Science.gov

Sample records for annual publication ngs

  1. NGS for the Masses: Empowering Biologists to Improve Bioinformatics Productivity ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Qaadri, Kashef [Biomatters

    2016-07-12

    Kashef Qaadri on "NGS for the Masses: Empowering biologists to improve bioinformatic productivity" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  2. NGS for the Masses: Empowering Biologists to Improve Bioinformatics Productivity ( 7th Annual SFAF Meeting, 2012)

    SciTech Connect

    Qaadri, Kashef

    2012-06-01

    Kashef Qaadri on "NGS for the Masses: Empowering biologists to improve bioinformatic productivity" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  3. Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Gilbert, Tom

    2013-03-01

    Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  4. 78 FR 23960 - Annual Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-23

    ... THE FOOD AND DRUG ADMINISTRATION Annual Public Meeting ACTION: Notice of annual meeting. SUMMARY: The Reagan-Udall Foundation for the Food and Drug Administration (FDA), which was created by Title VI of the Food and Drug Amendments of 2007, is announcing an annual open public meeting. The Foundation...

  5. 77 FR 26585 - Annual Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-04

    ... THE FOOD AND DRUG ADMINISTRATION Annual Public Meeting ACTION: Notice of annual meeting. SUMMARY: The Reagan-Udall Foundation for the Food and Drug Administration (FDA), which was created by Title VI of the Food and Drug Amendments of 2007, is announcing an annual open public meeting. The Foundation...

  6. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

    PubMed Central

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J.; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  7. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    PubMed

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  8. Alabama Public Library Service, 1987 Annual Report.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    Designed to provide an overview of the range and quality of services provided by the Alabama Public Library Service (APLS), this annual report focuses on the 1987 activities of APLS. A report on the activities of the Library Development Division shows the allocation of state aid and Library Services and Construction Act (LCSA) Titles I and III…

  9. Alabama Public Library Service Annual Report, 1989.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This annual report highlights the accomplishments of the Alabama Public Library Service (APLS) during 1989. Introductory materials include a map of Alabama's Congressional districts, photographs of the executive board of APLS, and comments from the chairman of the executive board and from APLS' director. The following accomplishments are then…

  10. Alabama Public Library Service Annual Report, 1990.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This annual report highlights the accomplishments of the Alabama Public Library Service (APLS) during 1990. Introductory materials include a map of Alabama's Congressional districts, photographs of the executive board of APLS, and comments from the chairman of the executive board and from APLS' director. Accomplishments are reported under the…

  11. Alabama Public Library Service Annual Report, 1990.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This annual report highlights the accomplishments of the Alabama Public Library Service (APLS) during 1990. Introductory materials include a map of Alabama's Congressional districts, photographs of the executive board of APLS, and comments from the chairman of the executive board and from APLS' director. Accomplishments are reported under the…

  12. Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS

    PubMed Central

    Tosar, Juan Pablo; Rovira, Carlos; Naya, Hugo; Cayota, Alfonso

    2014-01-01

    The report that exogenous plant miRNAs are able to cross the mammalian gastrointestinal tract and exert gene-regulation mechanism in mammalian tissues has yielded a lot of controversy, both in the public press and the scientific literature. Despite the initial enthusiasm, reproducibility of these results was recently questioned by several authors. To analyze the causes of this unease, we searched for diet-derived miRNAs in deep-sequencing libraries performed by ourselves and others. We found variable amounts of plant miRNAs in publicly available small RNA-seq data sets of human tissues. In human spermatozoa, exogenous RNAs reached extreme, biologically meaningless levels. On the contrary, plant miRNAs were not detected in our sequencing of human sperm cells, which was performed in the absence of any known sources of plant contamination. We designed an experiment to show that cross-contamination during library preparation is a source of exogenous RNAs. These contamination-derived exogenous sequences even resisted oxidation with sodium periodate. To test the assumption that diet-derived miRNAs were actually contamination-derived, we sought in the literature for previous sequencing reports performed by the same group which reported the initial finding. We analyzed the spectra of plant miRNAs in a small RNA sequencing study performed in amphioxus by this group in 2009 and we found a very strong correlation with the plant miRNAs which they later reported in human sera. Even though contamination with exogenous sequences may be easy to detect, cross-contamination between samples from the same organism can go completely unnoticed, possibly affecting conclusions derived from NGS transcriptomics. PMID:24729469

  13. NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

    PubMed Central

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2015-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. PMID:22517761

  14. NGS catalog: A database of next generation sequencing studies in humans.

    PubMed

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2012-06-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. © 2012 Wiley Periodicals, Inc.

