01

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).

Chapter 21: Programmatic Interfaces - STILTS

NASA Astrophysics Data System (ADS)

Fitzpatrick, M. J.

STILTS is the Starlink Tables Infrastructure Library Tool Set developed by Mark Taylor of the former Starlink Project. STILTS is a command-line tool (see the NVOSS_HOME/bin/stilts command) providing access to the same functionality driving the TOPCAT application and can be run using either the STILTS-specific jar file, or the more general TOPCAT jar file (both are available in the NVOSS_HOME/java/lib directory and are included in the default software environment classpath). The heart of both STILTS and TOPCAT is the STIL Java library. STIL is designed to efficiently handle the input, output and processing of very large tabular datasets and the STILTS task interface makes it an ideal tool for the scripting environment. Multiple formats are supported (including FITS Binary Tables, VOTable, CSV, SQL databases and ASCII, amongst others) and while some tools will generically handle all supported formats, others are specific to the VOTable format. Converting a VOTable to a more script-friendly format is the first thing most users will encounter, but there are many other useful tools as well.

GIANT API: an application programming interface for functional genomics.

PubMed

Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

2016-07-08

GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Benefits of Using a Mars Forward Strategy for Lunar Surface Systems

NASA Technical Reports Server (NTRS)

Mulqueen, Jack; Griffin, Brand; Smitherman, David; Maples, Dauphne

2009-01-01

This paper identifies potential risk reduction, cost savings and programmatic procurement benefits of a Mars Forward Lunar Surface System architecture that provides commonality or evolutionary development paths for lunar surface system elements applicable to Mars surface systems. The objective of this paper is to identify the potential benefits for incorporating a Mars Forward development strategy into the planned Project Constellation Lunar Surface System Architecture. The benefits include cost savings, technology readiness, and design validation of systems that would be applicable to lunar and Mars surface systems. The paper presents a survey of previous lunar and Mars surface systems design concepts and provides an assessment of previous conclusions concerning those systems in light of the current Project Constellation Exploration Architectures. The operational requirements for current Project Constellation lunar and Mars surface system elements are compared and evaluated to identify the potential risk reduction strategies that build on lunar surface systems to reduce the technical and programmatic risks for Mars exploration. Risk reduction for rapidly evolving technologies is achieved through systematic evolution of technologies and components based on Moore's Law superimposed on the typical NASA systems engineering project development "V-cycle" described in NASA NPR 7120.5. Risk reduction for established or slowly evolving technologies is achieved through a process called the Mars-Ready Platform strategy in which incremental improvements lead from the initial lunar surface system components to Mars-Ready technologies. The potential programmatic benefits of the Mars Forward strategy are provided in terms of the transition from the lunar exploration campaign to the Mars exploration campaign. By utilizing a sequential combined procurement strategy for lunar and Mars exploration surface systems, the overall budget wedges for exploration systems are reduced and the costly technological development gap between the lunar and Mars programs can be eliminated. This provides a sustained level of technological competitiveness as well as maintaining a stable engineering and manufacturing capability throughout the entire duration of Project Constellation.

Community health workers and mobile technology: a systematic review of the literature.

PubMed

Braun, Rebecca; Catalani, Caricia; Wimbush, Julian; Israelski, Dennis

2013-01-01

In low-resource settings, community health workers are frontline providers who shoulder the health service delivery burden. Increasingly, mobile technologies are developed, tested, and deployed with community health workers to facilitate tasks and improve outcomes. We reviewed the evidence for the use of mobile technology by community health workers to identify opportunities and challenges for strengthening health systems in resource-constrained settings. We conducted a systematic review of peer-reviewed literature from health, medical, social science, and engineering databases, using PRISMA guidelines. We identified a total of 25 unique full-text research articles on community health workers and their use of mobile technology for the delivery of health services. Community health workers have used mobile tools to advance a broad range of health aims throughout the globe, particularly maternal and child health, HIV/AIDS, and sexual and reproductive health. Most commonly, community health workers use mobile technology to collect field-based health data, receive alerts and reminders, facilitate health education sessions, and conduct person-to-person communication. Programmatic efforts to strengthen health service delivery focus on improving adherence to standards and guidelines, community education and training, and programmatic leadership and management practices. Those studies that evaluated program outcomes provided some evidence that mobile tools help community health workers to improve the quality of care provided, efficiency of services, and capacity for program monitoring. Evidence suggests mobile technology presents promising opportunities to improve the range and quality of services provided by community health workers. Small-scale efforts, pilot projects, and preliminary descriptive studies are increasing, and there is a trend toward using feasible and acceptable interventions that lead to positive program outcomes through operational improvements and rigorous study designs. Programmatic and scientific gaps will need to be addressed by global leaders as they advance the use and assessment of mobile technology tools for community health workers.

Surgical interventions for pulmonary tuberculosis in Mumbai, India: surgical outcomes and programmatic challenges.

PubMed

Shirodkar, S; Anande, L; Dalal, A; Desai, C; Corrêa, G; Das, M; Laxmeshwar, C; Mansoor, H; Remartinez, D; Trelles, M; Isaakidis, P

2016-09-01

Setting: While surgery for pulmonary tuberculosis (PTB) is considered an important adjunct for specific cases, including drug-resistant tuberculosis, operational evidence on its feasibility and effectiveness is limited. Objective: To describe surgical outcomes and programmatic challenges of providing surgery for PTB in Mumbai, India. Design: A descriptive study of routinely collected data of surgical interventions for PTB from 2010 to 2014 in two Mumbai hospitals, one public, one private. Results: Of 85 patients, 5 (6%) died and 17 (20%) had complications, with wound infection being the most frequent. Repeat operation was required in 12 (14%) patients. Most procedures were performed on an emergency basis, and eligibility was established late in the course of treatment. Median time from admission to surgery was 51 days. Drug susceptibility test (DST) patterns and final treatment outcomes were not systematically collected. Conclusion: In a high-burden setting such as Mumbai, important data on surgery for PTB were surprisingly limited in both the private and public sectors. Eligibility for surgery was established late, culture and DST were not systematically offered, the interval between admission and surgery was long and TB outcomes were not known. Systematic data collection would allow for proper evaluation of surgery as adjunctive therapy for all forms of TB under programmatic conditions.

Surgical interventions for pulmonary tuberculosis in Mumbai, India: surgical outcomes and programmatic challenges

PubMed Central

Shirodkar, S.; Anande, L.; Dalal, A.; Desai, C.; Corrêa, G.; Laxmeshwar, C.; Mansoor, H.; Remartinez, D.; Trelles, M.; Isaakidis, P.

2016-01-01

Setting: While surgery for pulmonary tuberculosis (PTB) is considered an important adjunct for specific cases, including drug-resistant tuberculosis, operational evidence on its feasibility and effectiveness is limited. Objective: To describe surgical outcomes and programmatic challenges of providing surgery for PTB in Mumbai, India. Design: A descriptive study of routinely collected data of surgical interventions for PTB from 2010 to 2014 in two Mumbai hospitals, one public, one private. Results: Of 85 patients, 5 (6%) died and 17 (20%) had complications, with wound infection being the most frequent. Repeat operation was required in 12 (14%) patients. Most procedures were performed on an emergency basis, and eligibility was established late in the course of treatment. Median time from admission to surgery was 51 days. Drug susceptibility test (DST) patterns and final treatment outcomes were not systematically collected. Conclusion: In a high-burden setting such as Mumbai, important data on surgery for PTB were surprisingly limited in both the private and public sectors. Eligibility for surgery was established late, culture and DST were not systematically offered, the interval between admission and surgery was long and TB outcomes were not known. Systematic data collection would allow for proper evaluation of surgery as adjunctive therapy for all forms of TB under programmatic conditions. PMID:27695683

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

PubMed Central

Wei, Chih-Hsuan; Hakala, Kai; Pyysalo, Sampo; Ananiadou, Sophia; Kao, Hung-Yu; Lu, Zhiyong; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip

2013-01-01

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license. PMID:23613707

'Beyond the willing & the waiting' - The role of peer-based approaches in hepatitis C diagnosis & treatment.

PubMed

Henderson, Charles; Madden, Annie; Kelsall, Jenny

2017-12-01

This commentary seeks to examine the role, value and importance of peer-based programmatic approaches for ensuring the effective roll-out of the new hepatitis C (HCV) treatments among those most affected - that is, people who inject drugs (PWID). The authors examine recent approaches to HCV treatment in Australia including the provision of universal access to the new DAA regimens regardless of acquisition, genotype or severity of disease. These approaches are contextualised within wider global strategies to support HCV elimination as a public health threat by 2030 (WHO, 2016). Despite the unprecedented opportunity presented by the availability of the new treatments, the fact remains that those most affected by hepatitis C are still largely hidden and disconnected from the health system and are likely to stay that way without targeted education and support. There is a need to for greater investment in new and innovative HCV+ PWID peer education approaches for HCV diagnosis and treatment that add value to existing models of care to improve pathways and support people across their entire treatment journey. Key components include expanding existing peer-based programmes and developing new innovative peer initiatives, supporting the development of the PWID peer workforce, developing new, targeted peer education resources and promoting linkages and partnerships between peer based and HCV treatment service providers in primary and community settings. Our approach to HCV elimination needs to take account of people's broader lives, their vulnerabilities, their life journeys and their potential points of connection, engagement and access. Peer-based organisations and networks provide that unique point of engagement and access for those HCV+ PWID for whom the health system is an unfamiliar even forbidding place or for whom hepatitis C can be but one of many overwhelming issues in the lives. Copyright © 2017 Elsevier B.V. All rights reserved.

Employing human rights frameworks to realize access to an HIV cure

PubMed Central

Meier, Benjamin Mason; Gelpi, Adriane; Kavanagh, Matthew M; Forman, Lisa; Amon, Joseph J

2015-01-01

Introduction The scale of the HIV pandemic – and the stigma, discrimination and violence that surrounded its sudden emergence – catalyzed a public health response that expanded human rights in principle and practice. In the absence of effective treatment, human rights activists initially sought to protect individuals at high risk of HIV infection. With advances in antiretroviral therapy, activists expanded their efforts under international law, advocating under the human right to health for individual access to treatment. Discussion As a clinical cure comes within reach, human rights obligations will continue to play a key role in political and programmatic decision-making. Building upon the evolving development and implementation of the human right to health in the global response to HIV, we outline a human rights research agenda to prepare for HIV cure access, investigating the role of human rights law in framing 1) resource allocation, 2) international obligations, 3) intellectual property and 4) freedom from coercion. Conclusions The right to health is widely recognized as central to governmental, intergovernmental and non-governmental responses to the pandemic and critical both to addressing vulnerability to infection and to ensuring universal access to HIV prevention, treatment, care and support. While the advent of an HIV cure will raise new obligations for policymakers in implementing the right to health, the resolution of past debates surrounding HIV prevention and treatment may inform claims for universal access. PMID:26568056

Employing human rights frameworks to realize access to an HIV cure.

PubMed

Meier, Benjamin Mason; Gelpi, Adriane; Kavanagh, Matthew M; Forman, Lisa; Amon, Joseph J

2015-01-01

The scale of the HIV pandemic - and the stigma, discrimination and violence that surrounded its sudden emergence - catalyzed a public health response that expanded human rights in principle and practice. In the absence of effective treatment, human rights activists initially sought to protect individuals at high risk of HIV infection. With advances in antiretroviral therapy, activists expanded their efforts under international law, advocating under the human right to health for individual access to treatment. As a clinical cure comes within reach, human rights obligations will continue to play a key role in political and programmatic decision-making. Building upon the evolving development and implementation of the human right to health in the global response to HIV, we outline a human rights research agenda to prepare for HIV cure access, investigating the role of human rights law in framing 1) resource allocation, 2) international obligations, 3) intellectual property and 4) freedom from coercion. The right to health is widely recognized as central to governmental, intergovernmental and non-governmental responses to the pandemic and critical both to addressing vulnerability to infection and to ensuring universal access to HIV prevention, treatment, care and support. While the advent of an HIV cure will raise new obligations for policymakers in implementing the right to health, the resolution of past debates surrounding HIV prevention and treatment may inform claims for universal access.

