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Sample records for annotation assessment project

  1. nGASP – the nematode genome annotation assessment project

    PubMed Central

    Coghlan, Avril; Fiedler, Tristan J; McKay, Sheldon J; Flicek, Paul; Harris, Todd W; Blasiar, Darin; Stein, Lincoln D

    2008-01-01

    Background While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders. Conclusion This experiment establishes a baseline of gene prediction accuracy in Caenorhabditis genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of Caenorhabditis and other nematode species. We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders. PMID:19099578

  2. nGASP - the nematode genome annotation assessment project

    SciTech Connect

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome

  3. Managing Development Projects: A Selected, Annotated Bibliography. Annotated Bibliography #5.

    ERIC Educational Resources Information Center

    Chuenyane, Zachariah; And Others

    A selected annotated bibliography on managing development projects, intended for rural development practitioners, highlights items that outline some pressing issues and concerns confronting those involved in rural development in general and rural project management in particular. A section of annotated entries lists 21 publications on project…

  4. Meaningful Assessment: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Thrond, Mary A.

    The annotated bibliography contains citations of nine references on alternative student assessment methods in second language programs, particularly at the secondary school level. The references include a critique of conventional reading comprehension assessment, a discussion of performance assessment, a proposal for a multi-trait, multi-method…

  5. Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

    PubMed

    Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

    2015-02-01

    Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  6. Harnessing Collaborative Annotations on Online Formative Assessments

    ERIC Educational Resources Information Center

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  7. Harnessing Collaborative Annotations on Online Formative Assessments

    ERIC Educational Resources Information Center

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  8. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

    PubMed Central

    Overbeek, Ross; Begley, Tadhg; Butler, Ralph M.; Choudhuri, Jomuna V.; Chuang, Han-Yu; Cohoon, Matthew; de Crécy-Lagard, Valérie; Diaz, Naryttza; Disz, Terry; Edwards, Robert; Fonstein, Michael; Frank, Ed D.; Gerdes, Svetlana; Glass, Elizabeth M.; Goesmann, Alexander; Hanson, Andrew; Iwata-Reuyl, Dirk; Jensen, Roy; Jamshidi, Neema; Krause, Lutz; Kubal, Michael; Larsen, Niels; Linke, Burkhard; McHardy, Alice C.; Meyer, Folker; Neuweger, Heiko; Olsen, Gary; Olson, Robert; Osterman, Andrei; Portnoy, Vasiliy; Pusch, Gordon D.; Rodionov, Dmitry A.; Rückert, Christian; Steiner, Jason; Stevens, Rick; Thiele, Ines; Vassieva, Olga; Ye, Yuzhen; Zagnitko, Olga; Vonstein, Veronika

    2005-01-01

    The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms. PMID:16214803

  9. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

    PubMed

    Overbeek, Ross; Begley, Tadhg; Butler, Ralph M; Choudhuri, Jomuna V; Chuang, Han-Yu; Cohoon, Matthew; de Crécy-Lagard, Valérie; Diaz, Naryttza; Disz, Terry; Edwards, Robert; Fonstein, Michael; Frank, Ed D; Gerdes, Svetlana; Glass, Elizabeth M; Goesmann, Alexander; Hanson, Andrew; Iwata-Reuyl, Dirk; Jensen, Roy; Jamshidi, Neema; Krause, Lutz; Kubal, Michael; Larsen, Niels; Linke, Burkhard; McHardy, Alice C; Meyer, Folker; Neuweger, Heiko; Olsen, Gary; Olson, Robert; Osterman, Andrei; Portnoy, Vasiliy; Pusch, Gordon D; Rodionov, Dmitry A; Rückert, Christian; Steiner, Jason; Stevens, Rick; Thiele, Ines; Vassieva, Olga; Ye, Yuzhen; Zagnitko, Olga; Vonstein, Veronika

    2005-01-01

    The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

  10. Annotated Bibliography for the DEWPOINT project

    SciTech Connect

    Oehmen, Christopher S.

    2009-04-21

    This bibliography covers aspects of the Detection and Early Warning of Proliferation from Online INdicators of Threat (DEWPOINT) project including 1) data management and querying, 2) baseline and advanced methods for classifying free text, and 3) algorithms to achieve the ultimate goal of inferring intent from free text sources. Metrics for assessing the quality and correctness of classification are addressed in the second group. Data management and querying include methods for efficiently storing, indexing, searching, and organizing the data we expect to operate on within the DEWPOINT project.

  11. Project for Global Education: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Institute for World Order, New York, NY.

    Over 260 books, textbooks, articles, pamphlets, periodicals, films, and multi-media packages appropriate for the analysis of global issues at the college level are briefly annotated. Entries include classic books and articles as well as a number of recent (1976-1981) publications. The purpose is to assist students and educators in developing a…

  12. Project for Global Education: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Institute for World Order, New York, NY.

    Over 260 books, textbooks, articles, pamphlets, periodicals, films, and multi-media packages appropriate for the analysis of global issues at the college level are briefly annotated. Entries include classic books and articles as well as a number of recent (1976-1981) publications. The purpose is to assist students and educators in developing a…

  13. The caBIG annotation and image Markup project.

    PubMed

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

    2010-04-01

    Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

  14. Child and Adolescent Health Profile Project: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simkin, Linda; And Others

    Developed as part of the Child and Adolescent Health Profile Project, this annotated bibliography is intended as a reference for professionals interested in key dimensions of children's health. Citations are grouped into the following four categories: (1) background information on child health issues, (2) child health indicators and health status…

  15. Project PRISM: PRISM's Annotated Resource List.

    ERIC Educational Resources Information Center

    Cunnion, Maryellen; And Others

    The final of three volumes on Project PRISM, a program to help middle school teachers meet the needs of gifted and talented children in their classes without removing them from the mainstream, lists resources on the education of gifted and talented children. Materials are organized according to four basic types: books, periodicals, curriculum aids…

  16. Annotated Bibliography for the MATADOR Project

    SciTech Connect

    Janik, Tadeusz; White, Amanda M.; Pawley, Norma H.; Myers, Kary L.; Oehmen, Christopher S.

    2012-06-07

    The MATADOR project is focused on developing methods to infer the operational mode of facilities that have the potential to be used in weapons development programs. Our central hypothesis is that by persistent, non-intrusive monitoring of such facilities, differences between various use scenarios can be reliably discovered. The impact of success in this area is that new tools and techniques for monitoring and treaty verification would make it easier to reliably discover and document weapons development activities. This document captures the literature that will serve as a basis to approach this task. The relevant literature is divided into topical areas that relate to the various aspects of expected MATADOR project development. We have found that very little work that is directly applicable for our purposes has been published, which has motivated the development of novel methods under the project. Therefore, the manuscripts referenced in this document were selected based on their potential use as foundational blocks for the methods we anticipate developing, or so that we can understand the limitations of existing methods.

  17. Trade-off analysis for environmental projects: An annotated bibliography

    SciTech Connect

    Feather, T.D.; Harrington, K.W.; Capan, D.T.

    1995-08-01

    This is a report with an attached annotated bibliography. This study explores the literature for analytical techniques that can support the complex decision-making process associated with Corps of Engineers environmental projects. The literature review focuses on opportunities for using trade-off methodologies and group processes in environmental plan formulation and evaluation. The work was conducted under the Evaluation Framework Work Unit within the Evaluation of Environmental Investments Research Program.

  18. The RNA WikiProject: Community annotation of RNA families

    PubMed Central

    Daub, Jennifer; Gardner, Paul P.; Tate, John; Ramsköld, Daniel; Manske, Magnus; Scott, William G.; Weinberg, Zasha; Griffiths-Jones, Sam; Bateman, Alex

    2008-01-01

    The online encyclopedia Wikipedia has become one of the most important online references in the world and has a substantial and growing scientific content. A search of Google with many RNA-related keywords identifies a Wikipedia article as the top hit. We believe that the RNA community has an important and timely opportunity to maximize the content and quality of RNA information in Wikipedia. To this end, we have formed the RNA WikiProject (http://en.wikipedia.org/wiki/Wikipedia:WikiProject_RNA) as part of the larger Molecular and Cellular Biology WikiProject. We have created over 600 new Wikipedia articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct these articles. The Rfam database now redistributes this Wikipedia content as the primary textual annotation of its RNA families. Users can, therefore, for the first time, directly edit the content of one of the major RNA databases. We believe that this Wikipedia/Rfam link acts as a functioning model for incorporating community annotation into molecular biology databases. PMID:18945806

  19. A Novel Method for Learner Assessment Based on Learner Annotations

    ERIC Educational Resources Information Center

    Noorbehbahani, Fakhroddin; Samani, Elaheh Biglar Beigi; Jazi, Hossein Hadian

    2013-01-01

    Assessment is one of the most essential parts of any instructive learning process which aims to evaluate a learner's knowledge about learning concepts. In this work, a new method for learner assessment based on learner annotations is presented. The proposed method exploits the M-BLEU algorithm to find the most similar reference annotations…

  20. Behavioral Assessment Instruments, Techniques, and Procedures: Summary and Annotated Bibliography.

    ERIC Educational Resources Information Center

    Shorkey, Clayton T.; Williams, Harry

    This annotated bibliography cites 223 articles related to behavioral assessment reported in 18 professional journals between January 1960 and Spring 1976. A summary and a reference grouping of the articles are included to allow for identification of articles related to (1) electromechanical devices used in identification, measurement, and storage…

  1. Behavioral Assessment Instruments, Techniques, and Procedures: Summary and Annotated Bibliography.

    ERIC Educational Resources Information Center

    Shorkey, Clayton T.; Williams, Harry

    This annotated bibliography cites 223 articles related to behavioral assessment reported in 18 professional journals between January 1960 and Spring 1976. A summary and a reference grouping of the articles are included to allow for identification of articles related to (1) electromechanical devices used in identification, measurement, and storage…

  2. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

    PubMed

    Horton, Roger; Gibson, Richard; Coggill, Penny; Miretti, Marcos; Allcock, Richard J; Almeida, Jeff; Forbes, Simon; Gilbert, James G R; Halls, Karen; Harrow, Jennifer L; Hart, Elizabeth; Howe, Kevin; Jackson, David K; Palmer, Sophie; Roberts, Anne N; Sims, Sarah; Stewart, C Andrew; Traherne, James A; Trevanion, Steve; Wilming, Laurens; Rogers, Jane; de Jong, Pieter J; Elliott, John F; Sawcer, Stephen; Todd, John A; Trowsdale, John; Beck, Stephan

    2008-01-01

    The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.

  3. GENCODE: The reference human genome annotation for The ENCODE Project

    PubMed Central

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M.; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L.; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J.

    2012-01-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  4. GENCODE: the reference human genome annotation for The ENCODE Project.

    PubMed

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

    2012-09-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

  5. Assessment of protein set coherence using functional annotations

    PubMed Central

    Chagoyen, Monica; Carazo, Jose M; Pascual-Montano, Alberto

    2008-01-01

    Background Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational methods have been devised that rely on the analysis of functional annotations. Although current methods provide valuable information (e.g. significantly enriched annotations, pairwise functional similarities), they do not specifically measure the degree of homogeneity of a protein set. Results In this work we present a method that scores the degree of functional homogeneity, or coherence, of a set of proteins on the basis of the global similarity of their functional annotations. The method uses statistical hypothesis testing to assess the significance of the set in the context of the functional space of a reference set. As such, it can be used as a first step in the validation of sets expected to be homogeneous prior to further functional interpretation. Conclusion We evaluate our method by analysing known biologically relevant sets as well as random ones. The known relevant sets comprise macromolecular complexes, cellular components and pathways described for Saccharomyces cerevisiae, which are mostly significantly coherent. Finally, we illustrate the usefulness of our approach for validating 'functional modules' obtained from computational analysis of protein-protein interaction networks. Matlab code and supplementary data are available at PMID:18937846

  6. Mouse genome annotation by the RefSeq project.

    PubMed

    McGarvey, Kelly M; Goldfarb, Tamara; Cox, Eric; Farrell, Catherine M; Gupta, Tripti; Joardar, Vinita S; Kodali, Vamsi K; Murphy, Michael R; O'Leary, Nuala A; Pujar, Shashikant; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Webb, David; Wright, Mathew W; Murphy, Terence D; Pruitt, Kim D

    2015-10-01

    Complete and accurate annotation of the mouse genome is critical to the advancement of research conducted on this important model organism. The National Center for Biotechnology Information (NCBI) develops and maintains many useful resources to assist the mouse research community. In particular, the reference sequence (RefSeq) database provides high-quality annotation of multiple mouse genome assemblies using a combinatorial approach that leverages computation, manual curation, and collaboration. Implementation of this conservative and rigorous approach, which focuses on representation of only full-length and non-redundant data, produces high-quality annotation products. RefSeq records explicitly link sequences to current knowledge in a timely manner, updating public records regularly and rapidly in response to nomenclature updates, addition of new relevant publications, collaborator discussion, and user feedback. Whole genome re-annotation is also conducted at least every 12-18 months, and often more frequently in response to assembly updates or availability of informative data. This article highlights key features and advantages of RefSeq genome annotation products and presents an overview of NCBI processes to generate these data. Further discussion of NCBI's resources highlights useful features and the best methods for accessing our data.

  7. Office of Maternal and Child Health Active Projects FY 1989. An Annotated Listing.

    ERIC Educational Resources Information Center

    National Center for Education in Maternal and Child Health, Washington, DC.

    An annotated listing is presented of projects offering maternal and child health care services. These projects, referred to as special projects of regional and national significance (SPRANS), are supported by the Office of Maternal and Child Health of the Department of Health and Human Services. The first section provides information on services…

  8. Experiential Learning: An Annotated Literature Guide. CAEL Project Report.

    ERIC Educational Resources Information Center

    Stutz, Jane Porter, Ed.; Knapp, Joan, Ed.

    This guide is organized into three parts. Parts A and B contain bibliographic citations and brief annotations; Part C is an alphabetical listing of all references. Topics included in Part A are: the rationale and history of experiential learning, types of programs, program planning and implementation, program evaluation and quality assurance,…

  9. Annotated Football Bibliography. An Applied Project in Physical Education.

    ERIC Educational Resources Information Center

    Clemence, William J., Jr.; Pitts, James Walter

    This annotated bibliography was compiled to assist physical education majors, especially those having a major interest in football and football coaching. The bibliography is limited to the areas of coaching techniques and philosophy, fundamentals, offense, defense, injuries, and conditioning at the high school and college level. These broader…

  10. Annotated Football Bibliography. An Applied Project in Physical Education.

    ERIC Educational Resources Information Center

    Clemence, William J., Jr.; Pitts, James Walter

    This annotated bibliography was compiled to assist physical education majors, especially those having a major interest in football and football coaching. The bibliography is limited to the areas of coaching techniques and philosophy, fundamentals, offense, defense, injuries, and conditioning at the high school and college level. These broader…

  11. Maternal and Child Health Bureau Active Projects FY 1991: An Annotated Listing.

    ERIC Educational Resources Information Center

    National Center for Education in Maternal and Child Health, Washington, DC.

    This annotated listing provides brief descriptions of the 591 projects funded during 1991 by federal set-aside funds of the Maternal and Child Health (MCH) Services Block Grant and identified as special projects of regional and national significance (SPRANS). Preliminary information includes an introduction, an organization chart of the Maternal…

  12. Gene Characterization Index: Assessing the Depth of Gene Annotation

    PubMed Central

    Yusuf, Dimas; Brumm, Jochen; Cheung, Warren; Wahlestedt, Claes; Lenhard, Boris; Wasserman, Wyeth W.

    2008-01-01

    Background We introduce the Gene Characterization Index, a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described. Inherently a reflection of human perception, the Gene Characterization Index is applied for assessing the characterization status of individual genes, thus serving the advancement of both genome annotation and applied genomics research by rapid and unbiased identification of groups of uncharacterized genes for diverse applications such as directed functional studies and delineation of novel drug targets. Methodology/Principal Findings The scoring procedure is based on a global survey of researchers, who assigned characterization scores from 1 (poor) to 10 (extensive) for a sample of genes based on major online resources. By evaluating the survey as training data, we developed a bioinformatics procedure to assign gene characterization scores to all genes in the human genome. We analyzed snapshots of functional genome annotation over a period of 6 years to assess temporal changes reflected by the increase of the average Gene Characterization Index. Applying the Gene Characterization Index to genes within pharmaceutically relevant classes, we confirmed known drug targets as high-scoring genes and revealed potentially interesting novel targets with low characterization indexes. Removing known drug targets and genes linked to sequence-related patent filings from the entirety of indexed genes, we identified sets of low-scoring genes particularly suited for further experimental investigation. Conclusions/Significance The Gene Characterization Index is intended to serve as a tool to the scientific community and granting agencies for focusing resources and efforts on unexplored areas of the genome. The Gene Characterization Index is available from http://cisreg.ca/gci/. PMID:18213364

  13. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

    PubMed

    Holt, Carson; Yandell, Mark

    2011-12-22

    Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

  14. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

    PubMed Central

    2011-01-01

    Background Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. Results We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. Conclusions MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets. PMID:22192575

  15. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    PubMed

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project.

  16. Automatic assessment of voice quality in the context of multiple annotations.

    PubMed

    Gil González, Julián; Álvarez, Mauricio A; Orozco, Álvaro A

    2015-01-01

    Approaches to evaluate voice quality include perceptual analysis, and acoustical analysis. Perceptual analysis is subjective and depends mostly on the ability of a specialist to assess a pathology, whereas acoustical analysis is objective, but highly relies on the quality of the so called annotations that the specialist assigns to the voice signal. The quality of the annotations for acoustical analysis depends heavily on the expertise and knowledge of the specialist. We face a scenario where we have annotations performed by several specialists with different levels of expertise and knowledge. Traditional pattern recognition methods employed in acoustical analysis are no longer applicable, since these methods are designed for scenarios where a "ground-truth" label is assigned by the specialist. In this paper, we apply recent developments in machine learning for taking into account multiple annotators for acoustical analysis of voice signals. For the classification step we compare two techniques, one of them based on Gaussian Processes for regression with multiple annotators, and the other is a multi-class Logistic Regression model that measures the annotator performance in terms of sensitivity and specificity. The performance of classifiers is assessed in terms of Cohen's Kappa index. Results show that the multi-annotator classification schemes have better performance when compared to techniques based on a traditional classifier where the true label is estimated from the multiple annotations available using majority voting.

  17. An Assessment of Reliability of Dialogue-Annotation Instructions.

    ERIC Educational Resources Information Center

    Mann, William C.; And Others

    This report is part of ongoing research engaged in transforming knowledge of how human communication works into improvements in man-machine communication of existing and planned computer systems. The methodology includes having a trained "Observer" annotate transcripts of human communication in a prescribed manner. One of the issues,…

  18. An Assessment of Reliability of Dialogue Annotation Instructions

    DTIC Science & Technology

    1977-01-01

    This report is part of an ongoing research effort on man-machine communication, which is engaged in transforming knowledge of how human communication works...certain kinds of recurring features in transcripts of human communication . These methods involve having a trained person, called an Observer, annotate...right kind of data for developing human communication theory. It is a confirmation of the appropriateness and potential effectiveness of using this

  19. The Ensembl gene annotation system

    PubMed Central

    Aken, Bronwen L.; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J.; Murphy, Daniel N.; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y. Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. Database URL: http://www.ensembl.org/index.html PMID:27337980

  20. Coordinated international action to accelerate genome-to-phenome with FAANG, The Functional Annotation of Animal Genomes project

    USDA-ARS?s Scientific Manuscript database

    We describe the organization of a nascent international effort - the "Functional Annotation of ANimal Genomes" project - whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species....

  1. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    PubMed

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

  2. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    PubMed

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  3. A Pilot Study on Developing a Standardized and Sensitive School Violence Risk Assessment with Manual Annotation.

    PubMed

    Barzman, Drew H; Ni, Yizhao; Griffey, Marcus; Patel, Bianca; Warren, Ashaki; Latessa, Edward; Sorter, Michael

    2017-09-01

    School violence has increased over the past decade and innovative, sensitive, and standardized approaches to assess school violence risk are needed. In our current feasibility study, we initialized a standardized, sensitive, and rapid school violence risk approach with manual annotation. Manual annotation is the process of analyzing a student's transcribed interview to extract relevant information (e.g., key words) to school violence risk levels that are associated with students' behaviors, attitudes, feelings, use of technology (social media and video games), and other activities. In this feasibility study, we first implemented school violence risk assessments to evaluate risk levels by interviewing the student and parent separately at the school or the hospital to complete our novel school safety scales. We completed 25 risk assessments, resulting in 25 transcribed interviews of 12-18 year olds from 15 schools in Ohio and Kentucky. We then analyzed structured professional judgments, language, and patterns associated with school violence risk levels by using manual annotation and statistical methodology. To analyze the student interviews, we initiated the development of an annotation guideline to extract key information that is associated with students' behaviors, attitudes, feelings, use of technology and other activities. Statistical analysis was applied to associate the significant categories with students' risk levels to identify key factors which will help with developing action steps to reduce risk. In a future study, we plan to recruit more subjects in order to fully develop the manual annotation which will result in a more standardized and sensitive approach to school violence assessments.

  4. Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum

    PubMed Central

    2010-01-01

    Background Plasmodium falciparum is the main causative agent of malaria. Of the 5 484 predicted genes of P. falciparum, about 57% do not have sufficient sequence similarity to characterized genes in other species to warrant functional assignments. Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes. Gene expression data have been widely used in the recent years to help functional annotation in an intra-species way via the so-called Guilt By Association (GBA) principle. Results We propose a new method that uses gene expression data to assess inter-species annotation transfers. Our approach starts from a set of likely orthologs between a reference species (here S. cerevisiae and D. melanogaster) and a query species (P. falciparum). It aims at identifying clusters of coexpressed genes in the query species whose coexpression has been conserved in the reference species. These conserved clusters of coexpressed genes are then used to assess annotation transfers between genes with low sequence similarity, enabling reliable transfers of annotations from the reference to the query species. The approach was used with transcriptomic data sets of P. falciparum, S. cerevisiae and D. melanogaster, and enabled us to propose with high confidence new/refined annotations for several dozens hypothetical/putative P. falciparum genes. Notably, we revised the annotation of genes involved in ribosomal proteins and ribosome biogenesis and assembly, thus highlighting several potential drug targets. Conclusions Our approach uses both sequence similarity and gene expression data to help inter-species gene annotation transfers. Experiments show that this strategy improves the accuracy achieved when using solely sequence similarity and outperforms the accuracy of the GBA approach. In addition, our experiments with P. falciparum show that it can infer a function for numerous hypothetical genes. PMID:20078859

  5. Workflow and web application for annotating NCBI BioProject transcriptome data.

    PubMed

    Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

    2017-01-01

    The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/.

  6. Workflow and web application for annotating NCBI BioProject transcriptome data

    PubMed Central

    Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

    2017-01-01

    Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

  7. Assessment of disease named entity recognition on a corpus of annotated sentences

    PubMed Central

    Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

    2008-01-01

    Background In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. Results As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. Conclusions The annotated corpus is publicly available at and can serve as a benchmark to other systems. In addition, we found that dictionary look

  8. Assessment and management of animal damage in Pacific Northwest forests: an annotated bibliography.

    Treesearch

    D.M. Loucks; H.C. Black; M.L. Roush; S.R. Radosevich

    1990-01-01

    This annotated bibliography of published literature provides a comprehensive source of information on animal damage assessment and management for forest land managers and others in the Pacific Northwest. Citations and abstracts from more than 900 papers are indexed by subject and author. The publication complements and supplements A Silvicultural Approach to...

  9. Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome

    PubMed Central

    Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/. PMID:24489955

  10. Foreign Language Assessment in Grades K-8: An Annotated Bibliography of Assessment Instruments. Language in Education: Theory and Practice 90.

    ERIC Educational Resources Information Center

    Thompson, Lynn, Comp.

    The annotated bibliography describes foreign language assessment instruments currently used in elementary and middle schools. The instruments are drawn from a wide variety of program models: Foreign Language in the Elementary School (FLES), middle school sequential instruction, and immersion (total, two-way, partial). The bibliography has six…

  11. A Review and Annotated Bibliography of Training Performance Measurement and Assessment Literature

    DTIC Science & Technology

    1988-10-01

    in the design of this research effort, the collection of data, and the preparation and review of the draft and final reports. It can truly be said that...Manager for Training Devices (PM TRADE) helped to guide the design of the effort and kept the authors focused on objectives meaningful to the Army. The...data and prepare and format the report. vi A REVIEW AND ANNOTATED BIBLIOGRAPHY OF TRAINING PERFORMANCE MEASUREMENT AND ASSESSMENT LITERATURE EXECUTIVE

  12. Report on the 2011 Critical Assessment of Function Annotation (CAFA) meeting

    SciTech Connect

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA). The meeting was exciting and, based on feedback, quite successful. There were 73 registered participants. The schedule was only slightly different from the one proposed, due to two cancellations. Dr. Olga Troyanskaya has canceled and we invited Dr. David Jones instead. Similarly, instead of Dr. Richard Roberts, Dr. Simon Kasif gave a closing keynote. The remaining invited speakers were Janet Thornton (EBI) and Amos Bairoch (University of Geneva).

  13. Assessment of disease named entity recognition on a corpus of annotated sentences.

    PubMed

    Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

    2008-04-11

    In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to other systems. In addition, we found

  14. Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction.

    PubMed

    Névéol, Aurélie; Islamaj Doğan, Rezarta; Lu, Zhiyong

    2011-04-01

    Information processing algorithms require significant amounts of annotated data for training and testing. The availability of such data is often hindered by the complexity and high cost of production. In this paper, we investigate the benefits of a state-of-the-art tool to help with the semantic annotation of a large set of biomedical queries. Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories. About half of the queries were annotated from scratch, while the other half were automatically pre-annotated and manually corrected. The impact of the automatic pre-annotations was assessed on several aspects of the task: time, number of actions, annotator satisfaction, inter-annotator agreement, quality and number of the resulting annotations. The analysis of annotation results showed that the number of required hand annotations is 28.9% less when using pre-annotated results from automatic tools. As a result, the overall annotation time was substantially lower when pre-annotations were used, while inter-annotator agreement was significantly higher. In addition, there was no statistically significant difference in the semantic distribution or number of annotations produced when pre-annotations were used. The annotated query corpus is freely available to the research community. This study shows that automatic pre-annotations are found helpful by most annotators. Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations.

  15. Semi-automatic semantic annotation of PubMed Queries: a study on quality, efficiency, satisfaction

    PubMed Central

    Névéol, Aurélie; Islamaj-Doğan, Rezarta; Lu, Zhiyong

    2010-01-01

    Information processing algorithms require significant amounts of annotated data for training and testing. The availability of such data is often hindered by the complexity and high cost of production. In this paper, we investigate the benefits of a state-of-the-art tool to help with the semantic annotation of a large set of biomedical information queries. Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories. About half of the queries were annotated from scratch, while the other half were automatically pre-annotated and manually corrected. The impact of the automatic pre-annotations was assessed on several aspects of the task: time, number of actions, annotator satisfaction, inter-annotator agreement, quality and number of the resulting annotations. The analysis of annotation results showed that the number of required hand annotations is 28.9% less when using pre-annotated results from automatic tools. As a result, the overall annotation time was substantially lower when pre-annotations were used, while inter-annotator agreement was significantly higher. In addition, there was no statistically significant difference in the semantic distribution or number of annotations produced when pre-annotations were used. The annotated query corpus is freely available to the research community. This study shows that automatic pre-annotations are found helpful by most annotators. Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations. PMID:21094696

  16. Assessing identity, redundancy and confounds in Gene Ontology annotations over time.

    PubMed

    Gillis, Jesse; Pavlidis, Paul

    2013-02-15

    The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored. We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction databases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks. Data available at http://chibi.ubc.ca/assessGO.

  17. Quality assessment of digital annotated ECG data from clinical trials by the FDA ECG Warehouse.

    PubMed

    Sarapa, Nenad

    2007-09-01

    The FDA mandates that digital electrocardiograms (ECGs) from 'thorough' QTc trials be submitted into the ECG Warehouse in Health Level 7 extended markup language format with annotated onset and offset points of waveforms. The FDA did not disclose the exact Warehouse metrics and minimal acceptable quality standards. The author describes the Warehouse scoring algorithms and metrics used by FDA, points out ways to improve FDA review and suggests Warehouse benefits for pharmaceutical sponsors. The Warehouse ranks individual ECGs according to their score for each quality metric and produces histogram distributions with Warehouse-specific thresholds that identify ECGs of questionable quality. Automatic Warehouse algorithms assess the quality of QT annotation and duration of manual QT measurement by the central ECG laboratory.

  18. Annotated bibliography of methodology for assessment of undiscovered oil and gas resources

    USGS Publications Warehouse

    Charpentier, R.R.; Dolton, G.L.; Ulmishek, G.F.

    1995-01-01

    An annotated bibliography of methodology of assessment of undiscovered oil and gas resources is presented as a useful reference for those engaged in resource assessment. The articles that are included deal only with quantitative assessment of undiscovered or inferred resources. the articles in this bibliography are classified largely according to the major assessment method that was applied in each situation. Major assessment methods include areal and volumetric yield methods, field size distributions, historical extrapolation, deposit modeling, organic geochemical mass balance methods, and direct expert assessment. Other categories include mathematical tools, reserve growth/confirmation, quantitative characterization of undiscovered resources, and general topics. For the purpose of future updates, we solicit contributions of articles that may have been missed in the preparation of this bibliography. ?? 1995 Oxford University Press.

  19. Pre Teacher Assessment Project.

    ERIC Educational Resources Information Center

    Millward, Robert E.; Gerlach, Gail J.

    The goal of the Pre Teacher Assessment Center is to give college sophomores a diagnostic assessment of their potential teaching skills across 13 skill dimensions felt to be prerequisites for teaching. The pre teacher assessment provides students with detailed information about potential teaching strengths and weaknesses and helps remediate…

  20. An Introduction to Genome Annotation.

    PubMed

    Campbell, Michael S; Yandell, Mark

    2015-12-17

    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  1. The integrated landscape assessment project

    Treesearch

    Miles A. Hemstrom; Janine Salwasser; Joshua Halofsky; Jimmy Kagan; Cyndi Comfort

    2012-01-01

    The Integrated Landscape Assessment Project (ILAP) is a three-year effort that produces information, models, data, and tools to help land managers, policymakers, and others examine mid- to broad-scale (e.g., watersheds to states and larger areas) prioritization of land management actions, perform landscape assessments, and estimate potential effects of management...

  2. Bacterial genome annotation.

    PubMed

    Beckloff, Nicholas; Starkenburg, Shawn; Freitas, Tracey; Chain, Patrick

    2012-01-01

    Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among organisms is not impeded. Functional annotation is dependent on sequence similarity to other known genes or proteins in an effort to assess the function of the gene. Combining structural and functional annotation across genomes in a comparative manner promotes higher levels of accurate annotation as well as an advanced understanding of genome evolution. As the availability of bacterial sequences increases and annotation methods improve, the value of comparative annotation will increase.

  3. Health Education and Physical Education (Healthy, Active Living). Grades 5 and 9. Assessment Annotations for the Curriculum Frameworks.

    ERIC Educational Resources Information Center

    Missouri State Dept. of Elementary and Secondary Education, Jefferson City.

    This document provides supplemental assessment information to "Missouri's Framework for Curriculum Development in Health Education and Physical Education (Healthy, Active Living) K-12." The assessment annotations found in the third column of this document are intended to provide information for administrators, curriculum directors, and…

  4. Health Education and Physical Education (Healthy, Active Living). Grades 5 and 9. Assessment Annotations for the Curriculum Frameworks.

    ERIC Educational Resources Information Center

    Missouri State Dept. of Elementary and Secondary Education, Jefferson City.

    This document provides supplemental assessment information to "Missouri's Framework for Curriculum Development in Health Education and Physical Education (Healthy, Active Living) K-12." The assessment annotations found in the third column of this document are intended to provide information for administrators, curriculum directors, and…

  5. Computing human image annotation.

    PubMed

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities.

  6. Information integration for environmental monitoring and assessment: An annotated bibliography. Professional paper

    SciTech Connect

    Rajagopal, R.; Natarajan, U.; Wacker, J.

    1992-01-01

    Annual federal and state investments in the collection, storage, and maintenance of resource and environmental data are enormous (estimated in the range of a few to tens of billions of dollars). Despite these investments, the use of information from these databases for societal endpoints has been limited. Further research to evaluate the utility of large environmental databases in the analysis of selected scientific and regulatory questions therefore would be timely. The primary purpose of the paper is to provide an annotated review of selected literature on the topic of information integration in the context of environmental monitoring and assessment. Based on a review of this literature, significant scholarly contributions to this field have been identified as falling into the following four issue areas: institutional, resource/ecological, design, and technological. The publications are grouped, indexed, associated with keywords and organized under these four major issue areas.

  7. Assessing the impact of human genome annotation choice on RNA-seq expression estimates.

    PubMed

    Wu, Po-Yen; Phan, John H; Wang, May D

    2013-01-01

    Genome annotation is a crucial component of RNA-seq data analysis. Much effort has been devoted to producing an accurate and rational annotation of the human genome. An annotated genome provides a comprehensive catalogue of genomic functional elements. Currently, at least six human genome annotations are publicly available, including AceView Genes, Ensembl Genes, H-InvDB Genes, RefSeq Genes, UCSC Known Genes, and Vega Genes. Characteristics of these annotations differ because of variations in annotation strategies and information sources. When performing RNA-seq data analysis, researchers need to choose a genome annotation. However, the effect of genome annotation choice on downstream RNA-seq expression estimates is still unclear. This study (1) investigates the effect of different genome annotations on RNA-seq quantification and (2) provides guidelines for choosing a genome annotation based on research focus. We define the complexity of human genome annotations in terms of the number of genes, isoforms, and exons. This definition facilitates an investigation of potential relationships between complexity and variations in RNA-seq quantification. We apply several evaluation metrics to demonstrate the impact of genome annotation choice on RNA-seq expression estimates. In the mapping stage, the least complex genome annotation, RefSeq Genes, appears to have the highest percentage of uniquely mapped short sequence reads. In the quantification stage, RefSeq Genes results in the most stable expression estimates in terms of the average coefficient of variation over all genes. Stable expression estimates in the quantification stage translate to accurate statistics for detecting differentially expressed genes. We observe that RefSeq Genes produces the most accurate fold-change measures with respect to a ground truth of RT-qPCR gene expression estimates. Based on the observed variations in the mapping, quantification, and differential expression calling stages, we demonstrate

  8. Video Annotation Software Application for Thorough Collaborative Assessment of and Feedback on Microteaching Lessons in Geography Education

    ERIC Educational Resources Information Center

    van der Westhuizen, Christo P.; Golightly, Aubrey

    2015-01-01

    This article discusses the process and findings of a study in which video annotation (VideoANT) and a learning management system (LMS) were implemented together in the microteaching lessons of fourth-year geography student teachers. The aim was to ensure adequate assessment of and feedback for each student, since these aspects are, in general, a…

  9. Video Annotation Software Application for Thorough Collaborative Assessment of and Feedback on Microteaching Lessons in Geography Education

    ERIC Educational Resources Information Center

    van der Westhuizen, Christo P.; Golightly, Aubrey

    2015-01-01

    This article discusses the process and findings of a study in which video annotation (VideoANT) and a learning management system (LMS) were implemented together in the microteaching lessons of fourth-year geography student teachers. The aim was to ensure adequate assessment of and feedback for each student, since these aspects are, in general, a…

  10. ASSESSMENT OF THE SWINE PROTEIN-ANNOTATED OLIGONUCLEOTIDE MICROARRAY AND UTILITY OF THE ARRAYS FOR EQTL AND TRANSCRIPTIONAL PROFILING STUDIES

    USDA-ARS?s Scientific Manuscript database

    We have evaluated the new Swine Protein-Annotated Oligonucleotide Microarray (http://www.pigoligoarray.org) by analyzing transcriptional profiles for longissimus dorsi muscle (LD), Bronchial lymph node (BLN) and Lung. Four LD samples were used to assess the stringency of hybridization conditions com...

  11. SEED Software Annotations.

    ERIC Educational Resources Information Center

    Bethke, Dee; And Others

    This document provides a composite index of the first five sets of software annotations produced by Project SEED. The software has been indexed by title, subject area, and grade level, and it covers sets of annotations distributed in September 1986, April 1987, September 1987, November 1987, and February 1988. The date column in the index…

  12. Assessment of community-submitted ontology annotations from a novel database-journal partnership

    PubMed Central

    Berardini, Tanya Z.; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

    2012-01-01

    As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org PMID:22859749

  13. Assessment of community-submitted ontology annotations from a novel database-journal partnership.

    PubMed

    Berardini, Tanya Z; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

    2012-01-01

    As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org.

  14. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

    PubMed

    Shameer, Khader; Tripathi, Lokesh P; Kalari, Krishna R; Dudley, Joel T; Sowdhamini, Ramanathan

    2016-09-01

    Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  15. WESTERN AIRBORNE CONTAMINANTS ASSESSMENT PROJECT RESEARCH PLAN

    EPA Science Inventory

    The goal of the Western Airborne Contaminants Assessment Project (WACAP) is to assess the deposition of airborne contaminants in Western National Parks, providing regional and local information on exposure, accumulation, impacts, and probable sources. This project is being desig...

  16. WESTERN AIRBORNE CONTAMINANTS ASSESSMENT PROJECT RESEARCH PLAN

    EPA Science Inventory

    The goal of the Western Airborne Contaminants Assessment Project (WACAP) is to assess the deposition of airborne contaminants in Western National Parks, providing regional and local information on exposure, accumulation, impacts, and probable sources. This project is being desig...

  17. Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study

    PubMed Central

    Raethong, Nachon; Wong-ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa

    2016-01-01

    Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction. PMID:27274991

  18. International Arctic Seas Assessment Project.

    PubMed

    Sjöblom, K L; Salo, A; Bewers, J M; Cooper, J; Dyer, R S; Lynn, N M; Mount, M E; Povinec, P P; Sazykina, T G; Schwarz, J; Scott, E M; Sivintsev, Y V; Tanner, J E; Warden, J M; Woodhead, D

    1999-09-30

    The International Atomic Energy Agency responded to the news that the former Soviet Union had dumped radioactive wastes in the shallow waters of the Arctic Seas, by launching the International Arctic Seas Assessment Project in 1993. The project had two objectives: to assess the risks to human health and to the environment associated with the radioactive wastes dumped in the Kara and Barents Seas; and to examine possible remedial actions related to the dumped wastes and to advise on whether they are necessary and justified. The current radiological situation in the Arctic waters was examined to assess whether there is any evidence for releases from the dumped waste. Potential future releases from the dumped wastes were predicted, concentrating on the high-level waste objects containing the major part of the radionuclide inventory of the wastes. Environmental transport of released radionuclides was modelled and the associated radiological impact on humans and the biota was assessed. The feasibility, costs and benefits of possible remedial measures applied to a selected high-level waste object were examined. Releases from identified dumped objects were found to be small and localised to the immediate vicinity of the dumping sites. Projected future annual doses to members of the public in typical local population groups were very small, less than 1 microSv--corresponding to a trivial risk. Projected future doses to a hypothetical group of military personnel patrolling the foreshore of the fjords in which wastes have been dumped were higher, up to 4 mSv/year, which still is of the same order as the average annual natural background dose. Moreover, since any of the proposed remedial actions were estimated to cost several million US$ to implement, remediation was not considered justified on the basis of potentially removing a collective dose of 10 man Sv. Doses calculated to marine fauna were insignificant, orders of magnitude below those at which detrimental effects on

  19. Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

    PubMed

    Arloth, Janine; Bader, Daniel M; Röh, Simone; Altmann, Andre

    2015-01-01

    Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.

  20. Chemical facility vulnerability assessment project.

    PubMed

    Jaeger, Calvin D

    2003-11-14

    Sandia National Laboratories, under the direction of the Office of Science and Technology, National Institute of Justice, conducted the chemical facility vulnerability assessment (CFVA) project. The primary objective of this project was to develop, test and validate a vulnerability assessment methodology (VAM) for determining the security of chemical facilities against terrorist or criminal attacks (VAM-CF). The project also included a report to the Department of Justice for Congress that in addition to describing the VAM-CF also addressed general observations related to security practices, threats and risks at chemical facilities and chemical transport. In the development of the VAM-CF Sandia leveraged the experience gained from the use and development of VAs in other areas and the input from the chemical industry and Federal agencies. The VAM-CF is a systematic, risk-based approach where risk is a function of the severity of consequences of an undesired event, the attack potential, and the likelihood of adversary success in causing the undesired event. For the purpose of the VAM-CF analyses Risk is a function of S, L(A), and L(AS), where S is the severity of consequence of an event, L(A) is the attack potential and L(AS) likelihood of adversary success in causing a catastrophic event. The VAM-CF consists of 13 basic steps. It involves an initial screening step, which helps to identify and prioritize facilities for further analysis. This step is similar to the prioritization approach developed by the American Chemistry Council (ACC). Other steps help to determine the components of the risk equation and ultimately the risk. The VAM-CF process involves identifying the hazardous chemicals and processes at a chemical facility. It helps chemical facilities to focus their attention on the most critical areas. The VAM-CF is not a quantitative analysis but, rather, compares relative security risks. If the risks are deemed too high, recommendations are developed for

  1. Total Quality Management in Higher Education: From Assessment to Improvement. An Annotated Bibliography, Second Edition.