  15. Advancing Public Health in Cancer - Annual Plan

    Cancer.gov

    Cancer is the leading cause of death from disease among Americans under 85. Learn how NCI advances public health by conducting research to improve the delivery of quality cancer prevention, screening, and treatment to all Americans.

  16. Airborne Gravity Data Enhances NGS Experimental Gravimetric Geoid in Alaska

    NASA Astrophysics Data System (ADS)

    Holmes, S. A.; Childers, V. A.; Li, X.; Roman, D. R.

    2014-12-01

    The U.S. National Geodetic Survey [NGS], through their Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, continues to update its gravimetry holdings by flying new airborne gravity surveys over a large fraction of the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field by using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Several airborne campaigns have already been flown over Alaska and its coastline. Some of this Alaskan coastal data have been incorporated into a new NGS experimental geoid model - xGEOID14. The xGEOID14 model is the first in a series of annual experimental geoid models that will incorporate NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques by which the airborne and land-survey data are filtered and cleaned, and then combined with satellite gravity models, elevation data (etc.) with the ultimate aim of computing a geoid model that can support a national physical height system by 2022. Here we will examine the NGS GRAV-D airborne data in Alaska, and assess its contribution to xGEOID14. Future prospects for xGEOID15 will also be considered.

  17. National Alliance for Public Charter Schools 2015 Annual Report

    ERIC Educational Resources Information Center

    National Alliance for Public Charter Schools, 2016

    2016-01-01

    This 2015 annual report shares many of the accomplishments achieved by the National Alliance for Public Charter Schools in 2015 including the celebration of their 10th anniversary. Among other achievements, the report highlights: (1) At the end of 2015 Congress and the President agreed to an $80 million increase in support for the federal Charter…

  18. Utah Public Library Service, 2001: An Annual Report.

    ERIC Educational Resources Information Center

    Long, Sandi

    This annual report of Utah public library services presents data useful for local library planning. This information is presented in two sections: core performance measures and general tables. Statewide summary data and breakouts by the populations of the library jurisdictions are provided for the following core performance measures: (1) visits…

  19. The 41st Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Bushaw, William J.; McNee, John A.

    2009-01-01

    The authors report the findings of the 41st Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools. The annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools is unique because it's not an advocacy poll, but rather a thoughtful study of Americans' current perceptions of their public schools. Each…

  20. Public expectations and attitudes for annual physical examinations and testing.

    PubMed

    Oboler, Sylvia K; Prochazka, Allan V; Gonzales, Ralph; Xu, Stanley; Anderson, Robert J

    2002-05-07

    Recent guidelines for adult prevention do not recommend a comprehensive annual physical examination, but current public expectations in light of this change are unknown. To determine public belief in the need for and content of an annual physical examination and to examine the effect of financial charges on these beliefs. Telephone survey. Three U.S. cities. Adult English-speaking respondents. Percentage of respondents answering that an annual physical examination is necessary and percentage desiring individual components of the history, physical examination, and laboratory testing, with and without knowledge of charges. Of 1203 respondents, 66% (67% in Denver, Colorado; 71% in Boston, Massachusetts; and 58% in San Diego, California) believed that in addition to regular care, an annual physical examination is necessary. Among the 600 respondents presented with charge information, interest decreased from 63% to 33% if payment were required. For history, greater than 90% believed that diet, exercise, and tobacco and alcohol use should be discussed, while 60% believed that seatbelt use and sexual history should be discussed. For the physical examination, greater than 90% felt that blood pressure should be measured and that the heart and lungs, abdomen, reflexes, and prostate should be examined. However, fewer than 80% thought that hearing and vision should be tested. Many tests, including the Papanicolaou smear (75%), mammography (71%), cholesterol measurement (65%), prostate-specific antigen test (65%), urinalysis (40%), blood glucose measurement (41%), fecal occult blood testing (39%), and chest radiography (36%), were desired. Interest in these tests decreased substantially when the charges were known. Public desire for a comprehensive annual physical examination is high across the United States and is sensitive to charges.