A Change Will Do You Good

ERIC Educational Resources Information Center

Mc Taggart, Breda; Cavaliero, Tamsin

2016-01-01

Programmatic review processes within higher education institutions provide programme teams with the opportunity to reflect on their practices. An output of such self-examination is often changes, not only to the content of programmes, but also to delivery methodologies. These changes are influenced by the environment, cultural norms, attitudes and…

75 FR 34465 - Statement of Organization, Functions, and Delegations of Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-17

... public health and women's health issues. Dated June 6, 2010. William P. Nichols, Chief Operating Officer... the Office of Chief of Public Health Practice (CAR) and insert the following: Office of the Associate... guide further science, policy, and programmatic efforts; (12) provides financial support to conduct both...

78 FR 73555 - Deepwater Horizon Oil Spill; Draft Programmatic and Phase III Early Restoration Plan and Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-06

...-making. U.S. Environmental Protection Agency (USEPA); State of Louisiana Coastal Protection and... of Alabama; State of Florida Department of Environmental Protection and Fish and Wildlife... Coastal and Marine Resources, and (2) Contribute to Providing and Enhancing Recreational Opportunities...

77 FR 28891 - National Flood Insurance Program Programmatic Environmental Impact Statement

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-16

... critical habitat. This effort will result in a comprehensive series of policy recommendations designed to transition the NFIP toward a more resilient, sustainable, and comprehensive approach to flood risk management... insurance is designed to provide a financial alternative and to reduce the escalating costs of Federal...

Assurance of Learning in a Writing-Intensive Business Course

ERIC Educational Resources Information Center

Carnes, Lana; Awang, Faridah; Smith, Halie

2015-01-01

Writing intensive courses provide a means of addressing declining student writing proficiency. Programmatic learning goals accomplished through a writing-intensive course can be used to develop students' writing skills. For business communication faculty members to maximize the value of their courses to business programs, they should demonstrate…

75 FR 17940 - Draft Programmatic Environmental Assessment for the Evaluation of the Grant Programs Directorate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-08

... and emergency preparedness grant programs that it administers. These programs provide grant funding to... effects of communication facilities construction or modification subject to review by the Federal... have or are likely to have a measurable negative effect on migratory bird populations. Avian mortality...

Teaching Them to Teach: Programmatic Evaluation of Graduate Assistants' Teaching Performance

ERIC Educational Resources Information Center

Sobel, Karen; Avery, Susan; Ferrer-Vinent, Ignacio J.

2016-01-01

Academic libraries are one of the most important sources of "on the job" training for future library instructors. Librarians who supervise and assess these future library instructors (often in graduate assistant positions) often choose to provide observations and feedback each semester to these instructors in training. Scholarly…

78 FR 74159 - Programmatic Candidate Conservation Agreement With Assurances for Least Chub Receipt of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-10

... voluntarily undertake management activities on their property to enhance, restore, or maintain habitat... FR 32726) and applicable regulations. The conservation goal of this CCAA is to reduce the threats to... goals for least chub. Least chub conservation will be enhanced by providing ESA regulatory assurances...

Using Mixed Methods to Assess Initiatives with Broad-Based Goals

ERIC Educational Resources Information Center

Inkelas, Karen Kurotsuchi

2017-01-01

This chapter describes a process for assessing programmatic initiatives with broad-ranging goals with the use of a mixed-methods design. Using an example of a day-long teaching development conference, this chapter provides practitioners step-by-step guidance on how to implement this assessment process.

Strategic Directions for Extension Health and Wellness Programs

ERIC Educational Resources Information Center

Rodgers, Michelle; Braun, Bonnie

2015-01-01

The new Cooperative Extension National Framework for Health and Wellness is a tool to help Extension systematically address the programmatic area of health and wellness at the individual, community, environmental, and policy levels. Key strategies of the framework tool are provided and suggestions for ways that Extension can use this framework…

20 CFR 641.864 - What functions and activities constitute programmatic activity costs?

Code of Federal Regulations, 2012 CFR

2012-04-01

..., DEPARTMENT OF LABOR PROVISIONS GOVERNING THE SENIOR COMMUNITY SERVICE EMPLOYMENT PROGRAM Administrative... training, as described in § 641.540, which may be provided before commencing or during a community service..., including job development and job search assistance, job fairs, job clubs, and job referrals; and (e...

20 CFR 641.864 - What functions and activities constitute programmatic activity costs?

Code of Federal Regulations, 2013 CFR

2013-04-01

..., DEPARTMENT OF LABOR PROVISIONS GOVERNING THE SENIOR COMMUNITY SERVICE EMPLOYMENT PROGRAM Administrative... training, as described in § 641.540, which may be provided before commencing or during a community service..., including job development and job search assistance, job fairs, job clubs, and job referrals; and (e...

Benefits of the NADE Certification Process: Self-Knowledge, Informed Choices & Programmatic Strength

ERIC Educational Resources Information Center

Greci, Dana

2016-01-01

Research shows that systematic, ongoing program evaluation is needed to adequately assess the effectiveness of developmental programs. Ongoing evaluation provides both (1) validation of programs to educational institutions and legislators; and (2) impetus for program improvement. The author of this article works in the Developmental Education…

Selected DOE headquarters publications

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

1979-04-01

This publication provides listings of (mainly policy and programmatic) publications which have been issued by headquarters organizations of the Department of Energy; assigned a DOE/XXX- type report number code, where XXX is the 1- to 4-letter code for the issuing headquarters organization; received by the Energy Library; and made available to the public.

Does Greater Autonomy Improve School Performance? Evidence from a Regression Discontinuity Analysis in Chicago

ERIC Educational Resources Information Center

Steinberg, Matthew P.

2014-01-01

School districts throughout the United States are increasingly providing greater autonomy to local public (non-charter) school principals. In 2005-06, Chicago Public Schools initiated the Autonomous Management and Performance Schools program, granting academic, programmatic, and operational freedoms to select principals. This paper provides…

Benefits and costs of programmatic agreements

DOT National Transportation Integrated Search

2015-02-01

The performing organization, on behalf of the FHWA Office of Planning, Environment, and Realty, conducted a benefit-cost assessment of programmatic agreements and approaches. The assessment consisted of a case study approach that evaluated three agre...

76 FR 50249 - Notice of Extension of Public Comment Period for the Draft Environmental Impact Statement...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-12

... the Draft Environmental Impact Statement, Including a Draft Programmatic Agreement, for the Clark... Programmatic Agreement, for the Southern Nevada Water Authority's (SNWA) proposed Clark, Lincoln, and White...

The National Aeronautics and Space Administration (NASA) Tracking and Data Relay Satellite System (TDRSS) program Economic and programmatic, considerations

NASA Technical Reports Server (NTRS)

Aller, R. O.

1985-01-01

The Tracking and Data Relay Satellite System (TDRSS) represents the principal element of a new space-based tracking and communication network which will support NASA spaceflight missions in low earth orbit. In its complete configuration, the TDRSS network will include a space segment consisting of three highly specialized communication satellites in geosynchronous orbit, a ground segment consisting of an earth terminal, and associated data handling and control facilities. The TDRSS network has the objective to provide communication and data relay services between the earth-orbiting spacecraft and their ground-based mission control and data handling centers. The first TDRSS spacecraft has been now in service for two years. The present paper is concerned with the TDRSS experience from the perspective of the various programmatic and economic considerations which relate to the program.

Programmatic management of multidrug-resistant tuberculosis: models from three countries.

PubMed

Furin, J; Bayona, J; Becerra, M; Farmer, P; Golubkov, A; Hurtado, R; Joseph, J K; Keshavjee, S; Ponomarenko, O; Rich, M; Shin, S

2011-10-01

Although multidrug-resistant tuberculosis (MDR-TB) is a major global health problem, there is a gap in programmatic treatment implementation. This study describes MDR-TB treatment models in three countries--Peru, Russia and Lesotho-- using qualitative data collected over a 13-year period. A program analysis is presented for each country focusing on baseline medical care, initial implementation and program evolution. A pattern analysis revealed six overarching themes common to all three programs: 1) importance of baseline assessments, 2) early identification of key collaborators, 3) identification of initial locus of care, 4) minimization of patient-incurred costs, 5) targeted interventions for vulnerable populations and 6) importance of technical assistance and funding. Site commonalities and differences in each of these areas were analyzed. It is recommended that all programs providing MDR-TB treatment address these six areas during program development and implementation.

Conceptual design and programmatics studies of space station accommodations for Life Sciences Research Facilities (LSRF)

NASA Technical Reports Server (NTRS)

1985-01-01

Conceptual designs and programmatics of the space station accommodations for the Life Sciences Research Facilities (LSRF) are presented. The animal ECLSS system for the LSRF provides temperature-humidity control, air circulation, and life support functions for experimental subjects. Three ECLSS were studied. All configurations presented satisfy the science requirements for: animal holding facilities with bioisolation; facilities interchangeable to hold rodents, small primates, and plants; metabolic cages interchangeable with standard holding cages; holding facilities adaptable to restrained large primates and rodent breeding/nesting cages; volume for the specified instruments; enclosed ferm-free workbench for manipulation of animals and chemical procedures; freezers for specimen storage until return; and centrifuge to maintain animals and plants at fractional g to 1 g or more, with potential for accommodating humans for short time intervals.

The impact of programmatic assessment on student learning: theory versus practice.

PubMed

Heeneman, Sylvia; Oudkerk Pool, Andrea; Schuwirth, Lambert W T; van der Vleuten, Cees P M; Driessen, Erik W

2015-05-01

It is widely acknowledged that assessment can affect student learning. In recent years, attention has been called to 'programmatic assessment', which is intended to optimise both learning functions and decision functions at the programme level of assessment, rather than according to individual methods of assessment. Although the concept is attractive, little research into its intended effects on students and their learning has been conducted. This study investigated the elements of programmatic assessment that students perceived as supporting or inhibiting learning, and the factors that influenced the active construction of their learning. The study was conducted in a graduate-entry medical school that implemented programmatic assessment. Thus, all assessment information, feedback and reflective activities were combined into a comprehensive, holistic programme of assessment. We used a qualitative approach and interviewed students (n = 17) in the pre-clinical phase of the programme about their perceptions of programmatic assessment and learning approaches. Data were scrutinised using theory-based thematic analysis. Elements from the comprehensive programme of assessment, such as feedback, portfolios, assessments and assignments, were found to have both supporting and inhibiting effects on learning. These supporting and inhibiting elements influenced students' construction of learning. Findings showed that: (i) students perceived formative assessment as summative; (ii) programmatic assessment was an important trigger for learning, and (iii) the portfolio's reflective activities were appreciated for their generation of knowledge, the lessons drawn from feedback, and the opportunities for follow-up. Some students, however, were less appreciative of reflective activities. For these students, the elements perceived as inhibiting seemed to dominate the learning response. The active participation of learners in their own learning is possible when learning is supported by programmatic assessment. Certain features of the comprehensive programme of assessment were found to influence student learning, and this influence can either support or inhibit students' learning responses. © 2015 John Wiley & Sons Ltd.

77 FR 38796 - Alabama Power Company; Holt Hydroelectric Project; Notice of Revised Restricted Service List for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-29

... Power Company; Holt Hydroelectric Project; Notice of Revised Restricted Service List for a Programmatic... Hydroelectric Project No. 2203. The programmatic agreement, when executed by the Commission, the Alabama SHPO...