    ERIC Educational Resources Information Center

    Peterson, Marvin W.; And Others

    This publication is an annotated bibliography of articles and key organizational sources on Total Quality Management (TQM) in higher education. The list was developed through searches of local and national data bases including Education Resources Information Center (ERIC), Public Affairs Information System (PAIS), Wilson Indexes to Journal…

  2. Apollo: a sequence annotation editor.

    PubMed

    Lewis, S E; Searle, S M J; Harris, N; Gibson, M; Lyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, M A; Kaminker, J S; Matthews, B B; Prochnik, S E; Smithy, C D; Tupy, J L; Rubin, G M; Misra, S; Mungall, C J; Clamp, M E

    2002-01-01

    The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.

  3. Annotated directory of US Government information system projects of potential interest to NASA/SSPO

    NASA Technical Reports Server (NTRS)

    Legrand, Sue

    1988-01-01

    The purpose of this research activity was to develop a list for NASA of major U.S. government information systems contacts who are able to cooperate with NASA on technical interchange. The list contains the names of appropriate managers involved in major information system projects, U.S. government office officials, and their hierarchy up to the highest officials whose major responsibilities include government information systems development.

  4. Strategies for annotation and curation of translational databases: the eTUMOUR project.

    PubMed

    Julià-Sapé, Margarida; Lurgi, Miguel; Mier, Mariola; Estanyol, Francesc; Rafael, Xavier; Candiota, Ana Paula; Barceló, Anna; García, Alina; Martínez-Bisbal, M Carmen; Ferrer-Luna, Rubén; Moreno-Torres, Ángel; Celda, Bernardo; Arús, Carles

    2012-01-01

    The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database--the eTDB--was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved.

  5. Strategies for annotation and curation of translational databases: the eTUMOUR project

    PubMed Central

    Julià-Sapé, Margarida; Lurgi, Miguel; Mier, Mariola; Estanyol, Francesc; Rafael, Xavier; Candiota, Ana Paula; Barceló, Anna; García, Alina; Martínez-Bisbal, M. Carmen; Ferrer-Luna, Rubén; Moreno-Torres, Àngel; Celda, Bernardo; Arús, Carles

    2012-01-01

    The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database—the eTDB—was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved. PMID:23180768

  6. Using video-annotation software to identify interactions in group therapies for schizophrenia: assessing reliability and associations with outcomes.

    PubMed

    Orfanos, Stavros; Akther, Syeda Ferhana; Abdul-Basit, Muhammad; McCabe, Rosemarie; Priebe, Stefan

    2017-02-10

    Research has shown that interactions in group therapies for people with schizophrenia are associated with a reduction in negative symptoms. However, it is unclear which specific interactions in groups are linked with these improvements. The aims of this exploratory study were to i) develop and test the reliability of using video-annotation software to measure interactions in group therapies in schizophrenia and ii) explore the relationship between interactions in group therapies for schizophrenia with clinically relevant changes in negative symptoms. Video-annotation software was used to annotate interactions from participants selected across nine video-recorded out-patient therapy groups (N = 81). Using the Individual Group Member Interpersonal Process Scale, interactions were coded from participants who demonstrated either a clinically significant improvement (N = 9) or no change (N = 8) in negative symptoms at the end of therapy. Interactions were measured from the first and last sessions of attendance (>25 h of therapy). Inter-rater reliability between two independent raters was measured. Binary logistic regression analysis was used to explore the association between the frequency of interactive behaviors and changes in negative symptoms, assessed using the Positive and Negative Syndrome Scale. Of the 1275 statements that were annotated using ELAN, 1191 (93%) had sufficient audio and visual quality to be coded using the Individual Group Member Interpersonal Process Scale. Rater-agreement was high across all interaction categories (>95% average agreement). A higher frequency of self-initiated statements measured in the first session was associated with improvements in negative symptoms. The frequency of questions and giving advice measured in the first session of attendance was associated with improvements in negative symptoms; although this was only a trend. Video-annotation software can be used to reliably identify interactive behaviors in groups

  7. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

    PubMed Central

    Hughes, Jim R.; Cheng, Jan-Fang; Ventress, Nicki; Prabhakar, Shyam; Clark, Kevin; Anguita, Eduardo; De Gobbi, Marco; de Jong, Pieter; Rubin, Eddy; Higgs, Douglas R.

    2005-01-01

    An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple, divergent species. This approach distinguishes multispecies conserved sequences (MCS) in noncoding regions from more rapidly evolving neutral DNA. Here, we have analyzed a region of ≈238kb containing the human α globin cluster that was sequenced and/or annotated across the syntenic region in 22 species spanning 500 million years of evolution. Using a variety of bioinformatic approaches and correlating the results with many aspects of chromosome structure and function in this region, we were able to identify and evaluate the importance of 24 individual MCSs. This approach sensitively and accurately identified previously characterized regulatory elements but also discovered unidentified promoters, exons, splicing, and transcriptional regulatory elements. Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs. PMID:15998734

  8. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

    PubMed Central

    Bergman, Casey M; Pfeiffer, Barret D; Rincón-Limas, Diego E; Hoskins, Roger A; Gnirke, Andreas; Mungall, Chris J; Wang, Adrienne M; Kronmiller, Brent; Pacleb, Joanne; Park, Soo; Stapleton, Mark; Wan, Kenneth; George, Reed A; de Jong, Pieter J; Botas, Juan; Rubin, Gerald M; Celniker, Susan E

    2002-01-01

    Background It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. Results We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. Conclusions Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone. PMID:12537575

  9. The Nozoe Autograph Books Project: An Assessment.

    PubMed

    Seeman, Jeffrey I; Johnson, Brian P

    2015-12-01

    Bonding beyond Borders is a fitting title to the Nozoe Autograph Books project, as the books and their publication involved innumerable contributors from around the globe all in the spirit of personal collaboration. The editors of this project share details of how the project came into being and give their own personal assessment of what it has become and what it means.

  10. Automated annotation and classification of BI-RADS assessment from radiology reports.

    PubMed

    Castro, Sergio M; Tseytlin, Eugene; Medvedeva, Olga; Mitchell, Kevin; Visweswaran, Shyam; Bekhuis, Tanja; Jacobson, Rebecca S

    2017-05-01

    The Breast Imaging Reporting and Data System (BI-RADS) was developed to reduce variation in the descriptions of findings. Manual analysis of breast radiology report data is challenging but is necessary for clinical and healthcare quality assurance activities. The objective of this study is to develop a natural language processing (NLP) system for automated BI-RADS categories extraction from breast radiology reports. We evaluated an existing rule-based NLP algorithm, and then we developed and evaluated our own method using a supervised machine learning approach. We divided the BI-RADS category extraction task into two specific tasks: (1) annotation of all BI-RADS category values within a report, (2) classification of the laterality of each BI-RADS category value. We used one algorithm for task 1 and evaluated three algorithms for task 2. Across all evaluations and model training, we used a total of 2159 radiology reports from 18 hospitals, from 2003 to 2015. Performance with the existing rule-based algorithm was not satisfactory. Conditional random fields showed a high performance for task 1 with an F-1 measure of 0.95. Rules from partial decision trees (PART) algorithm showed the best performance across classes for task 2 with a weighted F-1 measure of 0.91 for BIRADS 0-6, and 0.93 for BIRADS 3-5. Classification performance by class showed that performance improved for all classes from Naïve Bayes to Support Vector Machine (SVM), and also from SVM to PART. Our system is able to annotate and classify all BI-RADS mentions present in a single radiology report and can serve as the foundation for future studies that will leverage automated BI-RADS annotation, to provide feedback to radiologists as part of a learning health system loop. Copyright © 2017. Published by Elsevier Inc.

  11. Environmental Assessment Lakeview Geothermal Project

    SciTech Connect

    Treis, Tania

    2012-04-30

    The Town of Lakeview is proposing to construct and operate a geothermal direct use district heating system in Lakeview, Oregon. The proposed project would be in Lake County, Oregon, within the Lakeview Known Geothermal Resources Area (KGRA). The proposed project includes the following elements: Drilling, testing, and completion of a new production well and geothermal water injection well; construction and operation of a geothermal production fluid pipeline from the well pad to various Town buildings (i.e., local schools, hospital, and Lake County Industrial Park) and back to a geothermal water injection well. This EA describes the proposed project, the alternatives considered, and presents the environmental analysis pursuant to the National Environmental Policy Act. The project would not result in adverse effects to the environment with the implementation of environmental protection measures.

  12. Environmental assessment: The Eden project

    NASA Astrophysics Data System (ADS)

    Roza, Christodoulaki

    Non domestic buildings account for about one-sixth of the U.K.'s entire C02 emissions and one-third of the building related ones 2 . Their proportion of energy consumption, particularly electricity, has also been growing 2 . New buildings are not necessarily better, with energy use often proving to be much higher than their designers anticipated 2 . Annual C02 emissions of two- and sometimes three- times design expectations are far from unusual, leaving a massive credibility gap 2 . These and other global environmental and human health related concerns have motivated an increasing number of designers, developers and building users to pursue more environmentally sustainable designs and construction strategies 5 . However, these buildings can be difficult to evaluate, since they are large in scale, complex in materials and function and temporally dynamic due to limited service life of building components and changing user requirements 5 . All of these factors make environmental assessment of the buildings challenging. Previous Post Occupancy Review of Buildings and their Engineering (PROBE) building investigations have uncovered serious shortcomings in facilities management, or at least mismatches between a building's management needs and the ability of the occupiers to provide the right level of management 1 . Consequently, large differences between energy performance expectations and outcomes can occur virtually unnoticed, while designers continue to repeat flawed descriptions 2 . This investigation attempts to evaluate the building's operation and to help achieving demonstrable improvements in terms of energy efficiency and occupant satisfaction. The scope of this study is to evaluate the actual environmental performance of a building notable for its advanced design. The Education Resource Centre at the Eden Project was selected to compare design expectations with post occupancy performance. This report contains a small-scale survey of user satisfaction with the

  13. Morphosyntactic Annotation of CHILDES Transcripts

    ERIC Educational Resources Information Center

    Sagae, Kenji; Davis, Eric; Lavie, Alon; MacWhinney, Brian; Wintner, Shuly

    2010-01-01

    Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database…

  14. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  15. RATT: Rapid Annotation Transfer Tool

    PubMed Central

    Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

    2011-01-01

    Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

  16. Review of Projective Personality Assessment Techniques.

    ERIC Educational Resources Information Center

    Obrzut, John E.

    This paper reviews the literatuare on projective techniques of personality assessment and their use by school psychologists. Following a brief survey of the development of projective techniques, several of the most widely used techniques are briefly discussed, i.e., the Thematic Apperception Test (TAT), the Childrens Apperception Test (CAT), the…

  17. Review of Projective Personality Assessment Techniques.

    ERIC Educational Resources Information Center

    Obrzut, John E.

    This paper reviews the literatuare on projective techniques of personality assessment and their use by school psychologists. Following a brief survey of the development of projective techniques, several of the most widely used techniques are briefly discussed, i.e., the Thematic Apperception Test (TAT), the Childrens Apperception Test (CAT), the…

  18. Quality of computationally inferred gene ontology annotations.

    PubMed

    Skunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-05-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon-an important outcome given that >98% of all annotations are inferred without direct curation.

  19. Ares Project Technology Assessment: Approach and Tools

    NASA Technical Reports Server (NTRS)

    Hueter, Uwe; Tyson, Richard

    2010-01-01

    Technology assessments provide a status of the development maturity of specific technologies. Along with benefit analysis, the risks the project assumes can be quantified. Normally due to budget constraints, the competing technologies are prioritized and decisions are made which ones to fund. A detailed technology development plan is produced for the selected technologies to provide a roadmap to reach the desired maturity by the project s critical design review. Technology assessments can be conducted for both technology only tasks or for product development programs. This paper is primarily biased toward the product development programs. The paper discusses the Ares Project s approach to technology assessment. System benefit analysis, risk assessment, technology prioritization, and technology readiness assessment are addressed. A description of the technology readiness level tool being used is provided.

  20. Mexico Wind Resource Assessment Project

    SciTech Connect

    Schwartz, M.N.; Elliott, D.L.

    1995-05-01

    A preliminary wind energy resource assessment of Mexico that produced wind resource maps for both utility-scale and rural applications was undertaken as part of the Mexico-U.S. Renewable Energy Cooperation Program. This activity has provided valuable information needed to facilitate the commercialization of small wind turbines and windfarms in Mexico and to lay the groundwork for subsequent wind resource activities. A surface meteorological data set of hourly data in digital form was utilized to prepare a more detailed and accurate wind resource assessment of Mexico than otherwise would have been possible. Software was developed to perform the first ever detailed analysis of the wind characteristics data for over 150 stations in Mexico. The hourly data set was augmented with information from weather balloons (upper-air data), ship wind data from coastal areas, and summarized wind data from sources in Mexico. The various data were carefully evaluated for their usefulness in preparing the wind resource assessment. The preliminary assessment has identified many areas of good-to-excellent wind resource potential and shows that the wind resource in Mexico is considerably greater than shown in previous surveys.

  1. Human Genome Annotation

    NASA Astrophysics Data System (ADS)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  2. Hawaii Geothermal Project annotated bibliography: Biological resources of the geothermal subzones, the transmission corridors and the Puna District, Island of Hawaii

    SciTech Connect

    Miller, S.E.; Burgett, J.M.

    1993-10-01

    Task 1 of the Hawaii Geothermal Project Interagency Agreement between the Fish and Wildlife Service and the Department of Energy-Oak Ridge National Laboratory (DOE) includes an annotated bibliography of published and unpublished documents that cover biological issues related to the lowland rain forest in Puna, adjacent areas, transmission corridors, and in the proposed Hawaii Geothermal Project (HGP). The 51 documents reviewed in this report cover the main body of biological information for these projects. The full table of contents and bibliography for each document is included along with two copies (as requested in the Interagency Agreement) of the biological sections of each document. The documents are reviewed in five main categories: (1) geothermal subzones (29 documents); (2) transmission cable routes (8 documents); (3) commercial satellite launching facility (Spaceport; 1 document); (4) manganese nodule processing facility (2 documents); (5) water resource development (1 document); and (6) ecosystem stability and introduced species (11 documents).

  3. Project Assessment Skills Web Application

    NASA Technical Reports Server (NTRS)

    Goff, Samuel J.

    2013-01-01

    The purpose of this project is to utilize Ruby on Rails to create a web application that will replace a spreadsheet keeping track of training courses and tasks. The goal is to create a fast and easy to use web application that will allow users to track progress on training courses. This application will allow users to update and keep track of all of the training required of them. The training courses will be organized by group and by user, making readability easier. This will also allow group leads and administrators to get a sense of how everyone is progressing in training. Currently, updating and finding information from this spreadsheet is a long and tedious task. By upgrading to a web application, finding and updating information will be easier than ever as well as adding new training courses and tasks. Accessing this data will be much easier in that users just have to go to a website and log in with NDC credentials rather than request the relevant spreadsheet from the holder. In addition to Ruby on Rails, I will be using JavaScript, CSS, and jQuery to help add functionality and ease of use to my web application. This web application will include a number of features that will help update and track progress on training. For example, one feature will be to track progress of a whole group of users to be able to see how the group as a whole is progressing. Another feature will be to assign tasks to either a user or a group of users. All of these together will create a user friendly and functional web application.

  4. River Protection Project information systems assessment

    SciTech Connect

    JOHNSON, A.L.

    1999-07-28

    The Information Systems Assessment Report documents the results from assessing the Project Hanford Management Contract (PHMC) Hanford Data Integrator 2000 (HANDI 2000) system, Business Management System (BMS) and Work Management System phases (WMS), with respect to the System Engineering Capability Assessment Model (CAM). The assessment was performed in accordance with the expectations stated in the fiscal year (FY) 1999 Performance Agreement 7.1.1, item (2) which reads, ''Provide an assessment report on the selected Integrated Information System by July 31, 1999.'' This report assesses the BMS and WMS as implemented and planned for the River Protection Project (RPP). The systems implementation is being performed under the PHMC HANDI 2000 information system project. The project began in FY 1998 with the BMS, proceeded in FY 1999 with the Master Equipment List portion of the WMS, and will continue the WMS implementation as funding provides. This report constitutes an interim quality assessment providing information necessary for planning RPP's information systems activities. To avoid confusion, HANDI 2000 will be used when referring to the entire system, encompassing both the BMS and WMS. A graphical depiction of the system is shown in Figure 2-1 of this report.

  5. Annotated Videography.

    ERIC Educational Resources Information Center

    United States Holocaust Memorial Museum, Washington, DC.

    This annotated list of 43 videotapes recommended for classroom use addresses various themes for teaching about the Holocaust, including: (1) overviews of the Holocaust; (2) life before the Holocaust; (3) propaganda; (4) racism, anti-Semitism; (5) "enemies of the state"; (6) ghettos; (7) camps; (8) genocide; (9) rescue; (10) resistance;…

  6. The International Arctic Seas Assessment Project

    SciTech Connect

    Linsley, G.S.; Sjoeblom, K.L.

    1994-07-01

    The International Arctic Seas Assessment Project (IASAP) was initiated in 1993 to address widespread concern over the possible health and environmental impacts associated with the radioactive waste dumped into the shallow waters of the Arctic Seas. This article discusses the project with these general topics: A brief history of dumping activities; the international control system; perspectives on arctic Seas dumping; the IASAP aims and implementation; the IASAP work plan and progress. 2 figs.

  7. Algal functional annotation tool

    SciTech Connect

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG

  8. Tidd PFBC Demonstration Project, A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2001-08-31

    The Clean Coal Technology (CCT) Demonstration Program is a government and industry co-funded technology development effort to demonstrate a new generation of innovative coal utilization processes. One goal of the program is to furnish the energy marketplace with a variety of energy efficient, environmentally superior coal-based technologies. Demonstration projects seek to establish the commercial feasibility of the most promising coal technologies that have proceeded beyond the proof-of-concept stage. This report is a post-project assessment of the DOE CCT Demonstration Program, the Tidd PFBC Demonstration Project. A major objective of the CCT Program is to provide the technical data necessary for the private sector to proceed confidently with the commercial replication of the demonstrated technologies. An essential element of meeting this goal is the dissemination of results from the demonstration projects. This post-project assessment (PPA) report is an independent DOE appraisal of the successes that the completed project had in achieving its objectives and aiding in the commercialization of the demonstrated technology. The report also provides an assessment of the expected technical, environmental, and economic performance of the commercial version of the technology, as well as an analysis of the commercial market.

  9. Facility interface capability assessment (FICA) project

    SciTech Connect

    Mote, N.

    1990-10-01

    This paper discusses the Facility Interface Capability Assessment Project to determine current and potential facility capabilities for storage and shipment of spent fuel. The project includes performing site visits to all 122 commercial facilities from which spent fuel will be accepted by the Federal Waste Management System (FWMS). The Near-Site Transportation Infrastructure Project, which includes site surveys to determine the current and potential cask transportation capabilities in the vicinity of the 76 commercial sites on which are located the commercial facilities relevant to the FWMS is also addressed.

  10. Subjective risk assessment for planning conservation projects

    NASA Astrophysics Data System (ADS)

    Game, Edward T.; Fitzsimons, James A.; Lipsett-Moore, Geoff; McDonald-Madden, Eve

    2013-12-01

    Conservation projects occur under many types of uncertainty. Where this uncertainty can affect achievement of a project’s objectives, there is risk. Understanding risks to project success should influence a range of strategic and tactical decisions in conservation, and yet, formal risk assessment rarely features in the guidance or practice of conservation planning. We describe how subjective risk analysis tools can be framed to facilitate the rapid identification and assessment of risks to conservation projects, and how this information should influence conservation planning. Our approach is illustrated with an assessment of risks to conservation success as part of a conservation plan for the work of The Nature Conservancy in northern Australia. Risks can be both internal and external to a project, and occur across environmental, social, economic and political systems. Based on the relative importance of a risk and the level of certainty in its assessment we propose a series of appropriate, project level responses including research, monitoring, and active amelioration. Explicit identification, prioritization, and where possible, management of risks are important elements of using conservation resources in an informed and accountable manner.

  11. Student Query Trend Assessment with Semantical Annotation and Artificial Intelligent Multi-Agents

    ERIC Educational Resources Information Center

    Malik, Kaleem Razzaq; Mir, Rizwan Riaz; Farhan, Muhammad; Rafiq, Tariq; Aslam, Muhammad

    2017-01-01

    Research in era of data representation to contribute and improve key data policy involving the assessment of learning, training and English language competency. Students are required to communicate in English with high level impact using language and influence. The electronic technology works to assess students' questions positively enabling…

  12. Morphosyntactic annotation of CHILDES transcripts*

    PubMed Central

    SAGAE, KENJI; DAVIS, ERIC; LAVIE, ALON; MACWHINNEY, BRIAN; WINTNER, SHULY

    2014-01-01

    Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database with grammatical relations in the form of labeled dependency structures. We have produced a corpus of over 18,800 utterances (approximately 65,000 words) with manually curated gold-standard grammatical relation annotations. Using this corpus, we have developed a highly accurate data-driven parser for the English CHILDES data, which we used to automatically annotate the remainder of the English section of CHILDES. We have also extended the parser to Spanish, and are currently working on supporting more languages. The parser and the manually and automatically annotated data are freely available for research purposes. PMID:20334720

  13. Assessing uncertainties in land cover projections.

    PubMed

    Alexander, Peter; Prestele, Reinhard; Verburg, Peter H; Arneth, Almut; Baranzelli, Claudia; Batista E Silva, Filipe; Brown, Calum; Butler, Adam; Calvin, Katherine; Dendoncker, Nicolas; Doelman, Jonathan C; Dunford, Robert; Engström, Kerstin; Eitelberg, David; Fujimori, Shinichiro; Harrison, Paula A; Hasegawa, Tomoko; Havlik, Petr; Holzhauer, Sascha; Humpenöder, Florian; Jacobs-Crisioni, Chris; Jain, Atul K; Krisztin, Tamás; Kyle, Page; Lavalle, Carlo; Lenton, Tim; Liu, Jiayi; Meiyappan, Prasanth; Popp, Alexander; Powell, Tom; Sands, Ronald D; Schaldach, Rüdiger; Stehfest, Elke; Steinbuks, Jevgenijs; Tabeau, Andrzej; van Meijl, Hans; Wise, Marshall A; Rounsevell, Mark D A

    2017-02-01

    Understanding uncertainties in land cover projections is critical to investigating land-based climate mitigation policies, assessing the potential of climate adaptation strategies and quantifying the impacts of land cover change on the climate system. Here, we identify and quantify uncertainties in global and European land cover projections over a diverse range of model types and scenarios, extending the analysis beyond the agro-economic models included in previous comparisons. The results from 75 simulations over 18 models are analysed and show a large range in land cover area projections, with the highest variability occurring in future cropland areas. We demonstrate systematic differences in land cover areas associated with the characteristics of the modelling approach, which is at least as great as the differences attributed to the scenario variations. The results lead us to conclude that a higher degree of uncertainty exists in land use projections than currently included in climate or earth system projections. To account for land use uncertainty, it is recommended to use a diverse set of models and approaches when assessing the potential impacts of land cover change on future climate. Additionally, further work is needed to better understand the assumptions driving land use model results and reveal the causes of uncertainty in more depth, to help reduce model uncertainty and improve the projections of land cover.

  14. Project Assessment Framework through Design (PAFTD) - A Project Assessment Framework in Support of Strategic Decision Making

    NASA Technical Reports Server (NTRS)

    Depenbrock, Brett T.; Balint, Tibor S.; Sheehy, Jeffrey A.

    2014-01-01

    Research and development organizations that push the innovation edge of technology frequently encounter challenges when attempting to identify an investment strategy and to accurately forecast the cost and schedule performance of selected projects. Fast moving and complex environments require managers to quickly analyze and diagnose the value of returns on investment versus allocated resources. Our Project Assessment Framework through Design (PAFTD) tool facilitates decision making for NASA senior leadership to enable more strategic and consistent technology development investment analysis, beginning at implementation and continuing through the project life cycle. The framework takes an integrated approach by leveraging design principles of useability, feasibility, and viability and aligns them with methods employed by NASA's Independent Program Assessment Office for project performance assessment. The need exists to periodically revisit the justification and prioritization of technology development investments as changes occur over project life cycles. The framework informs management rapidly and comprehensively about diagnosed internal and external root causes of project performance.

  15. FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation.

    PubMed

    Chen, Ting-Wen; Gan, Ruei-Chi; Fang, Yi-Kai; Chien, Kun-Yi; Liao, Wei-Chao; Chen, Chia-Chun; Wu, Timothy H; Chang, Ian Yi-Feng; Yang, Chi; Huang, Po-Jung; Yeh, Yuan-Ming; Chiu, Cheng-Hsun; Huang, Tzu-Wen; Tang, Petrus

    2017-09-05

    Along with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/ . This new web-based annotator will shed light on field studies involving organisms without a reference genome.

  16. Project Approval, Environmental Assessment and Public Participation.

    ERIC Educational Resources Information Center

    Elder, P. S.

    1982-01-01

    Presents a case study of a heavy oil project proposed by Esso Resources Canada Limited at Cold Lake, Alberta, Canada. Focuses on the approval process, environmental and social impact assessments, and public participation. Evaluates the case and makes recommendations concerning the approval process. (DC)

  17. GSV Annotated Bibliography

    SciTech Connect

    Roberts, Randy S.; Pope, Paul A.; Jiang, Ming; Trucano, Timothy G.; Aragon, Cecilia R.; Ni, Kevin; Wei, Thomas; Chilton, Lawrence K.; Bakel, Alan

    2011-06-14

    The following annotated bibliography was developed as part of the Geospatial Algorithm Veri cation and Validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Veri cation and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following ve topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models.

  18. The surplus facility inventory and assessment project

    SciTech Connect

    Weiner, L.A.; Szilagyi, A.P.; Rae, L.J.

    1994-12-31

    As a result of the ending of the Cold War, the Department of Energy (DOE) is experiencing a downsizing of the DOE nuclear weapons complex similar to the downsizing and base closures being experienced by the armed forces. Declining budgets across all DOE programs have further contributed to the extent and rate at which DOE`s assets are being declared surplus. The Surplus Facility Inventory and Assessment (SFIA) Project will define the magnitude of risk associated with the DOE surplus, contaminated assets. The results of the SFIA Project will be fundamental to all planning, budgeting, and management associated with the surplus, contaminated inventory.

  19. Facility Interface Capability Assessment (FICA) project report

    SciTech Connect

    Pope, R.B.; MacDonald, R.R.; Viebrock, J.M.; Mote, N.

    1995-09-01

    The US Department of Energy`s (DOE) Office of Civilian Radioactive Waste Management (OCRWM) is responsible for developing the Civilian Radioactive Waste Management System (CRWMS) to accept spent nuclear fuel from commercial facilities. The objective of the Facility Interface Capability Assessment (FICA) project was to assess the capability of each commercial spent nuclear fuel (SNF) storage facility, at which SNF is stored, to handle various SNF shipping casks. The purpose of this report is to present and analyze the results of the facility assessments completed within the FICA project. During Phase 1, the data items required to complete the facility assessments were identified and the database for the project was created. During Phase 2, visits were made to 122 facilities on 76 sites to collect data and information, the database was updated, and assessments of the cask-handling capabilities at each facility were performed. Each assessment of cask-handling capability contains three parts: the current capability of the facility (planning base); the potential enhanced capability if revisions were made to the facility licensing and/or administrative controls; and the potential enhanced capability if limited physical modifications were made to the facility. The main conclusion derived from the planning base assessments is that the current facility capabilities will not allow handling of any of the FICA Casks at 49 of the 122 facilities evaluated. However, consideration of potential revisions and/or modifications showed that all but one of the 49 facilities could be adapted to handle at least one of the FICA Casks. For this to be possible, facility licensing, administrative controls, and/or physical aspects of the facility would need to be modified.

  20. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    SciTech Connect

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus

  1. FASTER project - data fusion for trafficability assessment

    NASA Astrophysics Data System (ADS)

    Skocki, K.; Nevatia, Y.

    2013-09-01

    Martian surface missions since Sojourner mission typically use robotic rover platform for carrying the science instrumentation. Such concept, successfully demonstrated by twin MER rovers, is however risky due to low trafficability soil patches unrecognized. Idea of soil traversability assessment is the base for FASTER project activities. This article shortly presents topics of special interest for planetary rover safe path finding and decision making process. The data fusion aspect of such process is analyzed shortly.

  2. Confined Zone Dispersion Project: A DOE assessment

    SciTech Connect

    1999-11-30

    The goal of the US Department of Energy (DOE) Clean Coal Technology (CCT) program is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have developed beyond the proof-of-concept (POC) stage. This document serves as a DOE post-project assessment of the Confined Zone Dispersion Project in CCT Round 3. In 1990, Bechtel Corporation entered into a cooperative agreement to conduct the demonstration project. The Seward Power Station of Pennsylvania Electric Company (now GPU Genco) was the host site. DOE funded 43 percent of the total project cost of $12,173,000. The project was started in June 1990 and was scheduled to be completed in June 1993. As a result of various operating problems, the schedule was extended into 1994 without additional cost to DOE. Bechtel provided the additional financing and GPU Genco provided electricity, steam, and water to operate the unit. The independent evaluation contained herein is based primarily on information from Bechtel's final technical report (1994) as well as other references cited. Confined Zone Dispersion (CZD) is a flue gas desulfurization (FGD) process that removes sulfur dioxide (SO{sub 2}). A finely atomized slurry of reactive lime, calcium hydroxide or Ca(OH){sub 2} is injected into the flue-gas duct work, between the air preheater and the second-stage ESP. The lime reacts with the SO{sub 2}, forming dry solid reaction products. The downstream ESP captures the 2 reaction products along with the fly ash entrained in the flue gas. The CZD process was demonstrated on Unit 5, a 147-MWe utility unit with two flue gas ducts. One of the ducts was extended to provide the requisite residence time and retrofitted with the CZD lime injection equipment.

  3. The West Virginia Health Education Assessment Project.

    PubMed

    Tompkins, Nancy O'Hara; Kamal, Khalid M; Chapman, Don

    2005-08-01

    Well-designed school health education should provide students with the knowledge and skills to prevent the health risk behaviors most responsible for the major causes of morbidity and mortality. This paper reports the methodology and findings of a West Virginia statewide health education assessment initiative and describes how the findings are used to design professional development training for school health educators. Selected response items from the State Collaborative on Assessment and Student Standards, Health Education Assessment Project were used to develop a 40-item assessment instrument for 6 health education content areas. In West Virginia, 51 counties and 242 schools were recruited (county response rate = 93%; school response rate = 53%); 17,549 students were tested in grades 6, 8, and high school health education classes. Mean total scores by grade were 30.61 (grade 6), 26.55 (grade 8), and 26.53 (high school), indicating a slight decline in scores as grade level increased. Females in each grade level scored higher on total Health Education Assessment Project (HEAP) scores and subtest scores than males. The results suggest notable differences across grade levels. High school students failed to meet the standard on any health education content areas, indicating the need for enhanced knowledge and skill development. During professional development training, HEAP scores were examined in the context of results from the West Virginia Youth Risk Behavior Survey to underscore the importance of providing quality skills-based health education in West Virginia schools.

  4. ParsEval: parallel comparison and analysis of gene structure annotations

    PubMed Central

    2012-01-01

    Background Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license) at http://parseval.sourceforge.net/. PMID:22852583

  5. Ranking Biomedical Annotations with Annotator's Semantic Relevancy

    PubMed Central

    2014-01-01

    Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator's knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user's vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large. PMID:24899918

  6. Ranking biomedical annotations with annotator's semantic relevancy.

    PubMed

    Wu, Aihua

    2014-01-01

    Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator's knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user's vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large.

  7. Healy Clean Coal Project: A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2003-09-01

    The goal of the U.S. Department of Energy's (DOE) Clean Coal Technology (CCT) Program is to provide the energy marketplace with advanced, more efficient, and environmentally responsible coal utilization options by conducting demonstrations of new technologies. These demonstration projects are intended to establish the commercial feasibility of promising advanced coal technologies that have been developed to a level at which they are ready for demonstration testing under commercial conditions. This document serves as a DOE post-project assessment (PPA) of the Healy Clean Coal Project (HCCP), selected under Round III of the CCT Program, and described in a Report to Congress (U.S. Department of Energy, 1991). The desire to demonstrate an innovative power plant that integrates an advanced slagging combustor, a heat recovery system, and both high- and low-temperature emissions control processes prompted the Alaska Industrial Development and Export Authority (AIDEA) to submit a proposal for this project. In April 1991, AIDEA entered into a cooperative agreement with DOE to conduct this project. Other team members included Golden Valley Electric Association (GVEA), host and operator; Usibelli Coal Mine, Inc., coal supplier; TRW, Inc., Space & Technology Division, combustor technology provider; Stone & Webster Engineering Corp. (S&W), engineer; Babcock & Wilcox Company (which acquired the assets of Joy Environmental Technologies, Inc.), supplier of the spray dryer absorber technology; and Steigers Corporation, provider of environmental and permitting support. Foster Wheeler Energy Corporation supplied the boiler. GVEA provided oversight of the design and provided operators during demonstration testing. The project was sited adjacent to GVEA's Healy Unit No. 1 in Healy, Alaska. The objective of this CCT project was to demonstrate the ability of the TRW Clean Coal Combustion System to operate on a blend of run-of-mine (ROM) coal and waste coal, while meeting strict

  8. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

    PubMed Central

    Thomas, Paul D.; Wood, Valerie; Mungall, Christopher J.; Lewis, Suzanna E.; Blake, Judith A.

    2012-01-01

    A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the “ortholog conjecture” (or, more properly, the “ortholog functional conservation hypothesis”). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the

  9. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

    PubMed

    Thomas, Paul D; Wood, Valerie; Mungall, Christopher J; Lewis, Suzanna E; Blake, Judith A

    2012-01-01

    A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis"). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a

  10. Ecological Compliance Assessment Project: 1994 Summary report

    SciTech Connect

    Brandt, C.A.

    1994-11-01

    The Ecological Compliance Assessment Project (ECAP) began full operation on March 1, 1994. The project is designed around a baseline environmental data concept that includes intensive biological field surveys of key areas of the Hanford Site where the majority of Site activities occur. These surveys are conducted at biologically appropriate times of year to ensure that the data gathered are current and accurate. The data are entered into the ECAP database, which serves as a reference for the evaluation of review requests coming in to the project. This methodology provided the basis for over 90 percent of the review requests received. Field surveys conducted under ECAP are performed to document occurrence information for species of concern and to obtain habitat descriptions. There are over 200 species of concern on the Hanford Site, including plants, birds, mammals, reptiles, amphibians, fish, and invertebrates. In addition, Washington State has designated mature sagebrush-steppe habitat as a Priority Habitat meriting special protective measures. Of the projects reviewed, 17 resulted or will result in impacts to species or habitats of concern on the Hanford Site. The greatest impact has been on big sagebrush habitat. Most of the impact has been or will be within the 600 Area of the Site.

  11. Klickitat Cogeneration Project : Final Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration; Klickitat Energy Partners

    1994-09-01

    To meet BPA`s contractual obligation to supply electrical power to its customers, BPA proposes to acquire power generated by Klickitat Cogeneration Project. BPA has prepared an environmental assessment evaluating the proposed project. Based on the EA analysis, BPA`s proposed action is not a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act of 1969 for the following reasons: (1)it will not have a significant impact land use, upland vegetation, wetlands, water quality, geology, soils, public health and safety, visual quality, historical and cultural resources, recreation and socioeconomics, and (2) impacts to fisheries, wildlife resources, air quality, and noise will be temporary, minor, or sufficiently offset by mitigation. Therefore, the preparation of an environmental impact statement is not required and BPA is issuing this FONSI (Finding of No Significant Impact).

  12. Nationwide tsunami hazard assessment project in Japan

    NASA Astrophysics Data System (ADS)

    Hirata, K.; Fujiwara, H.; Nakamura, H.; Osada, M.; Ohsumi, T.; Morikawa, N.; Kawai, S.; Aoi, S.; Yamamoto, N.; Matsuyama, H.; Toyama, N.; Kito, T.; Murashima, Y.; Murata, Y.; Inoue, T.; Saito, R.; Akiyama, S.; Korenaga, M.; Abe, Y.; Hashimoto, N.

    2014-12-01

    In 2012, we began a project of nationwide Probabilistic Tsunami Hazard Assessment (PTHA) in Japan to support various measures (Fujiwara et al., 2013, JpGU; Hirata et al., 2014, AOGS). The most important strategy in the nationwide PTHA is predominance of aleatory uncertainty in the assessment but use of epistemic uncertainty is limited to the minimum, because the number of all possible combinations among epistemic uncertainties diverges quickly when the number of epistemic uncertainties in the assessment increases ; we consider only a type of earthquake occurrence probability distribution as epistemic uncertainty. We briefly show outlines of the nationwide PTHA as follows; (i) we consider all possible earthquakes in the future, including those that the Headquarters for Earthquake Research Promotion (HERP) of Japanese Government, already assessed. (ii) We construct a set of simplified earthquake fault models, called "Characterized Earthquake Fault Models (CEFMs)", for all of the earthquakes by following prescribed rules (Toyama et al., 2014, JpGU; Korenaga et al., 2014, JpGU). (iii) For all of initial water surface distributions caused by a number of the CEFMs, we calculate tsunamis by solving a nonlinear long wave equation, using FDM, including runup calculation, over a nesting grid system with a minimum grid size of 50 meters. (iv) Finally, we integrate information about the tsunamis calculated from the numerous CEFMs to get nationwide tsunami hazard assessments. One of the most popular representations of the integrated information is a tsunami hazard curve for coastal tsunami heights, incorporating uncertainties inherent in tsunami simulation and earthquake fault slip heterogeneity (Abe et al., 2014, JpGU). We will show a PTHA along the eastern coast of Honshu, Japan, based on approximately 1,800 tsunami sources located within the subduction zone along the Japan Trench, as a prototype of the nationwide PTHA. This study is supported by part of the research

  13. Session: Pre-development project risk assessment

    SciTech Connect

    Curry, Richard; Linehan, Andy

    2004-09-01

    This second session at the Wind Energy and Birds/Bats workshop consisted of two presentations followed by a discussion/question and answer period. The focus of the presentations was on the practices and methodologies used in the wind energy industry for assessing risk to birds and bats at candidate project sites. Presenters offered examples of pre-development siting evaluation requirements set by certain states. Presentation one was titled ''Practices and Methodologies and Initial Screening Tools'' by Richard Curry of Curry and Kerlinger, LLC. Presentation two was titled ''State of the Industry in the Pacific Northwest'' by Andy Linehan, CH2MHILL.

  14. Maturation of the Asteroid Threat Assessment Project

    NASA Technical Reports Server (NTRS)

    Arnold, J. O..; Burkhard, C. D.

    2017-01-01

    As described at IPPW 12 [1], NASA initiated a new research activity focused on Planetary Defense (PD) on October 1, 2014. The overarching function of the Asteroid Threat Assessment Project (ATAP) is to provide capabilities to assess impact damage of any Near-Earth Object (NEO) that could inflict on the Earth. The activity includes four interrelated efforts: Initial Conditions (at the atmospheric entry interface); Entry Modeling (energy deposition in the atmosphere); Hazards (on the surface including winds, over pressures, thermal exposures, craters, tsunami and earthquakes) and Risk (physics-based). This paper outlines progress by ATAP and highlights achievements that are complimentary to activities of interest to the International Planetary Probe community. The ATAPs work is sponsored by NASAs Planetary Defense Coordination Office (PDCO), a part of the agency's Science Mission Directorate [1] Arnold, J. O., et. al., Overview of a New NASA Activity Focused on Planetary Defense, IPPW 12 Cologne Germany, June 15-19. 2015.

  15. IV&V Project Assessment Process Validation

    NASA Technical Reports Server (NTRS)

    Driskell, Stephen

    2012-01-01

    The Space Launch System (SLS) will launch NASA's Multi-Purpose Crew Vehicle (MPCV). This launch vehicle will provide American launch capability for human exploration and travelling beyond Earth orbit. SLS is designed to be flexible for crew or cargo missions. The first test flight is scheduled for December 2017. The SLS SRR/SDR provided insight into the project development life cycle. NASA IV&V ran the standard Risk Based Assessment and Portfolio Based Risk Assessment to identify analysis tasking for the SLS program. This presentation examines the SLS System Requirements Review/System Definition Review (SRR/SDR), IV&V findings for IV&V process validation correlation to/from the selected IV&V tasking and capabilities. It also provides a reusable IEEE 1012 scorecard for programmatic completeness across the software development life cycle.