  1. Why School? The 48th Annual PDK Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Phi Delta Kappan, 2016

    2016-01-01

    Why school? The 48th Annual PDK Poll of the Public's Attitudes Toward the Public Schools included questions about the purpose of schooling, standards, homework, school funding, and parents' relationships with their schools. The 2016 poll, which was conducted by Langer Research Associates, was based on a telephone poll of 1,221 adults during April…

  2. CPB and the Public Interest. The Corporation for Public Broadcasting 1976 Annual Report.

    ERIC Educational Resources Information Center

    Corporation for Public Broadcasting, Washington, DC.

    The mission of the Corporation for Public Broadcasting (CPB) is to take the lead in helping develop a uniquely American non-commercial public radio-television system that will inform, enlighten, entertain, and enrich the lives of people. In their annual report for fiscal year 1976, CPB lists as its activities: (1) a satellite interconnection plan…

  3. 78 FR 57378 - Proposed Information Collection Request; Comment Request; Annual Public Water System Compliance...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-18

    ... AGENCY Proposed Information Collection Request; Comment Request; Annual Public Water System Compliance... Protection Agency is planning to submit an information collection request (ICR), ``Annual Public Water System... available to the public, and submit to the Administrator of EPA, an annual report of violations of...

  4. 86(th) Annual Georgia Public Health Association Meeting & Conference Report.

    PubMed

    Smith, Selina A; Abbott, Regina; Sims, Christy

    2015-01-01

    The 86(th) annual meeting of the Georgia Public Health Association (GPHA) and joint conference with the Southern Health Association was held in Atlanta, Georgia, on April 13-14, 2015, with pre-conference (April 12(th)) and post-conference (April 14(th)) Executive Board meetings. As Georgia's leading forum for public health researchers, practitioners, and students, the annual meeting of the GPHA brings together participants from across the state to explore recent developments in the field and to exchange techniques, tools, and experiences. Historically, the GPHA conference has been held in Savannah (n=24); Jekyll Island (n=20); Atlanta (n=16); Augusta (n=4); and Gainesville (n=1). There was no annual meeting during the early years (1929-1936); during World War II (1941-1943 and 1945); and for four years during the 1980s. Between 2006 and 2010, GPHA held one-day annual meetings and business sessions with educational workshops. Several new initiatives were highlighted as part of this year's conference. These included a "move and groove" physical activity lounge, registration scholarships for students with a dedicated meet-and-greet reception, an expanded exhibit hall, presentation and approval of three resolutions (related to healthy foods at official activities and events; weapons at official activities and events; and memorials), and approval of the 2015 legislative policy positions and amended association bylaws. The theme for the conference was Advocacy in Action for Public Health. Specifically, the program addressed ensuring access to care; protecting funding for core programs, services, and infrastructure; eliminating health disparities; and addressing key public health issues important to the state of Georgia. One hundred and nine (109) abstracts were submitted for peer review; 36 were accepted for poster and 40 for workshop presentations. Four plenary sessions with keynote speakers covered the intersection between advocacy and policy, Georgia's response to the

  5. 86th Annual Georgia Public Health Association Meeting & Conference Report

    PubMed Central

    Smith, Selina A.; Abbott, Regina; Sims, Christy

    2015-01-01

    EXECUTIVE SUMMARY The 86th annual meeting of the Georgia Public Health Association (GPHA) and joint conference with the Southern Health Association was held in Atlanta, Georgia, on April 13–14, 2015, with pre-conference (April 12th) and post-conference (April 14th) Executive Board meetings. As Georgia’s leading forum for public health researchers, practitioners, and students, the annual meeting of the GPHA brings together participants from across the state to explore recent developments in the field and to exchange techniques, tools, and experiences. Historically, the GPHA conference has been held in Savannah (n=24); Jekyll Island (n=20); Atlanta (n=16); Augusta (n=4); and Gainesville (n=1). There was no annual meeting during the early years (1929–1936); during World War II (1941–1943 and 1945); and for four years during the 1980s. Between 2006 and 2010, GPHA held one-day annual meetings and business sessions with educational workshops. Several new initiatives were highlighted as part of this year’s conference. These included a “move and groove” physical activity lounge, registration scholarships for students with a dedicated meet-and-greet reception, an expanded exhibit hall, presentation and approval of three resolutions (related to healthy foods at official activities and events; weapons at official activities and events; and memorials), and approval of the 2015 legislative policy positions and amended association bylaws. The theme for the conference was Advocacy in Action for Public Health. Specifically, the program addressed ensuring access to care; protecting funding for core programs, services, and infrastructure; eliminating health disparities; and addressing key public health issues important to the state of Georgia. One hundred and nine (109) abstracts were submitted for peer review; 36 were accepted for poster and 40 for workshop presentations. Four plenary sessions with keynote speakers covered the intersection between advocacy and policy

  6. 46 CFR 503.34 - Annual report of public information request activity.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 9 2010-10-01 2010-10-01 false Annual report of public information request activity... PUBLIC INFORMATION Requests for Records Under the Freedom of Information § 503.34 Annual report of public information request activity. (a) On or before February 1 of each year, the Commission shall submit to the...