Ecological risks of DOE`s programmatic environmental restoration alternatives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-06-01

This report assesses the ecological risks of the Department of Energy`s (DOE) Environmental Restoration Program. The assessment is programmatic in that it is directed at evaluation of the broad programmatic alternatives outlined in the DOE Implementation Plan. It attempts to (1) characterize the ecological resources present on DOE facilities, (2) describe the occurrence and importance of ecologically significant contamination at major DOE facilities, (3) evaluate the adverse ecological impacts of habitat disturbance caused by remedial activities, and (4) determine whether one or another of the programmatic alternatives is clearly ecologically superior to the others. The assessment focuses on six representativemore » facilities: the Idaho National Engineering Laboratory (INEL); the Fernald Environmental Management Project (FEMP); the Oak Ridge Reservation (ORR), including the Oak Ridge National Laboratory (ORNL), Y-12 plant, and K-25 plant; the Rocky Flats Plant; the Hanford Reservation; and the Portsmouth Gaseous Diffusion Plant.« less

Data Publishing and Sharing Via the THREDDS Data Repository

NASA Astrophysics Data System (ADS)

Wilson, A.; Caron, J.; Davis, E.; Baltzer, T.

2007-12-01

The terms "Team Science" and "Networked Science" have been coined to describe a virtual organization of researchers tied via some intellectual challenge, but often located in different organizations and locations. A critical component to these endeavors is publishing and sharing of content, including scientific data. Imagine pointing your web browser to a web page that interactively lets you upload data and metadata to a repository residing on a remote server, which can then be accessed by others in a secure fasion via the web. While any content can be added to this repository, it is designed particularly for storing and sharing scientific data and metadata. Server support includes uploading of data files that can subsequently be subsetted, aggregrated, and served in NetCDF or other scientific data formats. Metadata can be associated with the data and interactively edited. The THREDDS Data Repository (TDR) is a server that provides client initiated, on demand, location transparent storage for data of any type that can then be served by the THREDDS Data Server (TDS). The TDR provides functionality to: * securely store and "own" data files and associated metadata * upload files via HTTP and gridftp * upload a collection of data as single file * modify and restructure repository contents * incorporate metadata provided by the user * generate additional metadata programmatically * edit individual metadata elements The TDR can exist separately from a TDS, serving content via HTTP. Also, it can work in conjunction with the TDS, which includes functionality to provide: * access to data in a variety of formats via -- OPeNDAP -- OGC Web Coverage Service (for gridded datasets) -- bulk HTTP file transfer * a NetCDF view of datasets in NetCDF, OPeNDAP, HDF-5, GRIB, and NEXRAD formats * serving of very large volume datasets, such as NEXRAD radar * aggregation into virtual datasets * subsetting via OPeNDAP and NetCDF Subsetting services This talk will discuss TDR/TDS capabilities as well as how users can install this software to create their own repositories.

Online-to-offline models in HIV service delivery.

PubMed

Anand, Tarandeep; Nitpolprasert, Chattiya; Phanuphak, Nittaya

2017-09-01

Half the world's population has access to Internet and technologies, and utilization is near-ubiquitous among providers and key populations. Despite being so well connected; identifying, reaching and linking vulnerable populations to HIV clinical services remains a global challenge. This review highlights the emerging online-to-offline (O2O) models, their potential in scaling up services, and evaluating impact, and implications for future research. Globally, four major types of O2O models have been implemented, primarily in the West and Asia, especially among MSM and transgender women. These models have varying levels of impact in terms of reach, engagement, participation, linkage, and ability to track and monitor participants, and assess outcomes. Those integrated with offline sites enable seamless transition, dramatically reduce the O2O linkage time and demonstrate high linkage success (>73%). O2O models are ideal for at-risk, stigmatized, criminalized populations and for scaling-up biomedical prevention interventions such as preexposure and postexposure prophylaxis. O2O models represent novel and powerful solutions to reverse the pandemic and could help fill significant programmatic gaps in tracking individuals through HIV cascades. Providers, especially in resource-limited settings, could choose between a variety of current approaches highlighted in this review and employ no-cost or cost-effective technologies to transform their traditional models and leverage O2O models.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

2008-07-01

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

The Control Unit of KM3NeT data acquisition

NASA Astrophysics Data System (ADS)

Bozza, Cristiano

2016-04-01

The KM3NeT Collaboration is building a new generation of neutrino telescopes in the Mediterranean Sea. With the telescopes, scientists will search for cosmic neutrinos to study highly energetic objects in the Universe, while one neutrino detector will be dedicated to measure the properties of the high-energy neutrino particles themselves. Control of the KM3NeT data acquisition processes is handled by the KM3NeT Control Unit, which has been designed to maximise the detector live time. The Control Unit features software programs with different roles, following the philosophy of having no single point of failure. While all programs are interconnected, each one can also work alone for most of the time in case other services are unavailable. All services run on the Common Language Runtime, which ensures portability, flexibility and automatic memory management. Each service has an embedded Web server, providing a user interface as well as programmatic access to data and functions. Data to and from detector components for monitoring and management purposes are transmitted using a custom designed protocol. The Control Unit is interfaced to one or more Message Dispatchers to control the data acquisition chain. A Data Base Interface provides fast and fault-tolerant connection to a remote Data Base.

Gramene 2016: comparative plant genomics and pathway resources

PubMed Central

Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

2016-01-01

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

Michigan dentists' attitudes toward Medicaid and an alternative public dental insurance system for children.

PubMed

Nebeker, Cordell D; Briskie, Daniel M; Maturo, Raymond A; Piskorowski, Wilhelm A; Sohn, Woosung; Boynton, James R

2014-01-01

Healthy Kids Dental (HKD) was created as a pilot program of the Michigan State Medicaid program to increase access to care for Medicaid-eligible children. The purpose of this study was to evaluate dentist's attitudes toward Healthy Kids Dental and Medicaid in Michigan. An online survey was sent to practitioners with an e-mail address registered with the Michigan Dental Association (N=4,285). Surveys were returned from 965 practitioners (~23 percent). Although practitioners were not fully satisfied with the HKD, their satisfaction with the program was significantly higher than their satisfaction with the traditional Medicaid program (P<.001). Sixty-four percent of providers that accept Medicaid limit the number of children seen in some manner, while 28 percent of providers that accept HKD limit the number of children seen. Families with traditional Medicaid who contact an office are significantly less likely to receive treatment for their child than families with HKD insurance who contact the same office (P<.001). Practitioners were more satisfied with programmatic and patient-related factors of the Healthy Kids Dental program than they were with Medicaid. Dentists were more likely to treat children with HKD than children with Medicaid when the parent contacts a dentist in Michigan.

Smoothing Data Friction through building Service Oriented Data Platforms

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Richards, C. J.; Evans, B. J. K.; Wang, J.; Druken, K. A.

2017-12-01

Data Friction has been commonly defined as the costs in time, energy and attention required to simply collect, check, store, move, receive, and access data. On average, researchers spend a significant fraction of their time finding the data for their research project and then reformatting it so that it can be used by the software application of their choice. There is an increasing role for both data repositories and software to be modernised to help reduce data friction in ways that support the better use of the data. Many generic data repositories simply accept data in the format as supplied: the key check is that the data have sufficient metadata to enable discovery and download. Few generic repositories have both the expertise and infrastructure to support the multiple domain specific requirements that facilitate the increasing need for integration and reusability. In contrast, major science domain-focused repositories are increasingly able to implement and enforce community endorsed best practices and guidelines that ensure reusability and harmonization of data for use within the community by offering semi-automated QC workflows to improve quality of submitted data. The most advanced of these science repositories now operate as service-oriented data platforms that extend the use of data across domain silos and increasingly provide server-side programmatically-enabled access to data via network protocols and community standard APIs. To provide this, more rigorous QA/QC procedures are needed to validate data against standards and community software and tools. This ensures that the data can be accessed in expected ways and also demonstrates that the data works across different (non-domain specific) packages, tools and programming languages deployed by the various user communities. In Australia, the National Computational Infrastructure (NCI) has created such a service-oriented data platform which is demonstrating how this approach can reduce data friction, servicing both individual domains as well as facilitating cross-domain collaboration. The approach has required an increase in effort for the repository to provide the additional expertise, so as to enable a better capability and efficient system which ultimately saves time by the individual researcher.

Python scripting in the nengo simulator.

PubMed

Stewart, Terrence C; Tripp, Bryan; Eliasmith, Chris

2009-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models.

Python Scripting in the Nengo Simulator

PubMed Central

Stewart, Terrence C.; Tripp, Bryan; Eliasmith, Chris

2008-01-01

Nengo (http://nengo.ca) is an open-source neural simulator that has been greatly enhanced by the recent addition of a Python script interface. Nengo provides a wide range of features that are useful for physiological simulations, including unique features that facilitate development of population-coding models using the neural engineering framework (NEF). This framework uses information theory, signal processing, and control theory to formalize the development of large-scale neural circuit models. Notably, it can also be used to determine the synaptic weights that underlie observed network dynamics and transformations of represented variables. Nengo provides rich NEF support, and includes customizable models of spike generation, muscle dynamics, synaptic plasticity, and synaptic integration, as well as an intuitive graphical user interface. All aspects of Nengo models are accessible via the Python interface, allowing for programmatic creation of models, inspection and modification of neural parameters, and automation of model evaluation. Since Nengo combines Python and Java, it can also be integrated with any existing Java or 100% Python code libraries. Current work includes connecting neural models in Nengo with existing symbolic cognitive models, creating hybrid systems that combine detailed neural models of specific brain regions with higher-level models of remaining brain areas. Such hybrid models can provide (1) more realistic boundary conditions for the neural components, and (2) more realistic sub-components for the larger cognitive models. PMID:19352442

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

An Application Programming Interface for Synthetic Snowflake Particle Structure and Scattering Data

NASA Technical Reports Server (NTRS)

Lammers, Matthew; Kuo, Kwo-Sen

2017-01-01

The work by Kuo and colleagues on growing synthetic snowflakes and calculating their single-scattering properties has demonstrated great potential to improve the retrievals of snowfall. To grant colleagues flexible and targeted access to their large collection of sizes and shapes at fifteen (15) microwave frequencies, we have developed a web-based Application Programming Interface (API) integrated with NASA Goddard's Precipitation Processing System (PPS) Group. It is our hope that the API will enable convenient programmatic utilization of the database. To help users better understand the API's capabilities, we have developed an interactive web interface called the OpenSSP API Query Builder, which implements an intuitive system of mechanisms for selecting shapes, sizes, and frequencies to generate queries, with which the API can then extract and return data from the database. The Query Builder also allows for the specification of normalized particle size distributions by setting pertinent parameters, with which the API can also return mean geometric and scattering properties for each size bin. Additionally, the Query Builder interface enables downloading of raw scattering and particle structure data packages. This presentation will describe some of the challenges and successes associated with developing such an API. Examples of its usage will be shown both through downloading output and pulling it into a spreadsheet, as well as querying the API programmatically and working with the output in code.

75 FR 56092 - Notice Modifying Restricted Service List for a Programmatic Agreement for Managing Properties...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

... Inclusion in the National Register of Historic Places; Marseilles Land and Water Company September 3, 2010... Programmatic Agreement for Managing Properties Included in or Eligible for Inclusion in the National Register...

The Open Data Repository's Data Publisher

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

2015-12-01

Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A, Mars Science Laboratory Investigations and University of Arizona Geosciences.

36 CFR 800.14 - Federal agency program alternatives.

Code of Federal Regulations, 2010 CFR

2010-07-01

... program or the resolution of adverse effects from certain complex project situations or multiple... by the agreement. (3) Developing programmatic agreements for complex or multiple undertakings. Consultation to develop a programmatic agreement for dealing with the potential adverse effects of complex...