  16. Assessment of CO{sub 2} projections

    SciTech Connect

    Enting, I.G.; Wigley, T.M.L.; Heimann, M.

    1994-07-01

    Various projections of the relation between future CO{sub 2} concentrations and future emissions were undertaken as part of the scientific assessment for Working Group 1 of the Intergovernmental Panel on Climate Change. There were three type of calculation: (1) forward projections, calculating the atmospheric CO{sub 2} concentrations resulting from specified emission scenarios, (2) inverse calculations determining the emission rates that would be required to achieve stabilization of CO{sub 2} concentrations via specified pathways and (3) impulse response function calculations required for determining Global Warming Potentials. The use of a standardized set of conditions allows an intercomparison of models. The ocean models used in the calculations presented here span a range of forms from response function descriptions to general circulation models. The general issue for all levels of modelling is whether the model parameters can reasonably be regarded as being the same in the future as at present. Sensitivity studies explore other aspects of the uncertainties of such projections. This report documents the specifications, the models that were used and the results that were obtained. Some preliminary interpretations of the results are included.

  17. A beginner's guide to eukaryotic genome annotation.

    PubMed

    Yandell, Mark; Ence, Daniel

    2012-04-18

    The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches.

  18. A New Field of Dreams: The Collegiate Learning Assessment Project.

    ERIC Educational Resources Information Center

    Benjamin, Roger; Clum, Marc

    2003-01-01

    Describes the key features of the Collegiate Learning Assessment (CLA) project, which assesses the "value added" of an institution. The project assesses the institutional contribution to student learning through a focus on general education skills and the assessment of student performance relative to other students and through a…

  19. Staff Differentiation. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Marin County Superintendent of Schools, Corte Madera, CA.

    This annotated bibliography reviews selected literature focusing on the concept of staff differentiation. Included are 62 items (dated 1966-1970), along with a list of mailing addresses where copies of individual items can be obtained. Also a list of 31 staff differentiation projects receiving financial assistance from the U.S. Office of Education…

  20. Final rapid reactivation project environmental assessment

    SciTech Connect

    1999-02-10

    The US Department of Energy (DOE) has prepared an environmental assessment (EA) for the Rapid Reactivation Project at Sandia National Laboratories, New Mexico. The EA analyzes the potential effects of a proposal to increase production of neutron generators from the current capability of 600 units per year up to 2,000 units per year. The project would use existing buildings and infrastructure to the maximum extent possible to meet the additional production needs. The increased production levels would necessitate modifications and additions involving a total area of approximately 26,290 gross square feet at Sandia National Laboratories, New Mexico, Technical Area 1. Additional production equipment would be procured and installed. The no-action alternative would be to continue production activities at the current capability of 600 units per year. The EA analyzes effects on health, safety, and air quality, resulting from construction and operation and associated cumulative effects. A detailed description of the proposed action and its environmental consequences is presented in the EA.

  1. Regional Assessment of Supplementation Project : Status Report.

    SciTech Connect

    Unknown author

    1991-10-01

    The Fish and Wildlife Program of the Northwest Power Planning Council (NPPC) prescribes several approaches to achieve its goal of doubling the salmon and steelhead runs of the Columbia River. Among those approaches are habitat restoration, improvements in adult and juvenile passage at dams and artificial propagation. Supplementation will be a major part of the new hatchery programs. The purpose of the Regional Assessment of Supplementation Project (RASP) is to provide an overview of ongoing and planned supplementation activities, to construct a conceptual framework and model for evaluating the potential benefits and risks of supplementation and to develop a plan for better regional coordination of research and monitoring and evaluation of supplementation. RASP has completed its first year of work. Progress toward meeting the first year's objectives and recommendations for future tasks are contained in this report.

  2. Regional Assessment of Supplementation Project. Status report

    SciTech Connect

    Not Available

    1991-10-01

    The Fish and Wildlife Program of the Northwest Power Planning Council (NPPC) prescribes several approaches to achieve its goal of doubling the salmon and steelhead runs of the Columbia River. Among those approaches are habitat restoration, improvements in adult and juvenile passage at dams and artificial propagation. Supplementation will be a major part of the new hatchery programs. The purpose of the Regional Assessment of Supplementation Project (RASP) is to provide an overview of ongoing and planned supplementation activities, to construct a conceptual framework and model for evaluating the potential benefits and risks of supplementation and to develop a plan for better regional coordination of research and monitoring and evaluation of supplementation. RASP has completed its first year of work. Progress toward meeting the first year`s objectives and recommendations for future tasks are contained in this report.

  3. Modular Sequence: Teaching Reading to Bilingual Learners. TTP 002.15B; An Annotated Bibliography of Reading Materials for Spanish-Speaking Students. Teacher Corps Bilingual Project.

    ERIC Educational Resources Information Center

    Rodriguez, Norma, Comp.

    The majority of the material cited in this annotated bibliography is in Spanish although bilingual and English materials are also included. Each annotation is presented both in English and in Spanish. The bibliography is part of a modular sequence for teaching reading to bilingual learners. The bibliography covers the following areas: (a) general…

  4. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

    PubMed

    Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

  5. Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome.

    PubMed

    Lange, Philipp F; Huesgen, Pitter F; Nguyen, Karen; Overall, Christopher M

    2014-04-04

    A goal of the Chromosome-centric Human Proteome Project is to identify all human protein species. With 3844 proteins annotated as "missing", this is challenging. Moreover, proteolytic processing generates new protein species with characteristic neo-N termini that are frequently accompanied by altered half-lives, function, interactions, and location. Enucleated and largely void of internal membranes and organelles, erythrocytes are simple yet proteomically challenging cells due to the high hemoglobin content and wide dynamic range of protein concentrations that impedes protein identification. Using the N-terminomics procedure TAILS, we identified 1369 human erythrocyte natural and neo-N-termini and 1234 proteins. Multiple semitryptic N-terminal peptides exhibited improved mass spectrometric identification properties versus the intact tryptic peptide enabling identification of 281 novel erythrocyte proteins and six missing proteins identified for the first time in the human proteome. With an improved bioinformatics workflow, we developed a new classification system and the Terminus Cluster Score. Thereby we described a new stabilizing N-end rule for processed protein termini, which discriminates novel protein species from degradation remnants, and identified protein domain hot spots susceptible to cleavage. Strikingly, 68% of the N-termini were within genome-encoded protein sequences, revealing alternative translation initiation sites, pervasive endoproteolytic processing, and stabilization of protein fragments in vivo. The mass spectrometry proteomics data have been deposited to ProteomeXchange with the data set identifier .

  6. Mining GO annotations for improving annotation consistency.

    PubMed

    Faria, Daniel; Schlicker, Andreas; Pesquita, Catia; Bastos, Hugo; Ferreira, António E N; Albrecht, Mario; Falcão, André O

    2012-01-01

    Despite the structure and objectivity provided by the Gene Ontology (GO), the annotation of proteins is a complex task that is subject to errors and inconsistencies. Electronically inferred annotations in particular are widely considered unreliable. However, given that manual curation of all GO annotations is unfeasible, it is imperative to improve the quality of electronically inferred annotations. In this work, we analyze the full GO molecular function annotation of UniProtKB proteins, and discuss some of the issues that affect their quality, focusing particularly on the lack of annotation consistency. Based on our analysis, we estimate that 64% of the UniProtKB proteins are incompletely annotated, and that inconsistent annotations affect 83% of the protein functions and at least 23% of the proteins. Additionally, we present and evaluate a data mining algorithm, based on the association rule learning methodology, for identifying implicit relationships between molecular function terms. The goal of this algorithm is to assist GO curators in updating GO and correcting and preventing inconsistent annotations. Our algorithm predicted 501 relationships with an estimated precision of 94%, whereas the basic association rule learning methodology predicted 12,352 relationships with a precision below 9%.

  7. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    DOE PAGES

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; ...

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genesmore » and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary

  8. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    SciTech Connect

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.; Maranas, Costas D.

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to

  9. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models.

    PubMed

    Benedict, Matthew N; Mundy, Michael B; Henry, Christopher S; Chia, Nicholas; Price, Nathan D

    2014-10-01

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to

  10. A review of methodological factors in performance assessments of time-varying aircraft noise effects. [with annotated bibliography

    NASA Technical Reports Server (NTRS)

    Coates, G. D.; Alluisi, E. A.; Adkins, C. J., Jr.

    1977-01-01

    Literature on the effects of general noise on human performance is reviewed in an attempt to identify (1) those characteristics of noise that have been found to affect human performance; (2) those characteristics of performance most likely to be affected by the presence of noise, and (3) those characteristics of the performance situation typically associated with noise effects. Based on the characteristics identified, a theoretical framework is proposed that will permit predictions of possible effects of time-varying aircraft-type noise on complex human performance. An annotated bibliography of 50 articles is included.

  11. Quality of Computationally Inferred Gene Ontology Annotations

    PubMed Central

    Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-01-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

  12. Assessing the Relationship between Ethical Project Management and Information Technology Project Success

    ERIC Educational Resources Information Center

    Howell, Byron Winter

    2010-01-01

    The purpose of this quantitative study was to assess the relationship between ethical project management and information technology (IT) project success. The success of IT projects is important for organizational success, but the rate of IT projects is historically low, costing billions of dollars annually. Using four key ethical variables…

  13. Assessing the Relationship between Ethical Project Management and Information Technology Project Success

    ERIC Educational Resources Information Center

    Howell, Byron Winter

    2010-01-01

    The purpose of this quantitative study was to assess the relationship between ethical project management and information technology (IT) project success. The success of IT projects is important for organizational success, but the rate of IT projects is historically low, costing billions of dollars annually. Using four key ethical variables…

  14. Assessing temperature pattern projections made in 1989

    NASA Astrophysics Data System (ADS)

    Stouffer, Ronald J.; Manabe, Syukuro

    2017-03-01

    Successful projection of the distribution of surface temperature change increases our confidence in climate models. Here we evaluate projections of global warming from almost 30 years ago using the observations made during the past half century.

  15. Kalispell Maintenance Headquarters Project : Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1991-01-01

    The facilities needed to maintain and repair Bonneville Power Administration (BPA's) electrical equipment in northwest Montana are currently in two locations: A maintenance headquarters at the Kalispell Substation, and a temporary leased facility south of Kalispell. The present situation is not efficient. There is not enough space to accommodate the equipment needed at each site, and coordination and communication between the two sites is difficult. Also, two sites means duplication of equipment and facilities. BPA needs a single, centralized facility that would efficiently accommodate all the area's maintenance activities and equipment. BPA proposes to build a maintenance headquarters facility consisting of 2 to 4 single-story buildings totaling about 35,000 square feet (office spaces and workshop areas); an open-ended vehicle storage building (carport style); a fenced-in storage year; a storage building for flammables, herbicides, and hazardous wastes; and a parking lot. The facility would require developing about 6 to 10 acres of land. Two sites are being considered for the proposed project (see the attached map for locations). This report is the environmental assessment of the two options.

  16. Annotated Catalog of Bilingual Vocational Training Materials.

    ERIC Educational Resources Information Center

    Miranda (L.) and Associates, Bethesda, MD.

    This catalog contains annotations for 170 bilingual vocational training materials. Most of the materials are written in English, but materials written in 13 source languages and directed toward speakers of 17 target languages are provided. Annotations are provided for the following different types of documents: administrative, assessment and…

  17. Direct functional assessment of the composite phenotype through multivariate projection strategies.

    PubMed

    Conesa, Ana; Bro, Rasmus; García-García, Francisco; Prats, José Manuel; Götz, Stefan; Kjeldahl, Karin; Montaner, David; Dopazo, Joaquín

    2008-12-01

    We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

  18. Chapter 13 - Perspectives on LANDFIRE Prototype Project Accuracy Assessment

    Treesearch

    James Vogelmann; Zhiliang Zhu; Jay Kost; Brian Tolk; Donald Ohlen

    2006-01-01

    The purpose of this chapter is to provide a general overview of the many aspects of accuracy assessment pertinent to the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project). The LANDFIRE Prototype formed a large and complex research and development project with many broad-scale data sets and products developed throughout...

  19. Portfolio Assessment of an Undergraduate Group Project

    ERIC Educational Resources Information Center

    Kuisma, Raija

    2007-01-01

    Students in the Physiotherapy Programme carried out a group project in their final year of studies. The objectives of the project were that the students learn and appreciate the process and activities involved in research, acquire deeper understanding of a topic in their professional interest, learn to work as a team, manage their own time,…

  20. Multiple Intelligences: Curriculum and Assessment Project. Final Report

    ERIC Educational Resources Information Center

    Hyland, Aine, Ed.

    2011-01-01

    The "Multiple Intelligences, Curriculum and Assessment Project" at University College Cork was a collaborative project carried out between 1995 and 1999. The key research question focused on whether Howard Gardner's theory of Multiple Intelligences could be applied to, and enhance, aspects of curriculum and assessment at primary and…

  1. A Pilot Project for Assessing Nonacademic Characteristics of Premedical Students

    ERIC Educational Resources Information Center

    Middents, Gerald J.

    1977-01-01

    The University of Texas Medical Branch at Galveston and Austin College cooperated in an experimental project to assess the quality and readiness of premedical students for medical schools and careers. The project and assessment process were mutually beneficial and it is hoped that they will be useful to those involved in career guidance. (LBH)

  2. Assessment and Improvement of Related Services (AIRS) Project. Final Report.

    ERIC Educational Resources Information Center

    McClelland, Robert A.; Hirata, Glenn T.

    The document presents the final report of the Assessment and Improvement of Related Services (AIRS) Project, an effort to assess the impact and effectiveness of special education related services in Hawaii. Each of the four project objectives focused on accomplishment of one of the evaluation types specified in the Context-Input-Process-Product…

  3. An Outcomes Assessment Project: Basic Writing and Essay Structure

    ERIC Educational Resources Information Center

    Caldwell, David; DeRusha, Jeanine; Stanton-Hammond, Gail; Straight, Steve; Sullivan, Patrick

    2011-01-01

    In this article, the authors report on an assessment project they recently conducted at their open admissions community college to assess student work at the end of the basic writing sequence. The authors' focus for this project was on the way students used essay structure. They gathered artifacts from students who were deemed "ready" by…

  4. A Pilot Project for Assessing Nonacademic Characteristics of Premedical Students

    ERIC Educational Resources Information Center

    Middents, Gerald J.

    1977-01-01

    The University of Texas Medical Branch at Galveston and Austin College cooperated in an experimental project to assess the quality and readiness of premedical students for medical schools and careers. The project and assessment process were mutually beneficial and it is hoped that they will be useful to those involved in career guidance. (LBH)

  5. Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

    PubMed

    Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young; Bada, Michael; Baumgartner, William A; Panteleyeva, Natalya; Verspoor, Karin; Palmer, Martha; Hunter, Lawrence E

    2017-08-17

    Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not

  6. Benefits Analysis of Past Projects. Volume 2. Individual Project Assessments.

    DTIC Science & Technology

    1984-11-01

    feasible for aluminum alloy 2024 -T3 bare, 0.063-inch in thickness, modified FPL surface preparation, and A1396B paste and PL729 film (with PL728...resulted in the adoption of a project design consisting of an integrally machined 2124 -T851 aluminum frame to which a one-piece pseudo-isotropic horon...production program. The 2124 -T851 aluminum frame was N/C machined from a 4.5-inch by 24-inch by 96-inch plate. A 24-inch by 73-inch, 40-ply boron/ aluminum

  7. Environmental Assessment : Happy Valley [Substation Project].

    SciTech Connect

    United States. Bonneville Power Administration.

    1982-05-01

    The proposed Happy Valley project consists of construction of a new BPA customer service 69-kV substation south of Sequim in Clallam County, Washington. A tie line, to be constructed by the customer as part of this project, will link the new BPA facility to the existing customer's transmission system in the area. This project responds to rapid load growth in the Olympic Peninsula, and will strengthen the existing BPA system and interconnected utility systems. It will reduce transmission losses presently incurred, especially on the BPA system supplying power to the Olympic Peninsula. This report describes the potential environmental impact of the proposed actions. 2 figs., 1 tab.

  8. Solar Resource and Meteorological Assessment Project (SOLRMAP)

    SciTech Connect

    Wilcox, S.

    2008-10-29

    The purpose of this collaborative project between NREL and industry is: (1) provide high quality solar measurements in support of deploying Concentrating Solar Thermal projects; and (2) provide NREL with research-quality data sets for refining solar models and developing solar forecasting capabilities. The benefits of this project are: (1) lends NREL credibility to data sets used for economic analyses and commercial justification; (2) helps minimize costly mistakes in estimating capacity and economic return on investment; (3) helps maximize the development of projects for which adequate solar resources exist; (4) provides data to NREL for research to improve/validate models and explore RA innovations; and (5) helps maintain collaborative channels between NREL and industry.

  9. Cyanobacteria Assessment Network (CyAN) Project

    EPA Pesticide Factsheets

    CyAN is a multi-agency project among the National Aeronautics and Space Administration (NASA), National Oceanic and Atmospheric Administration (NOAA), US Geological Survey (USGS), and EPA to develop an early warning indicator system to detect algal blooms.

  10. Spiral and Project-Based Learning with Peer Assessment in a Computer Science Project Management Course

    ERIC Educational Resources Information Center

    Jaime, Arturo; Blanco, José Miguel; Domínguez, César; Sánchez, Ana; Heras, Jónathan; Usandizaga, Imanol

    2016-01-01

    Different learning methods such as project-based learning, spiral learning and peer assessment have been implemented in science disciplines with different outcomes. This paper presents a proposal for a project management course in the context of a computer science degree. Our proposal combines three well-known methods: project-based learning,…

  11. Spiral and Project-Based Learning with Peer Assessment in a Computer Science Project Management Course

    ERIC Educational Resources Information Center

    Jaime, Arturo; Blanco, José Miguel; Domínguez, César; Sánchez, Ana; Heras, Jónathan; Usandizaga, Imanol

    2016-01-01

    Different learning methods such as project-based learning, spiral learning and peer assessment have been implemented in science disciplines with different outcomes. This paper presents a proposal for a project management course in the context of a computer science degree. Our proposal combines three well-known methods: project-based learning,…

  12. Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text.

    PubMed

    South, Brett R; Mowery, Danielle; Suo, Ying; Leng, Jianwei; Ferrández, Óscar; Meystre, Stephane M; Chapman, Wendy W

    2014-08-01

    The Health Insurance Portability and Accountability Act (HIPAA) Safe Harbor method requires removal of 18 types of protected health information (PHI) from clinical documents to be considered "de-identified" prior to use for research purposes. Human review of PHI elements from a large corpus of clinical documents can be tedious and error-prone. Indeed, multiple annotators may be required to consistently redact information that represents each PHI class. Automated de-identification has the potential to improve annotation quality and reduce annotation time. For instance, using machine-assisted annotation by combining de-identification system outputs used as pre-annotations and an interactive annotation interface to provide annotators with PHI annotations for "curation" rather than manual annotation from "scratch" on raw clinical documents. In order to assess whether machine-assisted annotation improves the reliability and accuracy of the reference standard quality and reduces annotation effort, we conducted an annotation experiment. In this annotation study, we assessed the generalizability of the VA Consortium for Healthcare Informatics Research (CHIR) annotation schema and guidelines applied to a corpus of publicly available clinical documents called MTSamples. Specifically, our goals were to (1) characterize a heterogeneous corpus of clinical documents manually annotated for risk-ranked PHI and other annotation types (clinical eponyms and person relations), (2) evaluate how well annotators apply the CHIR schema to the heterogeneous corpus, (3) compare whether machine-assisted annotation (experiment) improves annotation quality and reduces annotation time compared to manual annotation (control), and (4) assess the change in quality of reference standard coverage with each added annotator's annotations.

  13. Summary of Project Assessments through April 2008

    DTIC Science & Technology

    2008-07-24

    the potable water supply for the airport were not functioning because the water treatment plant that generates the required processed water was non...deficiencies. PA-05-001 Al Wahda Water Treatment Plant ($7.4M, IRRF, FluorAMEC LLC): The objective included refurbishment or replacement of chlorination...construction met the standards, the project was significantly de-scoped, and project results were not achieved. PA-05-002 Al Wathba Water Treatment Plant ($7.4M

  14. Technology Assessment Requirements for Programs and Projects

    NASA Technical Reports Server (NTRS)

    Bilbro, James W.

    2006-01-01

    Program/project uncertainty can most simply be defined as the unpredictability of its outcome. As might be expected, the degree of uncertainty depends substantially on program/project type. For hi-tech programs/projects, uncertainty all too frequently translates into schedule slips, cost overruns and occasionally even to cancellations or failures - consummations root cause of such events is often attributed to inadequate definition of requirements. If such were indeed the root cause, then correcting the situation would simply be a matter of requiring better requirements definition, but since history seems frequently to repeat itself, this must not be the case - at least not in total. There are in fact many contributors to schedule slips, cost overruns, project cancellations and failures, among them lack of adequate requirements definition. The case can be made, however, that many of these contributors are related to the degree of uncertainty at the outset of the project. And further, that a dominant factor in the degree of uncertainty is the maturity of the technology required to bring the project to fruition. This presentation discusses the concept of relating degrees of uncertainty to Technology Readiness Levels (TRL) and their associated Advancement Degree of Difficulty (AD2) levels. It also briefly describes a quantifiable process to establish the appropriate TRL for a given technology and quantifies through the AD2 what is required to move it from its current TRL to the desired TRL in order to reduce risk and maximize likelihood of successfully infusing the technology.

  15. Automated Knowledge Annotation for Dynamic Collaborative Environments

    SciTech Connect

    Cowell, Andrew J.; Gregory, Michelle L.; Marshall, Eric J.; McGrath, Liam R.

    2009-05-19

    This paper describes the Knowledge Encapsulation Framework (KEF), a suite of tools to enable automated knowledge annotation for modeling and simulation projects. This framework can be used to capture evidence (e.g., facts extracted from journal articles and government reports), discover new evidence (from similar peer-reviewed material as well as social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks.

  16. Spiral and Project-Based Learning with Peer Assessment in a Computer Science Project Management Course

    NASA Astrophysics Data System (ADS)

    Jaime, Arturo; Blanco, José Miguel; Domínguez, César; Sánchez, Ana; Heras, Jónathan; Usandizaga, Imanol

    2016-06-01

    Different learning methods such as project-based learning, spiral learning and peer assessment have been implemented in science disciplines with different outcomes. This paper presents a proposal for a project management course in the context of a computer science degree. Our proposal combines three well-known methods: project-based learning, spiral learning and peer assessment. Namely, the course is articulated during a semester through the structured (progressive and incremental) development of a sequence of four projects, whose duration, scope and difficulty of management increase as the student gains theoretical and instrumental knowledge related to planning, monitoring and controlling projects. Moreover, the proposal is complemented using peer assessment. The proposal has already been implemented and validated for the last 3 years in two different universities. In the first year, project-based learning and spiral learning methods were combined. Such a combination was also employed in the other 2 years; but additionally, students had the opportunity to assess projects developed by university partners and by students of the other university. A total of 154 students have participated in the study. We obtain a gain in the quality of the subsequently projects derived from the spiral project-based learning. Moreover, this gain is significantly bigger when peer assessment is introduced. In addition, high-performance students take advantage of peer assessment from the first moment, whereas the improvement in poor-performance students is delayed.

  17. Dynamic multimedia annotation tool

    NASA Astrophysics Data System (ADS)

    Pfund, Thomas; Marchand-Maillet, Stephane

    2001-12-01

    Annotating image collections is crucial for different multimedia applications. Not only this provides an alternative access to visual information but it is a critical step to perform the evaluation of content-based image retrieval systems. Annotation is a tedious task so that there is a real need for developing tools that lighten the work of annotators. The tool should be flexible and offer customization so as to make the annotator the most comfortable. It should also automate the most tasks as possible. In this paper, we present a still image annotation tool that has been developed with the aim of being flexible and adaptive. The principle is to create a set of dynamic web pages that are an interface to a SQL database. The keyword set is fixed and every image receives from concurrent annotators a set of keywords along with time stamps and annotator Ids. Each annotator has the possibility of going back and forth within the collection and its previous annotations. He is helped by a number of search services and customization options. An administrative section allows the supervisor to control the parameter of the annotation, including the keyword set, given via an XML structure. The architecture of the tool is made flexible so as to accommodate further options through its development.

  18. Fuzzy based risk register for construction project risk assessment

    NASA Astrophysics Data System (ADS)

    Kuchta, Dorota; Ptaszyńska, Ewa

    2017-07-01

    The paper contains fuzzy based risk register used to identify risks which appear in construction projects and to assess their attributes. Risk is considered here as a possible event with negative consequences for the project [4]. We use different risk attributes in the proposed risk register. Values of risk attributes are generated by using fuzzy numbers. Specific risk attributes have different importance for project managers of construction projects. To compare specific risk attributes we use methods of fuzzy numbers ranking. The main strengths of the proposed concept in managing construction projects are also presented in the paper.

  19. Preliminary assessment of potential CDM early start projects in Brazil

    SciTech Connect

    Meyers, S.; Sathaye, J.; Lehman, B.; Schumacher, K.; van Vliet, O.; Moreira, J.R.

    2000-11-01

    The Brazil/US Aspen Global Forum on Climate Change Policies and Programs has facilitated a dialogue between key Brazil and US public and private sector leaders on the subject of the Clean Development Mechanism (CDM). With support from the US government, a cooperative effort between Lawrence Berkeley National Laboratory and the University of Sao Paulo conducted an assessment of a number of projects put forth by Brazilian sponsors. Initially, we gathered information and conducted a screening assessment for ten projects in the energy sector and six projects in the forestry sector. Some of the projects appeared to offer greater potential to be attractive for CDM, or had better information available. We then conducted a more detailed assessment of 12 of these projects, and two other projects that were submitted after the initial screening. An important goal was to assess the potential impact of Certified Emission Reductions (CERs) on the financial performance of projects. With the exception of the two forestry-based fuel displacement projects, the impact of CERs on the internal rate of return (IRR) is fairly small. This is true for both the projects that displace grid electricity and those that displace local (diesel-based) electricity production. The relative effect of CERs is greater for projects whose IRR without CERs is low. CERs have a substantial effect on the IRR of the two short-rotation forestry energy substitution projects. One reason is that the biofuel displaces coke and oil, both of which are carbon-intensive. Another factor is that the product of these projects (charcoal and woodfuel, respectively) is relatively low value, so the revenue from carbon credits has a strong relative impact. CERs also have a substantial effect on the NPV of the carbon sequestration projects. Financial and other barriers pose a challenge for implementation of most of the projects. In most cases, the sponsor lacks sufficient capital, and loans are available only at high interest

  20. The Contribution of Project Environmental Assessment to Assessing and Managing Cumulative Effects: Individually and Collectively Insignificant?

    NASA Astrophysics Data System (ADS)

    Noble, Bram; Liu, Jialang; Hackett, Paul

    2017-04-01

    This paper explores the opportunities and constraints to project-based environmental assessment as a means to support the assessment and management of cumulative environmental effects. A case study of the hydroelectric sector is used to determine whether sufficient information is available over time through project-by-project assessments to support an adequate understanding of cumulative change. Results show inconsistency from one project to the next in terms of the components and indicators assessed, limited transfer of baseline information between project assessments over time, and the same issues and concerns being raised by review panels-even though the projects reviewed are operating in the same watershed and operated by the same proponent. Project environmental assessments must be managed, and coordinated, as part of a larger system of impact assessment, if project-by-project assessments are to provide a meaningful forum for learning and understanding cumulative change. The paper concludes with recommendations for improved project-based assessment practice in support of cumulative effects assessment and management.

  1. Assessing Projection Bias in Consumers’ Food Preferences

    PubMed Central

    de-Magistris, Tiziana; Gracia, Azucena

    2016-01-01

    The aim of this study is to test whether projection bias exists in consumers’ purchasing decisions for food products. To achieve our aim, we used a non-hypothetical experiment (i.e., experimental auction), where hungry and non-hungry participants were incentivized to reveal their willingness to pay (WTP). The results confirm the existence of projection bias when consumers made their decisions on food products. In particular, projection bias existed because currently hungry participants were willing to pay a higher price premium for cheeses than satiated ones, both in hungry and satiated future states. Moreover, participants overvalued the food product more when they were delivered in the future hungry condition than in the satiated one. Our study provides clear, quantitative and meaningful evidence of projection bias because our findings are based on economic valuation of food preferences. Indeed, the strength of this study is that findings are expressed in terms of willingness to pay which is an interpretable amount of money. PMID:26828930

  2. Promoting Health Literacy through the Health Education Assessment Project

    ERIC Educational Resources Information Center

    Marx, Eva; Hudson, Nancy; Deal, Tami B.; Pateman, Beth; Middleton, Kathleen

    2007-01-01

    Background: The Council of Chief State School Officers' State Collaborative on Assessment and Student Standards Health Education Assessment Project (SCASS-HEAP) allows states to pool financial and human resources to develop effective ready-to-use health education assessment resources through a collaborative process. The purpose of this article is…

  3. Promoting Health Literacy through the Health Education Assessment Project

    ERIC Educational Resources Information Center

    Marx, Eva; Hudson, Nancy; Deal, Tami B.; Pateman, Beth; Middleton, Kathleen

    2007-01-01

    Background: The Council of Chief State School Officers' State Collaborative on Assessment and Student Standards Health Education Assessment Project (SCASS-HEAP) allows states to pool financial and human resources to develop effective ready-to-use health education assessment resources through a collaborative process. The purpose of this article is…

  4. The Comprehensive Social Studies Assessment Project (CSSAP) Professional Development Manual.

    ERIC Educational Resources Information Center

    Missouri State Dept. of Elementary and Secondary Education, Jefferson City.

    The purpose of this professional development manual is to provide materials and activities for developing and using assessments in social studies. The manual came about through the efforts of the 25 state consortium Comprehensive Social Studies Assessment Project (CSSAP) to make the alignment of assessments, curricula, and instructional programs…

  5. A Selective Annotated Guide to Materials on Latin America Suitable for Use at the Secondary School Level. Latin American Studies Project.

    ERIC Educational Resources Information Center

    Jamieson, Alfred

    This selective annotated bibliography is designed to provide reference materials on Latin America that are useful at the secondary level. The guide includes materials on traditionally ignored areas of study, and reflects, as much as possible, an awareness of the problem of relevance and reality in Latin America, in social studies education, and in…

  6. Using the CAS Standards in Assessment Projects

    ERIC Educational Resources Information Center

    Dean, Laura A.

    2013-01-01

    This chapter provides an overview of the use of professional standards of practice in assessment and of the Council for the Advancement of Standards in Higher Education (CAS). It outlines a model for conducting program self-studies and discusses the importance of implementing change based on assessment results.

  7. Using the CAS Standards in Assessment Projects

    ERIC Educational Resources Information Center

    Dean, Laura A.

    2013-01-01

    This chapter provides an overview of the use of professional standards of practice in assessment and of the Council for the Advancement of Standards in Higher Education (CAS). It outlines a model for conducting program self-studies and discusses the importance of implementing change based on assessment results.

  8. Marion Industrial Substation Project : Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-04-01

    Consumers Power, Inc. (CPI), proposes to construct a new distribution substation under the existing Bonneville Power Administration (BPA) Albay-Lebanon transmission line near the city of Albany in Linn County, Oregon. BPA is proposing to grant a new Point of Delivery to CPI at this substation. The purpose of the project is to serve the developing industrial needs in the Marion Industrial Park and on the 550 acres of nearby land within CPI`s service area that are zoned for residential use. CPI prepared, and the Rural Electrification Administration (REA) has approved a Borrower`s Environmental Report (BER) which addresses this action along with several other proposed projects in the CPI service area. Portions of this BER are summarized in this brief EA. BPA is preparing its own EA since Department of Energy National Environmental Policy Act (NEPA) guidelines require additional environmental concerns to be addressed than are required by REA`s NEPA guidelines.

  9. Marion Industrial Substation Project : Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-04-01

    Consumers Power, Inc. (CPI), proposes to construct a new distribution substation under the existing Bonneville Power Administration (BPA) Albay-Lebanon transmission line near the city of Albany in Linn County, Oregon. BPA is proposing to grant a new Point of Delivery to CPI at this substation. The purpose of the project is to serve the developing industrial needs in the Marion Industrial Park and on the 550 acres of nearby land within CPI's service area that are zoned for residential use. CPI prepared, and the Rural Electrification Administration (REA) has approved a Borrower's Environmental Report (BER) which addresses this action along with several other proposed projects in the CPI service area. Portions of this BER are summarized in this brief EA. BPA is preparing its own EA since Department of Energy National Environmental Policy Act (NEPA) guidelines require additional environmental concerns to be addressed than are required by REA's NEPA guidelines.

  10. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes

    PubMed Central

    2002-01-01

    Background Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene) is imbedded in the approach. Results We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank. Conclusions The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific characteristics of some

  11. Antelope-Fossil Rebuild Project : Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-04-01

    The Columbia Power Cooperative Association (CPCA), Monument, Oregon, proposes to upgrade a 69-kV transmission line in Wasco and Wheeler Counties, Oregon, between the Antelope Substation and the Bonneville Power Administration`s (BPA) Fossil Substation. The project involves rebuilding and reconductoring 23.2 miles of transmission line, including modifying it for future use at 115 kV. Related project activities will include setting new wood pole structures, removing and disposing of old structures, conductors, and insulators, and stringing new conductor, all within the existing right-of-way. No new access roads will be required. A Borrower`s Environmental Report was prepared for the 1992--1993 Work Plan for Columbia Power Cooperative Association in March 1991. This report investigated cultural resources, threatened or endangered species, wetlands, and floodplains, and other environmental issues, and included correspondence with appropriate Federal, state, and local agencies. The report was submitted to the Rural Electrification Administration for their use in preparing their environmental documentation for the project.

  12. Antelope-Fossil Rebuild Project : Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-04-01

    The Columbia Power Cooperative Association (CPCA), Monument, Oregon, proposes to upgrade a 69-kV transmission line in Wasco and Wheeler Counties, Oregon, between the Antelope Substation and the Bonneville Power Administration's (BPA) Fossil Substation. The project involves rebuilding and reconductoring 23.2 miles of transmission line, including modifying it for future use at 115 kV. Related project activities will include setting new wood pole structures, removing and disposing of old structures, conductors, and insulators, and stringing new conductor, all within the existing right-of-way. No new access roads will be required. A Borrower's Environmental Report was prepared for the 1992--1993 Work Plan for Columbia Power Cooperative Association in March 1991. This report investigated cultural resources, threatened or endangered species, wetlands, and floodplains, and other environmental issues, and included correspondence with appropriate Federal, state, and local agencies. The report was submitted to the Rural Electrification Administration for their use in preparing their environmental documentation for the project.

  13. Book Reviews, Annotation, and Web Technology.

    ERIC Educational Resources Information Center

    Schulze, Patricia

    From reading texts to annotating web pages, grade 6-8 students rely on group cooperation and individual reading and writing skills in this research project that spans six 50-minute lessons. Student objectives for this project are that they will: read, discuss, and keep a journal on a book in literature circles; understand the elements of and…

  14. Galileo Reader and Annotator

    NASA Astrophysics Data System (ADS)

    Besomi, O.

    2011-06-01

    In his readings, Galileo made frequent use of annotations. Here, I will offer a general glance at them by discussing the case of the annotations to the Libra astronomica published in 1619 by Orazio Grassi, a Jesuit mathematician of the Collegio Romano. The annotations directly reflect Galileo's reaction to Grassi's book in a heated debate between the two astronomers. Galileo and Grassi had opposite ideas about the nature of the comets, which resulted in different scientific and theological implications. The annotations represent the starting point for Galileo's reply to the Libra, namely Il Saggiatore, which was published four years later and dedicated to the new pope Urban VIII.

  15. A Correlational Study Assessing the Relationships among Information Technology Project Complexity, Project Complication, and Project Success

    ERIC Educational Resources Information Center

    Williamson, David J.

    2011-01-01

    The specific problem addressed in this study was the low success rate of information technology (IT) projects in the U.S. Due to the abstract nature and inherent complexity of software development, IT projects are among the most complex projects encountered. Most existing schools of project management theory are based on the rational systems…

  16. A Correlational Study Assessing the Relationships among Information Technology Project Complexity, Project Complication, and Project Success

    ERIC Educational Resources Information Center

    Williamson, David J.

    2011-01-01

    The specific problem addressed in this study was the low success rate of information technology (IT) projects in the U.S. Due to the abstract nature and inherent complexity of software development, IT projects are among the most complex projects encountered. Most existing schools of project management theory are based on the rational systems…

  17. Undergraduate Lab Project in Personality Assessment: Measurement of Anal Character.

    ERIC Educational Resources Information Center

    Davidson, William B.

    1987-01-01

    This article describes a project which required students to write assessment items for a personality inventory. The 104 items generated were administered to 126 subjects. Results showed the items were reasonably reliable and valid. The pedagogical value of the project is discussed. (Author/JDH)

  18. The ECLSS Advanced Automation Project Evolution and Technology Assessment

    NASA Technical Reports Server (NTRS)

    Dewberry, Brandon S.; Carnes, James R.; Lukefahr, Brenda D.; Rogers, John S.; Rochowiak, Daniel M.; Mckee, James W.; Benson, Brian L.

    1990-01-01

    Viewgraphs on Environmental Control and Life Support System (ECLSS) advanced automation project evolution and technology assessment are presented. Topics covered include: the ECLSS advanced automation project; automatic fault diagnosis of ECLSS subsystems descriptions; in-line, real-time chemical and microbial fluid analysis; and object-oriented, distributed chemical and microbial modeling of regenerative environmental control systems description.

  19. Projecting national forest inventories for the 2000 RPA timber assessment.

    Treesearch

    John R. Mills; Xiaoping. Zhou

    2003-01-01

    National forest inventories were projected in a study that was part of the 2000 USDA Forest Service Resource Planning Act (RPA) timber assessment. This paper includes an overview of the status and structure of timber inventory of the National Forest System and presents 50-year projections under several scenarios. To examine a range of possible outcomes, results are...

  20. Multi-County Assessment of Adult Needs Project: Final Report.

    ERIC Educational Resources Information Center

    McLennan Community Coll., TX.

    The document is a summarized final report of the Multi-County Assessment of Adult Needs Project (MAP) which took place in central Texas (Bosque, Falls, Hill, and McLennan Counties). It summarizes the major activities and accomplishments of the project and contains all materials except Attachments 1 and 2, the reports on Phase I (Survey of Adult…

  1. A Function-Based Framework for Stream Assessment & Restoration Projects

    EPA Pesticide Factsheets

    This report lays out a framework for approaching stream assessment and restoration projects that focuses on understanding the suite of stream functions at a site in the context of what is happening in the watershed.

  2. Conducting Site and Economic Renewable Energy Project Feasibility Assessments

    EPA Pesticide Factsheets

    This page provides information on how organizations can take advantage of available tools and resources to take the initial steps in evaluating a renewable energy project, such as site and economic feasibility assessments.

  3. Involving Assessment Buddies in the Assessment of Design Project Work

    ERIC Educational Resources Information Center

    Osmond, Jane; Clough, Brian

    2012-01-01

    This paper discusses the impact of a specially developed assessment and feedback system implemented within a second year industrial design module at Coventry University, UK. The "Assessment Buddy" system was developed in response to the need for a successful assessment and feedback method that could cope with the complexities of a…

  4. Project M: An Assessment of Mission Assumptions

    NASA Technical Reports Server (NTRS)

    Edwards, Alycia

    2010-01-01

    Project M is a mission Johnson Space Center is working on to send an autonomous humanoid robot to the moon (also known as Robonaut 2) in l000 days. The robot will be in a lander, fueled by liquid oxygen and liquid methane, and land on the moon, avoiding any hazardous obstacles. It will perform tasks like maintenance, construction, and simple student experiments. This mission is also being used as inspiration for new advancements in technology. I am considering three of the design assumptions that contribute to determining the mission feasibility: maturity of robotic technology, launch vehicle determination, and the LOX/Methane fueled spacecraft

  5. Resource Assessment Project: User needs survey results

    NASA Astrophysics Data System (ADS)

    Hulstrom, R. L.

    1989-11-01

    This document presents the results of an extensive survey conducted by the Solar Energy Research Institute's (SERI) Resource Assessment and Instrumentation Branch. This survey addressed the needs for solar radiation data, models, algorithms, forecasts, and instrumentation, according to the various solar energy conversion technologies (photovoltaics, solar thermal, passive heating/cooling/daylighting, active solar heating/cooling (ASHC), and biomass). The survey was actually conducted during fiscal years 1984 and 1985 as input to the establishment of a formal Department of Energy (DOE) Resource Assessment Program. The survey included only solar radiation, as opposed to wind and other renewable resources. SERI is responsible for the solar radiation portion of the DOE Resource Assessment Program. The survey was conducted by sending a questionnaire to 135 individuals at DOE, the Department of Agriculture, industry, and various national laboratories, universities, and utilities, to represent a cross section of the previously named solar energy conversion technologies. The results of the survey were analyzed and summarized. The exact needs for solar radiation data, models, algorithms, forecasts, and instrumentation will surely change with time. Therefore, the SERI Resource Assessment and Instrumentation Branch will update the list continually.