  7. Oak Ridge Reservation Public Warning Siren System Annual Test Report

    SciTech Connect

    R. F. Gee

    2000-10-01

    The full operational test of the Oak Ridge Reservation (ORR) Public Warning Siren System (PWSS) was successfully conducted on September 27, 2000. The annual test is a full-scale sounding of the individual siren systems around each of the three Department of Energy (DOE) sites in Oak Ridge, Tennessee. The purpose of the annual test is to demonstrate and validate the siren systems' ability to alert personnel outdoors in the Immediate Notification Zones (INZ) (approximately two miles) around each site. The success of this test is based on two critical functions of the siren system. The first function is system operability. The system is considered operable if 90% of the sirens are operational. System diagnostics and direct field observations were used to validate the operability of the siren systems. Based on the diagnostic results and field observations, greater than 90% of the sirens were considered operational. The second function is system audibility. The system is considered audible if the siren could be heard in the immediate notification zones around each of the three sites. Direct field observations, along with sound level measurements, were used to validate the audibility of the siren system. Based on the direct field observations and sound level measurements, the siren system was considered audible. The combination of field observations, system diagnostic status reports, and sound level measurements provided a high level of confidence that the system met and would meet operational requirements upon demand. As part of the overall system test, the Tennessee Emergency Management Agency (TEMA) activated the Emergency Alerting System (EAS), which utilized area radio stations to make announcements regarding the test and to remind residents of what to do in the event of an actual emergency.

  8. 5 CFR 831.681 - Annual notice required by Public Law 95-317.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Annual notice required by Public Law 95-317. 831.681 Section 831.681 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL... Statutes § 831.681 Annual notice required by Public Law 95-317. At least once every 12 consecutive...

  9. 78 FR 13912 - Sunshine Act; Cancellation Notice of Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-01

    ... From the Federal Register Online via the Government Publishing Office OVERSEAS PRIVATE INVESTMENT CORPORATION Sunshine Act; Cancellation Notice of Annual Public Hearing OPIC's Sunshine Act notice of its Annual Public Hearing was published in the Federal Register (Volume 78, Number 17, Page 5516) on...

  10. The 38th Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Rose, Lowell C.; Gallup, Alec M.

    2006-01-01

    Rose and Gallup report on the results of the 38th Annual PDK/Gallup Poll of the Public's Attitude Toward the Public Schools. This year's survey examined No Child Left Behind and the public's perception of the law, the appropriate role of standardized testing, the achievement gap between white students and black and Hispanic students, the…

  11. Privacy Act of 1974; annual publication of systems of records--PHS.

    PubMed

    1985-10-10

    PHS is publishing a complete inventory of its current systems of records. Pub. L. 97-375, the Congressional Reports Elimination Act, amended the Privacy Act to eliminate the requirement for an annual republication of the system notices themselves. PHS agencies have reviewed their systems of records and found no significant changes since the 1984 annual publication. PHS has added four new systems of records to its inventory since the 1984 annual review; eleven systems have been deleted.

  12. TOGGLE: toolbox for generic NGS analyses.

    PubMed

    Monat, Cécile; Tranchant-Dubreuil, Christine; Kougbeadjo, Ayité; Farcy, Cédric; Ortega-Abboud, Enrique; Amanzougarene, Souhila; Ravel, Sébastien; Agbessi, Mawussé; Orjuela-Bouniol, Julie; Summo, Maryline; Sabot, François

    2015-11-09

    The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The creation of dedicated, robust and reliable pipelines able to handle dozens of samples from raw FASTQ data to relevant biological data is a time-consuming task in all projects relying on NGS. To address this, we created a generic and modular toolbox for developing such pipelines. TOGGLE (TOolbox for Generic nGs anaLysEs) is a suite of tools able to design pipelines that manage large sets of NGS softwares and utilities. Moreover, TOGGLE offers an easy way to manipulate the various options of the different softwares through the pipelines in using a single basic configuration file, which can be changed for each assay without having to change the code itself. We also describe one implementation of TOGGLE in a complete analysis pipeline designed for SNP discovery for large sets of genomic data, ready to use in different environments (from a single machine to HPC clusters). TOGGLE speeds up the creation of robust pipelines with reliable log tracking and data flow, for a large range of analyses. Moreover, it enables Biologists to concentrate on the biological relevance of results, and change the experimental conditions easily. The whole code and test data are available at https://github.com/SouthGreenPlatform/TOGGLE .