75 FR 40820 - City of Broken Bow, Oklahoma; Project No. 12470-001-Oklahoma Broken Bow Re-Regulation Dam...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-14

... Service List for a Programmatic Agreement for Managing Properties Included in or Eligible for Inclusion in... programmatic agreement for managing properties included in, or eligible for inclusion in, the National Register...

78 FR 71561 - Notice of Intent To Prepare a Supplemental Programmatic Environmental Impact Statement for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-29

... of documents #0;appearing in this section. #0; #0; #0; #0;#0;Federal Register / Vol. 78, No. 230... contracts. The 2008 CRP Programmatic EA (PEA) and FONSI, which evaluated mandatory changes to CRP...

33 CFR 385.1 - Purpose of the programmatic regulations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... regulations. 385.1 Section 385.1 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION PLAN General... of Project Implementation Reports, Project Cooperation Agreements, plans and specifications, Pilot...

33 CFR 385.1 - Purpose of the programmatic regulations.

Code of Federal Regulations, 2011 CFR

2011-07-01

... regulations. 385.1 Section 385.1 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION PLAN General... of Project Implementation Reports, Project Cooperation Agreements, plans and specifications, Pilot...

33 CFR 385.1 - Purpose of the programmatic regulations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... regulations. 385.1 Section 385.1 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION PLAN General... of Project Implementation Reports, Project Cooperation Agreements, plans and specifications, Pilot...

33 CFR 385.1 - Purpose of the programmatic regulations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... regulations. 385.1 Section 385.1 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION PLAN General... of Project Implementation Reports, Project Cooperation Agreements, plans and specifications, Pilot...

33 CFR 385.1 - Purpose of the programmatic regulations.

Code of Federal Regulations, 2010 CFR

2010-07-01

... regulations. 385.1 Section 385.1 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION PLAN General... of Project Implementation Reports, Project Cooperation Agreements, plans and specifications, Pilot...

Space station accommodations for life sciences research facilities. Phase 1: Conceptual design and programmatics studies for Missions SAAX0307, SAAX0302 and the transition from SAAX0307 to SAAX0302. Volume 2: Study results

NASA Technical Reports Server (NTRS)

1986-01-01

Lockheed Missiles and Space Company's conceptual designs and programmatics for a Space Station Nonhuman Life Sciences Research Facility (LSRF) are presented. Conceptual designs and programmatics encompass an Initial Orbital Capability (IOC) LSRF, a growth or follow-on Orbital Capability (FOC), and the transitional process required to modify the IOC LSFR to the FOC LSFR. The IOC and FOC LSFRs correspond to missions SAAX0307 and SAAX0302 of the Space Station Mission Requirements Database, respectively.

A Broader Conceptual Approach to Clinical Practice for the 21st Century

ERIC Educational Resources Information Center

Frey, Andy J.; Dupper, David R.

2005-01-01

The need for school social workers and other mental health providers to move away from specialist oriented services to comprehensive general programmatic approaches has been gaining increasing support among leaders in education and mental health. The "clinical quadrant" highlighted in this article is offered to better conceptualize the complex and…

Peer Review of Teaching: Best Practices for a Non-Programmatic Approach

ERIC Educational Resources Information Center

Alabi, Jaena; Weare, William H., Jr.

2014-01-01

Many academic librarians who provide library instruction have never received formal training in educational theory and methods. To bridge this gap and improve the teaching skills of instruction librarians, some academic libraries have established peer review of teaching programs. Despite the recognized benefits of peer review, it may not be…

Dropping Out of School. State Programs in Dropout Prevention.

ERIC Educational Resources Information Center

Sherman, Joel D.; Levine, Andrea B.

This document discusses state initiatives to address the dropout problem by presenting an overview of programmatic strategies states are using to meet the needs of dropout-prone youth and school dropouts and strategies to finance these efforts. It provides a framework for understanding current state programs and then presents an overview of…

Providing the Support Services Needed by Students Who Are Deaf or Hard of Hearing.

ERIC Educational Resources Information Center

Luetke-Stahlman, Barbara

1998-01-01

Discusses programmatic and curricular modifications often needed for students included in public school settings who are deaf or hard of hearing, such as adapting the mode/flow of classroom communication, linguistic-level changes, and adapting the listening and physical environment. Possible curricular modifications are suggested for…

An Intergenerational Partnership between a College and Congregate Housing Facility: How It Works, What It Means.

ERIC Educational Resources Information Center

Krout, John A.; Pogorzala, Christine H.

2002-01-01

Describes the goals, development, operation, and outcomes of an intergenerational programmatic relationship between a private college and a congregate facility for older adults. Faculty and students report that partnership activities provide excellent opportunities for increasing the understanding of aging and older adults. Residents report…

Self-Reflection and Math Performance in an Online Learning Environment

ERIC Educational Resources Information Center

Choi, Jinnie; Walters, Alyssa; Hoge, Pat

2017-01-01

According to recent reports, K-12 full-time virtual school students have shown lower performance in math than their counterparts in brick-and-mortar schools. However, research is lacking in what kind of programmatic interventions virtual schools might be particularly well-suited to provide to improve math performance. Engaging students in…

Procedure for estimating orbital debris risks

NASA Technical Reports Server (NTRS)

Crafts, J. L.; Lindberg, J. P.

1985-01-01

A procedure for estimating the potential orbital debris risk to the world's populace from payloads or spent stages left in orbit on future missions is presented. This approach provides a consistent, but simple, procedure to assess the risk due to random reentry with an adequate accuracy level for making programmatic decisions on planned low Earth orbit missions.

Transformational Leadership and Programmatic Outcomes: A Correlational Study of Athletic Training Programs

ERIC Educational Resources Information Center

Gerakos, Donna S.

2017-01-01

The study of leadership practices of athletic training program directors is severely limited and the lack of clearly defined program director qualifications combined to provide the underpinnings for this research. The purpose of this quantitative correlational study was to identify if a relationship existed between athletic training program…

Not Just for Novices: The Programmatic Impact of Practice-Based Teacher Education

ERIC Educational Resources Information Center

Francis, Anthony Tuf; Olson, Mark; Weinberg, Paul J.; Stearns-Pfeiffer, Amanda

2018-01-01

This article describes how a secondary teacher education program at a midsized university made the turn toward a practice-based program in teacher education. The authors argue that efforts to recenter the program around practices have not only improved opportunities for novice teachers, but also have provided teacher educators a programmatic…

Peer Facilitated Writing Groups: A Programmatic Approach to Doctoral Student Writing

ERIC Educational Resources Information Center

Kumar, Vijay; Aitchison, Claire

2018-01-01

Very few empirical studies have investigated programmes in which doctoral students act as peer facilitators in faculty writing groups. We report on the development of a centrally delivered doctoral student writing programme in which twenty student participants were mentored and provided with the resources to initiate their own faculty-based…

Policy Issues in Education for the Health Professions. Item #5B.

ERIC Educational Resources Information Center

Illinois State Board of Higher Education, Springfield.

This report re-examines the State of Illinois' Board of Higher Education's 1980 policies on education for the health professions and recommends revised general policies for the Board's consideration. An update on occupational demand and program developments are provided and programmatic directions are recommended for institutions to consider in…

34 CFR 611.52 - What are a grantee's programmatic responsibilities for ensuring that scholarship recipients...

Code of Federal Regulations, 2014 CFR

2014-07-01

... ensuring that scholarship recipients become successful teachers in high-need schools? 611.52 Section 611.52... teachers in high-need schools? In implementing its approved project, the grantee must— (a) Provide...) Upon graduation, scholarship recipients are able to secure teaching positions in high-need schools of...

34 CFR 611.52 - What are a grantee's programmatic responsibilities for ensuring that scholarship recipients...

Code of Federal Regulations, 2013 CFR

2013-07-01

... ensuring that scholarship recipients become successful teachers in high-need schools? 611.52 Section 611.52... teachers in high-need schools? In implementing its approved project, the grantee must— (a) Provide...) Upon graduation, scholarship recipients are able to secure teaching positions in high-need schools of...

34 CFR 611.52 - What are a grantee's programmatic responsibilities for ensuring that scholarship recipients...

Code of Federal Regulations, 2011 CFR

2011-07-01

... ensuring that scholarship recipients become successful teachers in high-need schools? 611.52 Section 611.52... teachers in high-need schools? In implementing its approved project, the grantee must— (a) Provide...) Upon graduation, scholarship recipients are able to secure teaching positions in high-need schools of...

34 CFR 611.52 - What are a grantee's programmatic responsibilities for ensuring that scholarship recipients...

Code of Federal Regulations, 2012 CFR

2012-07-01

... ensuring that scholarship recipients become successful teachers in high-need schools? 611.52 Section 611.52... teachers in high-need schools? In implementing its approved project, the grantee must— (a) Provide...) Upon graduation, scholarship recipients are able to secure teaching positions in high-need schools of...

Embracing Scientific and Engineering Practices in 4-H

ERIC Educational Resources Information Center

Worker, Steven M.

2013-01-01

The 4-H Science Initiative has renewed efforts to strengthen 4-H programmatic and evaluation efforts in science and engineering education. A fundamental component of this initiative is to provide opportunities to youth to aid in their development of science process skills; however, emerging research stresses the importance of engaging youth in…

Current directions in military health-care provider resilience.

PubMed

Lester, Paul B; Taylor, Lauren C; Hawkins, Stacy Ann; Landry, Lisa

2015-02-01

After more than a decade of war, the US military continues to place significant emphasis on psychological health and resilience. While research and programs that focus on the broader military community's resilience continue to emerge, less is known about and until recently little focus has been placed on military medical provider resilience. In this article, we review the literature on military medical provider resilience, provide an overview of the programmatic and technological advances designed to sustain and develop military medical provider resilience, and finally offer recommendations for future research.

78 FR 56869 - Nuclear Infrastructure Programmatic Environmental Impact Statement Supplement Analysis...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-16

... DEPARTMENT OF ENERGY Nuclear Infrastructure Programmatic Environmental Impact Statement Supplement... Statement for Accomplishing Expanded Civilian Nuclear Energy Research and Development and Isotope Production...), Office of Nuclear Energy, U.S. Department of Energy, 1000 Independence Ave. SW., Washington, DC 20585...

33 CFR 385.20 - Restoration Coordination and Verification (RECOVER).

Code of Federal Regulations, 2013 CFR

2013-07-01

... Verification (RECOVER). 385.20 Section 385.20 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION... technical team described in the “Final Integrated Feasibility Report and Programmatic Environmental Impact...

33 CFR 385.20 - Restoration Coordination and Verification (RECOVER).

Code of Federal Regulations, 2014 CFR

2014-07-01

... Verification (RECOVER). 385.20 Section 385.20 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION... technical team described in the “Final Integrated Feasibility Report and Programmatic Environmental Impact...

33 CFR 385.20 - Restoration Coordination and Verification (RECOVER).

Code of Federal Regulations, 2012 CFR

2012-07-01

... Verification (RECOVER). 385.20 Section 385.20 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION... technical team described in the “Final Integrated Feasibility Report and Programmatic Environmental Impact...

33 CFR 385.20 - Restoration Coordination and Verification (RECOVER).

Code of Federal Regulations, 2011 CFR

2011-07-01

... Verification (RECOVER). 385.20 Section 385.20 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE PROGRAMMATIC REGULATIONS FOR THE COMPREHENSIVE EVERGLADES RESTORATION... technical team described in the “Final Integrated Feasibility Report and Programmatic Environmental Impact...

CSM in Latin America: new developments.