  6. The West Virginia Health Education Assessment Project

    ERIC Educational Resources Information Center

    Tompkins, Nancy O'Hara; Kamal, Khalid M.; Chapman, Don

    2005-01-01

    Well-designed school health education should provide students with the knowledge and skills to prevent the health risk behaviors most responsible for the major causes of morbidity and mortality. This paper reports the methodology and findings of a West Virginia statewide health education assessment initiative and describes how the findings are…

  7. The West Virginia Health Education Assessment Project

    ERIC Educational Resources Information Center

    Tompkins, Nancy O'Hara; Kamal, Khalid M.; Chapman, Don

    2005-01-01

    Well-designed school health education should provide students with the knowledge and skills to prevent the health risk behaviors most responsible for the major causes of morbidity and mortality. This paper reports the methodology and findings of a West Virginia statewide health education assessment initiative and describes how the findings are…

  8. Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

    PubMed Central

    Childs, Kevin L.; Davidson, Rebecca M.; Buell, C. Robin

    2011-01-01

    With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa) gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional annotation of those

  9. Annotated Humanities Programs.

    ERIC Educational Resources Information Center

    Adler, Richard R.; Applebee, Arthur

    The humanities programs offered in 1968 by 227 United States secondary schools are listed alphabetically by state, including almost 100 new programs not annotated in the 1967 listing (see TE 000 224). Each annotation presents a brief description of the approach to study used in the particular humanities course (e.g., American Studies, Culture…

  10. WormBase: Annotating many nematode genomes.

    PubMed

    Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

    2012-01-01

    WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

  11. Omics data management and annotation.

    PubMed

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter.

  12. Final Report of the Vocational Assessment Project, 1979-80.

    ERIC Educational Resources Information Center

    Rutgers, The State Univ., New Brunswick, NJ. School of Medicine.

    To improve vocational rehabilitation programs for schizophrenic persons, a project sought to design an effective assessment strategy. Inactive records of schizophrenic clients at New Jersey sheltered workshops were examined to determine validity and reliability of assessment instruments being used. General Aptitude Test Battery (GATB) profiles of…

  13. Final Report of the Vocational Assessment Project, 1979-80.

    ERIC Educational Resources Information Center

    Rutgers, The State Univ., New Brunswick, NJ. School of Medicine.

    To improve vocational rehabilitation programs for schizophrenic persons, a project sought to design an effective assessment strategy. Inactive records of schizophrenic clients at New Jersey sheltered workshops were examined to determine validity and reliability of assessment instruments being used. General Aptitude Test Battery (GATB) profiles of…

  14. Assessment in Open and Distance Learning. Teeode Project.

    ERIC Educational Resources Information Center

    Steffens, Karl; Underwood, Jean; Bartolome, Antonio; Grave, Lidia

    The aim of the TEEODE project was to develop a representative survey of the models of assessment and evaluation used by institutions supporting distance learning in the 15 member states of the European Union. This paper focuses on issues of course development and assessment, and, in particular, on how effective learning outcomes are achieved and…

  15. Assessment of Inquiry Skills in the SAILS Project

    ERIC Educational Resources Information Center

    Harrison, Chris

    2014-01-01

    Inquiry provides both the impetus and experience that helps students acquire problem solving and lifelong learning skills. Teachers on the Strategies for Assessment of Inquiry Learning in Science Project (SAILS) strengthened their inquiry pedagogy, through focusing on seeking assessment evidence for formative action. This paper reports on both the…

  16. Environmental projects. Volume 16: Waste minimization assessment

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The Goldstone Deep Space Communications Complex (GDSCC), located in the MoJave Desert, is part of the National Aeronautics and Space Administration's (NASA's) Deep Space Network (DSN), the world's largest and most sensitive scientific telecommunications and radio navigation network. The Goldstone Complex is operated for NASA by the Jet Propulsion Laboratory. At present, activities at the GDSCC support the operation of nine parabolic dish antennas situated at five separate locations known as 'sites.' Each of the five sites at the GDSCC has one or more antennas, called 'Deep Space Stations' (DSS's). In the course of operation of these DSS's, various hazardous and non-hazardous wastes are generated. In 1992, JPL retained Kleinfelder, Inc., San Diego, California, to quantify the various streams of hazardous and non-hazardous wastes generated at the GDSCC. In June 1992, Kleinfelder, Inc., submitted a report to JPL entitled 'Waste Minimization Assessment.' This present volume is a JPL-expanded version of the Kleinfelder, Inc. report. The 'Waste Minimization Assessment' report did not find any deficiencies in the various waste-management programs now practiced at the GDSCC, and it found that these programs are being carried out in accordance with environmental rules and regulations.

  17. The NASA Space Radiobiology Risk Assessment Project

    NASA Astrophysics Data System (ADS)

    Cucinotta, Francis A.; Huff, Janice; Ponomarev, Artem; Patel, Zarana; Kim, Myung-Hee

    The current first phase (2006-2011) has the three major goals of: 1) optimizing the conventional cancer risk models currently used based on the double-detriment life-table and radiation quality functions; 2) the integration of biophysical models of acute radiation syndromes; and 3) the development of new systems radiation biology models of cancer processes. The first-phase also includes continued uncertainty assessment of space radiation environmental models and transport codes, and relative biological effectiveness factors (RBE) based on flight data and NSRL results, respectively. The second phase of the (2012-2016) will: 1) develop biophysical models of central nervous system risks (CNS); 2) achieve comphrensive systems biology models of cancer processes using data from proton and heavy ion studies performed at NSRL; and 3) begin to identify computational models of biological countermeasures. Goals for the third phase (2017-2021) include: 1) the development of a systems biology model of cancer risks for operational use at NASA; 2) development of models of degenerative risks, 2) quantitative models of counter-measure impacts on cancer risks; and 3) indiviudal based risk assessments. Finally, we will support a decision point to continue NSRL research in support of NASA's exploration goals beyond 2021, and create an archival of NSRL research results for continued analysis. Details on near term goals, plans for a WEB based data resource of NSRL results, and a space radiation Wikepedia are described.

  18. Balancing Formative and Summative Science Assessment Practices: Year One of the GenScope Assessment Project.

    ERIC Educational Resources Information Center

    Hickey, Daniel T.; Kruger, Ann Cale; Fredrick, Laura D.; Schafer, Nancy Jo; Kindfield, Ann C. H.

    This paper describes the GenScope Assessment Project, a project that is exploring ways of using multimedia computers to teach complex science content, refining sociocultural views of assessment and motivation, and considering different ways of reconciling the differences between these newer views and prior behavioral and cognitive views. The…

  19. "Triple-bottom-line" assessment of urban stormwater projects.

    PubMed

    Taylor, A C; Fletcher, T D

    2006-01-01

    New guidelines have been developed and trialled in Australia to assist urban stormwater managers to assess options for projects that aim to improve urban waterway health. These guidelines help users to examine the financial, ecological and social dimensions of projects (i.e., the so-called "triple-bottom-line"). Features of the assessment process described in the guidelines include use of multi criteria analysis, input from technical experts as well as non-technical stakeholders, and provision of three alternative levels of assessment to suit stormwater managers with differing needs and resources. This paper firstly provides a background to the new guidelines and triple-bottom-line assessment. The assessment methodology promoted in the new guidelines is then briefly summarised. This methodology is compared and contrasted with European guidelines from the "SWARD" project that have been primarily developed for assessing the relative sustainability of options involving urban water supply and sewerage assets. Finally, the paper discusses how assessment methodologies that evaluate the financial, ecological and social dimensions of projects can, under some circumstances, be used to evaluate the relative progress of options for urban water management on a journey towards the widely pursued, but vaguely defined goal of "sustainable development".

  20. Adaptive Peircean decision aid project summary assessments.

    SciTech Connect

    Senglaub, Michael E.

    2007-01-01

    This efforts objective was to identify and hybridize a suite of technologies enabling the development of predictive decision aids for use principally in combat environments but also in any complex information terrain. The technologies required included formal concept analysis for knowledge representation and information operations, Peircean reasoning to support hypothesis generation, Mill's's canons to begin defining information operators that support the first two technologies and co-evolutionary game theory to provide the environment/domain to assess predictions from the reasoning engines. The intended application domain is the IED problem because of its inherent evolutionary nature. While a fully functioning integrated algorithm was not achieved the hybridization and demonstration of the technologies was accomplished and demonstration of utility provided for a number of ancillary queries.

  1. Wabash River Coal Gasification Repowering Project: A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2002-01-15

    The goal of the U.S. Department of Energy (DOE) Clean Coal Technology Program (CCT) is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have developed beyond the proof-of-concept stage. This document serves as a DOE post-project assessment (PPA) of a project selected in CCT Round IV, the Wabash River Coal Gasification Repowering (WRCGR) Project, as described in a Report to Congress (U.S. Department of Energy 1992). Repowering consists of replacing an existing coal-fired boiler with one or more clean coal technologies to achieve significantly improved environmental performance. The desire to demonstrate utility repowering with a two-stage, pressurized, oxygen-blown, entrained-flow, integrated gasification combined-cycle (IGCC) system prompted Destec Energy, Inc., and PSI Energy, Inc., to form a joint venture and submit a proposal for this project. In July 1992, the Wabash River Coal Gasification Repowering Project Joint Venture (WRCGRPJV, the Participant) entered into a cooperative agreement with DOE to conduct this project. The project was sited at PSI Energy's Wabash River Generating Station, located in West Terre Haute, Indiana. The purpose of this CCT project was to demonstrate IGCC repowering using a Destec gasifier and to assess long-term reliability, availability, and maintainability of the system at a fully commercial scale. DOE provided 50 percent of the total project funding (for capital and operating costs during the demonstration period) of $438 million.

  2. Project W-420 Ventilation Stack Monitoring System Year 2000 Compliance Assessment Project Plan

    SciTech Connect

    BUSSELL, J.H.

    1999-08-25

    This assessment describes the potential Year 2000 (Y2K) problems and describes the methods for achieving Y2K Compliance for Project W-420, Ventilation Stack Monitoring Systems Upgrades. The purpose of this assessment is to give an overview of the project. This document will not be updated and any dates contained in this document are estimates and may change. The project work scope includes upgrades to ventilation stacks and generic effluent monitoring systems (GEMS) at the 244-A Double Contained Receiver Tank (DCRT), the 244-BX DCRT, the 244-CR Vault, tanks 241-C-105 and 241-C-106, the 244-S DCRT, and the 244-TX DCRT. A detailed description of system dates, functions, interfaces, potential Y2K problems, and date resolutions can not be described since the project is in the definitive design phase, This assessment will describe the methods, protocols, and practices to ensure that equipment and systems do not have Y2K problems.

  3. Needs assessment in health research projects: a new approach to project management in iran.

    PubMed

    Peykari, Niloofar; Owlia, Parviz; Malekafzali, Hossein; Ghanei, Mostafa; Babamahmoodi, Abdolreza; Djalalinia, Shirin

    2013-01-01

    The science and technology health plan has defined the outline of health research to the national vision of Iran by 2025. The aim of this study was to focus on the process of needs assessment of health research projects also health research priority setting in Iran. THE PROJECT MANAGEMENT LIFE CYCLE HAS FOUR PHASES: Initiation, Planning, Execution and Closure. Based on abovementioned points we conducted the study. Focusing on the needs assessment led to systematic implementation of needs assessment of health project in all of the medical sciences universities. Parallel with this achieved strategies health research priority setting was followed through specific process from empowerment to implementation. We should adopt with more systematic progressive methods of health project managements for both our national convenience as well as our international health research programs.

  4. Long-range global population projections, as assessed in 1980.

    PubMed

    1982-01-01

    UN medium range projections prepared in the 1980 assessment projected the population of individual countries up to the year 2025. The long range projections discussed here were prepared by projecting the population of 8 major world regions from 2025-2100. The purpose of the projection was to observe the implications of the changes from the 1978 assessment made in the 1980 medium range projections on the long range projections of the world's populations. As in previous projections, high, medium, and low variants were prepared in which fertility is assumed to be constant at the replacement level but at different times in the future. In addition, these projections contain 2 variants not previously prepared--namely, the growth and decline variants, in which the ultimate net reproduction rate is 1.05 and 0.95, respectively. In all the variants, expectation of life at birth is assumed to reach 75 years for males and 80 for females. According to the current medium variant projection, the earth's population will become stationary after 2095 at 10.2 billion persons, compared with a total of 10.5 billion projected in the 1978 assessment. The lower projection is largely attributable to a recent decline in the growth rate of several countries in South Asia which was greater than previously assumed. When the world population becomes stationary, both crude birth and death rates would be about 13/1000. In the decline variant, total population would peak at 7.7 billion in 2055, then decline gradually to 7.2 billion in 2100. The total population as projected by the growth variant would equal 14.9 billion in 2100 and would still be growing slowly. Between 1980 and 2050, 95% of the world's growth will occur in the currently less developed regions. Their share of total population will increase from 75-85% during that period. The age structure in all regions is expected to converge to 1 in which the median age is 39 years, the proportion both below age 15 and above age 64 is about 19

  5. Health Impact Assessment of Urban Development Project

    PubMed Central

    Shojaei, Parisa; Karimlou, Masoud; Mohammadi, Farahnaz; Malekafzali, Hosein

    2016-01-01

    Background: Health impact assessment (HIA) has emerged to identify those activities and policies likely to have major impacts on the health of a population. Method: In this research, qualitative method was applied to identifying health determinants that urban man made lake affect on them, formatting and weighing the hierarchy of the factors, calculating AHP, and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) method for decide and ranking alternatives. Results: According to the results of the study, from the structural determinants point of view, the most positive effect of man-made lake was on Recreational services by 89.5% and the most negative one was on housing. According to intermediary determinants and general average, the most positive effect of lake was on physical activity and quality of air by 88.9% and the most negative one was on noise pollution by 46.7%. Ultimately, considering the positive and negative effects of lake between constructing and not constructing the lake option, the construction option was selected. Conclusion: There is substantial potential to improve public health by bringing decision makers’ attention to the health consequences of their actions; city councilpersons, zoning commissioners, and other decision makers typically have little background in health. PMID:27157160

  6. Hellsgate Winter Range : Wildlife Mitigation Project. Preliminary Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1995-01-01

    The Bonneville Power Administration proposes funding the Hellsgate Winter Range Wildlife Mitigation Project in cooperation with the Colville Convederated Tribes and Bureau of Indian Affairs. This Preliminary Environmental Assessment examines the potential environmental effects of acquiring and managing property for wildlife and wildlife habitat within a large project area. The Propose action is intended to meet the need for mitigation of wildlife and wild life habitat that was adversely affected by the construction of Grand Coulee and Chief Joseph Dams and their reservoirs.

  7. Project Fox: Assessing Risks Posed By Asteroids

    NASA Astrophysics Data System (ADS)

    Reinhardt, J.; Chen, X.; Liu, W.; Manchev, P.; Paté-Cornell, M.

    2013-12-01

    In order to make decisions on how to invest limited research dollars on asteroid surveillance and mitigation options, an analytic understanding of the risks posed by impacts is necessary. Qualitative and quantitative studies have been performed to assess such risks, and some reasonable point estimates have been proposed. However, since consequential asteroid impacts tend to be rare events, point estimates and expected annual death rates do not adequately convey the heavy tail of the distribution, potentially leading to misguided resource allocations. We propose and develop a framework for new risk measures, including a distribution over the number of fatalities from asteroid impacts and the probability of a globally consequential impact. We implement a simulation of asteroid impacts using probabilistic inputs for impactor characteristics, and a Poisson process for asteroid arrivals over the next 100 years. Simulation results indicate that a significant portion of the risk to humans comes from asteroids in the 300-1000 meter diameter range; this is because asteroid impacts in this range can produce global effects, and are more frequent than those from asteroids greater than 1km in diameter. The relative importance of this size regime in overall asteroid impact risk is robust in simulation results, and we find the magnitude of risks is still sensitive to factors that contribute global effects from an asteroid impact. Initial results are provided on the sensitivity of impact risks to various mitigation measures, including 'civil defense' methods. These results underscore the need for next-generation survey missions, and can help provide the basis for setting future space telescope observation requirements.

  8. Digital imaging technology assessment: Digital document storage project

    NASA Technical Reports Server (NTRS)

    1989-01-01

    An ongoing technical assessment and requirements definition project is examining the potential role of digital imaging technology at NASA's STI facility. The focus is on the basic components of imaging technology in today's marketplace as well as the components anticipated in the near future. Presented is a requirement specification for a prototype project, an initial examination of current image processing at the STI facility, and an initial summary of image processing projects at other sites. Operational imaging systems incorporate scanners, optical storage, high resolution monitors, processing nodes, magnetic storage, jukeboxes, specialized boards, optical character recognition gear, pixel addressable printers, communications, and complex software processes.

  9. [Health impact assessment of building and investment projects].

    PubMed

    Thriene, B

    2003-02-01

    For regional planning and approval procedures for building projects of a certain order of magnitude and power rating according to the German Federal Act on the Prevention of Emissions with Integrated Environmental Impact Assessment (EIA), the German public health departments, acting as public authorities, increasingly perform health impact assessments (HIA). The amended Act on Environmental Impact Assessment, the Decree on industrial plants which require approval (4th Federal Decree on Emission Prevention) and the Health Service Acts of the Federal States of Germany form the legal basis for the assessment of health issues with regard to approval procedures for building and investment projects. In the framework of the "Action Programme for the Environment and Health", the present article aims at making this process binding and to ensure responsibility and general involvement of the Public Health departments in all German Federal States. Future criteria, basic principles and procedures for single-case testing as well as assessment standards should meet these requirements. The Federal Ministry for the Environment and the Federal Ministry for Health should agree on Health Impact Assessment (HIA ) as well as on the relaxant stipulations in their procedures and general administrative regulations for implementing the Environmental Impact Assessment Act (EIA). Current EIA procedures focus on urban development and road construction, industrial investment projects, intensive animal husbandry plants, waste incineration plants, and wind energy farms. This paper illustrates examples meeting with varying degrees of public acceptance. However, being involved in the regional planning procedure for the project "Extension of the federal motorway A 14 from Magdeburg to Schwerin", the Public Health Service also shares global responsibility for health and climate protection. Demands for shortest routing conflict with objectives of environmental protection which should be given long

  10. Engineering Systems Thinking: Definition, Assessing and Correlation with Project Success

    DTIC Science & Technology

    2011-05-01

    Engineering  Systems   Thinking :  Definition, Assessing and Correlation with  Project Success Moti Frank – HIT, Holon Institute of Technology, Israel...00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Engineering Systems Thinking : Definition, Assessing and Correlation with Project Success 5a...b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Engineering  Systems   Thinking : •Definition

  11. Directory of country environmental studies, 1993. An annotated bibliography of environmental and natural resource profiles and assessments

    SciTech Connect

    Tunstall, D.B.; van der Wansem, M.

    1992-11-01

    The 1993 edition of the Directory provides detailed citations and abstracts for 357 major natural resource and environmental studies (257 of which were added since the 1990 edition) covering 129 developing countries and 12 regional groupings. Most of the studies (93%) were prepared between 1987 and 1992. Included are 66 national reports prepared for the U.N. Conference on Environment and Development, held in Rio de Janeiro in June 1992. Thirty-three countries, including Algeria, Bhutan, Cuba, Republic of Korea, Laos, Namibia, South Africa, Suriname, Taiwan, and Venezuela, are new to this edition of the directory, which focuses on reports that link quantitative assessment of a country's natural resources to economic development and the maintenance of ecosystems, with particular emphasis on natural resource management strategies and action plans.

  12. An annotated energy bibliography

    NASA Technical Reports Server (NTRS)

    Blow, S. J.

    1979-01-01

    Comprehensive annotated compilation of books, journals, periodicals, and reports on energy and energy related topics, contains approximately 10,0000 tehcnical and nontechnical references from bibliographic and other sources dated January 1975 through May 1977.

  13. An annotated energy bibliography

    NASA Technical Reports Server (NTRS)

    Blow, S. J.

    1979-01-01

    Comprehensive annotated compilation of books, journals, periodicals, and reports on energy and energy related topics, contains approximately 10,0000 tehcnical and nontechnical references from bibliographic and other sources dated January 1975 through May 1977.

  14. The Groundwater Performance Assessment Project Quality Assurance Plan

    SciTech Connect

    Luttrell, Stuart P.

    2006-05-11

    U.S. Department of Energy (DOE) has monitored groundwater on the Hanford Site since the 1940s to help determine what chemical and radiological contaminants have made their way into the groundwater. As regulatory requirements for monitoring increased in the 1980s, there began to be some overlap between various programs. DOE established the Groundwater Performance Assessment Project (groundwater project) in 1996 to ensure protection of the public and the environment while improving the efficiency of monitoring activities. The groundwater project is designed to support all groundwater monitoring needs at the site, eliminate redundant sampling and analysis, and establish a cost-effective hierarchy for groundwater monitoring activities. This document provides the quality assurance guidelines that will be followed by the groundwater project. This QA Plan is based on the QA requirements of DOE Order 414.1C, Quality Assurance, and 10 CFR 830, Subpart A--General Provisions/Quality Assurance Requirements as delineated in Pacific Northwest National Laboratory’s Standards-Based Management System. In addition, the groundwater project is subject to the Environmental Protection Agency (EPA) Requirements for Quality Assurance Project Plans (EPA/240/B-01/003, QA/R-5). The groundwater project has determined that the Hanford Analytical Services Quality Assurance Requirements Documents (HASQARD, DOE/RL-96-68) apply to portions of this project and to the subcontractors. HASQARD requirements are discussed within applicable sections of this plan.

  15. Learning from partially annotated OPT images by contextual relevance ranking.

    PubMed

    Li, Wenqi; Zhang, Jianguo; Zheng, Wei-Shi; Coats, Maria; Carey, Frank A; McKenna, Stephen J

    2013-01-01

    Annotations delineating regions of interest can provide valuable information for training medical image classification and segmentation methods. However the process of obtaining annotations is tedious and time-consuming, especially for high-resolution volumetric images. In this paper we present a novel learning framework to reduce the requirement of manual annotations while achieving competitive classification performance. The approach is evaluated on a dataset with 59 3D optical projection tomography images of colorectal polyps. The results show that the proposed method can robustly infer patterns from partially annotated images with low computational cost.

  16. Rapid Response Risk Assessment in New Project Development

    NASA Technical Reports Server (NTRS)

    Graber, Robert R.

    2010-01-01

    A capability for rapidly performing quantitative risk assessments has been developed by JSC Safety and Mission Assurance for use on project design trade studies early in the project life cycle, i.e., concept development through preliminary design phases. A risk assessment tool set has been developed consisting of interactive and integrated software modules that allow a user/project designer to assess the impact of alternative design or programmatic options on the probability of mission success or other risk metrics. The risk and design trade space includes interactive options for selecting parameters and/or metrics for numerous design characteristics including component reliability characteristics, functional redundancy levels, item or system technology readiness levels, and mission event characteristics. This capability is intended for use on any project or system development with a defined mission, and an example project will used for demonstration and descriptive purposes, e.g., landing a robot on the moon. The effects of various alternative design considerations and their impact of these decisions on mission success (or failure) can be measured in real time on a personal computer. This capability provides a high degree of efficiency for quickly providing information in NASA s evolving risk-based decision environment

  17. Rapid Response Risk Assessment in New Project Development

    NASA Technical Reports Server (NTRS)

    Graber, Robert R.

    2010-01-01

    A capability for rapidly performing quantitative risk assessments has been developed by JSC Safety and Mission Assurance for use on project design trade studies early in the project life cycle, i.e., concept development through preliminary design phases. A risk assessment tool set has been developed consisting of interactive and integrated software modules that allow a user/project designer to assess the impact of alternative design or programmatic options on the probability of mission success or other risk metrics. The risk and design trade space includes interactive options for selecting parameters and/or metrics for numerous design characteristics including component reliability characteristics, functional redundancy levels, item or system technology readiness levels, and mission event characteristics. This capability is intended for use on any project or system development with a defined mission, and an example project will used for demonstration and descriptive purposes, e.g., landing a robot on the moon. The effects of various alternative design considerations and their impact of these decisions on mission success (or failure) can be measured in real time on a personal computer. This capability provides a high degree of efficiency for quickly providing information in NASA s evolving risk-based decision environment

  18. Environmental assessment, expanded Ponnequin wind energy project, Weld County, Colorado

    SciTech Connect

    1999-02-01

    The US Department of Energy (DOE) has considered a proposal from the State of Colorado, Office of Energy Conservation (OEC), for funding construction of the Expanded Ponnequin Wind Project in Weld County, Colorado. OEC plans to enter into a contracting arrangement with Public Service Company of Colorado (PSCo) for the completion of these activities. PSCo, along with its subcontractors and business partners, are jointly developing the Expanded Ponnequin Wind Project. The purpose of this Final Environmental Assessment (EA) is to provide DOE and the public with information on potential environmental impacts associated with the Expanded Ponnequin Wind Energy Project. This EA, and public comments received on it, were used in DOE`s deliberations on whether to release funding for the expanded project under the Commercialization Ventures Program.

  19. The Miami-Dade Juvenile Assessment Center National Demonstration Project

    ERIC Educational Resources Information Center

    Walters, Wansley; Dembo, Richard; Beaulaurier, Richard; Cocozza, Joseph; De La Rosa, Mario; Poythress, Norman; Skowyra, Kathy; Veysey, Bonita M.

    2005-01-01

    The Miami-Dade Juvenile Assessment Center National Demonstration Project (NDP) is serving as a national model for the transformation of front end services in the juvenile justice system in a unique sociocultural setting.We discuss the background and vision of the NDP, its implementation and accomplishments in six major program areas: (1)…

  20. Fine sediment sources in conservation effects assessment project watersheds

    USDA-ARS?s Scientific Manuscript database

    Two naturally occurring radionuclides, 7Be and 210Pbxs , were used as tracers to discriminate eroded surface soils from channel-derived sediments in the fine suspended sediment loads of eight Conservation Effects Assessment Project (CEAP) benchmark watersheds. Precipitation, source soils, and suspe...

  1. Integrated economic and climate projections for impact assessment

    EPA Science Inventory

    We designed scenarios for impact assessment that explicitly address policy choices and uncertainty in climate response. Economic projections and the resulting greenhouse gas emissions for the “no climate policy” scenario and two stabilization scenarios: at 4.5 W/m2 and 3.7 W/m2 b...

  2. Integrated economic and climate projections for impact assessment

    EPA Science Inventory

    We designed scenarios for impact assessment that explicitly address policy choices and uncertainty in climate response. Economic projections and the resulting greenhouse gas emissions for the “no climate policy” scenario and two stabilization scenarios: at 4.5 W/m2 and 3.7 W/m2 b...

  3. Cheney Lake CEAP Project: Conservation Practice Effects Assessment

    USDA-ARS?s Scientific Manuscript database

    AnnAGNPS was used to analyze Cheney Lake Watershed, a Special Emphasis Watershed, during the Conservation Evaluation Assessment Project (CEAP). Seven (7) best management conservation practice (BMP) scenarios, which would impact sediment and nutrient loading to Cheney Lake, were identified and evalu...

  4. Living memorials project: year 1 social and site assessment

    Treesearch

    Erika S. Svendsen; Lindsay K. Campbell

    2005-01-01

    The Living Memorials Project (LMP) social and site assessment identified more than 200 public open spaces created, used, or enhanced in memory of the tragic events of September 11, 2001 (9-11). A national registry of these sites is available for viewing and updating online. Researchers interviewed 100 community groups using social ecology methods of observation,...

  5. Report of the Palomar College Assessment of Learning Project.

    ERIC Educational Resources Information Center

    Palomar Coll., San Marcos, CA.

    Following the proposal of the Chancellor of the California Community to shift from attendance-based funding to performance-based funding, Palomar College (California) has articulated its intention to judge its quality and formulate its policies primarily on learning outcomes. Out of this imperative, the Assessment of Learning Project (ALP) was…

  6. Assessment of Individual Student Performance in Online Team Projects

    ERIC Educational Resources Information Center

    Alden, Jay

    2011-01-01

    The use of team projects has been shown to be beneficial in higher education. There is also general agreement that team efforts should be assessed and that the grading ought to represent both (1) the quality of the product developed jointly by the team, as well as (2) the degree of participation and quality of contribution by each individual…

  7. Expert Systems Based Clinical Assessment and Tutorial Project.

    ERIC Educational Resources Information Center

    Papa, Frank; Shores, Jay

    This project at the Texas College of Osteopathic Medicine (Fort Worth) evaluated the use of an artificial-intelligence-derived measure, "Knowledge-Based Inference Tool" (KBIT), as the basis for assessing medical students' diagnostic capabilities and designing instruction to improve diagnostic skills. The instrument was designed to…

  8. Wabash River Coal Gasification Repowering Project: A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2002-01-15

    The goal of the U.S. Department of Energy (DOE) Clean Coal Technology Program (CCT) is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have developed beyond the proof-of-concept stage. This document serves as a DOE post-project assessment (PPA) of a project selected in CCT Round IV, the Wabash River Coal Gasification Repowering (WRCGR) Project, as described in a Report to Congress (U.S. Department of Energy 1992). Repowering consists of replacing an existing coal-fired boiler with one or more clean coal technologies to achieve significantly improved environmental performance. The desire to demonstrate utility repowering with a two-stage, pressurized, oxygen-blown, entrained-flow, integrated gasification combined-cycle (IGCC) system prompted Destec Energy, Inc., and PSI Energy, Inc., to form a joint venture and submit a proposal for this project. In July 1992, the Wabash River Coal Gasification Repowering Project Joint Venture (WRCGRPJV, the Participant) entered into a cooperative agreement with DOE to conduct this project. The project was sited at PSI Energy's Wabash River Generating Station, located in West Terre Haute, Indiana. The purpose of this CCT project was to demonstrate IGCC repowering using a Destec gasifier and to assess long-term reliability, availability, and maintainability of the system at a fully commercial scale. DOE provided 50 percent of the total project funding (for capital and operating costs during the demonstration period) of $438 million. Construction for the demonstration project was started in July 1993. Pre-operational tests were initiated in August 1995, and construction was completed in November 1995. Commercial operation began in November 1995, and the demonstration period was completed in December

  9. Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data

    PubMed Central

    Peng, Xinxia; Pipes, Lenore; Xiong, Hao; Green, Richard R.; Jones, Daniel C.; Ruzzo, Walter L.; Schroth, Gary P.; Mason, Christopher E.; Palermo, Robert E.; Katze, Michael G.

    2014-01-01

    Background The genome annotations of rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques, two of the most common nonhuman primate animal models, are limited. Methods We analyzed large-scale macaque RNA-based next-generation sequencing (RNAseq) data to identify un-annotated macaque transcripts. Results For both macaque species, we uncovered thousands of novel isoforms for annotated genes and thousands of un-annotated intergenic transcripts enriched with non-coding RNAs. We also identified thousands of transcript sequences which are partially or completely ‘missing’ from current macaque genome assemblies. We showed that many newly identified transcripts were differentially expressed during SIV infection of rhesus macaques or during Ebola virus infection of cynomolgus macaques. Conclusions For two important macaque species, we uncovered thousands of novel isoforms and un-annotated intergenic transcripts including coding and non-coding RNAs, polyadenylated and non-polyadenylated transcripts. This resource will greatly improve future macaque studies, as demonstrated by their applications in infectious disease studies. PMID:24810475

  10. Semantic Annotation of Mutable Data

    PubMed Central

    Morris, Robert A.; Dou, Lei; Hanken, James; Kelly, Maureen; Lowery, David B.; Ludäscher, Bertram; Macklin, James A.; Morris, Paul J.

    2013-01-01

    Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema. PMID:24223697

  11. Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

    PubMed Central

    Nagel, Kevin; Jimeno-Yepes, Antonio; Rebholz-Schuhmann, Dietrich

    2009-01-01

    Background A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level. Results This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context written in the surrounding text. MEDLINE abstract texts have been processed to identify protein mentions in combination with taxonomic species and protein residues (F1-measure 0.52). The identified protein-species-residue triplets have been validated and benchmarked against reference data resources (UniProtKb, average F1-measure of 0.54). Then, contextual features were extracted through shallow and deep parsing and the features have been classified into predefined categories (F1-measure ranges from 0.15 to 0.67). Furthermore, the feature sets have been aligned with annotation types in UniProtKb to assess the relevance of the annotations for ongoing curation projects. Altogether, the annotations have been assessed automatically and manually against reference data resources. Conclusion This work proposes a solution for the automatic extraction of functional annotation for protein residues from biomedical articles. The presented approach is an extension to other existing systems in that a wider range of residue entities are considered and that features of residues are extracted as annotations. PMID:19758468

  12. The ClearEarth Project: Preliminary Findings from Experiments in Applying the CLEARTK NLP Pipeline and Annotation Tools Developed for Biomedicine to the Earth Sciences

    NASA Astrophysics Data System (ADS)

    Duerr, R.; Thessen, A.; Jenkins, C. J.; Palmer, M.; Myers, S.; Ramdeen, S.

    2016-12-01

    The ability to quickly find, easily use and effortlessly integrate data from a variety of sources is a grand challenge in Earth sciences, one around which entire research programs have been built. A myriad of approaches to tackling components of this challenge have been demonstrated, often with some success. Yet finding, assessing, accessing, using and integrating data remains a major challenge for many researchers. A technology that has shown promise in nearly every aspect of the challenge is semantics. Semantics has been shown to improve data discovery, facilitate assessment of a data set, and through adoption of the W3C's Linked Data Platform to have improved data integration and use at least for data amenable to that paradigm. Yet the creation of semantic resources has been slow. Why? Amongst a plethora of other reasons, it is because semantic expertise is rare in the Earth and Space sciences; the creation of semantic resources for even a single discipline is labor intensive and requires agreement within the discipline; best practices, methods and tools for supporting the creation and maintenance of the resources generated are in flux; and the human and financial capital needed are rarely available in the Earth sciences. However, other fields, such as biomedicine, have made considerable progress in these areas. The NSF-funded ClearEarth project is adapting the methods and tools from these communities for the Earth sciences in the expectation that doing so will enhance progress and the rate at which the needed semantic resources are created. We discuss progress and results to date, lessons learned from this adaptation process, and describe our upcoming efforts to extend this knowledge to the next generation of Earth and data scientists.

  13. Environmental Restoration Disposal Facility (Project W-296) Safety Assessment

    SciTech Connect

    Armstrong, D.L.

    1994-08-01

    This Safety Assessment is based on information derived from the Conceptual Design Report for the Environmental Restoration Disposal Facility (DOE/RL 1994) and ancillary documentation developed during the conceptual design phase of Project W-296. The Safety Assessment has been prepared to support the Solid Waste Burial Ground Interim Safety Basis document. The purpose of the Safety Assessment is to provide an evaluation of the design to determine if the process, as proposed, will comply with US Department of Energy (DOE) Limits for radioactive and hazardous material exposures and be acceptable from an overall health and safety standpoint. The evaluation considered affects on the worker, onsite personnel, the public, and the environment.

  14. Environmental Assessment Expanded Ponnequin Wind Energy Project Weld County, Colorado

    SciTech Connect

    N /A

    1999-03-02

    The U.S.Department of Energy (DOE) has considered a proposal from the State of Colorado, Office of Energy Conservation (OEC), for funding construction of the Expanded Ponnequin Wind Project in Weld County, Colorado. OEC plans to enter into a contracting arrangement with Public Service Company of Colorado (PSCO) for the completion of these activities. PSCo, along with its subcontractors and business partners, are jointly developing the Expanded Ponnequin Wind Project. DOE completed an environmental assessment of the original proposed project in August 1997. Since then, the geographic scope and the design of the project changed, necessitating additional review of the project under the National Environmental Policy Act. The project now calls for the possible construction of up to 48 wind turbines on State and private lands. PSCo and its partners have initiated construction of the project on private land in Weld County, Colorado. A substation, access road and some wind turbines have been installed. However, to date, DOE has not provided any funding for these activities. DOE, through its Commercialization Ventures Program, has solicited applications for financial assistance from state energy offices, in a teaming arrangement with private-sector organizations, for projects that will accelerate the commercialization of emerging renewable energy technologies. The Commercialization Ventures Program was established by the Renewable Energy and Energy Efficiency Technology Competitiveness Act of 1989 (P.L. 101-218) as amended by the Energy Policy Act of 1992 (P.L. 102-486). The Program seeks to assist entry into the marketplace of newly emerging renewable energy technologies, or of innovative applications of existing technologies. In short, an emerging renewable energy technology is one which has already proven viable but which has had little or no operational experience. The Program is managed by the Department of Energy, Office of Energy Efficiency and Renewable Energy. The

  15. Health Communication and Literacy: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Beveridge, Jennifer

    This annotated bibliography lists publications and World Wide Web sites dealing with health communication and literacy. The 51 publications, which were all published between 1982 and 1998, contain information about and/or for use in the following areas: assessment, assessment tools, elderly adults, empowerment, maternal and child health, patient…

  16. Health Communication and Literacy: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Beveridge, Jennifer

    This annotated bibliography lists publications and World Wide Web sites dealing with health communication and literacy. The 51 publications, which were all published between 1982 and 1998, contain information about and/or for use in the following areas: assessment, assessment tools, elderly adults, empowerment, maternal and child health, patient…

  17. Use of course-embedded projects for program assessment.

    PubMed

    Krilowicz, B L; Downs, T

    1999-06-01

    There is increasing demand on science faculty to develop authentic assessment measures for both individual courses and undergraduate programs. We report here on a quarter-long group project used in a neurophysiology course that can be used for either purpose. Small groups of four to five students critically analyze at least 10 articles from the primary scientific literature. The end result of this process is the equivalent of a scientific review article that is presented in two formats, a 10-min oral presentation and a scientific poster presentation. Students perform better on application tasks than on analysis, synthesis, or evaluation tasks associated with the project (P < 0.025) and generally respond positively to process questions (59-82%) but less positively to task questions (36-76%) about group dynamics. The cognitive skills and basic content knowledge required to complete this project are developed throughout the undergraduate program. Thus the project is a type of culminating program experience. However, the project also assesses basic course proficiency, because students cannot analyze primary neuroscience research without an understanding of neurophysiological principles.

  18. Guidance on internal dose assessments from monitoring data (project IDEAS).

    PubMed

    Doerfel, H; Andrasi, A; Bailey, M; Berkovski, V; Castellani, C M; Hurtgen, C; Jourdain, J R; LeGuen, B

    2003-01-01

    Several international inter-comparison exercises on intake and internal dose assessments from monitoring data led to the conclusion that the results calculated by different participants varied significantly, mainly due to the broad variety of methods and assumptions applied in the assessment procedure. Based on these experiences, the need of harmonisation of the procedures has been formulated as an EU research project under the 5th Framework Programme, with the aim of developing general guidelines for standardising assessments of intakes and internal doses. In the IDEAS project, eight institutions from seven European countries are participating, also using inputs from internal dosimetry professionals from across Europe to ensure broad consensus in the outcome of the project. To ensure that the guidelines are applicable to a wide range of practical situations, the first step will be to compile a database on well documented cases of internal contamination. In parallel, an improved version of existing software will be developed and distributed to the partners for further use. Many cases from the database will be evaluated independently by more partners using the same software and the results will be discussed and the draft guidelines prepared. The guidelines will then be revised and refined on the basis of the experiences and discussions of two workshops, and an intercomparison exercise organised in the frame of the project which will be open to all internal dosimetry professionals.

  19. Mod-2 wind turbine project assessment and cluster test plans

    NASA Technical Reports Server (NTRS)

    Gordon, L. H.

    1982-01-01

    An assessment of the Mod-2 Wind Turbine project is presented based on initial goals and present results. Specifically, the Mod-2 background, project flow, and a chronology of events/results leading to Mod-2 acceptance is presented. After checkout/acceptance of the three operating turbines, NASA/LeRC will continue management of a two year test program performed at the DOE Goodnoe Hills test site. This test program is expected to yield data necessary for the continued development and optimization of wind energy systems. These test activities, the implementation of, and the results to date are also presented.

  20. Evaluating Computational Gene Ontology Annotations.

    PubMed

    Škunca, Nives; Roberts, Richard J; Steffen, Martin

    2017-01-01

    Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.

  1. Algal functional annotation tool

    SciTech Connect

    Lopez, D.; Casero, D.; Cokus, S. J.; Merchant, S. S.; Pellegrini, M.

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  2. Injectors and Annotations

    NASA Technical Reports Server (NTRS)

    Filman, Robert E.

    2004-01-01

    In a previous paper, we presented the Object Infrastructure Framework. The goal of that system is to simplify the creation of distributed applications. The primary claim of that work is that non-functional 'ilities' could be achieved by controlling and manipulating the communications between components, thereby simplifying the development of distributed systems. A secondary element of that paper is to argue for extending the conventional distributed objects model in two important ways: 1) The ability to insert injectors (filters, wrappers) into the communication path between components; 2) The ability to annotate communications with additional information, and to propagate these annotations through an application. Here we express the descriptions of that paper.

  3. Program of Research in the Field of Human Resources Development with Special Reference to Asia and the Far East; Annotated List of Research Projects Completed and Proposed.

    ERIC Educational Resources Information Center

    Mehta, M.M.

    Summaries of nine research projects completed and 26 research projects proposed or in progress, titles of papers produced in coordinated research and teaching programs, and a list of 13 international, national, or regional, seminars, conferences, or expert working group meetings contributing to human resources development in Asia and the Far East…

  4. Gene and alternative splicing annotation with AIR

    PubMed Central

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V.; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts. PMID:15632090

  5. Automated analysis and annotation of basketball video

    NASA Astrophysics Data System (ADS)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  6. Gene and alternative splicing annotation with AIR.

    PubMed

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts.

  7. A Novel Approach to Semantic and Coreference Annotation at LLNL

    SciTech Connect

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  8. Controls on project proponents and environmental impact assessment effectiveness

    SciTech Connect

    Ortolano, L. )

    1993-01-01

    The degree of effectiveness of environmental impact assessment (EIA) for particular projects is associated with the existence of mechanisms of organizational control. Five dimensions of EIA effectiveness are considered: procedural compliance, completeness of EIA documents, methods to assess impacts, influence on project decisions, and weight given to environmental factors. Six mechanisms of control are introduced and illustrated by programs and projects in several countries. Experience in the Philippines under President Marcos demonstrates that procedural control in the form of EIA regulations, when used without other control mechanisms, will lead at most to token compliance. Judicial control, as practiced in the US, yields high procedural compliance. Evaluative control can yield effective EIA, but some systems based on this form of control treat only a small fraction of the major projects proposed. Both control exerted by development assistance organizations and control by professionals have great potential for yielding effective EIA, but that potential has not been fully realized. Control exerted directly by citizens or agencies not otherwise involved in EIA is uncommon, but cases from Taiwan demonstrate that those controls can be significant. An understanding of relationships between control mechanisms and EIA effectiveness is useful in designing EIA policies and programs.

  9. Assessing local resources and culture before instituting quality improvement projects.

    PubMed

    Hawkins, C Matthew

    2014-12-01

    The planning phases of quality improvement projects are commonly overlooked. Disorganized planning and implementation can escalate chaos, intensify resistance to change, and increase the likelihood of failure. Two important steps in the planning phase are (1) assessing local resources available to aid in the quality improvement project and (2) evaluating the culture in which the desired change is to be implemented. Assessing local resources includes identifying and engaging key stakeholders and evaluating if appropriate expertise is available for the scope of the project. This process also involves engaging informaticists and gathering available IT tools to plan and automate (to the extent possible) the data-gathering, analysis, and feedback steps. Culture in a department is influenced by the ability and willingness to manage resistance to change, build consensus, span boundaries between stakeholders, and become a learning organization. Allotting appropriate time to perform these preparatory steps will increase the odds of successfully performing a quality improvement project and implementing change. Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  10. Quantification for complex assessment: uncertainty estimation in final year project thesis assessment

    NASA Astrophysics Data System (ADS)

    Kim, Ho Sung

    2013-12-01

    A quantitative method for estimating an expected uncertainty (reliability and validity) in assessment results arising from the relativity between four variables, viz examiner's expertise, examinee's expertise achieved, assessment task difficulty and examinee's performance, was developed for the complex assessment applicable to final year project thesis assessment including peer assessment. A guide map can be generated by the method for finding expected uncertainties prior to the assessment implementation with a given set of variables. It employs a scale for visualisation of expertise levels, derivation of which is based on quantified clarities of mental images for levels of the examiner's expertise and the examinee's expertise achieved. To identify the relevant expertise areas that depend on the complexity in assessment format, a graphical continuum model was developed. The continuum model consists of assessment task, assessment standards and criterion for the transition towards the complex assessment owing to the relativity between implicitness and explicitness and is capable of identifying areas of expertise required for scale development.

  11. Social cost impact assessment of pipeline infrastructure projects

    SciTech Connect

    Matthews, John C.; Allouche, Erez N.; Sterling, Raymond L.

    2015-01-15

    A key advantage of trenchless construction methods compared with traditional open-cut methods is their ability to install or rehabilitate underground utility systems with limited disruption to the surrounding built and natural environments. The equivalent monetary values of these disruptions are commonly called social costs. Social costs are often ignored by engineers or project managers during project planning and design phases, partially because they cannot be calculated using standard estimating methods. In recent years some approaches for estimating social costs were presented. Nevertheless, the cost data needed for validation of these estimating methods is lacking. Development of such social cost databases can be accomplished by compiling relevant information reported in various case histories. This paper identifies eight most important social cost categories, presents mathematical methods for calculating them, and summarizes the social cost impacts for two pipeline construction projects. The case histories are analyzed in order to identify trends for the various social cost categories. The effectiveness of the methods used to estimate these values is also discussed. These findings are valuable for pipeline infrastructure engineers making renewal technology selection decisions by providing a more accurate process for the assessment of social costs and impacts. - Highlights: • Identified the eight most important social cost factors for pipeline construction • Presented mathematical methods for calculating those social cost factors • Summarized social cost impacts for two pipeline construction projects • Analyzed those projects to identify trends for the social cost factors.

  12. Parallel optics technology assessment for the versatile link project

    SciTech Connect

    Chramowicz, J.; Kwan, S.; Rivera, R.; Prosser, A.; /Fermilab

    2011-01-01

    This poster describes the assessment of commercially available and prototype parallel optics modules for possible use as back end components for the Versatile Link common project. The assessment covers SNAP12 transmitter and receiver modules as well as optical engine technologies in dense packaging options. Tests were performed using vendor evaluation boards (SNAP12) as well as custom evaluation boards (optical engines). The measurements obtained were used to compare the performance of these components with single channel SFP+ components operating at a transmission wavelength of 850 nm over multimode fibers.

  13. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  14. Impact of the agricultural research service watershed assessment studies on the conservation effects assessment project cropland national assessment

    USDA-ARS?s Scientific Manuscript database

    USDA initiated the Conservation Effects Assessment Project (CEAP) in 2002 to analyze societal and environmental benefits gained from the increased conservation program funding provided in the 2002 Farm Bill. The Natural Resources Conservation Service (NRCS), Agricultural Research Service (ARS), and...

  15. Modeling loosely annotated images using both given and imagined annotations

    NASA Astrophysics Data System (ADS)

    Tang, Hong; Boujemaa, Nozha; Chen, Yunhao; Deng, Lei

    2011-12-01

    In this paper, we present an approach to learn latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: 1. ambiguous correspondences between visual features and annotated keywords; 2. incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning a topic model. In particular, some ``imagined'' keywords are poured into the incomplete annotation through measuring similarity between keywords in terms of their co-occurrence. Then, both given and imagined annotations are employed to learn probabilistic topic models for automatically annotating new images. We conduct experiments on two image databases (i.e., Corel and ESP) coupled with their loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods. The proposed method improves word-driven probability latent semantic analysis (PLSA-words) up to a comparable performance with the best discrete annotation method, while a merit of PLSA-words is still kept, i.e., a wider semantic range.

  16. Cheating. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M., Comp.

    This 89-item, annotated bibliography was compiled to provide access to research and discussions of cheating and, specifically, cheating on tests. It is not limited to any educational level, nor is it confined to any specific curriculum area. Two data bases were searched by computer, and a library search was conducted. A computer search of the…

  17. Automated Microbial Genome Annotation

    SciTech Connect

    Land, Miriam

    2009-05-29

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  18. Annotation: The Savant Syndrome

    ERIC Educational Resources Information Center

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  19. Ghostwriting: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Donald B.

    Drawn from communication journals, historical and news magazines, business and industrial magazines, political science and world affairs journals, general interest periodicals, and literary and political review magazines, the approximately 90 entries in this annotated bibliography discuss ghostwriting as practiced through the ages and reveal the…

  20. Annotated Bibliography. First Edition.

    ERIC Educational Resources Information Center

    Haring, Norris G.

    An annotated bibliography which presents approximately 300 references from 1951 to 1973 on the education of severely/profoundly handicapped persons. Citations are grouped alphabetically by author's name within the following categories: characteristics and treatment, gross motor development, sensory and motor development, physical therapy for the…

  1. Ghostwriting: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Donald B.

    Drawn from communication journals, historical and news magazines, business and industrial magazines, political science and world affairs journals, general interest periodicals, and literary and political review magazines, the approximately 90 entries in this annotated bibliography discuss ghostwriting as practiced through the ages and reveal the…

  2. Integrative neural networks models for stream assessment in restoration projects

    NASA Astrophysics Data System (ADS)

    Gazendam, Ed; Gharabaghi, Bahram; Ackerman, Josef D.; Whiteley, Hugh

    2016-05-01

    Stream-habitat assessment for evaluation of restoration projects requires the examination of many parameters, both watershed-scale and reach-scale, to incorporate the complex non-linear effects of geomorphic, riparian, watershed and hydrologic factors on aquatic ecosystems. Rapid geomorphic assessment tools used by many jurisdictions to assess natural channel design projects seldom include watershed-level parameters, which have been shown to have a significant effect on benthic habitat in stream systems. In this study, Artificial Neural Network (ANN) models were developed to integrate complex non-linear relationships between the aquatic ecosystem health indices and key watershed-scale and reach-scale parameters. Physical stream parameters, based on QHEI parameters, and watershed characteristics data were collected at 112 sites on 62 stream systems located in Southern Ontario. Benthic data were collected separately and benthic invertebrate summary indices, specifically Hilsenhoff's Biotic Index (HBI) and Richness, were determined. The ANN models were trained on the randomly selected 3/4 of the dataset of 112 streams in Ontario, Canada and validated on the remaining 1/4. The R2 values for the developed ANN model predictions were 0.86 for HBI and 0.92 for Richness. Sensitivity analysis of the trained ANN models revealed that Richness was directly proportional to Erosion and Riparian Width and inversely proportional to Floodplain Quality and Substrate parameters. HBI was directly proportional to Velocity Types and Erosion and inversely proportional to Substrate, % Treed and 1:2 Year Flood Flow parameters. The ANN models can be useful tools for watershed managers in stream assessment and restoration projects by allowing consideration of watershed properties in the stream assessment.

  3. Assessment of Smolt Condition for Travel Time Analysis Project, 1987-1997 Project Review.

    SciTech Connect

    Schrock, Robin M.; Hans, Karen M.; Beeman, John W.

    1997-12-01

    The assessment of Smolt Condition for Travel Time Analysis Project (Bonneville Power Administration Project 87-401) monitored attributes of salmonid smolt physiology in the Columbia and Snake River basins from 1987 to 1997, under the Northwest Power Planning Council Fish and Wildlife Program, in cooperation with the Smolt Monitoring Program of the Fish Passage Center. The primary goal of the project was to investigate the physiological development of juvenile salmonids related to migration rates. The assumption was made that the level of smolt development, interacting with environmental factos such as flow, would be reflected in travel times. The Fish Passage Center applied the physiological measurements of smolt condition to Water Budget management, to regulate flows so as to decrease travel time and increase survival.

  4. Environmentally Conscious Manufacturing Project: ECM assessment guidance manual

    SciTech Connect

    Not Available

    1994-11-01

    The purpose of this document is to provide a summary of the basic tools that will be used in conducting assessments under the Environmentally Conscious Manufacturing (ECM) Project assessment program. ECM can cover a wide range of issues including: finding safer alternatives to toxic materials; changing processes to become more efficient; environmental costs and regulatory compliance; waste reduction; energy conservation; product packaging; and product reuse/recycling. The assessments performed as part of this program will try to identify opportunities to implement technologies/actions that will promote the types of results listed above. The general methodology, or sequence of events, that will be used in conducting assessments is as follows: 1. Form an Assessment Team; 2. Map Process by flow diagrams and materials accounting; 3. Identify opportunities for ECM by activity based accounting and pareto analysis; 4. Identify and evaluate ECM/pollution prevention alternatives; 5. Implement alternatives; 6. Monitor progress. All of the assessment steps listed above are addressed in this document except forming the assessment team. The tools discussed in this document are well known, widely used process analysis or quality improvement tools which have been adapted for use in evaluating opportunities for ECM/Pollution prevention.

  5. Environmental Management Assessment of the Fernald Environmental Management Project (FEMP)

    SciTech Connect

    Not Available

    1993-04-01

    This report documents the results of the Environmental Management Assessment performed at the Fernald Environmental Management Project (FEMP) in Fernald, Ohio. During this assessment, the activities conducted by the assessment team included review of internal documents and reports from previous audits and assessments; interviews with US Department of Energy (DOE) and FEMP contractor personnel; and inspection and observation of selected facilities and operations. The onsite portion of the assessment was conducted from March 15 through April 1, 1993, by DOE`s Office of Environmental Audit (EH-24) located within the Office of the Assistant Secretary for Environment, Safety, and Health (EH-1). EH-24 carries out independent assessments of DOE facilities and activities as part of the EH-1 Environment, Safety, and Health (ES&H) Oversight Audit Program. The EH-24 program is designed to evaluate the status of DOE facilities and activities with respect to compliance with Federal, state, and local environmental laws and regulations; compliance with DOE Orders, Guidance and Directives; conformance with accepted industry practices and standards of performance; and the status and adequacy of management systems developed to address environmental requirements. The Environmental Management Assessment of FEMP focused on the adequacy of environmental management systems. Further, in response to requests by the Office of Environmental Restoration and Waste Management (EM) and Fernald Field Office (FN), Quality Assurance and Environmental Radiation activities at FEMP were evaluated from a programmatic standpoint. The results of the evaluation of these areas are contained in the Environmental Protection Programs section in this report.

  6. Comprehensive assessment of projected changes in water availability and aridity

    NASA Astrophysics Data System (ADS)

    Greve, Peter; Seneviratne, Sonia I.

    2015-04-01

    Substantial changes in the hydrological cycle are projected for the 21st century, with potential major impacts, particularly at regional scale. However, the projections are subject to major uncertainties and the metrics generally used to assess such changes do not fully account for the hydroclimatological characteristics of the land surface. In this context, the 'dry gets drier, wet gets wetter' paradigm is often used as a simplifying summary. However, recent studies have challenged the validity of the paradigm both for observations (Greve et al., 2014) and projections (Roderick et al., 2014), especially casting doubt on applying the widely used P-E (precipitation - evapotranspiration) metric over global land surfaces. Here we show in a comprehensive assessment that projected changes in mean annual P-E are generally not significant in most land areas, with the exception of the northern high latitudes where significant changes towards wetter conditions are found. We further show that the combination of decreasing P and increasing atmospheric demand (potential evapotranspiration, Ep) leads to a significant increase in aridity in many subtropical and neighbouring regions, thus confirming the paradigm for some dry regions, but invalidating it for the relative large fraction of the affected area which is currently in a humid or transitional climate regime. Combining both metrics (P-E and P-E_p) we conclude that the 'dry gets drier, wet gets wetter' paradigm is generally not confirmed for projected changes in most land areas (despite notable exceptions in the high latitudes and subtropics), because of a lack of robustness of the projected changes in some regions (tropics) and because humid to transitional regions are shifting to drier conditions, i.e. not following the paradigm. References Greve, P., Orlowsky, B., Mueller, B., Sheffield, J., Reichstein, M., & Seneviratne, S. I. Global assessment of trends in wetting and drying over land. Nature Geosci. 7, 716-721 (2014

  7. Wildlife Habitat Impact Assessment, Chief Joseph Dam Project, Washington : Project Report 1992.

    SciTech Connect

    Kuehn, Douglas; Berger, Matthew

    1992-01-01

    Under the Pacific Northwest Electric Power Planning and Conservation Act of 1980, and the subsequent Northwest Power Planning Council`s Columbia River Basin Fish and Wildlife Program, a wildlife habitat impact assessment and identification of mitigation objectives have been developed for the US Army Corps of Engineer`s Chief Joseph Dam Project in north-central Washington. This study will form the basis for future mitigation planning and implementation.

  8. Hellsgate Winter Range : Wildlife Mitigation Project. Final Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1995-03-01

    Bonneville Power Administration (BPA) proposes to fund the Hellsgate Winter Range Wildlife Mitigation Project (Project) in a cooperative effort with the Colville Confederated Tribes and the Bureau of Indian Affairs (BIA). The proposed action would allow the sponsors to secure property and conduct wildlife management activities within the boundaries of the Colville Indian Reservation. This Final Environmental Assessment (EA) examines the potential environmental effects of acquiring and managing property for wildlife and wildlife habitat within a large project area. This area consists of several separated land parcels, of which 2,000 hectares (4,943 acres) have been purchased by BPA and an additional 4,640 hectares (11,466 acres) have been identified by the Colville Confederated Tribes for inclusion in the Project. Four proposed activities (habitat protection, habitat enhancement, operation and maintenance, and monitoring and evaluation) are analyzed. The proposed action is intended to meet the need for mitigation of wildlife and wildlife habitat that was adversely affected by the construction of Grand Coulee and Chief Joseph Dams and their reservoirs.

  9. Project W-151 Tank 101-AZ Waste Retrieval System Year 2000 Compliance Assessment Project Plan

    SciTech Connect

    BUSSELL, J.H.

    1999-08-02

    This assessment describes the potential Year 2000 (Y2K) problems and describes the methods for achieving Y2K compliance for Project W-151, Tank 101-AZ Waste Retrieval System. The purpose of this assessment is to give an overview of the project. This document will not be updated and any dates contained in this document are estimates and may change. Two mixer pumps and instrumentation have been or are planned to be installed in waste tank 101-AZ to demonstrate solids mobilization. The information and experience gained during this process test will provide data for comparison with sludge mobilization prediction models and provide indication of the effects of mixer pump operation on an Aging Waste Facility tank. A limited description of system dates, functions, interfaces, potential Y2K problems, and date resolutions is presented. The project is presently on hold, and definitive design and procurement have been completed. This assessment will describe the methods, protocols, and practices to ensure that equipment and systems do not have Y2K problems.

  10. Project W-519 TWRS privatization phase 1 infrastructure year 2000 compliance assessment project plan

    SciTech Connect

    BUSSELL, J.H.

    1999-08-25

    This assessment describes the potential Year 2000 (Y2K) problems and describes the methods for achieving Y2K Compliance for Project W-519, Tank Waste Remediation System Privatization Phase I Infrastructure Support. The purpose of this assessment is to give an overview of the project. This assessment will describe the methods, protocols, and practices to assure that equipment and systems do not have Y2K problems. This document will not be updated and any dates contained in this document are estimates and may change. The scope of project W-519 is to provide utilities and infrastructure to support construction and operation of the private contractor's facility to treat, immobilize, and dispose of tank waste. The private contractor's facility will be located on east side of 200E-area and north of Route 4s (near the defunct grout vaults). The utilities include potable and process water, construction and operational electrical power systems, and liquid effluent disposal transfer lines to the existing effluent treatment facility (ETF) and the liquid effluent retention facility (LERF).

  11. The Vertebrate Genome Annotation browser 10 years on.

    PubMed

    Harrow, Jennifer L; Steward, Charles A; Frankish, Adam; Gilbert, James G; Gonzalez, Jose M; Loveland, Jane E; Mudge, Jonathan; Sheppard, Dan; Thomas, Mark; Trevanion, Stephen; Wilming, Laurens G

    2014-01-01

    The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.uk), initially designed as a community resource for browsing manual annotation of the human genome project, now contains five reference genomes (human, mouse, zebrafish, pig and rat). Its introduction pages have been redesigned to enable the user to easily navigate between whole genomes and smaller multi-species haplotypic regions of interest such as the major histocompatibility complex. The VEGA browser is unique in that annotation is updated via the Human And Vertebrate Analysis aNd Annotation (HAVANA) update track every 2 weeks, allowing single gene updates to be made publicly available to the research community quickly. The user can now access different haplotypic subregions more easily, such as those from the non-obese diabetic mouse, and display them in a more intuitive way using the comparative tools. We also highlight how the user can browse manually annotated updated patches from the Genome Reference Consortium (GRC).

  12. Solar Tutorial and Annotation Resource (STAR)

    NASA Astrophysics Data System (ADS)

    Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

    2009-12-01

    We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven

  13. SNOX flue gas cleaning demonstration project: A DOE assessment

    SciTech Connect

    2000-06-01

    The goal of the US Department of Energy (DOE) Clean Coal Technology (CCT) Program is to provide the energy marketplace with a suite of advanced, cost-effective, highly efficient, and environmentally responsible coal-utilization technologies through cooperatively implementing a series of demonstration projects with industry stake holders. These projects seek to establish at scale the commercial viability of the most promising advanced coal technologies that have developed beyond the proof-of-concept stage. This document serves as DOE's post-project assessment of a project selected in CCT Round 2, SNOX{trademark} Flue Gas Cleaning Demonstration Project. DOE's participation in this project through Cooperative Agreement No. DE-FC22-90PC89655 is consistent with Public Law 100-202 as amended by Public Law 100-446. The SNOX process is a combination of catalytic processes that remove sulfur dioxide (SO{sub 2}), nitrogen oxides (NO{sub x}) and residual particulate matter (PM) from flue gas that has been pre-cleaned with particulate removal. The process generates salable sulfuric acid (H{sub 2}SO{sub 4}) meeting an industry wide standard (US Government Specification O-S-801E) from the SO{sub 2} and converts the NO{sub x} to harmless nitrogen and water vapor. The integrated design of the process enables high-pollutant-removal efficiencies, no significant waste production (only very low quantities of flue gas ash and catalyst degradation fines), and significant heat recovery potential that can be used in the commercial application of the technology to attain increased thermal efficiency of the system. The host site chosen for this CCT demonstration project was Ohio Edison's Niles Station located along the Mahoning River in Niles, Ohio, just northwest of Youngstown. There are two cyclone coal-fired, steam electricity-generating units at the plant. The performance objectives of this project were as follows: to demonstrate SO{sub 2}-removal efficiency greater than 95%; to

  14. Assessing human rights impacts in corporate development projects

    SciTech Connect

    Salcito, Kendyl; Utzinger, Jürg; Weiss, Mitchell G.; Münch, Anna K.; Singer, Burton H.; Krieger, Gary R.; Wielga, Mark

    2013-09-15

    Human rights impact assessment (HRIA) is a process for systematically identifying, predicting and responding to the potential impact on human rights of a business operation, capital project, government policy or trade agreement. Traditionally, it has been conducted as a desktop exercise to predict the effects of trade agreements and government policies on individuals and communities. In line with a growing call for multinational corporations to ensure they do not violate human rights in their activities, HRIA is increasingly incorporated into the standard suite of corporate development project impact assessments. In this context, the policy world's non-structured, desk-based approaches to HRIA are insufficient. Although a number of corporations have commissioned and conducted HRIA, no broadly accepted and validated assessment tool is currently available. The lack of standardisation has complicated efforts to evaluate the effectiveness of HRIA as a risk mitigation tool, and has caused confusion in the corporate world regarding company duties. Hence, clarification is needed. The objectives of this paper are (i) to describe an HRIA methodology, (ii) to provide a rationale for its components and design, and (iii) to illustrate implementation of HRIA using the methodology in two selected corporate development projects—a uranium mine in Malawi and a tree farm in Tanzania. We found that as a prognostic tool, HRIA could examine potential positive and negative human rights impacts and provide effective recommendations for mitigation. However, longer-term monitoring revealed that recommendations were unevenly implemented, dependent on market conditions and personnel movements. This instability in the approach to human rights suggests a need for on-going monitoring and surveillance. -- Highlights: • We developed a novel methodology for corporate human rights impact assessment. • We piloted the methodology on two corporate projects—a mine and a plantation. • Human

  15. Idaho National Engineering Laboratory Sewer System Upgrade Project. Environmental Assessment

    SciTech Connect

    Not Available

    1994-04-01

    The Department of Energy (DOE) has prepared an environmental assessment for a proposed Sewer System Upgrade Project at the Idaho National Engineering Laboratory (INEL) near Idaho Falls, Idaho. The proposed action would include activities conducted at the Central Facilities Area, Test Reactor Area, and the Containment Test Facility at the Test Area North at INEL. The proposed action would consist of replacing or remodeling the existing sewage treatment plants at the Central Facilities Area, Test Reactor Area, and Containment Test Facility. Also, a new sewage testing laboratory would be constructed at the Central Facilities Area. Finally, the proposed action would include replacing, repairing, and/or adding sewer lines in areas where needed.

  16. Assessment of battery technologies, trends and projected business climate

    SciTech Connect

    1994-08-01

    This study, sponsored by the North American Defense Industrial Base Organization (NADIBO), assesses the long term health of the North American military battery production base. The objective of the report is to discuss the following areas: Batteries and battery chemistries that military systems use today; U.S. and Canadian production capabilities relative to these chemistries; Battery technology trends and research and development programs regarding current and future military battery systems; The current and projected business climate for producers of military batteries Marketplace issues and concerns.

  17. Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

    PubMed Central

    Andorf, Carson; Dobbs, Drena; Honavar, Vasant

    2007-01-01

    Background Incorrectly annotated sequence data are becoming more commonplace as databases increasingly rely on automated techniques for annotation. Hence, there is an urgent need for computational methods for checking consistency of such annotations against independent sources of evidence and detecting potential annotation errors. We show how a machine learning approach designed to automatically predict a protein's Gene Ontology (GO) functional class can be employed to identify potential gene annotation errors. Results In a set of 211 previously annotated mouse protein kinases, we found that 201 of the GO annotations returned by AmiGO appear to be inconsistent with the UniProt functions assigned to their human counterparts. In contrast, 97% of the predicted annotations generated using a machine learning approach were consistent with the UniProt annotations of the human counterparts, as well as with available annotations for these mouse protein kinases in the Mouse Kinome database. Conclusion We conjecture that most of our predicted annotations are, therefore, correct and suggest that the machine learning approach developed here could be routinely used to detect potential errors in GO annotations generated by high-throughput gene annotation projects. Editors Note : Authors from the original publication (Okazaki et al.: Nature 2002, 420:563–73) have provided their response to Andorf et al, directly following the correspondence. PMID:17683567

  18. The GATO gene annotation tool for research laboratories.

    PubMed

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

  19. LIMB demonstration project extension and Coolside demonstration: A DOE assessment

    SciTech Connect

    National Energy Technology Laboratory

    2000-04-30

    The goal of the US Department of Energy (DOE) Clean Coal Technology (CCT) program is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have already reached the proof-of-concept stage. This document serves as a DOE post-project assessment of the CCT Round 1 project ``LIMB Demonstration Project Extension and Coolside Demonstration'', described in a report to Congress (Babcock and Wilcox 1987), a paper by DePero et al. (1992), and in a report by Goots et al. (1992). The original limestone injection multistage burner (LIMB) demonstration work was conducted by Babcock and Wilcox Company (B and W) beginning in 1984, under the sponsorship of the US Environmental Protection Agency (EPA) and the State of Ohio Coal Development Office (OCDO). In 1987, B and W and the Ohio Edison Company agreed to extend the full-scale demonstration of LIMB technology under the sponsorship of DOE through its CCT Program, and with support from OCDO and Consolidation Coal Company, now known as CONSOL. In a separate effort, CONSOL had been developing another flue gas desulfurization (FGD) technology known as the Coolside process. Both LIMB and Coolside use sorbent injection to remove SO{sub 2}. The LIMB process injects the sorbent into the furnace and the Coolside injects the sorbent into the flue gas duct. In addition, LIMB uses low-NO{sub x} burners to reduce NO{sub x} emissions; hence it is categorized as a combination SO{sub 2}/NO{sub x} control technology. To take advantage of synergism between the two processes, the CCT project was structured to incorporate demonstration of both the LIMB and Coolside processes. Coolside testing was accomplished between July 1989 and February 1990, and the LIMB Extension test program was conducted between April 1990 and August

  20. Geometry Problem Solving Ability and Tolerance Character of Students 8th Grade with Assessment Project

    NASA Astrophysics Data System (ADS)

    Masrukan; Mufidah, N. A.

    2017-04-01

    The 4K model is a learning model that is characterized by character, performance, creative and conservative. The use of a 4K model in this research is to improve the character of tolerance and Geometry problem-solving ability of students. Assessment of learning done thoroughly and during the learning process, using project assessment that includes assessment at the time of student do the project and assessment of students’ project report. The result that the ability of geometry problem solving and tolerance character of students with project assessment achieve mastery and improved by project assessment.

  1. Charting the Course toward Instructionally Sound Assessment. A Report of the Alternative Assessment Pilot Project.

    ERIC Educational Resources Information Center

    California Assessment Collaborative, San Francisco.

    The California Assessment Collaborative (CAC) was designed as a three-year effort to identify, validate, and disseminate alternatives to standardized testing throughout the state. This report highlights the results from the first year and comments on the work of 22 diverse pilot projects that serve as examples of site-based development of…

  2. Charting the Course toward Instructionally Sound Assessment. A Report of the Alternative Assessment Pilot Project.

    ERIC Educational Resources Information Center

    California Assessment Collaborative, San Francisco.

    The California Assessment Collaborative (CAC) was designed as a three-year effort to identify, validate, and disseminate alternatives to standardized testing throughout the state. This report highlights the results from the first year and comments on the work of 22 diverse pilot projects that serve as examples of site-based development of…

  3. Willow Creek Wildlife Mitigation Project. Final Environmental Assessment.

    SciTech Connect

    1995-04-01

    Today`s notice announces BPA`s proposal to fund land acquisition or acquisition of a conservation easement and a wildlife management plan to protect and enhance wildlife habitat at the Willow Creek Natural Area in Eugene, Oregon. This action would provide partial mitigation for wildlife and wildlife habitat lost by the development of Federal hydroelectric projects in the Willamette River Basin. The project is consistent with BPA`s obligations under provisions of the Pacific Northwest Electric Power Planning and Conservation Act of 1980 as outlined by the Northwest Power Planning Council`s 1994 Columbia River Basin Fish and Wildlife Program. BPA has prepared an environmental assessment (DOE/EA-1023) evaluating the proposed project. Based on the analysis in the EA, BPA has determined that the proposed action is not a major Federal action significantly affecting the quality of the human environment, within the meaning of the National Environmental Policy Act (NEPA) of 1969. Therefore, the preparation of an environmental impact statement (EIS) is not required and BPA is issuing this FONSI.

  4. The abortion assessment project--India: key findings and recommendations.

    PubMed

    Duggal, Ravi; Ramachandran, Vimala

    2004-11-01

    The Abortion Assessment Project-India, begun in August 2000, is one of the largest studies on abortion ever undertaken in India. This article synthesises the findings of the six facility surveys, two community-based surveys, eight qualitative studies, policy review and commissioned working papers that were produced as part of the project by researchers from across India. Public investment in abortion services nationally was found to be grossly inadequate. 75% of facilities were found in the private sector in the six states and were overwhelmingly perceived to give better services. Although some important changes were made in the 1971 Medical Termination of Pregnancy Act related to clinic certification and medical abortion, further changes during the second phase of the government's Reproductive and Child Health Programme are recommended, based on this research and state and national-level consultations organised by the project These include integrating abortion services into primary and community health centres, increased investment in public facilities, promoting use of vacuum aspiration and medical abortion, convincing providers to stop using curettage, broadening the base of abortion providers by training paramedics to do first trimester abortions, and reskilling traditional providers to play alternative roles that support women's access to safe abortion services.

  5. Blue Creek Winter Range : Wildlife Mitigation Project : Final Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration; United States. Bureau of Indian Affairs; Spokane Tribe of the Spokane Reservation, Washington

    1994-11-01

    Bonneville Power Administration (BPA) proposes to fund that portion of the Washington Wildlife Agreement pertaining to the Blue Creek Winter Range Wildlife Mitigation Project (Project) in a cooperative effort with the Spokane Tribe, Upper Columbia United Tribes, and the Bureau of Indian Affairs (BIA). If fully implemented, the proposed action would allow the sponsors to protect and enhance 2,631 habitat units of big game winter range and riparian shrub habitat on 2,185 hectares (5,400 acres) of Spokane Tribal trust lands, and to conduct long term wildlife management activities within the Spokane Indian Reservation project area. This Final Environmental Assessment (EA) examines the potential environmental effects of securing land and conducting wildlife habitat enhancement and long term management activities within the boundaries of the Spokane Indian Reservation. Four proposed activities (habitat protection, habitat enhancement, operation and maintenance, and monitoring and evaluation) are analyzed. The proposed action is intended to meet the need for mitigation of wildlife and wildlife habitat adversely affected by the construction of Grand Coulee Dam and its reservoir.

  6. Tiering strategic environmental assessment and project environmental impact assessment in highway planning in Sao Paulo, Brazil

    SciTech Connect

    Sanchez, Luis E. Silva-Sanchez, Solange S.

    2008-10-15

    Constructing highways in dense urban areas is always a challenge. In Sao Paulo Metropolitan Region, heavy truck traffic contributes to clog streets and expressways alike. As part of the traffic neither originates nor head to the region, a peripheral highway has been proposed to reduce traffic problems. This project, called Rodoanel, is an expressway approximately 175 km long. The fact that the projected south and north sections would cross catchments that supply most of the metropolis water demand was strongly disputed and made the environmental permitting process particularly difficult. The agency in charge commissioned a strategic environmental assessment (SEA) of a revamped project, and called it the Rodoanel Programme. However, the SEA report failed to satisfactorily take account of significant strategic issues. Among these, the highway potential effect of inducing urban sprawl over water protection zones is the most critical issue, as it emerged later as a hurdle to project licensing. Conclusion is that, particularly where no agreed-upon framework for SEA exists, when vertical tiering with downstream project EIA is sought, then a careful scoping of strategic issues is more than necessary. If an agreement on 'what is strategic' is not reached and not recognized by influential stakeholders, then the unsettled conflicts will be transferred to project EIA. In such a context, SEA will have added another loop to the usually long road to project approval.

  7. Risk assessment in submarine outfall projects: the case of Portugal.

    PubMed

    Mendonça, Ana; Losada, Miguel Ángel; Reis, Maria Teresa; Neves, Maria Graça

    2013-02-15

    Submarine outfalls need to be evaluated as part of an integrated environmental protection system for coastal areas. Although outfalls are tight with the diversity of economic activities along a densely populated coastline being effluent treatment and effluent reuse a sign of economic prosperity, precautions must be taken in the construction of these structures. They must be designed so as to have the least possible impact on the environment and at the same time be economically viable. This paper outlines the initial phases of a risk assessment procedure for submarine outfall projects. This approach includes a cost-benefit analysis in which risks are systematically minimized or eliminated. The methods used in this study also allow for randomness and uncertainty. The input for the analysis is a wide range of information and data concerning the failure probability of outfalls and the consequences of an operational stoppage or failure. As part of this risk assessment, target design levels of reliability, functionality, and operationality were defined for the outfalls. These levels were based on an inventory of risks associated with such construction projects, and thus afforded the possibility of identifying possible failure modes. This assessment procedure was then applied to four case studies in Portugal. The results obtained were the values concerning the useful life of the outfalls at the four sites and their joint probability of failure against the principal failure modes assigned to ultimate and serviceability limit states. Also defined were the minimum operationality of these outfalls, the average number of admissible technical breakdowns, and the maximum allowed duration of a stoppage mode. It was found that these values were in consonance with the nature of the effluent (tourist-related, industrial, or mixed) as well as its importance for the local economy. Even more important, this risk assessment procedure was able to measure the impact of the outfalls on

  8. TVA commercial demonstration plant project. Volume 2. Basis of study assessments and project selection. Final report

    SciTech Connect

    Not Available

    1980-11-01

    The Tennessee Valley Authority (TVA) is considering the design, construction, and operation of a commercial scale coal gasification facility to produce a clean, medium Btu fuel gas (MBG). The project includes all process and support systems required to convert approximately 20,000 tons per day of Kentucky No. 9 bituminous coal, as fed to the gasifiers, into MBG equivalent to about 300 billion Btu per day. The first phase of the proposed project involves conceptual design, environmental and siting studies and economic analyses of commercial plants emphasizing the following gasification technologies: Babcock and Wilcox entrained flow gasifier, Lurgi dry ash gasifier, BGC/Lurgi slagging gasifier, Texaco entrained flow gasifier, and Koppers Totzek entrained flow gasifier. Foster Wheeler's study and assessments/process selection is summarized in this volume.

  9. Quantification of false positives within Moon Zoo crater annotations

    NASA Astrophysics Data System (ADS)

    Tar, P.; Thacker, N.

    2014-04-01

    The Moon Zoo citizen science project [1] allows members of the public to annotate lunar images, providing researchers with a wealth of location and size information regarding the population of small craters on the Moon. To date, approximately 4 million images have been inspected. Here, we show how a quantitative pattern recognition system can be used to estimate the quantity of contamination in Moon Zoo data from erroneous annotations. The proposed method produces not only estimates of true verses false crater annotations, but also a full error covariance, with additional conformity checks, which is essential for the meaningful interpretation of measurements, e.g. for plotting error bars.

  10. Coalescence and refinement of Moon Zoo crater annotations

    NASA Astrophysics Data System (ADS)

    Tar, P.; Thacker, N.

    2014-04-01

    The Moon Zoo citizen science project [1] allows members of the public to annotate lunar images, providing researchers with a wealth of location and size information regarding the population of small craters on the Moon. To date, approximately 4 million images have been inspected. Here, we show how data from multiple users can be combined to give a consensus as to the parameters of annotated craters. The process uses annotations and image data to provide Likelihood solutions, revealing the most probable crater parameters, from which crater Size-Frequency Distributions (SFDs) might be produced.

  11. Systematic Sustainability Assessment (SSA) Tool for Hydroelectric Project in Malaysia

    NASA Astrophysics Data System (ADS)

    Turan, Faiz Mohd; Johan, Kartina

    2017-08-01

    Sustainably developed and managed hydropower has enormous potential to contribute to global sustainability goals. It is known that hydroelectricity contributing small amounts to greenhouse gas emissions and other atmospheric pollutants. However, developing the remaining hydroelectric potential offers many challenges, and public pressure and expectations on the environmental and social performance of hydroelectric tend to increase over time. This paper aims to develop Systematic Sustainability Assessment (SSA) Tool that promotes and guides more sustainable hydroelectric projects in the context of Malaysia. The proposed SSA tool which not only provide a quality and quantitative report of sustainability performance but also act as Self-Assessment Report (SAR) to provide roadmap to achieve greater level of sustainability in project management for continuous improvement. It is expected to provide a common language that allow government, civil society, financial institutions and the hydroelectric sector to talk about and evaluate sustainability issues. The advantage of SSA tool is it can be used at any stage of hydroelectric development, from the earliest planning stages right through to operation.

  12. The ENCOAL Mild Coal Gasification Project, A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2002-03-15

    This report is a post-project assessment of the ENCOAL{reg_sign} Mild Coal Gasification Project, which was selected under Round III of the U.S. Department of Energy (DOE) Clean Coal Technology (CCT) Demonstration Program. The CCT Demonstration Program is a government and industry cofunded technology development effort to demonstrate a new generation of innovative coal utilization processes in a series of commercial-scale facilities. The ENCOAL{reg_sign} Corporation, a wholly-owned subsidiary of Bluegrass Coal Development Company (formerly SMC Mining Company), which is a subsidiary of Ziegler Coal Holding Company, submitted an application to the DOE in August 1989, soliciting joint funding of the project in the third round of the CCT Program. The project was selected by DOE in December 1989, and the Cooperative Agreement (CA) was approved in September 1990. Construction, commissioning, and start-up of the ENCOAL{reg_sign} mild coal gasification facility was completed in June 1992. In October 1994, ENCOAL{reg_sign} was granted a two-year extension of the CA with the DOE, that carried through to September 17, 1996. ENCOAL{reg_sign} was then granted a six-month, no-cost extension through March 17, 1997. Overall, DOE provided 50 percent of the total project cost of $90,664,000. ENCOAL{reg_sign} operated the 1,000-ton-per-day mild gasification demonstration plant at Triton Coal Company's Buckskin Mine near Gillette, Wyoming, for over four years. The process, using Liquids From Coal (LFC{trademark}) technology originally developed by SMC Mining Company and SGI International, utilizes low-sulfur Powder River Basin (PRB) coal to produce two new fuels, Process-Derived Fuel (PDF{trademark}) and Coal-Derived Liquids (CDL{trademark}). The products, as alternative fuel sources, are capable of significantly lowering current sulfur emissions at industrial and utility boiler sites throughout the nation thus reducing pollutants causing acid rain. In support of this overall objective

  13. Promoting health literacy through the health education assessment project.

    PubMed

    Marx, Eva; Hudson, Nancy; Deal, Tami B; Pateman, Beth; Middleton, Kathleen

    2007-04-01

    The Council of Chief State School Officers' State Collaborative on Assessment and Student Standards Health Education Assessment Project (SCASS-HEAP) allows states to pool financial and human resources to develop effective ready-to-use health education assessment resources through a collaborative process. The purpose of this article is to describe the extensive ongoing development of the SCASS-HEAP and its benefits for important stakeholders in health and education. A review of the products from the first decade of the SCASS-HEAP was undertaken. The SCASS-HEAP supports a comprehensive systems approach to helping educators focus effectively on the most important skills and issues in child and adolescent health and gives health education a place at the school reform table, providing visibility and credibility and promoting the essential links between health and learning. State education agencies and school districts can use SCASS-HEAP materials for assessment and, perhaps more importantly, to help teachers modify and improve instruction at the classroom level for increased student learning.