PubMed

1986-01-01

SOMARC is currently providing support to contraceptive social marketing efforts in Bolivia, Brazil, and Paraguay. The distinctly different family planning climates in these 3 countries have provided SOMARC with an opportunity to practice programmatic flexibility in project strategy and design. In Bolivia, the SOMARC strategy for implementing contraceptive social marketing is primarily a private sector venture in which donated products will be imported by local distributors and sold through the traditional channels. Distribution services through a network of local private family planning groups will provide SOMARC with direct access to Bolivian trade unions and work organizations. These family planning groups will in turn be strengthened by their association with the social marketing program as a potential source of revenue. In Brazil, where many low-priced contraceptives are already on the market, SOMARC's role will be in the areas of communication and promotion to increase contraceptive prevalence. The first task will be to identify target areas where there is a combination of low prevalence and an existing market infrastructure. A Brazil Contraceptive Social Marketing Program Advisory Council has been formed to provide a consolidated approach to family planning activities. Efforts toward developing a contraceptive social marketing program in Paraguay remain at an exploratory level. The introduction of social marketing in Paraguay is complicated by the existence of a pervasive contraband system. Although consumer awareness of contraception is high, the contraceptive prevalence rate is low. Efforts in all 3 countries reflect SOMAR's strategy of broadening the scope of project alternatives to meet the special needs of each nation.

A mixed-method evaluation of the New York State Eat Well Play Hard Community Projects: Building local capacity for sustainable childhood obesity prevention.

PubMed

Reid, Kaydian S; Sekhobo, Jackson P; Gantner, Leigh A; Holbrook, MaryEllen K; Allsopp, Marie; Whalen, Linda B; Koren-Roth, Amy

2018-04-01

This study used a mixed-method, comparative case study approach to assess the level of capacity built for childhood obesity prevention among seven New York State Eat Well Play Hard-Community Projects (EWPH-CP). Data were collected through a self-reported survey in 2007, semi-structured interviews in 2009, and EWPH-CP program documentation throughout the 2006-2010 funding cycle. Quantitative and qualitative analyses were used along with an integrative framework for assessing local capacity building to characterize the capacity built by the study coalitions. Four coalitions rated membership characteristics as a challenge at the beginning of the funding cycle. Towards the end of the funding cycle, all seven coalitions reported activities that were initially focused on building their membership (i.e., member capacity) or positive working relationships (i.e. relational capacity), before eventually pursuing support and resources (i.e., organizational capacity) for implementing their chosen community-oriented programmatic goals (i.e., programmatic capacity). Five coalitions reported environmental changes aimed at increasing physical activity or fruit and vegetable intake. Technical assistance provided to coalitions was credited with contributing to the achievement of programmatic goals. These results suggest that the coalitions succeeded in building local capacity for increasing age-appropriate physical activity or fruit and vegetables intake in the target communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohi, J.

Supporting analysis and assessments can provide a sound analytic foundation and focus for program planning, evaluation, and coordination, particularly if issues of hydrogen production, distribution, storage, safety, and infrastructure can be analyzed in a comprehensive and systematic manner. The overall purpose of this activity is to coordinate all key analytic tasks-such as technology and market status, opportunities, and trends; environmental costs and benefits; and regulatory constraints and opportunities-within a long-term and systematic analytic foundation for program planning and evaluation. Within this context, the purpose of the project is to help develop and evaluate programmatic pathway options that incorporate near andmore » mid-term strategies to achieve the long-term goals of the Hydrogen Program. In FY 95, NREL will develop a comprehensive effort with industry, state and local agencies, and other federal agencies to identify and evaluate programmatic pathway options to achieve the long-term goals of the Program. Activity to date is reported.« less

GMES Space Component: Programme overview

NASA Astrophysics Data System (ADS)

Aschbacher, J.; Milagro-Perez, M. P.

2012-04-01

The European Union (EU) and the European Space Agency (ESA) have developed the Global Monitoring for Environment and Security (GMES) programme as Europe's answer to the vital need for joined-up data about our climate, environment and security. Through a unique combination of satellite, atmospheric and Earth-based monitoring systems, the initiative will provide new insight into the state of the land, sea and air, providing policymakers, scientists, businesses and the public with accurate and timely information. GMES capabilities include monitoring and forecasting of climatic change, flood risks, soil and coastal erosion, crop and fish resources, air pollution, greenhouse gases, iceberg distribution and snow cover, among others. To accomplish this, GMES has been divided into three main components: Space, In-situ and Services. The Space Component, led by ESA, comprises five types of new satellites called Sentinels that are being developed by ESA specifically to meet the needs of GMES, the first of which to be launched in 2013. These missions carry a range of technologies, such as radar and multi-spectral imaging instruments for land, ocean and atmospheric monitoring. In addition, access to data from the so-called Contributing Missions guarantees that European space infrastructure is fully used for GMES. An integrated Ground Segment ensures access to Sentinels and Contributing Missions data. The in-situ component, under the coordination of the European Environment Agency (EEA), is composed of atmospheric and Earth based monitoring systems, and based on established networks and programmes at European and international levels. The European Commission is in charge of implementing the services component of GMES and of leading GMES overall. GMES services, fed with data from the Space and In-situ components, will provide essential information in five main domains, atmosphere, ocean and land monitoring as well as emergency response and security. Climate change has been added as a new GMES service and cross-cuts all these domains. Even if GMES is built to primarily serve operational services, there is a large benefit for science users as well. In addition, science will be crucial to advance services and provide critical input to the definition of new observation systems. Access to Sentinel data is governed by the Sentinel data policy, which is part of a wider GMES data and information access policy. The Sentinel data policy envisages free and open access, subject to restrictions only if security or other European interests need to be preserved. The programme will enter the operational phase in 2014, when the first dedicated spacecraft, the Sentinel missions, will be in orbit. The main programmatic challenge is to ensure the programme's long-term sustainability. This session aims at informing users about the current programme's overall status and its potential for users in the services and scientific fields.

Data Democratization - Promoting Real-Time Data Sharing and Use Worldwide

NASA Astrophysics Data System (ADS)

Yoksas, T. C.; Almeida, W. G.; Leon, V. C.

2007-05-01

The Unidata Program Center (Unidata) of the University Corporation of Atmospheric Research (UCAR) is actively involved in international collaborations whose goals are the free-and-open sharing of hydro-meteorological data; the distribution of analysis and visualization tools for those data; the establishment of server technologies that provide easy-to-use, programmatic remote-access to a wide variety of datasets, and in the building of a community where data, tools, and best practices in education and research are shared. The tools and services provided by Unidata are available to the research and education community free-of-charge. Data sharing capabilities are being provided by Unidata's Internet Data Distribution (IDD) system, a community-based effort that has been the primary source of real-time meteorological data in the US university community for over a decade. A collaboration among Unidata, Brazil's Centro de Previso de Tempo e Estudos Climaticos (CPTEC), the Universidad Federal do Rio de Janeiro (UFRJ), and the Universidade de Sao Paulo (USP) has resulted in the creation of a Brazilian peer of the North American IDD, the IDD-Brasil. Collaboration between Unidata and the Universidad de Costa Rica (UCR) seeks to extend IDD data sharing throughout Central America and the Caribbean in an IDD-Caribe. Efforts aimed at creating a data sharing network for researchers on the Antarctic continent have resulted in the establishment of the Antarctic-IDD. Most recently, explorations of data sharing between UCAR and select countries in Africa have begun. Data analysis and visualization capabilities are available through Unidata in a suite of freely-available applications: the National Centers for Environmental Prediction (NCEP) GEneral Meteorology PAcKage (GEMPAK); the Unidata Integrated Data Viewer (IDV); and University of Wisconsin, Space Science and Engineering Center (SSEC) Man-computer Interactive Data Access System (McIDAS). Remote data access capabilities are provided by Unidata's Thematic Realtime Environmental Data Services (THREDDS) servers (which incorporate Open-source Project for a Network Data Access (OPeNDAP) data services), and the Abstract Data Distribution Environment (ADDE) of McIDAS. It is envisioned that the data sharing capabilities available in the IDD, IDD-Brasil, IDD-Caribe, and Antarctic-IDD, remote data access capabilities available in THREDDS and ADDE, and analysis capabilities available in GEMPAK, the IDV, and McIDAS will help foster new collaborations among prominent universities, national meteorological agencies, and WMO Regional Meteorological Training Centers throughout North, Central, and South America, in the Antarctic research community, and eventually in Africa. This paper is intended to inform AGU 2007 Joint Assembly attendees, especially those in Mexico and Central America, of the availability of real-time data and tools to analyze/visualize those data, and to promote the free-and-open sharing of data, especially of locally-held datasets of general interest.

A Systematic Approach to Programmatic Assessment

ERIC Educational Resources Information Center

Moffit, Dani M.; Mansell, Jamie L.; Russ, Anne C.

2016-01-01

Context: Accrediting bodies and universities increasingly require evidence of student learning within courses and programs. Within athletic training, programmatic assessment has been a source of angst for program directors. While there are many ways to assess educational programs, this article introduces 1 systematic approach. Objective: This…

Programmatic Agreements for Project-Level Air Quality Analyses : NCHRP 25-25 Task 78

DOT National Transportation Integrated Search

2015-09-01

The research performed under Task 78 was divided into two phases. The first phase involved development of a draft Programmatic Agreement (PA) template and a draft Technical Support Document (TSD) template for project-level carbon monoxide (CO) hot-sp...

10 CFR 603.895 - Protection of information in programmatic reports.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Section 603.895 Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS TECHNOLOGY INVESTMENT AGREEMENTS Award Terms Related to Other Administrative Matters Financial and Programmatic Reporting § 603.895... transaction that would be trade secret, or commercial or financial information that is privileged or...

75 FR 69475 - Notice Regarding Changed Venue for Public Hearing On a Draft Programmatic Environmental Impact...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-12

... NATIONAL SCIENCE FOUNDATION Notice Regarding Changed Venue for Public Hearing On a Draft Programmatic Environmental Impact Statement/Overseas Environmental Impact Statement (PEIS) AGENCY: National Science Foundation. ACTION: Notice regarding changed venue for public hearing. SUMMARY: The National...

Transfer Function Control for Biometric Monitoring System

NASA Technical Reports Server (NTRS)

Chmiel, Alan J. (Inventor); Grodinsky, Carlos M. (Inventor); Humphreys, Bradley T. (Inventor)

2015-01-01

A modular apparatus for acquiring biometric data may include circuitry operative to receive an input signal indicative of a biometric condition, the circuitry being configured to process the input signal according to a transfer function thereof and to provide a corresponding processed input signal. A controller is configured to provide at least one control signal to the circuitry to programmatically modify the transfer function of the modular system to facilitate acquisition of the biometric data.

Enhancing GADRAS Source Term Inputs for Creation of Synthetic Spectra.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horne, Steven M.; Harding, Lee

The Gamma Detector Response and Analysis Software (GADRAS) team has enhanced the source term input for the creation of synthetic spectra. These enhancements include the following: allowing users to programmatically provide source information to GADRAS through memory, rather than through a string limited to 256 characters; allowing users to provide their own source decay database information; and updating the default GADRAS decay database to fix errors and include coincident gamma information.

Army Programmatic Environmental Assessment of the Mine Resistant Ambush Protected (MRAP) Vehicle Program

DTIC Science & Technology

2010-12-01

vehicles  with  a  blast  resistant  V‐shaped underbody designed to protect the crew from mine blasts, fragments  and direct  fire  weapons.  The CAT I vehicle...Army Programmatic Environmental  Assessment   of the  Mine  Resistant  Ambush Protected (MRAP)  Vehicle Program        December 2010...06-07-2010 to 20-11-2010 4. TITLE AND SUBTITLE Army Programmatic Environmental Assessment of the Mine Resistant Ambush Protected (MRAP) Vehicle

System analysis study of space platform and station accommodations for life sciences research facilities. Volume 2: Study results, attachment 2. Phase A: Conceptual design and programmatics

NASA Technical Reports Server (NTRS)

Wiley, Lowell F.