  14. Geohazard assessment lifecycle for a natural gas pipeline project

    NASA Astrophysics Data System (ADS)

    Lekkakis, D.; Boone, M. D.; Strassburger, E.; Li, Z.; Duffy, W. P.

    2015-09-01

    the assessment, further exploration was proposed. In cases where rerouting was constrained, mitigation via structural measures was proposed. This paper further discusses the cost, schedule and resource challenges of planning and executing such a large-scale geotechnical investigation, the interfaces between the various disciplines involved during the assessment, the innovative tools employed for the field mapping, the classifications developed for mapping landslides, karst geology, and trench excavatability, determining liquefaction stretches and the process for the site localization of the Above Ground Installations (AGI). It finally discusses the objectives of the FEED study in terms of providing a route, a ± 20% project cost estimate and a schedule, and the additional engineering work foreseen to take place in the detailed engineering phase of the project.

  15. Statistical mechanics of ontology based annotations

    NASA Astrophysics Data System (ADS)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  16. Open Ocean Assessments for Management in the GEF Transboundary Waters Assessment Project (TWAP)

    NASA Astrophysics Data System (ADS)

    Fischer, A. S.; Alverson, K. D.

    2010-12-01

    A methodology for a thematic and scientifically-credible assessment of Open Ocean waters as a part of the Global Environment Facility (GEF) Transboundary Waters Assessment Project (TWAP) has been developed in the last 18 months by the Intergovernmental Oceanographic Commission of UNESCO, and is presented for feedback and comment. While developed to help the GEF International Waters focal area target investment to manage looming environmental threats in interlinked freshwater and marine systems (a very focused decision support system), the assessment methodology could contribute to other assessment and management efforts in the UN system and elsewhere. Building on a conceptual framework that describes the relationships between human systems and open ocean natural systems, and on mapping of the human impact on the marine environment, the assessment will evaluate and make projections on a thematic basis, identifying key metrics, indices, and indicators. These themes will include the threats on key ecosystem services of climate change through sea level rise, changed stratification, warming, and ocean acidification; vulnerabilities of ecosystems, habitats, and living marine resources; the impact and sustainability of fisheries; and pollution. Global-level governance arrangements will also be evaluated, with an eye to identifying scope for improved global-level management. The assessment will build on sustained ocean observing systems, model projections, and an assessment of scientific literature, as well as tools for combining knowledge to support identification of priority concerns and in developing scenarios for management. It will include an assessment of key research and observing needs as one way to deal with the scientific uncertainty inherent in such an exercise, and to better link policy and science agendas.

  17. Life Cycle Assessment of Biochar - EuroChar Project

    NASA Astrophysics Data System (ADS)

    Rack, M.; Woods, J.

    2012-04-01

    One of the most significant challenges faced by modern-day society is that of global warming. An exclusive focus on reducing the greenhouse gas (GHG) emissions will not suffice and therefore technologies capable of removing CO2 directly from the atmosphere at low or minimal cost are gaining increased attention. The production and use of biochar is an example of such an emerging mitigation strategy. However, as with any novel product, process and technology it is vital to conduct an assessment of the entire life cycle in order to determine the environmental impacts of the new concept in addition to analysing the other sustainability criteria. Life Cycle Assessment (LCA), standardized by ISO (2006a), is an example of a tool used to calculate the environmental impacts of a product or process. Imperial College London will follow the guidelines and recommendations of the ISO 14040 series (ISO 2002, ISO 2006a-b) and the International Life Cycle Data System (ILCD) Handbook (EC JRC IES, 2010a-e), and will use the SimaPro software to conduct a LCA of the biochar supply chains for the EuroChar project. EuroChar ('biochar for Carbon sequestration and large-scale removal of GHG from the atmosphere') is a project funded by the European Commission under its Seventh Framework Programme (FP7). EuroChar aims to investigate and reduce uncertainties around the impacts of, and opportunities for, biochar and, in particular, explore a possible introduction into modern agricultural systems in Europe, thereby moving closer to the determination of the true potential of biochar. EuroChar will use various feedstocks, ranging from wheat straw to olive residues and poplar, as feedstocks for biochar production and will focus on two conversion technologies, Hydrothermal Carbonization (HTC) and Thermochemical Carbonization (TC), followed by the application of the biochar in crop-growth field trials in England, France and Italy. In April 2012, the EuroChar project will be at its halfway mark and

  18. Background and Reflections on the Life Cycle Assessment Harmonization Project

    SciTech Connect

    Heath, G. A.; Mann, M. K.

    2012-04-01

    Despite the ever-growing body of life cycle assessment (LCA) literature on electricity generation technologies, inconsistent methods and assumptions hamper comparison across studies and pooling of published results. Synthesis of the body of previous research is necessary to generate robust results to assess and compare environmental performance of different energy technologies for the benefit of policy makers, managers, investors, and citizens. With funding from the U.S. Department of Energy, the National Renewable Energy Laboratory initiated the LCA Harmonization Project in an effort to rigorously leverage the numerous individual studies to develop collective insights. The goals of this project were to: (1) understand the range of published results of LCAs of electricity generation technologies, (2) reduce the variability in published results that stem from inconsistent methods and assumptions, and (3) clarify the central tendency of published estimates to make the collective results of LCAs available to decision makers in the near term. The LCA Harmonization Project's initial focus was evaluating life cycle greenhouse gas (GHG) emissions from electricity generation technologies. Six articles from this first phase of the project are presented in a special supplemental issue of the Journal of Industrial Ecology on Meta-Analysis of LCA: coal (Whitaker et al. 2012), concentrating solar power (Burkhardt et al. 2012), crystalline silicon photovoltaics (PVs) (Hsu et al. 2012), thin-film PVs (Kim et al. 2012), nuclear (Warner and Heath 2012), and wind (Dolan and Heath 2012). Harmonization is a meta-analytical approach that addresses inconsistency in methods and assumptions of previously published life cycle impact estimates. It has been applied in a rigorous manner to estimates of life cycle GHG emissions from many categories of electricity generation technologies in articles that appear in this special supplemental supplemental issue, reducing the variability and

  19. Assess the flood resilience tools integration in the landuse projects

    NASA Astrophysics Data System (ADS)

    Moulin, E.; Deroubaix, J.-F.

    2012-04-01

    Despite a severe regulation concerning the building in flooding areas, 80% of these areas are already built in the Greater Paris (Paris, Val-de-Marne, Hauts-de-Seine and Seine-Saint-Denis). The land use in flooding area is presented as one of the main solutions to solve the ongoing real estate pressure. For instance some of the industrial wastelands located along the river are currently in redevelopment and residential buildings are planned. So the landuse in the flooding areas is currently a key issue in the development of the Greater Paris area. To deal with floods there are some resilience tools, whether structural (such as perimeter barriers or building aperture barriers, etc) or non structural (such as warning systems, etc.). The technical solutions are available and most of the time efficient1. Still, we notice that these tools are not much implemented. The people; stakeholders and inhabitants, literally seems to be not interested. This papers focus on the integration of resilience tools in urban projects. Indeed one of the blockages in the implementation of an efficient flood risk prevention policy is the lack of concern of the landuse stakeholders and the inhabitants for the risk2. We conducted an important number of interviews with stakeholders involved in various urban projects and we assess, in this communication, to what extent the improvement of the resilience to floods is considered as a main issue in the execution of an urban project? How this concern is maintained or could be maintained throughout the project. Is there a dilution of this concern? In order to develop this topic we rely on a case study. The "Ardoines" is a project aiming at redeveloping an industrial site (South-East Paris), into a project including residential and office buildings and other amenities. In order to elaborate the master plan, the urban planning authority brought together some flood risk experts. According to the comments of the experts, the architect in charge of the

  20. Comparative omics-driven genome annotation refinement: application across Yersiniae.

    PubMed

    Schrimpe-Rutledge, Alexandra C; Jones, Marcus B; Chauhan, Sadhana; Purvine, Samuel O; Sanford, James A; Monroe, Matthew E; Brewer, Heather M; Payne, Samuel H; Ansong, Charles; Frank, Bryan C; Smith, Richard D; Peterson, Scott N; Motin, Vladimir L; Adkins, Joshua N

    2012-01-01

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes) protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.

  1. Solving the Problem: Genome Annotation Standards before the Data Deluge

    PubMed Central

    Klimke, William; O'Donovan, Claire; White, Owen; Brister, J. Rodney; Clark, Karen; Fedorov, Boris; Mizrachi, Ilene; Pruitt, Kim D.; Tatusova, Tatiana

    2011-01-01

    The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries. PMID:22180819

  2. Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

    PubMed Central

    2010-01-01

    Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence. PMID:21092105

  3. Results of Needs Assessments Related to Citizen Science Projects

    NASA Astrophysics Data System (ADS)

    Buxner, Sanlyn; Bracey, Georgia; Glushko, Anna; Bakerman, Maya; Gay, Pamela L.; CosmoQuest Team

    2017-01-01

    The CosmoQuest Virtual Research Facility invites the public and classrooms to participate in NASA Science Mission Directorate related research that leads to publishable results and data catalogues. One of the main goals of the project is to support professional scientists in doing science and the general public--including parents, children, teachers, and students--in learning and doing science. Through the effort, the CosmoQuest team is developing a variety of supports and opportunities to support the doing and teaching of science. To inform our efforts, we have implemented a set of needs surveys to assess the needs of our different audiences. These surveys are being used to understand the interests, motivations, resources, challenges and demographics of our growing CosmoQuest community and others interested in engaging in citizen science projects. The surveys include those for teachers, parents, adult learners, planetarium professionals, subject matter experts (SMEs), and the general public. We will share the results of these surveys and discuss the implications of the results for broader education and outreach programs.

  4. Advanced Seismic Probabilistic Risk Assessment Demonstration Project Plan

    SciTech Connect

    Coleman, Justin

    2014-09-01

    Idaho National Laboratories (INL) has an ongoing research and development (R&D) project to remove excess conservatism from seismic probabilistic risk assessments (SPRA) calculations. These risk calculations should focus on providing best estimate results, and associated insights, for evaluation and decision-making. This report presents a plan for improving our current traditional SPRA process using a seismic event recorded at a nuclear power plant site, with known outcomes, to improve the decision making process. SPRAs are intended to provide best estimates of the various combinations of structural and equipment failures that can lead to a seismic induced core damage event. However, in general this approach has been conservative, and potentially masks other important events (for instance, it was not the seismic motions that caused the Fukushima core melt events, but the tsunami ingress into the facility).

  5. Assessing soil and groundwater contamination in a metropolitan redevelopment project.

    PubMed

    Yun, Junki; Lee, Ju Young; Khim, Jeehyeong; Ji, Won Hyun

    2013-08-01

    The purpose of this study was to assess contaminated soil and groundwater for the urban redevelopment of a rapid transit railway and a new mega-shopping area. Contaminated soil and groundwater may interfere with the progress of this project, and residents and shoppers may be exposed to human health risks. The study area has been remediated after application of first remediation technologies. Of the entire area, several sites were still contaminated by waste materials and petroleum. For zinc (Zn) contamination, high Zn concentrations were detected because waste materials were disposed in the entire area. For petroleum contamination, high total petroleum hydrocarbon (TPH) and hydrocarbon degrading microbe concentrations were observed at the depth of 7 m because the underground petroleum storage tank had previously been located at this site. Correlation results suggest that TPH (soil) concentration is still related with TPH (groundwater) concentration. The relationship is taken into account in the Spearman coefficient (α).

  6. Electric G-Van demonstration and commercial assessment project

    SciTech Connect

    Braga, B.D. )

    1992-12-01

    The Electric Power Research Institute was awarded this grant to continue the joint effort initiated by EPRI, and VE International to proceed beyond the prototype phase of the electric G-Van development. The goal of EPRI and VEHMA was to develop a market for the electric G-Van, and to distribute them to commercial fleet operators. The objective of this project was to produce G-Vans in a production facility that would be comparable to the GMC Truck internal combustion engine Vandura Van produced by General Motors in quality, reliability, durability and safety. An initial market assessment/demonstration phase of sixty (60) vehicles was to be undertaken, with the ability to expand production volume quickly to meet market demands. Brief description of each task of this grant is given and the actions taken by EPRI to complete them.

  7. Agents and Data Mining in Bioinformatics: Joining Data Gathering and Automatic Annotation with Classification and Distributed Clustering

    NASA Astrophysics Data System (ADS)

    Bazzan, Ana L. C.

    Multiagent systems and data mining techniques are being frequently used in genome projects, especially regarding the annotation process (annotation pipeline). This paper discusses annotation-related problems where agent-based and/or distributed data mining has been successfully employed.

  8. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  9. Phylogenetic molecular function annotation

    NASA Astrophysics Data System (ADS)

    Engelhardt, Barbara E.; Jordan, Michael I.; Repo, Susanna T.; Brenner, Steven E.

    2009-07-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called "phylogenomics") is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

  10. Annotation: the savant syndrome.

    PubMed

    Heaton, Pamela; Wallace, Gregory L

    2004-07-01

    Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area. Traditionally, savants have been defined as intellectually impaired individuals who nevertheless display exceptional skills within specific domains. However, within the extant literature, cases of savants with developmental and other clinical disorders, but with average intellectual functioning, are increasingly reported. We thus propose that focus should diverge away from IQ scores to encompass discrepancies between functional impairments and unexpected skills. It has long been observed that savant skills are more prevalent in individuals with autism than in those with other disorders. Therefore, in this annotation we seek to explore the parameters of the savant syndrome by considering these skills within the context of neuropsychological accounts of autism. A striking finding amongst those with savant skills, but without the diagnosis of autism, is the presence of cognitive features and behavioural traits associated with the disorder. We thus conclude that autism (or autistic traits) and savant skills are inextricably linked and we should therefore look to autism in our quest to solve the puzzle of the savant syndrome. Copyright 2004 Association for Child Psychology and Psychiatry

  11. Visualizing GO Annotations.

    PubMed

    Supek, Fran; Škunca, Nives

    2017-01-01

    Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that describe gene function and that can be used to summarize the results of the genome-scale experiments. However, making sense of such GO enrichment analyses may be challenging. For instance, overrepresented GO functions in a set of differentially expressed genes are typically output as a flat list, a format not adequate to capture the complexities of the hierarchical structure of the GO annotation labels.In this chapter, we survey various methods to visualize large, difficult-to-interpret lists of GO terms. We catalog their availability-Web-based or standalone, the main principles they employ in summarizing large lists of GO terms, and the visualization styles they support. These brief commentaries on each software are intended as a helpful inventory, rather than comprehensive descriptions of the underlying algorithms. Instead, we show examples of their use and suggest that the choice of an appropriate visualization tool may be crucial to the utility of GO in biological discovery.

  12. The effectiveness of annotated (vs. non-annotated) digital pathology slides as a teaching tool during dermatology and pathology residencies.

    PubMed

    Marsch, Amanda F; Espiritu, Baltazar; Groth, John; Hutchens, Kelli A

    2014-06-01

    With today's technology, paraffin-embedded, hematoxylin & eosin-stained pathology slides can be scanned to generate high quality virtual slides. Using proprietary software, digital images can also be annotated with arrows, circles and boxes to highlight certain diagnostic features. Previous studies assessing digital microscopy as a teaching tool did not involve the annotation of digital images. The objective of this study was to compare the effectiveness of annotated digital pathology slides versus non-annotated digital pathology slides as a teaching tool during dermatology and pathology residencies. A study group composed of 31 dermatology and pathology residents was asked to complete an online pre-quiz consisting of 20 multiple choice style questions, each associated with a static digital pathology image. After completion, participants were given access to an online tutorial composed of digitally annotated pathology slides and subsequently asked to complete a post-quiz. A control group of 12 residents completed a non-annotated version of the tutorial. Nearly all participants in the study group improved their quiz score, with an average improvement of 17%, versus only 3% (P = 0.005) in the control group. These results support the notion that annotated digital pathology slides are superior to non-annotated slides for the purpose of resident education. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. 75 FR 10500 - Environmental Assessment Prepared for Proposed Cape Wind Energy Project in Nantucket Sound, MA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-08

    ... Minerals Management Service Environmental Assessment Prepared for Proposed Cape Wind Energy Project in... review and comment of an EA and Draft FONNSI prepared by MMS for the Cape Wind Energy Project proposed... Environmental Impact Statement (FEIS) for the Cape Wind Energy Project. The FEIS assessed the...

  14. The Luneburg Sustainable University Project in International Comparison: An Assessment against North American Peers

    ERIC Educational Resources Information Center

    Beringer, Almut

    2007-01-01

    Purpose: To assess the Luneburg Sustainable University Project (the Project) in a non-European international context; to relate the project scholarly approach to selected scholarly and practice-oriented North American sustainability in higher education (SHE) methods; to analyze project innovations against North American initiatives.…

  15. Assessment of projected climate change signals over central Africa based on a multitude of global and regional climate projections

    NASA Astrophysics Data System (ADS)

    Hänsler, Andreas; Saeed, Fahad; Jacob, Daniela

    2013-04-01

    It is well accepted within the scientific community that only a large ensemble of different projections will allow achieving robust climate change information for a specific region. In the framework of the project "Climate changes scenarios for the Congo basin" (funded by the German Ministry for Environment, Nature Conservation and Nuclear Safety) a regional climate change assessment is conducted by the Climate Service Center (CSC) over the greater Congo basin region. The analysis is based on a state-of-the-art multi-model multi-scenario ensemble of global and regional climate change projections. In this ensemble the results of several GCM projections from the CMIP3 and the CMIP5 projects are combined with some of the recently downscaled regional CORDEX-Africa projections. Altogether data from 77 different climate change projections are analysed; separated into 31 projections for a "high" and 46 for a "low" emission scenario. In the study several parameters and indices related to temperature and precipitation are considered for the assessment of projected climate change. The large size of the analyzed ensemble is expected to be useful for not only quantifying the magnitude of projected changes, but also to analyze their robustness as well. Moreover, potential differences between projected changes from GCMs and RCMs can also be analysed.

  16. Assessment of projected climate change signals over central Africa based on a multitude of global and regional climate projections

    NASA Astrophysics Data System (ADS)

    Haensler, A.; Saeed, F.; Jacob, D.

    2013-05-01

    It is well accepted within the scientific community that only a large ensemble of different projections will allow achieving robust climate change information for a specific region. In the framework of the project "Climate changes scenarios for the Congo basin" (funded by the German Ministry for Environment, Nature Conservation and Nuclear Safety) a regional climate change assessment is conducted by the Climate Service Center (CSC) over the greater Congo basin region. The analysis is based on a state-of-the-art multi-model multi-scenario ensemble of global and regional climate change projections. In this ensemble the results of several GCM projections from the CMIP3 and the CMIP5 projects are combined with some of the recently downscaled regional CORDEX-Africa projections. Altogether data from 77 different climate change projections are analysed; separated into 31 projections for a "high" and 46 for a "low" emission scenario. In the study several parameters and indices related to temperature and precipitation are considered for the assessment of projected climate change. The large size of the analyzed ensemble is expected to be useful for not only quantifying the magnitude of projected changes, but also to analyze their robustness as well. Moreover, potential differences between projected changes from GCMs and RCMs can also be analysed.

  17. Considerations to improve functional annotations in biological databases.

    PubMed

    Benítez-Páez, Alfonso

    2009-12-01

    Despite the great effort to design efficient systems allowing the electronic indexation of information concerning genes, proteins, structures, and interactions published daily in scientific journals, some problems are still observed in specific tasks such as functional annotation. The annotation of function is a critical issue for bioinformatic routines, such as for instance, in functional genomics and the further prediction of unknown protein function, which are highly dependent of the quality of existing annotations. Some information management systems evolve to efficiently incorporate information from large-scale projects, but often, annotation of single records from the literature is difficult and slow. In this short report, functional characterizations of a representative sample of the entire set of uncharacterized proteins from Escherichia coli K12 was compiled from Swiss-Prot, PubMed, and EcoCyc and demonstrate a functional annotation deficit in biological databases. Some issues are postulated as causes of the lack of annotation, and different solutions are evaluated and proposed to avoid them. The hope is that as a consequence of these observations, there will be new impetus to improve the speed and quality of functional annotation and ultimately provide updated, reliable information to the scientific community.

  18. Genix: a new online automated pipeline for bacterial genome annotation.

    PubMed

    Kremer, Frederico Schmitt; Eslabão, Marcus Redü; Dellagostin, Odir Antônio; Pinto, Luciano da Silva

    2016-12-01

    Next-generation sequencing has significantly reduced the cost of genome-sequencing projects, resulting in an expressive increase in the availability of genomic data in public databases. The cheaper and easier is to sequence new genomes, the more accurate the annotation steps have to be to avoid both the loss of information and the accumulation of erroneous features that may affect the accuracy of further analysis. In the case of bacteria genomes, a range of web annotation software has been developed; however, many applications have yet to incorporate the steps required to improve their result, including the removal of false-positive/spurious and a more complete identification of non-coding features. We present Genix, a new web-based bacterial genome annotation pipeline. A comparison of the results generated by Genix for four reference genomes against those generated by other annotation tools indicated that our pipeline is able to provide results that are closer to the reference genome annotation, with a smaller amount of false-positive proteins and missing functional annotated proteins. Additionally, the metrics obtained by Genix were slightly better than those obtained by Prokka, a state-of-art standalone annotation system. Our results indicate that Genix is a useful tool that is able to provide a more refined result, and may be a user-friendly way to obtain high-quality results.

  19. Widowed Persons Service: Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Bressler, Dawn, Comp.; And Others

    This document presents an annotated bibliography of books and articles on topics relevant to widowhood. These annotations are included: (1) 21 annotations on the grief process; (2) 11 annotations on personal observations about widowhood; (3) 16 annotations on practical problems surrounding widowhood, including legal and financial problems and job…

  20. The Community Research Scholars Initiative: A Mid‐Project Assessment

    PubMed Central

    Pike, Earl; Sehgal, Ashwini R.; Fischer, Robert L.; Collins, Cyleste

    2015-01-01

    Abstract Community organizations addressing health and human service needs generally have minimal capacity for research and evaluation. As a result, they are often inadequately equipped to independently carry out activities that can be critical for their own success, such as conducting needs assessments, identifying best practices, and evaluating outcomes. Moreover, they are unable to develop equitable partnerships with academic researchers to conduct community‐based research. This paper reports on the progress of the Community Research Scholar Initiative (CRSI), a program that aims to enhance community research and evaluation capacity through training of selected employees from Greater Cleveland community organizations. The intensive 2‐year CRSI program includes didactic instruction, fieldwork, multiple levels of community and academic engagement, leadership training, and a mentored research project. The first cohort of CRSI Scholars, their community organizations, and other community stakeholders have incorporated program lessons into their practices and operations. The CRSI program evaluation indicates: the importance of careful Scholar selection; the need to engage executive leadership from Scholar organizations; the value of a curriculum integrating classwork, fieldwork, and community engagement; and the need for continual scholar skill and knowledge assessment. These findings and lessons learned guide other efforts to enhance community organization research and evaluation capacity. PMID:26073663

  1. Environmental assessment: Kotzebue Wind Installation Project, Kotzebue, Alaska

    SciTech Connect

    1998-05-01

    The DOE is proposing to provide financial assistance to the Kotzebue Electric Association to expand its existing wind installation near Kotzebue, Alaska. Like many rural Alaska towns, Kotzebue uses diesel-powered generators to produce its electricity, the high cost of which is currently subsidized by the Alaska State government. In an effort to provide a cost effective and clean source of electricity, reduce dependence on diesel fuel, and reduce air pollutants, the DOE is proposing to fund an experimental wind installation to test commercially available wind turbines under Arctic conditions. The results would provide valuable information to other Alaska communities experiencing similar dependence on diesel-powered generators. The environmental assessment for the proposed wind installation assessed impacts to biological resources, land use, electromagnetic interference, coastal zone, air quality, cultural resources, and noise. It was determined that the project does not constitute a major Federal action significantly affecting the quality of the human environment. Therefore, the preparation of an environmental impact statement is not required, and DOE has issued a Finding of No Significant Impact.

  2. The SKI repository performance assessment project Site-94

    SciTech Connect

    Andersson, J.; Dverstorp, B.; Sjoeblom, R.; Wingefors, S.

    1995-12-01

    SITE-94 is a research project conducted as a performance assessment of a hypothetical repository for spent nuclear fuel, but with real pre-excavation data from a real site. The geosphere, the engineered barriers and the processes for radionuclide release and transport comprise an integrated interdependent system, which is described by an influence diagram (PID) that reflects how different Features, Events or Processes (FEPs) inside the system interact. Site evaluation is used to determine information of transport paths in the geosphere and to deliver information on geosphere interaction with the engineered barriers. A three-dimensional geological structure model of the site as well as alternative conceptual models consistent with the existing hydrological field data, have been analyzed. Groundwater chemistry is evaluated and a model, fairly consistent with the flow model, for the origin of the different waters has been developed. The geological structure model is also used for analyzing the mechanical stability of the site. Several phenomena of relevance for copper corrosion in a repository environment have been investigated. For Reference Case conditions and regardless of flow variability, output is dominated by I-129, which, for a single canister, may give rise to drinking water well doses in the order of 10{sup -6}Sv/yr. Finally, it appears that the procedures involved in the development of influence diagrams may be a promising tool for quality assurance of performance assessments.

  3. NREL Solar Radiation Resource Assessment Project: Status and outlook

    SciTech Connect

    Renne, D.; Riordan, C.; Maxwell, E.; Stoffel, T.; Marion, B.; Rymes, M.; Wilcox, S.; Myers, D.

    1992-05-01

    This report summarizes the activities and accomplishments of NREL's Solar Radiation Resource Assessment Project during fiscal year 1991. Currently, the primary focus of the SRRAP is to produce a 1961--1990 National Solar Radiation Data Base, providing hourly values of global horizontal, diffuse, and direct normal solar radiation at approximately 250 sites around the United States. Because these solar radiation quantities have been measured intermittently at only about 50 of these sites, models were developed and applied to the majority of the stations to provide estimates of these parameters. Although approximately 93% of the data base consists of modeled data this represents a significant improvement over the SOLMET/ERSATZ 1952--1975 data base. The magnitude and importance of this activity are such that the majority of SRRAP human and financial in many other activities, which are reported here. These include the continued maintenance of a solar radiation monitoring network in the southeast United States at six Historically Black Colleges and Universities (HBCU's), the transfer of solar radiation resource assessment technology through a variety of activities, participation in international programs, and the maintenance and operation of NREL's Solar Radiation Research Laboratory. 17 refs.

  4. Rubrics, Portfolios, and Tests, Oh My! Assessing Understanding in Project-Based Learning.

    ERIC Educational Resources Information Center

    McGrath, Diane

    2003-01-01

    Presents an overview of features central to conducting assessment in project-based learning (PBL). Focuses on critical assessment issues and discusses multiple assessments; assessment as a learning activity; student involvement in setting standards for assessment; and outside assessment of the final artifact. Describes technological tools that can…

  5. WEGO: a web tool for plotting GO annotations

    PubMed Central

    Ye, Jia; Fang, Lin; Zheng, Hongkun; Zhang, Yong; Chen, Jie; Zhang, Zengjin; Wang, Jing; Li, Shengting; Li, Ruiqiang; Bolund, Lars; Wang, Jun

    2006-01-01

    Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at . There are two available mirror sites at and . Any suggestions are welcome at wego@genomics.org.cn. PMID:16845012

  6. Environmental Assessment: geothermal direct heat project, Marlin, Texas

    SciTech Connect

    Not Available

    1980-08-01

    The Federal action addressed by this Environmental Assessment (EA) is joint funding the retrofitting of a heating and hot water system in a hospital at Marlin, Texas, with a geothermal preheat system. The project will be located within the existing hospital boiler room. One supply well was drilled in an existing adjacent parking lot. It was necessary to drill the well prior to completion of this environmental assessment in order to confirm the reservoir and to obtain fluids for analysis in order to assess the environmental effects of fluid disposal. Fluid from operation will be disposed of by discharging it directly into existing street drains, which will carry the fluid to Park Lake and eventually the Brazos River. Fluid disposal activities are regulated by the Texas Railroad Commission. The local geology is determined by past displacements in the East Texas Basin. Boundaries are marked by the Balcones and the Mexia-Talco fault systems. All important water-bearing formations are in the cretaceous sedimentary rocks and are slightly to highly saline. Geothermal fluids are produced from the Trinity Group; they range from approximately 3600 to 4000 ppM TDS. Temperatures are expected to be above 64/sup 0/C (147/sup 0/F). Surface water flows southeastward as a part of the Brazos River Basin. The nearest perennial stream is the Brazos River 5.6 km (3.5 miles) away, to which surface fluids will eventually discharge. Environmental impacts of construction were small because of the existing structures and paved areas. Construction run-off and geothermal flow-test fluid passed through a small pond in the city park, lowering its water quality, at least temporarily. Construction noise was not out of character with existing noises around the hospital.

  7. Environmental assessment of USAID housing projects in the Russian Federation

    SciTech Connect

    Loran, B.; Miller, C.

    1995-12-01

    Parsons was selected by the United States Agency for International Development (USAID) as the general contractor for construction management for the construction of 2,500 housing units within the Russian Federation. These housing units, to be occupied by Russian officers returning from the Baltic States, are under construction on 15 sites, selected from an initial list of 200, based on habitability, capability of successful final construction. Cost meeting USAID guidelines, and impacts on the environment. USAID fulfilled NEPA requirements by preparing, with assistance of Parsons Engineering Science, a Programmatic Environmental Assessment and 15 site specific Environmental Assessments for the project. The sites were scattered over the entire Russian Federation west of the Ural Mountains. The site offerors completed an environmental checklist covering a broad range of possible impacts. Significant environmental issues and concerns were further identified during scoping meetings held at the site locations. The most important issues discussed were: soil contamination; gaseous, liquid, and solid pollutants to which the site may be exposed; incompatible adjacent land uses; ready access to utilities and social services; and socioeconomic situation favorable to resettlement of Russian military officers. No major environmental issues or concerns were identified for the 15 selected sites. Certificates indicating the absence of chemical and radiological surface and subsurface contamination at the proposed sites were provided by the local environmental officers. Polynuclear aromatic hydrocarbons were found present at one of the sites considered in a preliminary selection, and later rejected due to the failure of contractual negotiations. The environmental assessments included mitigation and monitoring measures for construction and operation (occupancy) impacts.

  8. An Annotated Bibliography on Children.

    ERIC Educational Resources Information Center

    Bureau of Libraries and Educational Technology (DHEW/OE), Washington, DC.

    This annotated bibliography is a highly selective list of materials published in the last five years on the major problems, trends, methodologies and achievements in the field of child development. It contains annotated references to approximately 500 books, periodicals, technical reports, government documents, legislative materials, professional…

  9. Drug Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mathieson, Moira B.

    This bibliography consists of a total of 215 entries dealing with drug education, including curriculum guides, and drawn from documents in the ERIC system. There are two sections, the first containing 130 annotated citations of documents and journal articles, and the second containing 85 citations of journal articles without annotations, but with…

  10. Managing and Querying Image Annotation and Markup in XML.

    PubMed

    Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

    2010-01-01

    Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

  11. Managing and Querying Image Annotation and Markup in XML

    PubMed Central

    Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

    2010-01-01

    Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

  12. Gene ontology annotation by density and gravitation models.

    PubMed

    Hou, Wen-Juan; Lin, Kevin Hsin-Yih; Chen, Hsin-Hsi

    2006-01-01

    Gene Ontology (GO) is developed to provide standard vocabularies of gene products in different databases. The process of annotating GO terms to genes requires curators to read through lengthy articles. Methods for speeding up or automating the annotation process are thus of great importance. We propose a GO annotation approach using full-text biomedical documents for directing more relevant papers to curators. This system explores word density and gravitation relationships between genes and GO terms. Different density and gravitation models are built and several evaluation criteria are employed to assess the effects of the proposed methods.

  13. How to scientifically assess a restoration project: a case study

    NASA Astrophysics Data System (ADS)

    Alvarez de Buergo, M.; Fort, R.; Freire, D. M.; Lopez-Arce, P.; Vazquez-Calvo, C.

    2012-04-01

    Commonly, it is said that there is lack of communication among scientists, conservators, restorers, project managers and architects. But sometimes this communication flows, and we can find enormous benefits from and for all the participating agents. This is the case we present in this work, in which technical agents in charge of the restoration of a building, asked for some scientific advice to perform the restoration of a heritage building. The results were successful and fantastic for both of them, in terms of one part asking for consultation and the other answering to the demands and resolving real problems. This is the case of a marvellous Renaissance building (Medinaceli Dukes palace, 15th-16th centuries) in the central area of Spain (Cogolludo, Guadalajara). Focused on the restoration project, we were asked for consultancy on how to solve matters like the assessment of the already fixed in project cleaning method for the stone façades, the efficacy and durability methods for some conservation products to be applied, the presence or not of a patina on the stone; the viability of using some restoration mortars, and the origin of some efflorescences that came out just after placed in the building a restoration rendering mortar. Responses to these matters were answered by performing tests both in the lab and on site in the building. The efficiency and effects on stone of the blasting cleaning method was assessed by first analysing the nature and thickness of the surface deposits to be removed (SEM-EDS analyses); secondly, roughness and colour measurements were performed, and thirdly, SEM-EDS analyses were carried out again to determine whether the cleaning method was able to remove part of the surface deposits, completely, or even part of the stone substrate. Some conservation products were tested on stone specimens, both their efficacy and their durability, concluding that it was better not to apply any of them. A patina was found on the stone façade under SEM

  14. Documentation assessment, Project C-018H, 200-E area effluent treatment facility

    SciTech Connect

    Peres, M.W.; Connor, M.D.; Mertelendy, J.I.

    1994-12-21

    Project C-018H is one of the fourteen subprojects to the Hanford Environmental Compliance (HEC) Project. Project C-018H provides treatment and disposal for the 242-A Evaporator and PUREX plant process condensate waste streams. This project used the Integrated Management Team (IMT) approach proposed by RL. The IMT approach included all affected organizations on the project team to coordinate and execute all required project tasks, while striving to integrate and satisfy all technical, operational, functional, and organizational objectives. The HEC Projects were initiated in 1989. Project C-018H began in early 1990, with completion of construction currently targeted for mid-1995. This assessment was performed to evaluate the effectiveness of the management control on design documents and quality assurance records developed and submitted for processing, use, and retention for the Project. The assessment focused primarily on the overall adequacy and quality of the design documentation currently being submitted to the project document control function.

  15. Genomic Data and Annotation from the SEED

    DOE Data Explorer

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  16. Health Impact Assessment of Indira Sagar Project: a paramount to studies on Water Development Projects.

    PubMed

    Anushrita; Nagpal, B N; Kapoor, Neera; Srivastava, Aruna; Saxena, Rekha; Singh, Shailendra; Gupta, Sanjeev; Singh, Sompal; Vikram, Kumar; Valecha, Neena

    2017-01-26

    Very limited studies on Health Impact Assessment (HIA) of Water Development Projects (WDP) in relation to mosquito-borne diseases have been carried out in India. The current study focuses on using HIA as a tool for finding impact of Indira Sagar Project, Madhya Pradesh on human health in relation to mosquito borne diseases, and emphasizing its incorporation as an integral part of any WDP. Screening, scoping, assessment, recommendation, reporting, and evaluation were carried out in selected study areas. Entomological, epidemiological, socio-economic and knowledge, attitudes and practices data related to malaria transmission in three dam components: Submergence (SUB), Command (CMD) and Resettlement and Rehabilitation (RR) colonies were generated for the period of January 2013-December 2014. Statistical analysis was attempted to compare data among dam components and to identify risk factors. Component-specific mitigation measures were suggested based on observations. Anopheles culicifacies was the dominating species in all three dam components and its man-hour density in CMD areas was higher compared to SUB and RR. The odds of finding a positive malaria case was much higher in CMD compared to SUB (OR 1.24, CI 95% 0.71-2.43) and RR (OR 5.48, CI 95% 0.73-40.63). Respondents of CMD stated more previous episodes of malaria (81.8%) compared to RR (61.4%) and SUB (55.7%). The canonical discriminant analysis concluded that distance from reservoir/Indira Sagar canal had the highest discriminating ability of malaria cases in different components followed by treatment-seeking behaviour and malaria history. The analysis identified these risk factors with 70% accuracy. Engineering manipulations may be carried out in CMD areas to control seepage and RR colonies should be established beyond 3 km from reservoir/Indira Sagar canal considering the flight range of A. culicifacies. Strengthening of surveillance with early detection and complete treatment was recommended for CMD areas

  17. California Groundwater Ambient Monitoring and Assessment (GAMA) Program Priority Basin Project--shallow aquifer assessment

    USGS Publications Warehouse

    ,

    2013-01-01

    The California State Water Resources Control Board’s (SWRCB) GAMA Program is a comprehensive assessment of statewide groundwater quality in California. From 2004 to 2012, the GAMA Program’s Priority Basin Project focused on assessing groundwater resources used for public drinking-water supplies. More than 2,000 public-supply wells were sampled by U.S. Geological Survey (USGS) for this effort. Starting in 2012, the GAMA Priority Basin Project began an assessment of water resources in shallow aquifers in California. These shallow aquifers provide water for domestic and small community-supply wells, which are often drilled to shallower depths in the groundwater system than public-supply wells. Shallow aquifers are of interest because shallow groundwater may respond more quickly and be more susceptible to contamination from human activities at the land surface, than the deeper aquifers. The SWRCB’s GAMA Program was developed in response to the Groundwater Quality Monitoring Act of 2001 (Water Code sections 10780-10782.3): a public mandate to assess and monitor the quality of groundwater resources used for drinking-water supplies, and to increase the availability of information about groundwater quality to the public. The U.S. Geological Survey is the technical lead of the Priority Basin Project. Stewardship of California’s groundwater resources is a responsibility shared between well owners, communities, and the State. Participants and collaborators in the GAMA Program include Regional Water Quality Control Boards, Department of Water Resources, Department of Public Health, local and regional groundwater management entities, county and local water agencies, community groups, and private citizens. Well-owner participation in the GAMA Program is entirely voluntary.

  18. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

    PubMed Central

    Livstone, Michael S.; Lewis, Suzanna E.; Thomas, Paul D.

    2011-01-01

    The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods. PMID:21873635

  19. A guide to best practices for Gene Ontology (GO) manual annotation

    PubMed Central

    Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

    2013-01-01

    The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all. Database URL: http://www.geneontology.org PMID:23842463

  20. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

    PubMed

    Gaudet, Pascale; Livstone, Michael S; Lewis, Suzanna E; Thomas, Paul D

    2011-09-01

    The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.

  1. Overview of the Texas Source Water Assessment Project

    USGS Publications Warehouse

    Ulery, Randy L.

    2000-01-01

    The 1996 Amendments to the Safe Drinking Water Act require, for the first time, that each state prepare a source water assessment for all PWS. Previously, Federal regulations focused on sampling and enforcement with emphasis on the quality of delivered water. These Amendments emphasize the importance of protecting the source water. States are required to determine the drinking-water source, the origin of contaminants monitored or the potential contaminants to be monitored, and the intrinsic susceptibility of the source water. Under the amendments to the Act, States must create SWAP Programs. The programs must include an individual source water assessment for each public water system regulated by the State. These assessments will determine whether an individual drinking water source is susceptible to contamination. During 1997?99, TNRCC and USGS staff met as subject-matter working groups to develop an approach to conducting Source Water Susceptibility Assessments (SWSA) and a draft workplan. The draft workplan was then presented to and reviewed by various stakeholder and technical advisory groups. Comments and suggestions from these groups were considered, and a final workplan was produced and presented to the EPA. After EPA approval, work formally began on the Texas SWAP Project. The project has an expected completion date of September 2002. At that time, initial SWSA of all Texas public water supplies should be complete. Ground-water supplies can be considered susceptible if a possible source of contamination (PSOC) exists in the contributing area for the public-supply well field or spring, the contaminant travel time to the well field or spring is short, and the soil zone, vadose zone, and aquifer-matrix materials are unlikely to adequately attenuate the contaminants associated with the PSOC. In addition, particular types of land use/cover within the contributing area may cause the supply to be deemed more susceptible to contamination. Finally, detection of

  2. The discrepancies in the results of bioinformatics tools for genomic structural annotation

    NASA Astrophysics Data System (ADS)

    Pawełkowicz, Magdalena; Nowak, Robert; Osipowski, Paweł; Rymuszka, Jacek; Świerkula, Katarzyna; Wojcieszek, Michał; Przybecki, Zbigniew

    2014-11-01

    A major focus of sequencing project is to identify genes in genomes. However it is necessary to define the variety of genes and the criteria for identifying them. In this work we present discrepancies and dependencies from the application of different bioinformatic programs for structural annotation performed on the cucumber data set from Polish Consortium of Cucumber Genome Sequencing. We use Fgenesh, GenScan and GeneMark to automated structural annotation, the results have been compared to reference annotation.

  3. Pulsed Photonuclear Assessment (PPA) Technique: CY-05 Project Summary Report

    SciTech Connect

    J.L. Jones; B.D. Bennett; K.J. Haskell; J.T. Johnson; D.R. Norman; J.W. Sterbentz; R.W. Watson; S.M. Watson; W.Y. Yoon; J.M. Zabriskie; C.E. Moss; K.L. Folkman; C.C. O'Neil; A.W. Hunt; R.J. Spaulding

    2005-12-01

    Idaho National Laboratory, along with Idaho State University’s Idaho Accelerator Center and Los Alamos National Laboratory, is developing an electron accelerator-based, photonuclear inspection technology, called the Pulsed Photonuclear Assessment (PPA) system, for the detection of nuclear material concealed within air-, rail-, and, primarily, maritime-cargo transportation containers. This report summarizes the advances and progress of the system’s development in 2005. The contents of this report include an overview of the prototype inspection system, selected Receiver-Operator-Characteristic curves for system detection performance characterization, a description of the approach used to integrate the three major detection components of the PPA inspection system, highlights of the gray-scale density mapping technique being used for significant shield material detection, and higher electron beam energy detection results to support an evaluation for an optimal interrogating beam energy. This project is supported by the Department of Homeland Security Office of Research and Development and, more recently, the Domestic Nuclear Detection Office.

  4. Human Variome Project Quality Assessment Criteria for Variation Databases.

    PubMed

    Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

    2016-06-01

    Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

  5. Designing of an environmental assessment algorithm for surface mining projects.

    PubMed

    Mirmohammadi, Mirsaleh; Gholamnejad, Javad; Fattahpour, Vahidoddin; Seyedsadri, Pejman; Ghorbani, Yousef

    2009-06-01

    This paper depicts the method used to quantify the environmental impact of mining activities in surface mine projects. The affected environment was broken down into thirteen components, such as Human health and immunity, Surface water, Air quality, etc. The effect of twenty impacting factors from the mining and milling activities was then calculated for each Environmental Component. Environmental assessments are often performed by using matrix methods in which one dimension of the matrix is the "Impacting Factor" and the other one is the "Environmental Components". For the presented matrix method, each Impacting Factor was first given a magnitude between -10 and 10. These factors are used to set up a matrix named Impacting Factor Matrix, whose elements represent the Impacting Factor values. The effects of each Impacting Factor on each Environmental Component were then quantified by multiplying the Impacting Factor Matrix by Weighting Factor Matrix. The elements of the weighting factors matrix reflect the effects of each Impacting Factor on each Environmental Component. The outlined method was originally developed for a mining and milling operation in Iran, but it can successfully be used for mining ventures and more general industrial activities in other countries in accordance to their environmental regulations and laws.

  6. Draft environmental assessment -- Test Area North pool stabilization project update

    SciTech Connect

    1997-06-01

    The purpose of this Environmental Assessment (EA) is to update the ``Test Area North Pool Stabilization Project`` EA (DOE/EA-1050) and finding of no significant impact (FONSI) issued May 6, 1996. This update analyzes the environmental and health impacts of a drying process for the Three Mile Island (TMI) nuclear reactor core debris canisters now stored underwater in a facility on the Idaho National Engineering and Environmental Laboratory (INEEL). A drying process was analyzed in the predecision versions of the EA released in 1995 but that particular process was determined to be ineffective and dropped form the Ea/FONSI issued May 6, 1996. The origin and nature of the TMI core debris and the proposed drying process are described and analyzed in detail in this EA. As did the 1996 EA, this update analyzes the environmental and health impacts of removing various radioactive materials from underwater storage, dewatering these materials, constructing a new interim dry storage facility, and transporting and placing the materials into the new facility. Also, as did the 1996 EA, this EA analyzes the removal, treatment and disposal of water from the pool, and placement of the facility into a safe, standby condition. The entire action would take place within the boundaries of the INEEL. The materials are currently stored underwater in the Test Area North (TAN) building 607 pool, the new interim dry storage facility would be constructed at the Idaho Chemical Processing Plant (ICPP) which is about 25 miles south of TAN.

  7. Environmental Assessment -- Test Area North pool stabilization project update

    SciTech Connect

    1997-08-01

    The purpose of this Environmental Assessment (EA) is to update the ``Test Area North Pool Stabilization Project`` EA (DOE/EA-1050) and finding of no significant impact (FONSI) issued May 6, 1996. This update analyzes the environmental and health impacts of a drying process for the Three Mile Island (TMI) nuclear reactor core debris canisters now stored underwater in a facility on the Idaho National Engineering and Environmental Laboratory (INEEL). A drying process was analyzed in the predecision versions of the EA released in 1995 but that particular process was determined to be ineffective and dropped from the EA/FONSI issued May 6, 1996. A new drying process was subsequently developed and is analyzed in Section 2.1.2 of this document. As did the 1996 EA, this update analyzes the environmental and health impacts of removing various radioactive materials from underwater storage, dewatering these materials, constructing a new interim dry storage facility, and transporting and placing the materials into the new facility. Also, as did the 1996 EA, this EA analyzes the removal, treatment and disposal of water from the pool, and placement of the facility into a safe, standby condition. The entire action would take place within the boundaries of the INEEL. The materials are currently stored underwater in the Test Area North (TAN) building 607 pool, the new interim dry storage facility would be constructed at the Idaho Chemical Processing Plant (ICPP) which is about 25 miles south of TAN.

  8. Jannovar: a java library for exome annotation.

    PubMed

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

  9. Gene Ontology annotations and resources.

    PubMed

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

  10. Assessing corporate project impacts in changeable contexts: A human rights perspective

    SciTech Connect

    Salcito, Kendyl; Singer, Burton H.; Krieger, Gary R.; Weiss, Mitchell G.; Wielga, Mark; Utzinger, Jürg

    2014-07-01

    Project-level impact assessment was originally conceived as a snapshot taken in advance of project implementation, contrasting current conditions with a likely future scenario involving a variety of predicted impacts. Current best practice guidance has encouraged a shift towards longitudinal assessments from the pre-project stage through the implementation and operating phases. Experience and study show, however, that assessment of infrastructure-intensive projects rarely endures past the project's construction phase. Negative consequences for environmental, social and health outcomes have been documented. Such consequences clarify the pressing need for longitudinal assessment in each of these domains, with human rights impact assessment (HRIA) as an umbrella over, and critical augmentation of, environmental, social and health assessments. Project impacts on human rights are more closely linked to political, economic and other factors beyond immediate effects of a company's policy and action throughout the project lifecycle. Delineating these processes requires an adequate framework, with strategies for collecting longitudinal data, protocols that provide core information for impact assessment and guidance for adaptive mitigation strategies as project-related effects change over time. This article presents general principles for the design and implementation of sustained, longitudinal HRIA, based on experience assessing and responding to human rights impact in a uranium mining project in Malawi. The case study demonstrates the value of longitudinal assessment both for limiting corporate risk and improving human welfare. - Graphical abstract: Assessing changes in human rights condition as affected by both project and context, over time. - Highlights: • Corporate capital projects affect human rights in myriad ways. • Ongoing, longitudinal impact assessment techniques are needed. • We present an approach for conducting longitudinal human rights impact assessment

  11. Evaluating Translational Correspondence Using Annotation Projection

    DTIC Science & Technology

    2003-02-01

    their rep- resentation of monolingual relationships than their predecessors ((Wu, 1995; Alshawi et al., 2000; Yamada and Knight, 2001); cf. (Brown et al...1990; Brown et al., 1993)). Using richer monolingual representations in statistical MT raises the challenge of how to characterize the cross-language...relationship be- tween two sets of monolingual syntactic rela- tions. In this paper, we investigate a character- ization that often appears

  12. DOE Hydropower Program biennial report 1990--1991 (with updated annotated bibliography)

    SciTech Connect

    Chappell, J.R.; Rinehart, B.N.; Sommers, G.L. ); Sale, M.J. )

    1991-07-01

    This report summarizes the activities of the US Department of Energy's (DOE) Hydropower Program for fiscal years 1990 and 1991, and provides an annotated bibliography of research, engineering, operations, regulations, and costs of projects pertinent to hydropower development. The Hydropower Program is organized as follows: background (including Technology Development and Engineering Research and Development); Resource Assessment; National Energy Strategy; Technology Transfer; Environmental Research; and, the bibliography discusses reports written by both private and non-Federal Government sectors. Most reports are available from the National Technical Information Service. 5 figs., 2 tabs.

  13. GLANET: genomic loci annotation and enrichment tool.

    PubMed

    Otlu, Burçak; Firtina, Can; Keles, Sündüz; Tastan, Oznur

    2017-09-15

    Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET . Tutorials are provided at https://glanet.readthedocs.org . burcak@ceng.metu.edu.tr or oznur.tastan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online.

  14. Metagenomic gene annotation by a homology-independent approach

    SciTech Connect

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  15. AutoFACT: An Automatic Functional Annotation and Classification Tool

    PubMed Central

    Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

    2005-01-01

    Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857

  16. MIPS: analysis and annotation of genome information in 2007.

    PubMed

    Mewes, H W; Dietmann, S; Frishman, D; Gregory, R; Mannhaupt, G; Mayer, K F X; Münsterkötter, M; Ruepp, A; Spannagl, M; Stümpflen, V; Rattei, T

    2008-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

  17. Environmental assessment -- Proposed neutrino beams at the Main Injector project

    SciTech Connect

    1997-12-01

    The US Department of Energy (DOE) proposes to build a beamline on the Fermi National Accelerator Laboratory (Fermilab) site to accommodate an experimental research program in neutrino physics. The proposed action, called Neutrino Beams at the Main Injector (NuMI), is to design, construct, operate and decommission a facility for producing and studying a high flux beam of neutrinos in the energy range of 1 to 40 GeV (1 GeV is one billion or 10{sup 9} electron volts). The proposed facility would initially be dedicated to two experiments, COSMOS (Cosmologically Significant Mass Oscillations) and MINOS (Main Injector Neutrino Oscillation Search). The neutrino beam would pass underground from Fermilab to northern Minnesota. A tunnel would not be built in this intervening region because the neutrinos easily pass through the earth, not interacting, similar to the way that light passes through a pane of glass. The beam is pointed towards the MINOS detector in the Soudan Underground Laboratory in Minnesota. Thus, the proposed project also includes construction, operation and decommissioning of the facility located in the Soudan Underground Laboratory in Minnesota that houses this MINOS detector. This environmental assessment (EA) has been prepared by the US Department of Energy (DOE) in accordance with the DOE`s National Environmental Policy Act (NEPA) Implementing Procedures (10 CFR 1021). This EA documents DOE`s evaluation of potential environmental impacts associated with the proposed construction and operation of NuMI at Fermilab and its far detector facility located in the Soudan Underground Laboratory in Minnesota. Any future use of the facilities on the Fermilab site would require the administrative approval of the Director of Fermilab and would undergo a separate NEPA review. Fermilab is a Federal high-energy physics research laboratory in Batavia, Illinois operated on behalf of the DOE by Universities Research Association, Inc.

  18. Augusta Newsprint: Paper Mill Pursues Five Projects Following Plant-Wide Energy Efficiency Assessment

    SciTech Connect

    Not Available

    2003-07-01

    Augusta Newsprint undertook a plant-wide energy efficiency assessment of its Augusta, Georgia, plant in 2001. The assessment helped the company decide to implement five energy efficiency projects. Four of the five projects will save the company 11,000 MWh of electrical energy (about$369,000) each year. The remaining project will produce more than$300,000 annually, from sale of the byproduct turpentine. The largest annual savings,$881,000, will come from eliminating Kraft pulp by using better process control. All of the projects could be applied to other paper mills and most of the projects could be applied in other industries.

  19. Lower Columbia River Terminal Fisheries Research Project : Final Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1995-04-01

    This notice announces BPA`S`s decision to fund the Oregon Department of Fish and Wildlife (ODFW), the Washington Department of Fish and Wildlife (WDFW), and the Clatsop Economic Development Committee for the Lower Columbia River Terminal Fisheries Research Project (Project). The Project will continue the testing of various species/stocks, rearing regimes, and harvest options for terminal fisheries, as a means to increase lower river sport and commercial harvest of hatchery fish, while providing both greater protection of weaker wild stocks and increasing the return of upriver salmon runs to potential Zone 6 Treaty fisheries. The Project involves relocating hatchery smolts to new, additional pen locations in three bays/sloughs in the lower Columbia River along both the Oregon and Washington sides. The sites are Blind Slough and Tongue Point in Clatsop County, Oregon, and Grays Bay/Deep River, Wahkiakum County, Washington. The smolts will be acclimated for various lengths of time in the net pens and released from these sites. The Project will expand upon an existing terminal fisheries project in Youngs Bay, Oregon. The Project may be expanded to other sites in the future, depending on the results of this initial expansion. BPA`S has determined the project is not a major Federal action significantly affecting the quality of the human environment, within the meaning of the National Environmental Policy Act (NEPA) of 1969. Therefore, the preparation of an environmental impact statement is not required, and BPA`S is issuing this FONSI.

  20. Milliken Clean Coal Demonstration Project: A DOE Assessment

    SciTech Connect

    National Energy Technology Laboratory

    2001-08-15

    The goal of the U.S. Department of Energy's (DOE) Clean Coal Technology (CCT) program is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal-utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have developed beyond the proof-of-concept stage.

  1. Evolving Project E-Scape for National Assessment

    ERIC Educational Resources Information Center

    Kimbell, Richard

    2012-01-01

    In the opening paper in this Special Edition I outlined the major issues that led to the establishment of "project e-scape". The project was intended to develop systems and approaches that enabled learners to build real-time web-based portfolios of their performance (initially) in design & technology and additionally to build systems…

  2. An assessment of uncertainty in forest carbon budget projections

    Treesearch

    Linda S. Heath; James E. Smith

    2000-01-01

    Estimates of uncertainty are presented for projections of forest carbon inventory and average annual net carbon flux on private timberland in the US using the model FORCARB. Uncertainty in carbon inventory was approximately ±9% (2000 million metric tons) of the estimated median in the year 2000, rising to 11% (2800 million metric tons) in projection year 2040...

  3. Assessment of Project-Based Learning in a MECHATRONICS Context

    ERIC Educational Resources Information Center

    Doppelt, Yaron

    2005-01-01

    Project-based learning (PBL) that has authenticity in the pupils' world enables the teaching of science and technology to pupils from a variety of backgrounds. PBL has the potential to enable pupils to research, plan, design, and reflect on the creation of technological projects (Doppelt, 2000). Engineering education, which is common in Israel,…

  4. Annotated Bibliography on Religious Development.

    ERIC Educational Resources Information Center

    Bucher, Anton A.; Reich, K. Helmut

    1991-01-01

    Presents an annotated bibliography on religious development that covers the areas of psychology and religion, measurement of religiousness, religious development during the life cycle, religious experiences, conversion, religion and morality, and images of God. (Author/BB)

  5. Patient Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Jeannette

    Topics included in this annotated bibliography on patient education are (1) background on development of patient education programs, (2) patient education interventions, (3) references for health professionals, and (4) research and evaluation in patient education. (TA)

  6. Hopi Linguistics: An Annotated Bibliography

    ERIC Educational Resources Information Center

    Seaman, P. David

    1977-01-01

    This is a preliminary research-oriented bibliography on the Hopi language. All known items, through mid-1976, are included, with an annotation for each item sketching its nature and/or possible value. (Author/RM)

  7. Butternut (Juglans cinerea) annotated bibliography.

    Treesearch

    M.E. Ostry; M.J. Moore; S.A.N. Worrall

    2003-01-01

    An annotated bibliography of the major literature related to butternut (Juglans cinerea) from 1890 to 2002. Includes 230 citations and a topical index. Topics include diseases, conservation, genetics, insect pests, silvics, nut production, propagation, silviculture, and utilization.

  8. Publication Production: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Firman, Anthony H.

    1994-01-01

    Offers brief annotations of 52 articles and papers on document production (from the Society for Technical Communication's journal and proceedings) on 9 topics: information processing, document design, using color, typography, tables, illustrations, photography, printing and binding, and production management. (SR)

  9. Publication Production: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Firman, Anthony H.

    1994-01-01

    Offers brief annotations of 52 articles and papers on document production (from the Society for Technical Communication's journal and proceedings) on 9 topics: information processing, document design, using color, typography, tables, illustrations, photography, printing and binding, and production management. (SR)

  10. The Assessment of Adult Needs: Phase 1 of Multi-County Assessment of Adult Needs Project (MAP).

    ERIC Educational Resources Information Center

    McLennan Community Coll., TX.

    The McLennan Community College Multi-County Needs Assessment Project's (MAP) survey, assessing the felt and perceived needs, problems, and interests of the local population relative to education and training programs, is discussed in the document. The Needs Assessment Survey, one component of MAP, was conducted in the central Texas area (Bosque,…

  11. Iterative performance assessments as a regulatory tool for evaluating repository safety: How experiences from SKI Project-90 were used in formulating the new performance assessment project SITE-94

    SciTech Connect

    Andersson, J.

    1993-12-31

    The Swedish Nuclear Power Inspectorate, SKI, regulatory research program has to prepare for the process of licensing a repository for spent nuclear fuel, by building up the necessary knowledge and review capacity. SKIs main strategy for meeting this demand is to develop an independent performance assessment capability. SKIs first own performance assessment project, Project-90, was completed in 1991 and is now followed by a new project, SITE-94. SITE-94 is based on conclusions reached within Project-90. An independent review of Project-90, carried out by a NEA team of experts, has also contributed to the formation of the project. Another important reason for the project is that the implementing organization in Sweden, SKB, has proposed to submit an application to start detailed investigation of a repository candidate site around 1997. SITE-94 is a performance assessment of a hypothetical repository at a real site. The main objective of the project is to determine how site specific data should be assimilated into the performance assessment process, and to evaluate how uncertainties inherent in site characterization will influence performance assessment results. This will be addressed by exploring multiple interpretations, conceptual models, and parameters consistent with the site data. The site evaluation will strive for consistency between geological, hydrological, rock mechanical, and geochemical descriptions. Other important elements of SITE-94 are the development of a practical and defensible methodology for defining, constructing and analyzing scenarios, the development of approaches for treatment of uncertainties, evaluation of canister integrity, and the development and application of an appropriate quality assurance plan for performance assessments.

  12. A Case Study of Teacher Learning in an Assessment for Learning Project in Hong Kong

    ERIC Educational Resources Information Center

    Tang, Sylvia Yee Fan; Leung, Pamela Pui Wan; Chow, Alice Wai Kwan; Wong, Ping Man

    2010-01-01

    Changes in assessment practices in the direction of assessment for learning (AfL) can be a powerful force to enhance student learning. This article presents a case study of teacher learning in an AfL project in Hong Kong. In the Project, AfL strategies were adopted in Chinese Language and English Language classrooms at the junior secondary level.…

  13. Centralisation of Assessment: Meeting the Challenges of Multi-Year Team Projects in Information Systems Education

    ERIC Educational Resources Information Center

    Cooper, Grahame; Heinze, Aleksej

    2007-01-01

    This paper focuses on the difficulties of assessing multi-year team projects, in which a team of students drawn from all three years of a full-time degree course works on a problem with and for a real-life organization. Although potential solutions to the problem of assessing team projects may be context-dependent, we believe that discussing these…

  14. Lessons Learned from Net Zero Energy Assessments and Renewable Energy Projects at Military Installations

    SciTech Connect

    Callahan, M.; Anderson, K.; Booth, S.; Katz, J.; Tetreault, T.

    2011-09-01

    Report highlights the increase in resources, project speed, and scale that is required to achieve the U.S. Department of Defense (DoD) energy efficiency and renewable energy goals and summarizes the net zero energy installation assessment (NZEI) process and the lessons learned from NZEI assessments and large-scale renewable energy projects implementations at DoD installations.

  15. Centralisation of Assessment: Meeting the Challenges of Multi-Year Team Projects in Information Systems Education

    ERIC Educational Resources Information Center

    Cooper, Grahame; Heinze, Aleksej

    2007-01-01

    This paper focuses on the difficulties of assessing multi-year team projects, in which a team of students drawn from all three years of a full-time degree course works on a problem with and for a real-life organization. Although potential solutions to the problem of assessing team projects may be context-dependent, we believe that discussing these…

  16. Project ADAPT: A Program to Assess Depression and Provide Proactive Treatment in Rural Areas

    ERIC Educational Resources Information Center

    Luptak, Marilyn; Kaas, Merrie J.; Artz, Margaret; McCarthy, Teresa

    2008-01-01

    Purpose: We describe and evaluate a project designed to pilot test an evidence-based clinical intervention for assessing and treating depression in older adults in rural primary care clinics. Project ADAPT--Assuring Depression Assessment and Proactive Treatment--utilized existing primary care resources to overcome barriers to sustainability…

  17. Project ADAPT: A Program to Assess Depression and Provide Proactive Treatment in Rural Areas

    ERIC Educational Resources Information Center

    Luptak, Marilyn; Kaas, Merrie J.; Artz, Margaret; McCarthy, Teresa

    2008-01-01

    Purpose: We describe and evaluate a project designed to pilot test an evidence-based clinical intervention for assessing and treating depression in older adults in rural primary care clinics. Project ADAPT--Assuring Depression Assessment and Proactive Treatment--utilized existing primary care resources to overcome barriers to sustainability…

  18. The Nucla Circulating Fluidized-Bed Demonstration Project: A U.S. DOE post-project assessment

    SciTech Connect

    1995-06-01

    This report is a post-project assessment of the Nucla Circulating Fluidized-Bed (CFB) Demonstration Project, the second project to be completed in the DOE Clean Coal Technology Program. Nucla was the first successful utility repowering project in the US, increasing the capacity of the original power station from 36 MW(e) to 110 MW(e) and extending its life by 30 years. In the CFB boiler, combustion and desulfurization both take place in the fluidized bed. Calcium in the sorbent captures sulfur dioxide and the relatively low combustion temperatures limit NOx formation. Hot cyclones separate the larger particles from the gas and recirculates them to the lower zones of the combustion chambers. This continuous circulation of coal char and sorbent particles is the novel feature of CFB technology. This demonstration project significantly advanced the environmental, operational, and economic potential of atmospheric CFB technology, precipitating a large number of orders for atmospheric CFB equipment. By 1994, more than 200 atmospheric CFB boilers have been constructed worldwide. Although at least six CFB units have been operated, the Nucla project`s CFB database continues to be an important and unique resource for the design of yet larger atmospheric CFB systems. The post-project assessment report is an independent DOE appraisal of the success a completed project had in achieving its objectives and aiding in the commercialization of the demonstrated technology. The report also provides an assessment of the expected technical, environmental, and economic performance of the commercial version of the technology as well as an analysis of the commercial market.

  19. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

    PubMed

    Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

    2015-01-01

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

  20. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

    SciTech Connect

    Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

    2015-10-26

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

  1. NCBI prokaryotic genome annotation pipeline.

    PubMed

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  2. Gene Ontology Annotations and Resources

    PubMed Central

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  3. An Annotated Bibliography of MANPRINT-Related Assessments and Evaluations Conducted by the U.S. Army, 2nd Edition: 1953 to 2009. Volume 2 - MANPRINT Assessment and Evaluations

    DTIC Science & Technology

    2010-02-01

    Cargo- HETS HETS Heavy Equipment Transport System (HETS), Which Includes M1000 Semitrailer and the M1070 Truck Tractor 1993 An Annotated...Vehicle- Wheeled- Cargo- HETS HETS Heavy Equipment Transporter System (HETS), Which Includes the M1000 Semitrailer and the M1070 Truck Tractor 1994...HETS a. The M1000 70-ton Semitrailer and the M1070 Truck Tractor combination is designated HETS. The HETS is required to effectively transport the 70

  4. Meta-Assessment in a Project-Based Systems Engineering Course

    ERIC Educational Resources Information Center

    Wengrowicz, Niva; Dori, Yehudit Judy; Dori, Dov

    2017-01-01

    Project-based learning (PBL) facilitates significant learning, but it poses a major assessment challenge for assessing individual content knowledge. We developed and implemented an assessment approach and tool for a mandatory undergraduate systems engineering PBL-based course. We call this type of assessment "student-oriented"…

  5. Meta-Assessment in a Project-Based Systems Engineering Course

    ERIC Educational Resources Information Center

    Wengrowicz, Niva; Dori, Yehudit Judy; Dori, Dov

    2017-01-01

    Project-based learning (PBL) facilitates significant learning, but it poses a major assessment challenge for assessing individual content knowledge. We developed and implemented an assessment approach and tool for a mandatory undergraduate systems engineering PBL-based course. We call this type of assessment "student-oriented"…

  6. Rapid Carbon Assessment Project: Data Summary and Availability

    NASA Astrophysics Data System (ADS)

    Wills, Skye; Loecke, Terry; Roecker, Stephen; Beaudette, Dylan; Libohova, Zamir; Monger, Curtis; Lindbo, David

    2017-04-01

    The Rapid Carbon Assessment (RaCA) project was undertaken to estimate regional soil organic carbon (SOC) stocks across the conterminous United States (CONUS) as a one-time event. Sample locations were selected randomly using the NRI (National Resource Inventory) sampling framework covering all areas in CONUS with SSURGO certified maps as of Dec 2012. Within each of 17 regions, sites were selected by a combination of soil and land use/cover groups (LUGR). At each of more than 6,000 sites five pedons were described and sampled to a depth of 100cm (one central and 4 satellites 30m in each cardinal direction). There were 144,833 samples described from 32,084 pedons at 6, 017 sites. A combination of measurement and modeled bulk density was used for all samples. A visible near-infrared (VNIR) spectrophotometer was used to scan each sample for prediction of soil carbon contents. The samples of each central pedon were analyzed by the Kellogg Soil Survey Laboratory for combustion carbon and calcimeter inorganic carbon. SOC stocks were calculated for each pedon using a standard fixed depth technique to depths of 5, 30 and 100cm. Pedon SOC stocks were transformed to better approach normality before LUGR, regional and land use/cover summaries were calculated. The values reported are geometric means. A detailed spatial map can be produced using LUGR mean assignment to correlated pixels. LUGR values range from 1 to 3,000 Mg ha-1. While some artifacts are visible due to the stratified nature of sampling and extrapolation, the predictions are generally smooth and highlight some distinct geomorphic features including the sandhills in the Great Plains in the central US, mountainous regions in the West and coastal wetlands in the East. Regional averages range from 46 Mg ha-1 in the desert Southwest to 182 Mg ha-1 in the Northeast. Regional trends correlate to climate variables such as precipitation and potential evapotranspiration. While land use/cover classes vary in mean values

  7. A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

    PubMed

    Huntley, Rachael P; Harris, Midori A; Alam-Faruque, Yasmin; Blake, Judith A; Carbon, Seth; Dietze, Heiko; Dimmer, Emily C; Foulger, Rebecca E; Hill, David P; Khodiyar, Varsha K; Lock, Antonia; Lomax, Jane; Lovering, Ruth C; Mutowo-Meullenet, Prudence; Sawford, Tony; Van Auken, Kimberly; Wood, Valerie; Mungall, Christopher J

    2014-05-21

    The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data. The core data structure is the annotation, an association between a gene product and a term from one of the three ontologies comprising the GO. Historically, it has not been possible to provide additional information about the context of a GO term, such as the target gene or the location of a molecular function. This has limited the specificity of knowledge that can be expressed by GO annotations. The GO Consortium has introduced annotation extensions that enable manually curated GO annotations to capture additional contextual details. Extensions represent effector-target relationships such as localization dependencies, substrates of protein modifiers and regulation targets of signaling pathways and transcription factors as well as spatial and temporal aspects of processes such as cell or tissue type or developmental stage. We describe the content and structure of annotation extensions, provide examples, and summarize the current usage of annotation extensions. The additional contextual information captured by annotation extensions improves the utility of functional annotation by representing dependencies between annotations to terms in the different ontologies of GO, external ontologies, or an organism's gene products. These enhanced annotations can also support sophisticated queries and reasoning, and will provide curated, directional links between many gene products to support pathway and network reconstruction.

  8. How can functional annotations be derived from profiles of phenotypic annotations?

    PubMed

    Serrano-Solano, Beatriz; Díaz Ramos, Antonio; Hériché, Jean-Karim; Ranea, Juan A G

    2017-02-10

    Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requires careful interpretation of phenotypic descriptions and assessment of phenotypic similarity. Understanding how functions and phenotypes are linked will be crucial for the development of methods for the automatic conversion of gene loss-of-function phenotypes to gene functional annotations. We explored the relation between cellular phenotypes from RNAi-based screens in human cells and gene annotations of cellular functions as provided by the Gene Ontology (GO). Comparing different similarity measures, we found that information content-based measures of phenotypic similarity were the best at capturing gene functional similarity. However, phenotypic similarities did not map to the Gene Ontology organization of gene function but to functions defined as groups of GO terms with shared gene annotations. Our observations have implications for the use and interpretation of phenotypic similarities as a proxy for gene functions both in RNAi screen data analysis and curation and in the prediction of disease genes.

  9. The Native Learner and Distance Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Confederation Coll. of Applied Arts and Technology, Thunder Bay (Ontario).

    This annotated bibliography consists of 76 entries dated 1975 through 1988, describing publications in the area of distance education and the Native learner. The bibliography represents one phase of a project entitled "Native Priorities for Distance Education," with the goal being the participation of Native peoples in the planning and…

  10. Program Evaluation in the Arts. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M., Comp.; Eichinger, Debra S., Comp.

    This 56-item annotated bibliography gives teachers and administrators access to information on the evaluation of school fine arts programs. Based upon a computer search of the Educational Resources Information Center (ERIC) data base, it cites project reports, journal articles, and dissertations published from 1963 to 1976. Citations of elementary…

  11. Adult Basic Education & Literacy, Media and Technology. An Annotated Bibliography

    ERIC Educational Resources Information Center

    Elliott, Claire

    2005-01-01

    This bibliography was compiled for The Centre for Literacy's 2005 Summer Institute: "Adult Basic Education & Literacy, Media and Technology." The references and annotations point to relevant research, project, strategy and evaluation reports that describe and analyze the current and future influences of changing technologies on…

  12. Minding the Gap: Annotation as Preparation for Discussion

    ERIC Educational Resources Information Center

    Feito, Jose Alfonso; Donahue, Patricia

    2008-01-01

    This research project examines classroom discussion in its relationship to reading as made visible through the practice of textual annotation. In order to develop a rich description of student reading/discussion processes, we targeted multiple undergraduate seminars at a liberal arts college as they encountered the first two Acts of Shakespeare's…

  13. Africa: An Annotated List of Printed Materials Suitable for Children.

    ERIC Educational Resources Information Center

    State Univ. of New York, Ithaca. School of Hotel Administration at Cornell Univ.

    This joint project of the American Library Association, Children's Services Division, and the African American Institute is intended to provide kindergarten through ninth grade children with an annotated listing of appropriate works concerning the land and peoples of the African continent. The listings are presented by country and include…

  14. Africa: An Annotated List of Printed Materials Suitable for Children.

    ERIC Educational Resources Information Center

    State Univ. of New York, Ithaca. School of Hotel Administration at Cornell Univ.

    This joint project of the American Library Association, Children's Services Division, and the African American Institute is intended to provide kindergarten through ninth grade children with an annotated listing of appropriate works concerning the land and peoples of the African continent. The listings are presented by country and include…

  15. Genome Annotation in a Community College Cell Biology Lab

    ERIC Educational Resources Information Center

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  16. WORKSHOPS FOR THE HANDICAPPED, AN ANNOTATED BIBLIOGRAPHY--NO. 3.

    ERIC Educational Resources Information Center

    PERKINS, DOROTHY C.; AND OTHERS

    THESE 126 ANNOTATIONS ARE THE THIRD VOLUME OF A CONTINUING SERIES OF BIBLIOGRAPHIES LISTING ARTICLES APPEARING IN JOURNALS AND CONFERENCE, RESEARCH, AND PROJECT REPORTS. LISTINGS INCLUDE TESTS, TEST RESULTS, STAFF TRAINING PROGRAMS, GUIDES FOR COUNSELORS AND TEACHERS, AND ARCHITECTURAL PLANNING, AND RELATE TO THE MENTALLY RETARDED, EMOTIONALLY…

  17. The Negro Freedom Movement: Past and Present. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Wayne County Intermediate School District, Detroit, MI. Desegregation Advisory Project.

    An annotated bibliography, prepared by the Desegregation Advisory Project and funded under Title IV of the Civil Rights Act of 1964, includes books for adults, children, and young adults. Also included is one section on audiovisual materials, and another on selected bibliographies. Pertinent periodicals and organizations providing resource…

  18. Genome Annotation in a Community College Cell Biology Lab

    ERIC Educational Resources Information Center

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  19. Short Mountain Landfill Gas Recovery Project : Stage 1 Environmental Assessment.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-05-01

    The Bonneville Power Administration (BPA), a Federal power marketing agency, has statutory responsibilities to supply electrical power to its utility, industrial, and other customers in the Pacific Northwest. BPA`s latest load/resource balance forecast, projects the capability of existing resources to satisfy projected Federal system loads. The forecast indicates a potential resource deficit. The underlying need for action is to satisfy BPA customers` demand for electrical power.

  20. An Economic Evaluation Framework for Assessing Renewable Energy Projects

    SciTech Connect

    Omitaomu, Olufemi A; Badiru, Adedeji B

    2012-01-01

    It is becoming increasingly imperative to integrate renewable energy, such as solar and wind, into electricity generation due to increased regulations on air and water pollution and a sociopolitical desire to develop more clean energy sources. This increased spotlight on renewable energy requires evaluating competing projects using either conventional economic analysis techniques or other economics-based models and approaches in order to select a subset of the projects to be funded. Even then, there are reasons to suspect that techniques applied to renewable energy projects may result in decisions that will reject viable projects due to the use of a limited number of quantifiable and tangible attributes about the projects. This paper presents a framework for economic evaluation of renewable energy projects. The framework is based on a systems approach in which the processes within the entire network of the system, from generation to consumption, are accounted for. Furthermore, the framework uses the concept of fuzzy system to calculate the value of information under conditions of uncertainty.

  1. Post-project geomorphic assessment of a large process-based river restoration project

    USGS Publications Warehouse

    Erwin, Susannah O.; Schmidt, John C.; Allred, Tyler M.

    2016-01-01

    This study describes channel changes following completion of the Provo River Restoration Project (PRRP), the largest stream restoration project in Utah and one of the largest projects in the United States in which a gravel-bed river was fully reconstructed. We summarize project objectives and the design process, and we analyze monitoring data collected during the first 7 years after project completion. Post-project channel adjustment during the study period included two phases: (i) an initial phase of rapid, but small-scale, adjustment during the first years after stream flow was introduced to the newly constructed channel and (ii) a subsequent period of more gradual topographic adjustment and channel migration. Analysis of aerial imagery and ground-survey data demonstrate that the channel has been more dynamic in the downstream 4 km where a local source contributes a significant annual supply of bed material. Here, the channel migrates and exhibits channel adjustments that are more consistent with project objectives. The upstream 12 km of the PRRP are sediment starved, the channel has been laterally stable, and this condition may not be consistent with large-scale project objectives.

  2. Post-project geomorphic assessment of a large process-based river restoration project

    NASA Astrophysics Data System (ADS)

    Erwin, Susannah O.; Schmidt, John C.; Allred, Tyler M.

    2016-10-01

    This study describes channel changes following completion of the Provo River Restoration Project (PRRP), the largest stream restoration project in Utah and one of the largest projects in the United States in which a gravel-bed river was fully reconstructed. We summarize project objectives and the design process, and we analyze monitoring data collected during the first 7 years after project completion. Post-project channel adjustment during the study period included two phases: (i) an initial phase of rapid, but small-scale, adjustment during the first years after stream flow was introduced to the newly constructed channel and (ii) a subsequent period of more gradual topographic adjustment and channel migration. Analysis of aerial imagery and ground-survey data demonstrate that the channel has been more dynamic in the downstream 4 km where a local source contributes a significant annual supply of bed material. Here, the channel migrates and exhibits channel adjustments that are more consistent with project objectives. The upstream 12 km of the PRRP are sediment starved, the channel has been laterally stable, and this condition may not be consistent with large-scale project objectives.

  3. Combining assessment and research during development of large technology integration projects.

    PubMed

    Koszalka, Tiffany A; Grabowski, Barbara L

    2003-05-01

    Descriptions of large technology integration projects can be found in the literature. Amongst reports of instructionally sound designs and increases in learning loom debates on the effectiveness and impact of the use of technology in education. Combining assessment and research components for large technology integration projects should yield results that inform this debate. The task of integrating assessment and research, however, is complex. Descriptions about how either assessment or research should be conducted can be found, but detailed examples illustrating integration of such strategies are scarce. This paper provides brief definitions of assessment, evaluation, and research and describes strategies for integrating and managing assessment and research activities for a large education technology development project. Examples of tools used to develop and manage a comprehensive assessment and research plan in a large technology integration development and research project are provided.

  4. Improving gene annotation using peptide mass spectrometry

    PubMed Central

    Tanner, Stephen; Shen, Zhouxin; Ng, Julio; Florea, Liliana; Guigó, Roderic; Briggs, Steven P.; Bafna, Vineet

    2007-01-01

    Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct and efficiently search spectra against a genomic database, with no prior knowledge of encoded proteins. By searching a corpus of 18.5 million tandem mass spectra (MS/MS) from human proteomic samples, we validate 39,000 exons and 11,000 introns at the level of translation. We present translation-level evidence for novel or extended exons in 16 genes, confirm translation of 224 hypothetical proteins, and discover or confirm over 40 alternative splicing events. Polymorphisms are efficiently encoded in our database, allowing us to observe variant alleles for 308 coding SNPs. Finally, we demonstrate the use of mass spectrometry to improve automated gene prediction, adding 800 correct exons to our predictions using a simple rescoring strategy. Our results demonstrate that proteomic profiling should play a role in any genome sequencing project. PMID:17189379

  5. A review of NASA-sponsored technology assessment projects

    NASA Technical Reports Server (NTRS)

    Mascy, A. C.; Alexander, A. D., III; Wood, R. D.

    1978-01-01

    Recent technology assessment studies sponsored by NASA are reviewed, and a summary of the technical results as well as a critique of the methodologies are presented. The reviews include Assessment of Lighter-Than-Air Technology, Technology Assessment of Portable Energy RDT&P, Technology Assessment of Future Intercity Passenger Transportation Systems, and Technology Assessment of Space Disposal of Radioactive Nuclear Waste. The use of workshops has been introduced as a unique element of some of these assessments. Also included in this report is a brief synopsis of a method of quantifying opinions obtained through such group interactions. Representative of the current technology assessments, these studies cover a broad range of socio-political factors and issues in greater depth than previously considered in NASA sponsored studies. In addition to the lessons learned through the conduct of these studies, a few suggestions for improving the effectiveness of future technology assessments are provided.

  6. Kinder Lernen Deutsch. Materials Project Part I. Revised.

    ERIC Educational Resources Information Center

    American Association of Teachers of German.

    The Kinder Lernen Deutsch (LKD) materials evaluation project identifies materials appropriate for the elementary school German classrooms in grades K-8. This guide consists of an annotated bibliography, with ratings, of these materials. The guiding principles by which the materials were assessed were: use of the communicative approach; integration…

  7. Current Knowledge and Projection on Assessing the Effectiveness of Training.

    ERIC Educational Resources Information Center

    Orlansky, Jesse

    This discussion of methods used to assess the effectiveness of training for U.S. Army personnel identifies various types of training, describes methods currently used, and suggests ways of improving the assessment process. The methodology and results of assessments of effectiveness, including the costs associated with the level of performance, are…

  8. Current Knowledge and Projection on Assessing the Effectiveness of Training.

    ERIC Educational Resources Information Center

    Orlansky, Jesse

    This discussion of methods used to assess the effectiveness of training for U.S. Army personnel identifies various types of training, describes methods currently used, and suggests ways of improving the assessment process. The methodology and results of assessments of effectiveness, including the costs associated with the level of performance, are…

  9. NRC assessment of the Department of Energy annealing demonstration project

    SciTech Connect

    Jackson, D.A.; Malik, S.N.