1985-01-01

The study results from the conceptual design and programmatics segment of the Space Platform and Station Accommodation for Life Sciences Research Facilities. The results and significant findings of the conceptual design and programmatics were generated by these tasks: (1) the review and update engineering and science requirements; (2) analysis of life sciences mission transition scenario; (3) the review and update of key trade issues; (4) the development of conceptual definition and designs; and (5) the development of the work breakdown schedule and its dictionary, program schedule, and estimated costs.

System analysis study of space platform and station accommodations for life sciences research facilities. Volume 1: Executive summary. Phase A: Conceptual design and programmatics

NASA Technical Reports Server (NTRS)

1985-01-01

The study was conducted in 3 parts over a 3 year period. The study schedule and the documentation associated with each study part is given. This document summarized selected study results from the conceptual design and programmatics segment of the effort. The objectives were: (1) to update requirements and tradeoffs and develop a detailed design and mission requirements document; (2) to develop conceptual designs and mission descriptions; and (3) to develop programmatic, i.e., work breakdown structure and work breakdown structure dictionary, estimated cost, and implementing plans and schedules.

Integrating HIV testing and care into tuberculosis services in Benin: programmatic aspects.

PubMed

Ferroussier, O; Dlodlo, R A; Capo-Chichi, D; Boillot, F; Gninafon, M; Trébucq, A; Fujiwara, P I

2013-11-01

Between 2005 and 2008, the diagnosis and care of human immunodeficiency virus (HIV) infection and tuberculosis (TB) services were integrated in Benin. The appointment of a TB-HIV Coordinator by the National Tuberculosis Control Programme and quarterly supervisory visits to TB clinics have bolstered the implementation of integrated HIV-TB activities. HIV testing and cotrimoxazole preventive therapy were integrated smoothly into the TB services. The strategy chosen to facilitate access of HIV-positive TB patients to antiretroviral treatment contributed to greater integration over time, but perpetuated, for some, the burden of attending two facilities. The integration and decentralisation of TB and HIV care services at national level in Benin resulted in a high uptake of HIV services among TB patients.

Identifying Inputs to Leadership Development within an Interdisciplinary Leadership Minor

ERIC Educational Resources Information Center

McKim, Aaron J.; Sorensen, Tyson J.; Velez, Jonathan J.

2015-01-01

Researchers conducted a qualitative analysis of students' experiences while enrolled in an interdisciplinary leadership minor with the intent to determine programmatic inputs that spur leadership development. Based on students' reflections, three domains of programmatic inputs for leadership development within the minor were identified. These…

Program Directors' Perceptions of Programmatic Attributes Contributing to Athletic Training Student Persistence

ERIC Educational Resources Information Center

Bowman, Thomas G.; Dodge, Thomas M.; Mazerolle, Stephanie M.

2015-01-01

Context: Graduates of athletic training programs (ATPs) have identified factors contributing to their persistence through professional education. However, program directors have yet to elaborate on programmatic attributes that might contribute to athletic training student retention in their respective ATPs. Objective: To determine program…

ACHP | News

Science.gov Websites

Conservation Service Develops Prototype Programmatic Agreement That Can Give States More Time Savings and ) is pleased to announce it has designated a Prototype Programmatic Agreement (PA) for the use of the ) without the need for ACHP participation in consultation or execution of the agreement. This program

Solar Energy Development PEIS Information Center

Science.gov Websites

skip navigation Solar Energy Development Programmatic EIS Home About the EIS Public Involvement Solar Energy Solar Energy Zones Maps Documents secondary menu News Frequently Asked Questions Glossary E the Programmatic Environmental Impact Statement for Solar Energy Development in Six Southwestern

Keep Writing Weird: A Call for Eco-Administration and Engaged Writing Programs

ERIC Educational Resources Information Center

House, Veronica

2016-01-01

Influenced by ecological theories of writing, the author proposes a new model for writing curriculum design and community-based projects. The article provides a project of the Writing Initiative for Service and Engagement at the University of Colorado Boulder as an example of programmatic engagement with a community issue using an ecological…

Cash Incentives and Turnover in Center-Based Child Care Staff

ERIC Educational Resources Information Center

Gable, Sara; Rothrauff, Tanja C.; Thornburg, Kathy R.; Mauzy, Denise

2007-01-01

The current study evaluates the Workforce INcentive Project (WIN), a programmatic effort to increase child care workforce stability in center- and home-based child care providers via the provision of bi-annual cash incentives based on educational attainment. Five hundred and thirteen center-based teaching staff (304 WIN and 209 comparison) and 167…

Breaking Down Barriers and Building Bridges: Transformative Practices in Community- and School-Based Urban Teacher Preparation

ERIC Educational Resources Information Center

Lee, Robert E.

2018-01-01

Attracting and retaining high-quality teachers is especially challenging in urban districts. It is in these communities where teacher candidates must begin their preparation. This article provides a conceptual framework and programmatic examples used to develop a community-based urban teacher preparation model within a third hybrid space where…

Seeking Clarity in New Jersey for Leadership Preparation Program Design: Confusion, Fragility, and Unintended Consequences

ERIC Educational Resources Information Center

Doolittle, Gini

2013-01-01

In 2004, the New Jersey Department of Education issued a mandate to the 17 leadership preparation program providers to revise their leadership preparation programs after completing a critical friends review. This case study explores the challenges, programmatic, and political experiences of one preparation program as state support dwindled.…

Benefits a Community College Can Realize by Providing Older Adult Programs: A Trustee's Viewpoint.

ERIC Educational Resources Information Center

Hartstein, Ray

Board members of community colleges need to carefully consider and actively support feasible programs for older people with a firm commitment to fiscal and programmatic decisions assuring lifelong learning opportunities and public service activities. Trustees must be aware of and understand problems and issues of older adults, secure data for…

Rural Oriented R&D Projects Supported by ETA/USDL: A Review and Synthesis. Papers in Employment and Training Studies.

ERIC Educational Resources Information Center

Leonardson, Gene S.; Nelson, David M.

Seventy-one 1963-75 Research & Development (R&D) reports were reviewed for purposes of providing a rural R&D synthesis useful to Comprehensive Employment and Training Act (CETA) planners and identifying labor market analysis techniques/implications successful rural programmatic initiations, data gaps, and broad policy issues. Conclusions and…

Knowledge Management in Public Health: Examining the Role of a Web-Based Reporting System for Tobacco Control

ERIC Educational Resources Information Center

Gottlieb, Amy Sue

2009-01-01

The importance and use of data and information to make sound programmatic decisions are receiving increased attention as state and federal funding for public health programs grows tighter and as demands for accountability continue. This dissertation provides insight into fundamental questions regarding the utilization of a Web-based reporting…

Proposal for a Venture Capital Grant: A Programmatic Approach to Excellence in Illinois Public Schools.

ERIC Educational Resources Information Center

Hickrod, G. Alan; And Others

A new formula proposed for categorically funding local education programs in Illinois can channel more money into programs for excellence than can general purpose grants. The formula, which would provide venture capital to stimulate local initiatives, would depend on district plans for using the money to improve instruction and on distribution of…

Long-term forest ecosystem research: a programmatic view

Treesearch

Wayne Swank; James Vose

2010-01-01

Long-term research provides the building blocks of knowledge needed to address natural resource and environmental issues. "Long-term" has frequently been considered to span decades with a time frame that usually encompasses at least one generation of scientists and frequently two or more generations. In the rich history of forest science, the origin of long-...

Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) - A New U.S. DOE Data Archive

NASA Astrophysics Data System (ADS)

Agarwal, D.; Varadharajan, C.; Cholia, S.; Snavely, C.; Hendrix, V.; Gunter, D.; Riley, W. J.; Jones, M.; Budden, A. E.; Vieglais, D.

2017-12-01

The ESS-DIVE archive is a new U.S. Department of Energy (DOE) data archive designed to provide long-term stewardship and use of data from observational, experimental, and modeling activities in the earth and environmental sciences. The ESS-DIVE infrastructure is constructed with the long-term vision of enabling broad access to and usage of the DOE sponsored data stored in the archive. It is designed as a scalable framework that incentivizes data providers to contribute well-structured, high-quality data to the archive and that enables the user community to easily build data processing, synthesis, and analysis capabilities using those data. The key innovations in our design include: (1) application of user-experience research methods to understand the needs of users and data contributors; (2) support for early data archiving during project data QA/QC and before public release; (3) focus on implementation of data standards in collaboration with the community; (4) support for community built tools for data search, interpretation, analysis, and visualization tools; (5) data fusion database to support search of the data extracted from packages submitted and data available in partner data systems such as the Earth System Grid Federation (ESGF) and DataONE; and (6) support for archiving of data packages that are not to be released to the public. ESS-DIVE data contributors will be able to archive and version their data and metadata, obtain data DOIs, search for and access ESS data and metadata via web and programmatic portals, and provide data and metadata in standardized forms. The ESS-DIVE archive and catalog will be federated with other existing catalogs, allowing cross-catalog metadata search and data exchange with existing systems, including DataONE's Metacat search. ESS-DIVE is operated by a multidisciplinary team from Berkeley Lab, the National Center for Ecological Analysis and Synthesis (NCEAS), and DataONE. The primarily data copies are hosted at DOE's NERSC supercomputing facility with replicas at DataONE nodes.

Closing up Shop: Perspectives on the Departmental/Programmatic Elimination Experience

ERIC Educational Resources Information Center

Donoff, Susan B.; Rosser, Vicki J.

2016-01-01

Departmental and programmatic eliminations represent a new paradigm in the history of American higher education. Hastened by a national economic recession and competing state funding priorities, public postsecondary institutions have turned to academic attrition as a solution to continuous budgetary shortfalls. As a means of addressing the lived…

Closing up Shop: Meditations on the Departmental/Programmatic Elimination Experience

ERIC Educational Resources Information Center

Donoff, Susan Beth

2012-01-01

Departmental and programmatic eliminations represent a new paradigm in the history of American higher education. Hastened by a national economic recession and competing state funding priorities, public post-secondary institutions have turned to academic attrition as a solution to continuous budgetary shortfalls. As a means of addressing the lived…

76 FR 24050 - Coral Reef Restoration Plan, Final Programmatic Environmental Impact Statement, Biscayne National...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-29

... DEPARTMENT OF THE INTERIOR National Park Service [2310-0003-422] Coral Reef Restoration Plan... for the Coral Reef Restoration Plan, Biscayne National Park. SUMMARY: Pursuant to the National... availability of a Final Programmatic Environmental Impact Statement for the Coral Reef Restoration Plan (Plan...

Progress toward a cosmic dust collection facility on space station

NASA Technical Reports Server (NTRS)

Mackinnon, Ian D. R. (Editor); Carey, William C. (Editor)

1987-01-01

Scientific and programmatic progress toward the development of a cosmic dust collection facility (CDCF) for the proposed space station is documented. Topics addressed include: trajectory sensor concepts; trajectory accuracy and orbital evolution; CDCF pointing direction; development of capture devices; analytical techniques; programmatic progress; flight opportunities; and facility development.

78 FR 16275 - Extension of the Duration of Programmatic Agreements Based on the Department of Energy Prototype...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-14

... ADVISORY COUNCIL ON HISTORIC PRESERVATION Extension of the Duration of Programmatic Agreements... Comment AGENCY: Advisory Council on Historic Preservation. ACTION: The Advisory Council on Historic... Program, and Energy Efficiency and Conservation Block Grant. SUMMARY: The Advisory Council on Historic...

75 FR 67084 - Notice of Availability of the Draft Programmatic Environmental Impact Statement for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-01

... Draft Programmatic Environmental Impact Statement for the Mechanical Creation and Maintenance of... the Mechanical Creation and Maintenance of Emergent Sandbar Habitat on the Riverine Segments of the... Environmental Impact Statement for the Mechanical Creation and Maintenance of Emergent Sandbar Habitat in the...