    1997-02-01

    Thermal annealing is the only known method for mitigating the effects of neutron irradiation embrittlement in reactor pressure vessel (RPV) steels. In May 1996, the US Department of Energy (DOE) in conjunction with the American Society of Mechanical Engineers, Westinghouse, Cooperheat, Electric Power Research Institute (with participating utilities), Westinghouse Owner`s Group, Consumers Power, Electricite` de France, Duquesne Light and the Central Research Institute of the Electric Power Industry (Japan) sponsored an annealing demonstration project (ADP) at Marble Hill. The Marble Hill Plant, located in Madison, Indiana, is a Westinghouse 4 loop design. The plant was nearly 70% completed when the project was canceled. Hence, the RPV was never irradiated. The paper will present highlights from the NRCs independent evaluation of the Marble Hill Annealing Demonstration Project.

  10. The state of play in higher eukaryote gene annotation.

    PubMed

    Mudge, Jonathan M; Harrow, Jennifer

    2016-12-01

    A genome sequence is worthless if it cannot be deciphered; therefore, efforts to describe - or 'annotate' - genes began as soon as DNA sequences became available. Whereas early work focused on individual protein-coding genes, the modern genomic ocean is a complex maelstrom of alternative splicing, non-coding transcription and pseudogenes. Scientists - from clinicians to evolutionary biologists - need to navigate these waters, and this has led to the design of high-throughput, computationally driven annotation projects. The catalogues that are being produced are key resources for genome exploration, especially as they become integrated with expression, epigenomic and variation data sets. Their creation, however, remains challenging.

  11. Performance Evaluation and Opportunity Assessment for St. Bernard Project

    SciTech Connect

    Dickson, Bruce

    2011-06-01

    This report describes efforts by IBACOS, a Building America research team, in the St. Bernard Project, a nonprofit, community-based organization whose mission is to assist Hurricane Katrina survivors to return to their homes in the New Orleans area. The report focuses on energy modeling results of two plans that the St. Bernard Project put forth as 'typical' building types and on quality issues that were observed during the field walk and best practice recommendations that could improve the energy efficiency and durability of the renovated homes.

  12. Performance Evaluation and Opportunity Assessment for St. Bernard Project

    SciTech Connect

    Dickson, B.

    2011-06-01

    This report describes efforts by IBACOS, a Department of Energy Building America research team, in the St. Bernard Project, a nonprofit, community-based organization whose mission is to assist Hurricane Katrina survivors return to their homes in the New Orleans area. The report focuses on energy modeling results of two plans that the St. Bernard Project put forth as 'typical' building types and on quality issues that were observed during the field walk and Best Practice recommendations that could improve the energy efficiency and durability of the renovated homes.

  13. Demonstration and Commercialization of the Sediment Ecosystem Assessment Protocol: Project ER-201130 Environmental Restoration Project

    DTIC Science & Technology

    2017-01-01

    Sustainability Branch (Code 71760) of the Advanced Systems and Applied Sciences Branch (71700), Space and Naval Warfare Systems Center Pacific, San Diego CA...Certification Program (ESTCP), project #ER-201130. Collaborators on this project were Gunther Rosen, PI; Dr. Bart Chadwick, Co-PI ( Space and Naval Warfare...Standard Operating Procedure SPAWAR Space and Naval Warfare Systems Command SPME Solid phase microextraction SPI Sediment Profile Imaging SWI

  14. Structural annotation of equine protein-coding genes determined by mRNA sequencing.

    PubMed

    Coleman, S J; Zeng, Z; Wang, K; Luo, S; Khrebtukova, I; Mienaltowski, M J; Schroth, G P; Liu, J; MacLeod, J N

    2010-12-01

    The horse, like the majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for the majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species. The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns. Sequencing of mRNA from eight equine tissues generated 293,758105 sequence tags of 35 bases each, equalling 10.28 gbp of total sequence data. The tag alignments represent approximately 207 × coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI. Tag coverage was sufficient to refine the structural annotation for 11,356 of these predicted genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI. Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq-derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci. Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.

  15. An assessment of adherence to basic ecological principles by payments for ecosystem service projects.

    PubMed

    Prager, C M; Varga, A; Olmsted, P; Ingram, J C; Cattau, M; Freund, C; Wynn-Grant, R; Naeem, S

    2016-08-01

    Programs and projects employing payments for ecosystem service (PES) interventions achieve their objectives by linking buyers and sellers of ecosystem services. Although PES projects are popular conservation and development interventions, little is known about their adherence to basic ecological principles. We conducted a quantitative assessment of the degree to which a global set of PES projects adhered to four ecological principles that are basic scientific considerations for any project focused on ecosystem management: collection of baseline data, identification of threats to an ecosystem service, monitoring, and attention to ecosystem dynamics or the formation of an adaptive management plan. We evaluated 118 PES projects in three markets-biodiversity, carbon, and water-compiled using websites of major conservation organizations; ecology, economic, and climate-change databases; and three scholarly databases (ISI Web of Knowledge, Web of Science, and Google Scholar). To assess adherence to ecological principles, we constructed two scientific indices (one additive [ASI] and one multiplicative [MSI]) based on our four ecological criteria and analyzed index scores by relevant project characteristics (e.g., sector, buyer, seller). Carbon-sector projects had higher ASI values (P < 0.05) than water-sector projects and marginally higher ASI scores (P < 0.1) than biodiversity-sector projects, demonstrating their greater adherence to ecological principles. Projects financed by public-private partnerships had significantly higher ASI values than projects financed by governments (P < 0.05) and marginally higher ASI values than those funded by private entities (P < 0.1). We did not detect differences in adherence to ecological principles based on the inclusion of cobenefits, the spatial extent of a project, or the size of a project's budget. These findings suggest, at this critical phase in the rapid growth of PES projects, that fundamental ecological principles should be

  16. Multimedia Projects in Education: Designing, Producing, and Assessing, Third Edition

    ERIC Educational Resources Information Center

    Ivers, Karen S.; Barron, Ann E.

    2005-01-01

    Building on the materials in the two previous successful editions, this book features approximately 40% all new material and updates the previous information. The authors use the DDD-E model (Decide, Design, Develop--Evaluate) to show how to select and plan multimedia projects, use presentation and development tools, manage graphics, audio, and…

  17. Multimedia Projects in Education: Designing, Producing, and Assessing. Second Edition.

    ERIC Educational Resources Information Center

    Ivers, Karen S.; Barron, Ann E.

    This handbook provides educators with strategies and ideas for incorporating multimedia projects into the curriculum for grades 4-12. With a focus on student learning, the authors show how to plan and implement multimedia activities and engage students in expressing themselves through a variety of media. Using the DDD-E model (Decide, Design,…

  18. Performance assessment of the PNM Prosperity electricity storage project

    SciTech Connect

    Roberson, Dakota; Ellison, James F.; Bhatnagar, Dhruv; Schoenwald, David A.

    2014-05-01

    The purpose of this study is to characterize the technical performance of the PNM Prosperity electricity storage project, and to identify lessons learned that can be used to improve similar projects in the future. The PNM Prosperity electricity storage project consists of a 500 kW/350 kWh advanced lead-acid battery with integrated supercapacitor (for energy smoothing) and a 250 kW/1 MWh advanced lead-acid battery (for energy shifting), and is co-located with a 500 kW solar photovoltaic (PV) resource. The project received American Reinvestment and Recovery Act (ARRA) funding. The smoothing system is e ective in smoothing intermittent PV output. The shifting system exhibits good round-trip efficiencies, though the AC-to-AC annual average efficiency is lower than one might hope. Given the current utilization of the smoothing system, there is an opportunity to incorporate additional control algorithms in order to increase the value of the energy storage system.

  19. Sequential Assessment of Engineering Design Projects at University Level

    ERIC Educational Resources Information Center

    Oehlers, Deric John

    2006-01-01

    Seven years of industrial experience followed by 30 years of academic research and teaching in structural engineering have led the author to believe that the prime objective of a university design course is not the design project itself but to train students to solve problems, as this will last them throughout their careers. It is shown how design…

  20. Alternative Assessment: A Monthly Portfolio Project Improves Student Performance.

    ERIC Educational Resources Information Center

    Valdez, Penelope S.

    2001-01-01

    Describes the use of monthly portfolio projects to track student progress and improve science performance in a 7th grade life science course. Students explain concepts they have learned, produce products to present what they have learned, and use the concepts to critique magazine articles, advertisements, or news stories. Provides an evaluation…

  1. Assessment of Communication Competencies in Engineering Design Projects.

    ERIC Educational Resources Information Center

    Brinkman, Gert W.; van der Geest, Thea M.

    2003-01-01

    Notes that reforms in engineering education have caused a shift from the traditional stand-alone courses in technical communication for engineering students towards communication training integrated in courses and design projects that allows students to develop four levels of competence. Describes three formats for integrated communication…

  2. Quantum Information Science Research and Technical Assessment Project

    DTIC Science & Technology

    2010-08-01

    Laboratories. We report here the successful initial experimental studies of removing applicable contaminants on metal surfaces. Heating in ion traps...fidelity quantum information processing operations [10]. These anomalous heating effects limit the fidelity of qubit gates. Understanding and improving...heating effects. Generation of Thin Metallic Films and Controlled Levels of Contamination One key aspect of this project is the ability produce

  3. The Application of Games Theory to Group Project Assessment.

    ERIC Educational Resources Information Center

    Pitt, M. J.

    2000-01-01

    Application of game theory to small-group project evaluation in higher education instruction finds that the best strategy for students wishing high grades may not be a strategy that promotes teamwork and cooperation. Suggests that putting students into groups may randomly disadvantage some students relative to others, producing serious unfairness…

  4. Multimedia Projects in Education: Designing, Producing, and Assessing. Second Edition.

    ERIC Educational Resources Information Center

    Ivers, Karen S.; Barron, Ann E.

    This handbook provides educators with strategies and ideas for incorporating multimedia projects into the curriculum for grades 4-12. With a focus on student learning, the authors show how to plan and implement multimedia activities and engage students in expressing themselves through a variety of media. Using the DDD-E model (Decide, Design,…

  5. Sequential Assessment of Engineering Design Projects at University Level

    ERIC Educational Resources Information Center

    Oehlers, Deric John

    2006-01-01

    Seven years of industrial experience followed by 30 years of academic research and teaching in structural engineering have led the author to believe that the prime objective of a university design course is not the design project itself but to train students to solve problems, as this will last them throughout their careers. It is shown how design…

  6. Peer Assessment of Group Projects in Civil Engineering.

    ERIC Educational Resources Information Center

    Rafiq, Yaqub; Fullerton, Hazel

    1996-01-01

    One university's use of peer evaluation to develop fair and reliable distribution of grades for group projects is described, and its adaptation to the specific requirements of civil engineering is examined. Results suggest the evaluation model is transferable to this discipline. In particular, use of student journals for grade allocation was found…

  7. The Interior Columbia Basin Ecosystem Management Project: scientific assessment.

    Treesearch

    1999-01-01

    This CD-ROM contains digital versions (PDF) of the major scientific documents prepared for the Interior Columbia Basin Ecosystem Management Project (ICBEMP). "A Framework for Ecosystem Management in the Interior Columbia Basin and Portions of the Klamath and Great Basins" describes a general planning model for ecosystem management. The "Highlighted...

  8. UMTRA project disposal cell cover biointrusion sensitivity assessment, Revision 1

    SciTech Connect

    1995-10-01

    This study provides an analysis of potential changes that may take place in a Uranium Mill Tailings Remedial Action (UMTRA) Project disposal cell cover system as a result of plant biointrusion. Potential changes are evaluated by performing a sensitivity analysis of the relative impact of root penetrations on radon flux out of the cell cover and/or water infiltration into the cell cover. Data used in this analysis consist of existing information on vegetation growth on selected cell cover systems and information available from published studies and/or other available project research. Consistent with the scope of this paper, no new site-specific data were collected from UMTRA Project sites. Further, this paper does not focus on the issue of plant transport of radon gas or other contaminants out of the disposal cell cover though it is acknowledged that such transport has the potential to be a significant pathway for contaminants to reach the environment during portions of the design life of a disposal cell where plant growth occurs. Rather, this study was performed to evaluate the effects of physical penetration and soil drying caused by plant roots that have and are expected to continue to grow in UMTRA Project disposal cell covers. An understanding of the biological and related physical processes that take place within the cover systems of the UMTRA Project disposal cells helps the U.S. Department of Energy (DOE) determine if the presence of a plant community on these cells is detrimental, beneficial, or of mixed value in terms of the cover system`s designed function. Results of this investigation provide information relevant to the formulation of a vegetation control policy.

  9. The Effect of Peer Assessment on Project Performance of Students at Different Learning Levels

    ERIC Educational Resources Information Center

    Li, Lan; Gao, Fei

    2016-01-01

    Peer assessment has been increasingly integrated in educational settings as a strategy to foster student learning. Yet little has been studied about how students at different learning levels may benefit from peer assessment. This study examined how peer-assessment and students' learning levels influenced students' project performance using a…

  10. Project RAILS: Lessons Learned about Rubric Assessment of Information Literacy Skills

    ERIC Educational Resources Information Center

    Belanger, Jackie; Zou, Ning; Mills, Jenny Rushing; Holmes, Claire; Oakleaf, Megan

    2015-01-01

    Rubric assessment of information literacy is an important tool for librarians seeking to show evidence of student learning. The authors, who collaborated on the Rubric Assessment of Informational Literacy Skills (RAILS) research project, draw from their shared experience to present practical recommendations for implementing rubric assessment in a…

  11. Utilizing Interactive Technology to Conduct Team Assessments: Teaming with Technology Research Project

    ERIC Educational Resources Information Center

    Thompson, Christy L.; Buchanan, Michelle L.; Westlake, Laura L.; Heinlein, Kenneth B.

    2005-01-01

    This article describes a project that used interactive technology to conduct arena assessments at a distance. Team building, technology requirements, technology employed, observational and quantitative results of assessment comparisons, and future directions are discussed. Real-time distance assessments were performed through the use of network…

  12. The Effect of Peer Assessment on Project Performance of Students at Different Learning Levels

    ERIC Educational Resources Information Center

    Li, Lan; Gao, Fei

    2016-01-01

    Peer assessment has been increasingly integrated in educational settings as a strategy to foster student learning. Yet little has been studied about how students at different learning levels may benefit from peer assessment. This study examined how peer-assessment and students' learning levels influenced students' project performance using a…

  13. Documenting Student Connectivity and Use of Digital Annotation Devices in Virginia Commonwealth University Connected Courses: An Assessment Toolkit for Digital Pedagogies in Higher Education

    ERIC Educational Resources Information Center

    Gogia, Laura Park

    2016-01-01

    Virginia Commonwealth University (VCU) is implementing a large scale exploration of digital pedagogies, including connected learning and open education, in an effort to promote digital fluency and integrative thinking among students. The purpose of this study was to develop a classroom assessment toolkit for faculty who wish to document student…

  14. Documenting Student Connectivity and Use of Digital Annotation Devices in Virginia Commonwealth University Connected Courses: An Assessment Toolkit for Digital Pedagogies in Higher Education

    ERIC Educational Resources Information Center

    Gogia, Laura Park

    2016-01-01

    Virginia Commonwealth University (VCU) is implementing a large scale exploration of digital pedagogies, including connected learning and open education, in an effort to promote digital fluency and integrative thinking among students. The purpose of this study was to develop a classroom assessment toolkit for faculty who wish to document student…

  15. Assessing English: A Trial Collaborative Standardised Marking Project

    ERIC Educational Resources Information Center

    Gibbons, Simon; Marshall, Bethan

    2010-01-01

    Recent policy developments in England have, to some extent, relaxed the hold of external, high-stakes assessment on teachers of students in the early years of secondary education. In such a context, there is the opportunity for teachers to reassert the importance of teacher assessment as the most reliable means of judging a student's abilities. A…

  16. The cumulative effects assessment of a coastal ecological restoration project in China: An integrated perspective.

    PubMed

    Ma, Deqiang; Zhang, Liyu; Fang, Qinhua; Jiang, Yuwu; Elliott, Michael

    2017-05-15

    Large scale coastal land-claim and sea-enclosing (CLASE) activities have caused habitat destruction, biodiversity losses and water deterioration, thus the local governments in China have recently undertaken seabed dredging and dyke opening (SDADO) as typical ecological restoration projects. However, some projects focus on a single impact on hydrodynamic conditions, water quality or marine organisms. In a case study in Xiamen, China, an integrated effects assessment framework centres on ecohydrology, using modeling of hydrodynamic conditions and statistical analysis of water quality, was developed to assess the effects of ecological restoration projects. The benefits of SDADO projects include improving hydrodynamic conditions and water quality, as a precursor to further marine biological improvements. This study highlights the need to comprehensively consider ecological effects of SDADO projects in the planning stage, and an integrative assessment method combining cumulative effects of hydrodynamic conditions, water quality and biological factors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Updating annotations with the distributed annotation system and the automated sequence annotation pipeline

    PubMed Central

    Speier, William; Ochs, Michael F.

    2012-01-01

    Summary: The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface allows pipeline plans in ASAP to be integrated into any system using HTTP and also allows the information returned by ASAP to be included in the DAS registry for use in any DAS-aware system. Three example implementations have been developed: the first accesses TRANSFAC information to automatically create gene sets for the Coordinated Gene Activity in Pattern Sets (CoGAPS) algorithm; the second integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client. Availability: Source code for ASAP 2.7 and the DAS 1.6 interface is available under the GNU public license. Proserver 2.20 is free software available from SourceForge. Scripts for installation and configuration on Linux are provided at our website: http://www.rits.onc.jhmi.edu/dbb/custom/A6/ Contact: Speier@mii.ucla.edu or mfo@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22945787

  18. Automatic annotation of outdoor photographs

    NASA Astrophysics Data System (ADS)

    Cusano, Claudio; Schettini, Raimondo

    2011-01-01

    We propose here a strategy for the automatic annotation of outdoor photographs. Images are segmented in homogeneous regions which may be then assigned to seven different classes: sky, vegetation, snow, water, ground, street, and sand. These categories allows for content-aware image processing strategies. Our annotation strategy uses a normalized cut segmentation to identify the regions to be classified by a multi-class Support Vector Machine. The strategy has been evaluated on a set of images taken from the LabelMe dataset.

  19. Projecting climate change in the United States: A technical document supporting the Forest Service RPA 2010 Assessment

    Treesearch

    Linda A. Joyce; David T. Price; David P. Coulson; Daniel W. McKenney; R. Martin Siltanen; Pia Papadopol; Kevin. Lawrence

    2014-01-01

    A set of climate change projections for the United States was developed for use in the 2010 USDA Forest Service RPA Assessment. These climate projections, along with projections for population dynamics, economic growth, and land use change in the United States, comprise the RPA scenarios and are used in the RPA Assessment to project future renewable resource conditions...

  20. Annotations of Mexican bullfighting videos for semantic index

    NASA Astrophysics Data System (ADS)

    Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

  1. Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

    NASA Astrophysics Data System (ADS)

    Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

    2006-12-01

    Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

  2. Alignment-Annotator web server: rendering and annotating sequence alignments.

    PubMed

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  4. Social impact evaluation: Some implications of the specific decisional context approach for Anticipatory Project Assessment (ARA)

    NASA Technical Reports Server (NTRS)

    Mayo, L. H.

    1975-01-01

    An anticipatory project assessment is discussed which is characterized as the capacity to perform, and the disposition to take into account in relevant decisional areas, the following operations: identification of the significant effects which will result from the introduction of a specified project configuration into alternative projected future social environments during the planning, implementation, and operational states; evaluation of such effects in terms of social impacts on affected participants and social value-institutional processes in accord with specified concepts of social justice.

  5. Social impact evaluation: Some implications of the specific decisional context approach for Anticipatory Project Assessment (ARA)

    NASA Technical Reports Server (NTRS)

    Mayo, L. H.

    1975-01-01

    An anticipatory project assessment is discussed which is characterized as the capacity to perform, and the disposition to take into account in relevant decisional areas, the following operations: identification of the significant effects which will result from the introduction of a specified project configuration into alternative projected future social environments during the planning, implementation, and operational states; evaluation of such effects in terms of social impacts on affected participants and social value-institutional processes in accord with specified concepts of social justice.

  6. Intelligent Vehicle Charging Benefits Assessment Using EV Project Data

    SciTech Connect

    Letendre, Steven; Gowri, Krishnan; Kintner-Meyer, Michael CW; Pratt, Richard M.

    2013-12-01

    PEVs can represent a significant power resource for the grid. An IVCI with bi-direction V2G capabilities would allow PEVs to provide grid support services and thus generate a source of revenue for PEV owners. The fleet of EV Project vehicles represents a power resource between 30 MW and 90 MW, depending on the power rating of the grid connection (5-15 kW). Aggregation of vehicle capacity would allow PEVs to participate in wholesale reserve capacity markets. One of the key insights from EV Project data is the fact that vehicles are connected to an EVSE much longer than is necessary to deliver a full charge. During these hours when the vehicles are not charging, they can be participating in wholesale power markets providing the high-value services of regulation and spinning reserves. The annual gross revenue potential for providing these services using the fleet of EV Project vehicles is several hundred thousands of dollars to several million dollars annually depending on the power rating of the grid interface, the number of hours providing grid services, and the market being served. On a per vehicle basis, providing grid services can generate several thousands of dollars over the life of the vehicle.

  7. An Annotated Bibliography of MANPRINT-Related Assessments and Evaluations Conducted by the U.S. Army, 2nd Edition: 1953 to 2009. Volume 1- Index

    DTIC Science & Technology

    2010-02-01

    22302-1458. FSTD, Ft. Sill, OK. DTIC ADB249574 Bayer , C., Kreko, Z., Raleigh, D., Dobbs, S., Thompson, P., & Shandle, G. (2005). System Assessment... Raymond , M. E., Rouse, J., & Padgett, D. (2006). System Evaluation Report (SER) for the Family of Medium Tactical Vehicles A1 Rebuy (FMTV A1R) Expansible...ADB322995. Sykes, M., Catalano, E., Horn, C., Emery, B., Halcisak, S., Rouse, J., Jennings, S., & Raymond , M. E. (2006). System Evaluation Report

  8. The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes.

    PubMed

    Vincze, Veronika; Szarvas, György; Farkas, Richárd; Móra, György; Csirik, János

    2008-11-19

    Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus). The corpus consists of three parts, namely medical free texts, biological full papers and biological scientific abstracts. The dataset contains annotations at the token level for negative and speculative keywords and at the sentence level for their linguistic scope. The annotation process was carried out by two independent linguist annotators and a chief linguist--also responsible for setting up the annotation guidelines --who resolved cases where the annotators disagreed. The resulting corpus consists of more than 20.000 sentences that were considered for annotation and over 10% of them actually contain one (or more) linguistic annotation suggesting negation or uncertainty. Statistics are reported on corpus size, ambiguity levels and the consistency of annotations. The corpus is accessible for academic purposes and is free of charge. Apart from the intended goal of serving as a common resource for the training, testing and comparing of biomedical Natural Language Processing systems, the corpus is also a good resource for the linguistic analysis of scientific and clinical texts.

  9. The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes

    PubMed Central

    Vincze, Veronika; Szarvas, György; Farkas, Richárd; Móra, György; Csirik, János

    2008-01-01

    Background Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus). Results The corpus consists of three parts, namely medical free texts, biological full papers and biological scientific abstracts. The dataset contains annotations at the token level for negative and speculative keywords and at the sentence level for their linguistic scope. The annotation process was carried out by two independent linguist annotators and a chief linguist – also responsible for setting up the annotation guidelines – who resolved cases where the annotators disagreed. The resulting corpus consists of more than 20.000 sentences that were considered for annotation and over 10% of them actually contain one (or more) linguistic annotation suggesting negation or uncertainty. Conclusion Statistics are reported on corpus size, ambiguity levels and the consistency of annotations. The corpus is accessible for academic purposes and is free of charge. Apart from the intended goal of serving as a common resource for the training, testing and comparing of biomedical Natural Language Processing systems, the corpus is also a good resource for the linguistic analysis of scientific and clinical texts. PMID:19025695

  10. Using Projects Scoring Rubrics to Assess Student Learning in an Information Systems Program

    ERIC Educational Resources Information Center

    Petkov, Doncho; Petkova, Olga; D'Onofrio, Marianne; Jarmoszko, A. T.

    2008-01-01

    This paper is about using projects for assessment of student learning in different courses of an Information Systems (IS) program. An overview of the role of educational projects in student learning is presented. The various aspects of defining standardized rubrics across an IS program are discussed. A methodology for the use of such rubrics in…

  11. Projecting other public inventories for the 2005 RPA timber assessment update.

    Treesearch

    Xiaoping Zhou; John R. Mills; Richard W. Haynes

    2007-01-01

    This study gives an overview of the current inventory status and the projection of future forest inventories on other public timberland. Other public lands are lands administered by state, local, and federal government but excluding National Forest System lands. These projections were used as part of the 2005 USDA Forest Service Resource Planning Act timber assessment...

  12. Implementation and Outcomes of Online Self and Peer Assessment on Group Based Honours Research Projects

    ERIC Educational Resources Information Center

    Wu, Chengqing; Chanda, Emmanuel; Willison, John

    2014-01-01

    Honours research projects in the School of Civil, Environmental and Mining Engineering at the University of Adelaide are run with small groups of students working with an academic supervisor in a chosen area for one year. The research project is mainly self-directed study, which makes it very difficult to fairly assess the contribution of…

  13. The Large Lecture Course Redesign Project: Pedagogical Goals and Assessment Results

    ERIC Educational Resources Information Center

    Aitken, Norman D.

    2005-01-01

    An analysis and assessment of the Course Redesign Project, which used technology to improve student learning and course satisfaction in large lecture courses at the University of Massachusetts Amherst. Six disciplinary-diverse departments participated in the project. Technology was selected for the purpose of introducing active learning into…

  14. Assessment of the Inquiry-Based Project Application in Science Education upon Turkish Science Teachers' Perspectives

    ERIC Educational Resources Information Center

    Akinoglu, Orhan

    2008-01-01

    Aim of the study is to assess the project works and application processes in science education of 6th, 7th and 8th grades in primary education upon teachers' perspectives. The research was fulfilled upon the descriptive survey model to collect data. Participants of the research were 90 teachers, having project management experience in science…

  15. Assessing Students' Conceptual Understanding in Science: An Introduction about a National Project in Taiwan

    ERIC Educational Resources Information Center

    Chiu, Mei-Hung; Guo, Chorng-Jee; Treagust, David F.

    2007-01-01

    In this article, we discuss several aspects of the national project, the National Science Concept Learning Study, designed to assess elementary, middle, and secondary students' conceptual understanding in science. After a short introduction to provide some history of the project, we describe the processes used in the integrative study, the…

  16. Understanding Project-Based Learning in Second Life with a Pedagogy, Training, and Assessment Trio

    ERIC Educational Resources Information Center

    Jarmon, Leslie; Traphagan, Tomoko; Mayrath, Michael

    2008-01-01

    This paper presents an empirical study of how Second Life (SL) was utilized for a highly successful project-based graduate interdisciplinary communication course. Researchers found that an integrated threefold approach emphasizing project-based pedagogy, technical training and support, and assessment/research was effective in cultivating and…

  17. Understanding Project-Based Learning in Second Life with a Pedagogy, Training, and Assessment Trio

    ERIC Educational Resources Information Center

    Jarmon, Leslie; Traphagan, Tomoko; Mayrath, Michael

    2008-01-01

    This paper presents an empirical study of how Second Life (SL) was utilized for a highly successful project-based graduate interdisciplinary communication course. Researchers found that an integrated threefold approach emphasizing project-based pedagogy, technical training and support, and assessment/research was effective in cultivating and…

  18. Implementation and Outcomes of Online Self and Peer Assessment on Group Based Honours Research Projects

    ERIC Educational Resources Information Center

    Wu, Chengqing; Chanda, Emmanuel; Willison, John

    2014-01-01

    Honours research projects in the School of Civil, Environmental and Mining Engineering at the University of Adelaide are run with small groups of students working with an academic supervisor in a chosen area for one year. The research project is mainly self-directed study, which makes it very difficult to fairly assess the contribution of…

  19. USGS National and Global Oil and Gas Assessment Project-Permian Basin Province, Midland Basin, Wolfcamp Shale Assessment Units

    USGS Publications Warehouse

    Gaswirth, Stephanie

    2016-01-01

    The Assessment Unit is the fundamental unit used in the National Assessment Project for the assessment of undiscovered oil and gas resources. The Assessment Unit is defined within the context of the higher-level Total Petroleum System. The Assessment Unit is shown herein as a geographic boundary interpreted, defined, and mapped by the geologist responsible for the province and incorporates a set of known or postulated oil and (or) gas accumulations sharing similar geologic, geographic, and temporal properties within the Total Petroleum System, such as source rock, timing, migration pathways, trapping mechanism, and hydrocarbon type. The Assessment Unit boundary is defined geologically as the limits of the geologic elements that define the Assessment Unit, such as limits of reservoir rock, geologic structures, source rock, and seal lithologies. The only exceptions to this are Assessment Units that border the Federal-State water boundary. In these cases, the Federal-State water boundary forms part of the Assessment Unit boundary.

  20. USGS National and Global Oil and Gas Assessment Project-Permian Basin Province, Val Verde Basin, Canyon Sandstones Assessment Units

    USGS Publications Warehouse

    Schenk, Christopher J.

    2016-01-01

    The Assessment Unit is the fundamental unit used in the National Assessment Project for the assessment of undiscovered oil and gas resources. The Assessment Unit is defined within the context of the higher-level Total Petroleum System. The Assessment Unit is shown herein as a geographic boundary interpreted, defined, and mapped by the geologist responsible for the province and incorporates a set of known or postulated oil and (or) gas accumulations sharing similar geologic, geographic, and temporal properties within the Total Petroleum System, such as source rock, timing, migration pathways, trapping mechanism, and hydrocarbon type. The Assessment Unit boundary is defined geologically as the limits of the geologic elements that define the Assessment Unit, such as limits of reservoir rock, geologic structures, source rock, and seal lithologies. The only exceptions to this are Assessment Units that border the Federal-State water boundary. In these cases, the Federal-State water boundary forms part of the Assessment Unit boundary.

  1. An Assessment of Stream Health in Urban Creeks with Community Led Improvement Projects

    NASA Astrophysics Data System (ADS)

    Sanchez, L.; Mercado, M.

    2016-12-01

    Small-scale restoration and improvement projects along urban creeks have become increasingly common and the need to assess their impact on stream health is necessary. Courtland and Peralta Creek have been subject to a variety of community, non-profit and city sponsored improvement projects. Assessment of nutrient contamination in the form of ammonia and nitrate indicate that these urban creeks have been impacted by human activity (Water Quality of Peralta and Courtland Creeks Oakland, CA, A. Ahumada). Continued assessment of the stream health through nitrate, ammonia and phosphate concentrations, benthic invertebrate derived biotic index and E. coli concentrations were used to assess site improvements. Youth and community site improvement project at Courtland Creek has resulted in the decline of nitrate contamination and an overall increase in benthic invertebrates species. Peralta Creek has a group of dedicated community volunteers that participate in clean up events but is just now implementing a planned restoration project increasing native plant diversity at the site.

  2. The Maricopa Integrated Risk Assessment Project: A New Way of Looking at Risk

    ERIC Educational Resources Information Center

    Unks, Ruth A.; Thor, Linda

    2008-01-01

    This article reviews the Maricopa Integrated Risk Assessment (MIRA) project and discusses its challenges and successes. Strategies and resources are offered for assisting community college administrators, faculty, and staff to successfully implement enterprise risk management at their institutions.

  3. Assessing Instructor Performance: A Classroom Project for an Industrial/Organizational Psychology Class.

    ERIC Educational Resources Information Center

    Kottke, Janet L.

    1984-01-01

    For a class project students in an industrial/organizational psychology course had to construct a performance appraisal instrument for assessing the instructor's performance. Evaluations revealed that students found the exercise useful. (RM)

  4. Assessing Instructor Performance: A Classroom Project for an Industrial/Organizational Psychology Class.

    ERIC Educational Resources Information Center

    Kottke, Janet L.

    1984-01-01

    For a class project students in an industrial/organizational psychology course had to construct a performance appraisal instrument for assessing the instructor's performance. Evaluations revealed that students found the exercise useful. (RM)

  5. Progress and implications from the grazing lands Conservation Effects Assessment Project (CEAP) literature syntheses

    USDA-ARS?s Scientific Manuscript database

    The Conservation Effects Assessment Project (CEAP) is a multiagency effort to quantify scientifically the environmental outcomes of conservation practices used by private landowners. Two syntheses of the scientific literature are underway, which will document the environmental outcomes of conservati...

  6. The Maricopa Integrated Risk Assessment Project: A New Way of Looking at Risk

    ERIC Educational Resources Information Center

    Unks, Ruth A.; Thor, Linda

    2008-01-01

    This article reviews the Maricopa Integrated Risk Assessment (MIRA) project and discusses its challenges and successes. Strategies and resources are offered for assisting community college administrators, faculty, and staff to successfully implement enterprise risk management at their institutions.

  7. 78 FR 43183 - Notice of Availability for Sharpe Permit Relinquishment Project Environmental Assessment Finding...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-19

    ... Availability (NOA) for Sharpe Permit Relinquishment Project Environmental Assessment (EA) Finding of No Significant Impact (FONSI). SUMMARY: On April 30, 2013, Defense Logistics Agency (DLA) published a NOA in...

  8. Preserving sequence annotations across reference sequences.

    PubMed

    Tatum, Zuotian; Roos, Marco; Gibson, Andrew P; Taschner, Peter Em; Thompson, Mark; Schultes, Erik A; Laros, Jeroen Fj

    2014-01-01

    Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO.

  9. Preserving sequence annotations across reference sequences

    PubMed Central

    2014-01-01

    Background Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. Results As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. Conclusions We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO. PMID:25093075

  10. LNG annotated bibliography

    SciTech Connect

    Bomelburg, H.J.; Counts, C.A.; Cowan, C.E.; Davis, W.E.; DeSteese, J.G.; Pelto, P.J.

    1982-09-01

    This document updates the bibliography published in Liquefied Gaseous Fuels Safety and Environmental Control Assessment Program: third status report (PNL-4172) and is a complete listing of literature reviewed and reported under the LNG Technical Surveillance Task. The bibliography is organized alphabetically by author.

  11. Polarimetric Interferometric SAR: Literature Review and an Assessment of its Utility for DND: TIF Project Memorandum

    DTIC Science & Technology

    2003-09-01

    SAR : Literature Review and an Assessment of its utility for DND TIF Project.Memorandum Karim E. Mattar, Maureen L. Yeremy and Chuck Livingstone...September 2003 Canada 20031119 057 Polarimetric Interferometric SAR : Literature Review and an Assessment of its utility for DND TIF Project Memorandum Karim...Radar ( SAR ) is a recent area of research that has had significant attention from the mid-1990s. This area of research has combined the utility of two SAR

  12. Facility assessment summary report for project W-314, tank farm restoration and safe operations

    SciTech Connect

    Jacobson, R.W.

    1996-06-13

    The Facility Assessment Summary Report (FSAR) is a key element in the systems engineering document hierarchy, and provides an evaluation overview of the physical conditions and requirements for upgrading facility systems, subsystems, and/or components (SSC). This Project W- 314 FASR was prepared to address the evaluations, inspections, and assessments conducted on the Tank Farm facilities associated with the preliminary Project W-314 scope, and to provide requirements for specifying necessary upgrades.

  13. Solar Radiation Resource Assessment Project. Program overview of fiscal year 1993

    SciTech Connect

    Not Available

    1994-06-01

    The mission of the Solar Radiation Resource Assessment Project is to provide essential information about the solar radiation resource to users and planners of solar technologies so that they can make informed and timely decisions concerning applications of those technologies. The project team accomplishes this by producing and disseminating relevant and reliable information about solar radiation. Topics include: Variability of solar radiation, measurements of solar radiation, spectral distribution of solar radiation, and assessment of the solar resource. FY 1993 accomplishments are detailed.

  14. Business and Industry Project-Based Capstone Courses: Selecting Projects and Assessing Learning Outcomes

    ERIC Educational Resources Information Center

    Maleki, Reza A.

    2009-01-01

    This is the first of two articles in which the author shares experiences gained from the development and delivery of a business/industry project-based capstone course. The course integrates research, proposal development and design experience based on knowledge and skills acquired in earlier coursework. The course also incorporates standards and…

  15. The Project on Assessing Long Distance Learning via Telecommunications. Project ALLTEL. A Summary Report.

    ERIC Educational Resources Information Center

    Chaloux, Bruce N.

    This summary report describes efforts to bridge developments in the use of technology in delivering higher education services with the traditional roles and responsibilities of state agencies, accrediting bodies, and institutions (Project ALLTEL). Designed to suggest policies and procedures to states and accrediting institutions charged with…

  16. The agricultural model intercomparison and improvement project (AgMIP) integrated regional assessment project

    USDA-ARS?s Scientific Manuscript database

    The worldwide sector faces the significant challenge of increasing production to provide food security for a population projected to rise to nine billion by mid-century, while protecting the environment and the sustainable functioning of ecosystems. This challenge is compounded by the need to adapt ...

  17. GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets

    PubMed Central

    Bastos, Hugo P.; Sousa, Lisete; Clarke, Luka A.; Couto, Francisco M.

    2015-01-01

    Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding the interpretation of actual functional similarity and overall functional coherence of such a group. One way to mitigate such issues is through the use of visualization and statistical techniques. Therefore, in order to help interpret this annotation heterogeneity we created a web application that generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and Information Content based metrics. The publicly accessible website http://xldb.di.fc.ul.pt/gryfun/ currently accepts lists of UniProt accession numbers in order to create user-defined protein sets for subsequent annotation visualization and statistical assessment. GRYFUN is a freely available web application that allows GO annotation visualization of protein sets and which can be used for annotation coherence and cohesiveness analysis and annotation extension assessments within under-annotated protein sets. PMID:25794277

  18. GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

    PubMed

    Bastos, Hugo P; Sousa, Lisete; Clarke, Luka A; Couto, Francisco M

    2015-01-01

    Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding the interpretation of actual functional similarity and overall functional coherence of such a group. One way to mitigate such issues is through the use of visualization and statistical techniques. Therefore, in order to help interpret this annotation heterogeneity we created a web application that generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and Information Content based metrics. The publicly accessible website http://xldb.di.fc.ul.pt/gryfun/ currently accepts lists of UniProt accession numbers in order to create user-defined protein sets for subsequent annotation visualization and statistical assessment. GRYFUN is a freely available web application that allows GO annotation visualization of protein sets and which can be used for annotation coherence and cohesiveness analysis and annotation extension assessments within under-annotated protein sets.

  19. Assessing Australian Rainfall Projections in Two Model Resolutions

    NASA Astrophysics Data System (ADS)

    Taschetto, A.; Haarsma, R. D.; Sen Gupta, A.

    2016-02-01

    Australian climate is projected to change with increases in greenhouse gases. The IPCC reports an increase in extreme daily rainfall across the country. At the same time, mean rainfall over southeast Australia is projected to reduce during austral winter, but to increase during austral summer, mainly associated with changes in the surrounding oceans. Climate models agree better on the future reduction of average rainfall over the southern regions of Australia compared to the increase in extreme rainfall events. One of the reasons for this disagreement may be related to climate model limitations in simulating the observed mechanisms associated with the mid-latitude weather systems, in particular due to coarse model resolutions. In this study we investigate how changes in sea surface temperature (SST) affect Australian mean and extreme rainfall under global warming, using a suite of numerical experiments at two model resolutions: about 126km (T159) and 25km (T799). The numerical experiments are performed with the earth system model EC-EARTH. Two 6-member ensembles are produced for the present day conditions and a future scenario. The present day ensemble is forced with the observed daily SST from the NOAA National Climatic Data Center from 2002 to 2006. The future scenario simulation is integrated from 2094 to 2098 using the present day SST field added onto the future SST change created from a 17-member ensemble based on the RCP4.5 scenario. Preliminary results show an increase in extreme rainfall events over Tasmania associated with enhanced convection driven by the Tasman Sea warming. We will further discuss how the projected changes in SST will impact the southern mid-latitude weather systems that ultimately affect Australian rainfall.

  20. Environment Assessment: Mill Creek - South Slough, Deauthorization Project, Milan, Illinois

    DTIC Science & Technology

    1992-03-01

    2004 Rock Island, Illinois 61204-2004 Sincerely, John R. Brown Colonel, U.S. Army District Engineer Enclosure DEPARTMENT OF THE ARMY ROCK ISLAND...the project area are anticipated. John R. Brown Date Colonel, U.S. Army District Engineer lt DAVErIL 4-- 1W ROK SLNDERý A ;;Q!-. -’.-.---- -r 4 .41a Vý...61201 COM: 309/793-5800 FTS: 782-5800 February 13, 1992 Colonel John R. Brown District Engineer U.S. Army Engineer District ATTN: Planning Division