47 CFR Appendix B to Part 1 - Nationwide Programmatic Agreement for the Collocation of Wireless Antennas

Code of Federal Regulations, 2010 CFR

2010-10-01

... Collocation of Wireless Antennas B Appendix B to Part 1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... the Collocation of Wireless Antennas Nationwide Programmatic Agreement for the Collocation of Wireless Antennas Executed by the Federal Communications Commission, the National Conference of State Historic...

47 CFR Appendix B to Part 1 - Nationwide Programmatic Agreement for the Collocation of Wireless Antennas

Code of Federal Regulations, 2014 CFR

2014-10-01

... Collocation of Wireless Antennas B Appendix B to Part 1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... the Collocation of Wireless Antennas Nationwide Programmatic Agreement for the Collocation of Wireless Antennas Executed by the Federal Communications Commission, the National Conference of State Historic...

47 CFR Appendix B to Part 1 - Nationwide Programmatic Agreement for the Collocation of Wireless Antennas

Code of Federal Regulations, 2011 CFR

2011-10-01

... Collocation of Wireless Antennas B Appendix B to Part 1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... the Collocation of Wireless Antennas Nationwide Programmatic Agreement for the Collocation of Wireless Antennas Executed by the Federal Communications Commission, the National Conference of State Historic...

47 CFR Appendix B to Part 1 - Nationwide Programmatic Agreement for the Collocation of Wireless Antennas

Code of Federal Regulations, 2013 CFR

2013-10-01

... Collocation of Wireless Antennas B Appendix B to Part 1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... the Collocation of Wireless Antennas Nationwide Programmatic Agreement for the Collocation of Wireless Antennas Executed by the Federal Communications Commission, the National Conference of State Historic...

47 CFR Appendix B to Part 1 - Nationwide Programmatic Agreement for the Collocation of Wireless Antennas

Code of Federal Regulations, 2012 CFR

2012-10-01

... Collocation of Wireless Antennas B Appendix B to Part 1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... the Collocation of Wireless Antennas Nationwide Programmatic Agreement for the Collocation of Wireless Antennas Executed by the Federal Communications Commission, the National Conference of State Historic...

77 FR 59395 - Grand River Dam Authority; Notice of Revised Restricted Service List for a Programmatic Agreement

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-27

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 2524-018--Oklahoma Salina Pumped Storage Project] Grand River Dam Authority; Notice of Revised Restricted Service List for a Programmatic Agreement Rule 2010 of the Federal Energy Regulatory Commission's (Commission) Rules of Practice...

20 CFR 645.210 - What is meant by the terms “entity” and “project” in the statutory phrase “an entity that...

Code of Federal Regulations, 2010 CFR

2010-04-01

... programmatic, supported by the total amount of one discrete award of WtW Governors' funds for long-term... programmatic, supported by the total amount of one discrete WtW competitive grant awarded to the entity...

Uranium Leasing Program PEIS Information Center

Science.gov Websites

Search Go search Uranium Leasing Program Programmatic Environmental Impact Statement Information Center Environmental Impact Statement (PEIS) for the Uranium Leasing Program. The United States Department of Energy (DOE) Office of Legacy Management (LM) has prepared a Programmatic Environmental Impact Statement (PEIS

77 FR 43808 - Supplement to the Draft Programmatic Restoration Plan and Programmatic Environmental Impact...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

...: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce... Liability Act of 1980 (CERCLA), the Oil Pollution Act (OPA) of 1990, the Clean Water Act (CWA), the National Oil and Hazardous Substances Pollution Contingency Plan (National Contingency Plan [NCP]), and other...

78 FR 25702 - Notice of Availability of a Draft Programmatic Environmental Assessment for Fisheries Research...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-02

... Availability of a Draft Programmatic Environmental Assessment for Fisheries Research Conducted and Funded by... Research Conducted and Funded by the Southwest Fisheries Science Center (SWFSC).'' Publication of this... cumulative impacts of conducting and funding fisheries and ecosystem research along the U.S. West Coast...

77 FR 39686 - Draft Programmatic Environmental Impact Statement and Restoration Plan To Compensate for Injuries...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-05

... Programmatic Environmental Impact Statement and Restoration Plan To Compensate for Injuries to Natural... Environmental Impact Statement and Restoration Plan; request for comments. SUMMARY: NOAA, the Department of the... Statement (PEIS) and Draft Restoration Plan are being released for public comment. The Restoration Plan...

36 CFR 800.13 - Post-review discoveries.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Post-review discoveries. 800... PROTECTION OF HISTORIC PROPERTIES The section 106 Process § 800.13 Post-review discoveries. (a) Planning for subsequent discoveries—(1) Using a programmatic agreement. An agency official may develop a programmatic...

36 CFR § 800.13 - Post-review discoveries.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 3 2013-07-01 2012-07-01 true Post-review discoveries. Â... PROTECTION OF HISTORIC PROPERTIES The section 106 Process § 800.13 Post-review discoveries. (a) Planning for subsequent discoveries—(1) Using a programmatic agreement. An agency official may develop a programmatic...

36 CFR 800.13 - Post-review discoveries.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Post-review discoveries. 800... PROTECTION OF HISTORIC PROPERTIES The section 106 Process § 800.13 Post-review discoveries. (a) Planning for subsequent discoveries—(1) Using a programmatic agreement. An agency official may develop a programmatic...

36 CFR 800.13 - Post-review discoveries.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Post-review discoveries. 800... PROTECTION OF HISTORIC PROPERTIES The section 106 Process § 800.13 Post-review discoveries. (a) Planning for subsequent discoveries—(1) Using a programmatic agreement. An agency official may develop a programmatic...

36 CFR 800.13 - Post-review discoveries.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Post-review discoveries. 800... PROTECTION OF HISTORIC PROPERTIES The section 106 Process § 800.13 Post-review discoveries. (a) Planning for subsequent discoveries—(1) Using a programmatic agreement. An agency official may develop a programmatic...

78 FR 21919 - Finding of No Significant Impact and Final Programmatic Environmental Assessment for Army 2020...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-12

... Programmatic Environmental Assessment for Army 2020 Force Structure Realignment AGENCY: Department of the Army... of the Finding of No Significant Impact (FNSI) for implementation of force structure realignment to... Structure Realignment (PEA), supporting studies, and comments received during the public review period, the...

Highlights of Programmatic, Interdisciplinary Research on Writing

ERIC Educational Resources Information Center

Berninger, Virginia W.

2009-01-01

An overview of research topics and findings from an interdisciplinary, programmatic line of research on writing over the past 25 years is presented. The cross-sectional assessment studies (grades 1 to 9) showed which measures uniquely explained variance in handwriting, spelling, and composing and thus validated their use in assessment. These and…

Leadership Development: An Examination of Individual and Programmatic Growth

ERIC Educational Resources Information Center

Conner, Jerusha Osberg; Strobel, Karen

2007-01-01

This study focuses on two girls' experiences in one youth leadership organization during a period of 3 years. Relying on an embedded case study design, the authors examine the links between leadership development and programmatic structures and supports. Specifically, the development of leadership capacities are analyzed along three dimensions:…

76 FR 53994 - Final Environmental Impact Statement, Single Nuclear Unit at the Bellefonte Plant Site, Jackson...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-30

... Programmatic Environmental Impact Statement (December 1995) and Reservoir Operations Study Final Programmatic.... Completion and operation of the 1,260-MW Bellefonte Unit 1 was one of the resource options analyzed in the..., Completion and Operation of Bellefonte Unit 1, as TVA's [[Page 53995

Satellite Power Systems (SPS) concept definition study (Exhibit D). Volume 4, Part 2: Cost and programmatics appendix

NASA Technical Reports Server (NTRS)

Hanley, G. M.

1981-01-01

Cost and programmatic aspects of a recommended satellite power system are documented. Computer generated summaries are presented, and the detailed computer runs structured in a Work Breakdown Structure are given. The six configurations developed during the study period are summarized.

75 FR 62433 - Notice of Public Hearings and the Availability of a Draft Programmatic Environmental Impact...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

... NATIONAL SCIENCE FOUNDATION Notice of Public Hearings and the Availability of a Draft Programmatic Environmental Impact Statement/Overseas Environmental Impact Statement (PEIS/OEIS) AGENCY: National Science... Seismic Research Funded by the National Science Foundation (NSF) or Conducted by the U.S. Geological...

77 FR 13095 - Intent To Prepare an Environmental Impact Statement for NOAA Restoration Center Programmatic...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-05

... Coastal Wetland Planning, Protection and Restoration Act (CWPPRA) Program, and the Great Lakes Habitat... Prepare an Environmental Impact Statement for NOAA Restoration Center Programmatic Coastal Habitat... (PEIS) to evaluate the potential environmental impacts of different ranges of coastal and marine habitat...

Programmatic Factors Associated with Undergraduate Athletic Training Student Retention and Attrition Decisions

ERIC Educational Resources Information Center

Bowman, Thomas G.; Hertel, Jay; Wathington, Heather D.

2015-01-01

Context: Athletic training programs (ATPs) are charged with meeting an increased demand for athletic trainers with adequate graduates. Currently, the retention rate of athletic training students in ATPs nationwide and the programmatic factors associated with these retention rates remain unknown. Objective: Determine the retention rate for athletic…

Toward Programmatic Research on Virtue Assessment: Challenges and Prospects

ERIC Educational Resources Information Center

Fowers, Blaine J.

2014-01-01

Poor construct definition has characterized research on virtue, beginning with Hartshorne and May's honesty studies and continuing to the present. Recently, scholars have begun to define virtues in ways that improve the prospects for measuring virtue constructs, but a coordinated, programmatic approach is necessary for success in virtue…

The 3D Elevation Program—Landslide recognition, hazard assessment, and mitigation support

USGS Publications Warehouse

Lukas, Vicki; Carswell, Jr., William J.

2017-01-27

The U.S. Geological Survey (USGS) Landslide Hazards Program conducts landslide hazard assessments, pursues landslide investigations and forecasts, provides technical assistance to respond to landslide emergencies, and engages in outreach. All of these activities benefit from the availability of high-resolution, three-dimensional (3D) elevation information in the form of light detection and ranging (lidar) data and interferometric synthetic aperture radar (IfSAR) data. Research on landslide processes addresses critical questions of where and when landslides are likely to occur as well as their size, speed, and effects. This understanding informs the development of methods and tools for hazard assessment and situational awareness used to guide efforts to avoid or mitigate landslide impacts. Such research is essential for the USGS to provide improved information on landslide potential associated with severe storms, earthquakes, volcanic activity, coastal wave erosion, and wildfire burn areas.Decisionmakers in government and the private sector increasingly depend on information the USGS provides before, during, and following disasters so that communities can live, work, travel, and build safely. The USGS 3D Elevation Program (3DEP) provides the programmatic infrastructure to generate and supply lidar-derived superior terrain data to address landslide applications and a wide range of other urgent needs nationwide. By providing data to users, 3DEP reduces users’ costs and risks and allows them to concentrate on their mission objectives. 3DEP includes (1) data acquisition partnerships that leverage funding, (2) contracts with experienced private mapping firms, (3) technical expertise, lidar data standards, and specifications, and (4) most important, public access to high-quality 3D elevation data.

Local in Practice: Professional Distinctions in Angolan Development Work

PubMed Central

Peters, Rebecca Warne

2017-01-01

Development workers employed by international nongovernmental organizations (NGOs) are commonly classified as national (local) or international (expatriate) staff members. The distinction is presumed to reflect the varieties of expertise required for the work and the workers’ different biographies. I examine the experiences of Angolans working in an international democratization program to demonstrate how some professionals at the lowest tiers of international development NGOs engage in social practices that strategically emphasize or conceal certain skills, kinds of knowledge, or family circumstances to fulfill industry expectations of “local staff.” Doing so allows them access to employment with international organizations and pursuit of a variety of personal and professional goals. These practices reinforce hierarchical inequalities within the development industry, however, limiting these workers’ influence over programmatic action. I argue that professional distinctions among development workers are social achievements and instruments of strategic manipulation by individuals and NGOs rather than accurate reflections of work or workers. The case study provides insight into the institutional reproduction of hierarchical inequalities and the complexly social reasons why those who suffer their limitations may act in ways that reinforce, rather than resist, unequal social structures. PMID:29430019

Iron for Africa—Report of an Expert Workshop

PubMed Central

Mwangi, Martin N.; Phiri, Kamija S.; Abkari, Abdelhak; Gbané, Mory; Bourdet-Sicard, Raphaelle; Braesco, Véronique Azaïs; Zimmermann, Michael B.; Prentice, Andrew M.

2017-01-01

Scientific experts from nine countries gathered to share their views and experience around iron interventions in Africa. Inappropriate eating habits, infections and parasitism are responsible for significant prevalence of iron deficiency, but reliable and country-comparable prevalence estimates are lacking: improvements in biomarkers and cut-offs values adapted to context of use are needed. Benefits of iron interventions on growth and development are indisputable and outweigh risks, which exist in populations with a high infectious burden. Indeed, pathogen growth may increase with enhanced available iron, calling for caution and preventive measures where malaria or other infections are prevalent. Most African countries programmatically fortify flour and supplement pregnant women, while iron deficiency in young children is rather addressed at individual level. Coverage and efficacy could improve through increased access for target populations, raised awareness and lower cost. More bioavailable iron forms, helping to decrease iron dose, or prebiotics, which both may lower risk of infections are attractive opportunities for Africa. Fortifying specific food products could be a relevant route, adapted to local context and needs of population groups while providing education and training. More globally, partnerships involving various stakeholders are encouraged, that could tackle all aspects of the issue. PMID:28587263

The MPO system for automatic workflow documentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abla, G.; Coviello, E. N.; Flanagan, S. M.

Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. Here, this article presents the Metadata, Provenance, and Ontology (MPO) System, the softwaremore » that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.« less

Sociocultural dimensions of tuberculosis: an overview of key concepts.

PubMed

Mason, P H; Degeling, C; Denholm, J

2015-10-01

Biomedical innovations are unlikely to provide effective and ethical tuberculosis (TB) control measures without complementary social science research. However, a strong interest in interdisciplinary work is often undermined by differences in language and concepts specific to each disciplinary approach. Accordingly, biological and social scientists need to learn how to communicate with each other. This article will outline key concepts relating to TB from medical anthropology and health sociology. Distilling these concepts in an introductory framework is intended to make this material accessible to researchers in laboratory, clinical and fieldwork settings, as well as to encourage more social scientists to engage with TB research among target groups critical for successful programmatic interventions. For pedagogical purposes, the relevant concepts are grouped into three categories: 1) structures and settings, which includes overarching themes such as syndemics, local biologies, medicalisation, structural violence and surveillance; 2) practices and processes, encompassing gender, stigma, taboo, and victim blaming; and 3) experience and enculturation, which includes illness narratives, biographical disruption and dynamic nominalism. By helping to navigate this literature, we hope to foster more cross-disciplinary conversations between qualitative and quantitative researchers. TB, a quintessential social disease, will be controlled more effectively using a multistranded research approach.

The MPO system for automatic workflow documentation

DOE PAGES

Abla, G.; Coviello, E. N.; Flanagan, S. M.; ...

2016-04-18

Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. Here, this article presents the Metadata, Provenance, and Ontology (MPO) System, the softwaremore » that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.« less

Preventing Mother-to-Child Transmission of HIV in Resource-Limited Settings: The Elizabeth Glaser Pediatric AIDS Foundation Experience

PubMed Central

Sripipatana, Tabitha; Turner, Abigail Norris; Hoblitzelle, Chuck; Robinson, Joanna; Wilfert, Catherine

2009-01-01

Objectives. In September 1999, the Elizabeth Glaser Pediatric AIDS Foundation initiated a multicountry, service-based programmatic effort in the developing world to reduce perinatally acquired HIV infection. We review 6½ years of one of the world's largest programs for the prevention of mother-to-child transmission (PMTCT) of HIV. Methods. Each PMTCT facility records patient data in antenatal clinics and labor and delivery settings about counseling, testing, HIV status, and antiretroviral prophylaxis and submits the data to foundation staff. Results. More than 2.6 million women have accessed foundation-affiliated services through June 2006. Overall, 92.9% of women who received antenatal care or were eligible for PMTCT services in labor and delivery have been counseled, and 82.8% of those counseled accepted testing. Among women identified as HIV positive, 75.0% received antiretroviral prophylaxis (most a single dose of nevirapine), as did 45.6% of their infants. Conclusions. The foundation's experience has demonstrated that opt-out testing, supplying mothers with medication at time of diagnosis, and providing the infant dose early have measurably improved program efficiency. PMTCT should be viewed as an achievable paradigm and an essential part of the continuum of care. PMID:18703458

Perceived Barriers and Facilitators to Healthy Eating and School Lunch Meals among Adolescents: A Qualitative Study.

PubMed

Payán, Denise D; Sloane, David C; Illum, Jacqueline; Farris, Tahirah; Lewis, LaVonna B

2017-09-01

We explored how perceived barriers and facilitators influence healthy eating and investigated the acceptability of changes to school lunch meals among adolescents after implementation of the Healthy, Hunger-Free Kids Act of 2010. We conducted 8 focus groups with adolescents (N = 64) at 3 South Los Angeles high schools. Data collection instruments included a semi-structured guide and questionnaire. Two researchers independently coded transcripts. Most participants believed fruits and vegetables were available in their community and reported high relative cost, poor quality, and lack of motivation as barriers to consumption. Many said school meals were an important source of healthy food and were aware of recent changes to the school lunch program. A primary facilitator to eating school lunches was access to fresh food items (eg, a salad bar). Perceived barriers included long cafeteria lines, time constraints, lack of variety, and limited quantities of preferred items. Adolescents viewed off-campus food establishments near the school as competition to school meals. Our findings suggest the need to measure perceived and actual barriers to healthy eating among adolescents and to examine the effect of these barriers on dietary behavior. We provide programmatic and policy recommendations.

"From me to HIV": a case study of the community experience of donor transition of health programs.

PubMed

Rodríguez, Daniela C; Tripathi, Vandana; Bohren, Meghan; Paul, Amy; Singh, Kriti; Chhabra, Vibha; Singh, Suneeta; Bennett, Sara

2015-08-19

Avahan, a large-scale HIV prevention program in India, transitioned over 130 intervention sites from donor funding and management to government ownership in three rounds. This paper examines the transition experience from the perspective of the communities targeted by these interventions. Fifteen qualitative longitudinal case studies were conducted across all three rounds of transition, including 83 in-depth interviews and 45 focus group discussions. Data collection took place between 2010 and 2013 in four states: Andhra Pradesh, Karnataka, Maharashtra and Tamil Nadu. We find that communication about transition was difficult at first but improved over time, while issues related to employment of peer educators were challenging throughout the transition. Clinical services were shifted to government providers resulting in mixed experiences depending on the population being targeted. Lastly, the loss of activities aimed at community ownership and mobilization negatively affected the beneficiaries' view of transition. While some programmatic changes resulted in improvements, additional opportunity costs for beneficiaries may pose barriers to accessing HIV prevention services. Communicating and engaging community stakeholders early on in future such transitions may mitigate negative feelings and lead to more constructive relationships and dialogue.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.

PubMed

Taminau, Jonatan; Meganck, Stijn; Lazar, Cosmin; Steenhoff, David; Coletta, Alain; Molter, Colin; Duque, Robin; de Schaetzen, Virginie; Weiss Solís, David Y; Bersini, Hugues; Nowé, Ann

2012-12-24

With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

Barriers to Expanding Advanced Pharmacy Practice Experience Site Availability in an Experiential Education Consortium

PubMed Central

Byrd, Debbie C.; Duke, Lori J.; Fetterman, James W.; Unterwagner, Whitney L.; Staton, April G.; Miller, Mindi S.; Sheffield, Melody C.; Kennedy, William K.; McDuffie, Charles H.; Stevenson, T. Lynn; Thompson, Paula A.; McCullough, Elizabeth S.

2009-01-01

Objectives To compare 2006-2007 and projected 2010-2011 advanced pharmacy practice experience (APPE) availability and needs for 4 colleges and schools of pharmacy in Georgia and Alabama and to examine barriers and offer potential solutions to increase APPE site and preceptor availability. Methods Data on APPE needs and availability were gathered prospectively and evaluated relative to current and projected enrollment and planned programmatic changes. Results Combined 2006-2007 non-community APPE needs and availabilities were 3,590 and 4,427, respectively, with a surplus availability of 837. Combined projected 2010-2011 non-community APPEs were estimated at 4,309. Assuming 2006-2007 non-community availability remained unchanged, the surplus availability declined to 118. Conclusions The need for quality experiential education represents a significant barrier and rate-limiting step to the matriculation of the increased numbers of pharmacists. Barriers to expanding APPE availability include: introductory pharmacy practice experience (IPPE) and APPE expansion, growth of new and existing pharmacy programs, financial instability of acute care facilities, and lack of preceptor development resources. Regional experiential education consortiums can provide a constructive approach to improve access to quality sites and preceptors through standardizing processes and leveraging resources. PMID:19777097

Aligning HST Images to Gaia: A Faster Mosaicking Workflow

NASA Astrophysics Data System (ADS)

Bajaj, V.

2017-11-01

We present a fully programmatic workflow for aligning HST images using the high-quality astrometry provided by Gaia Data Release 1. Code provided in a Jupyter Notebook works through this procedure, including parsing the data to determine the query area parameters, querying Gaia for the coordinate catalog, and using the catalog with TweakReg as reference catalog. This workflow greatly simplifies the normally time-consuming process of aligning HST images, especially those taken as part of mosaics.

Unpaved road dust management, a successful practitioner’s handbook

USGS Publications Warehouse

Jones, David; Kociolek, Angela; Surdahl, Roger; Bolander, Peter; Drewes, Bruce; Duran, Matthew; Fay, Laura; Huntington, George; James, David; Milne, Clark; Nahra, Mark; Scott, Andrew; Vitale, Bob; Williams, Bethany

2013-01-01

This handbook provides broad programmatic aspects of unpaved road management. It is based on observations made during a national scan tour and provides useful and insightful excerpts of realworld examples and includes practical how-to instructions for determining what type of treatment may be needed for different situations. It ultimately strives to encourage road managers to think broadly about the process of unpaved road management rather than just focusing on a specific type of chemical treatment.

Surplus Highly Enriched Uranium Disposition Program plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-10-01

The purpose of this document is to provide upper level guidance for the program that will downblend surplus highly enriched uranium for use as commercial nuclear reactor fuel or low-level radioactive waste. The intent of this document is to outline the overall mission and program objectives. The document is also intended to provide a general basis for integration of disposition efforts among all applicable sites. This plan provides background information, establishes the scope of disposition activities, provides an approach to the mission and objectives, identifies programmatic assumptions, defines major roles, provides summary level schedules and milestones, and addresses budget requirements.

Progressing from programmatic to discovery research: a case example with the overjustification effect.

PubMed

Roane, Henry S; Fisher, Wayne W; McDonough, Erin M

2003-01-01

Scientific research progresses along planned (programmatic research) and unplanned (discovery research) paths. In the current investigation, we attempted to conduct a single-case evaluation of the overjustification effect (i.e., programmatic research). Results of the initial analysis were contrary to the overjustification hypothesis in that removal of the reward contingency produced an increase in responding. Based on this unexpected finding, we conducted subsequent analyses to further evaluate the mechanisms underlying these results (i.e., discovery research). Results of the additional analyses suggested that the reward contingency functioned as punishment (because the participant preferred the task to the rewards) and that withdrawal of the contingency produced punishment contrast.