  13. Use of NGS in Commercial Broiler Production

    USDA-ARS?s Scientific Manuscript database

    With the development and evolution of next generation sequencing technologies, these powerful tools can be applied to a variety of aspect of commercial broiler production, especially in respect to food safety issues. NGS technologies allow for a deeper understanding of the complex microbiota inhere...

  14. 76 FR 69769 - Annual Public Meeting of the Interagency Steering Committee on Multimedia Environmental Modeling

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-09

    ... COMMISSION Annual Public Meeting of the Interagency Steering Committee on Multimedia Environmental Modeling... the Federal Interagency Steering Committee on Multimedia Environmental Modeling (ISCMEM) will convene...: Background: In 2001, six Federal agencies began formal cooperation under a Memorandum of Understanding...

  15. Publication rate of paper presentations from the Cervical Spine Research Society annual meeting.

    PubMed

    Okafor, Louis; Frost, Chelsea; Mesfin, Addisu

    2015-05-15

    Observational study. To evaluate the publication rate of podium presentations from the Cervical Spine Research Society (CSRS) annual meeting and to evaluate the publication rate of award-winning papers from the CSRS annual meeting. Although various publication rates from Orthopaedic meetings have been reported, the publication rates from the CSRS annual meetings are not known. Paper presentations and award-winning papers from the 2007 to 2011 annual CSRS meeting were identified. Using PubMed, we searched for publications with a title of the paper presentations or containing the same authors. The publication rate of the award-winning papers was evaluated in the same manner. We collected the title of the journals the papers were published in and identified the most common journals. Of the 321 podium presentations, 211 were published (65.7%). The publication rate was highest for 2007 abstracts (77.8%), followed by 2008 and 2011 (68.5%) and lowest for 2009 (58.5%). Of the 45 award-winning papers, 35 were published (77.8%), which was significantly different compared with the non-award-winning papers (63.8%, P=0.046). Spine, The Spine Journal, and Journal of Neurosurgery: Spine were the most common publication journals for the papers. In one of the first studies evaluating the publication rate of podium presentation from the CSRS annual meetings, we found an overall publication rate of 65.8% and 77.8% for award-winning papers. This high publication rate indicates the quality of papers presented at the CSRS annual meeting. 4.

  16. Annual State of Public Education Report, 2012-2013

    ERIC Educational Resources Information Center

    Guam Department of Education, 2013

    2013-01-01

    This report addresses the reporting requirements of Public Law 26-26 and the provisions of "No Child Left Behind" ("NCLB") as described in the Guam Department of Education Board adopted "District Action Plan" ("DAP"). Public Law 26-26, Section 3106 states that "No later than thirty (30) days following…

  17. SY 08-09 Annual State of Public Education Report

    ERIC Educational Resources Information Center

    Guam Department of Education, 2009

    2009-01-01

    The report addresses the reporting requirements of Public Law 26-26 and the provisions of No Child Left Behind (NCLB) as described in the Guam Department of Education Board adopted District Action Plan (DAP). Public Law 26-26, Section 3106 (a) states that "No later than thirty (30) days following the end of each fiscal year, the…

  18. Student Charges at Public Institutions. Annual Survey 1989-90.

    ERIC Educational Resources Information Center

    Nathanson, Jeanne H.; Ludwig, Meredith J.

    The 1990 report on student charges at public colleges and universities describes the costs of attending about 90 percent of the national publicly assisted, four-year institutions. The report uses data compiled by the American Association of State Colleges and Universities (AASCU) and the National Association of State Universities and Land-Grand…

  19. Student Charges at Public Institutions: Annual Survey 1988-89.

    ERIC Educational Resources Information Center

    Ludwig, Meredith; And Others

    The 1988 report on student charges at public colleges and universities compiled by the American Association of State Colleges and Universities (AASCU) and the National Association of State Universities and Land Grant Colleges (NASULGC) describes the costs of attending about 90% of the nation's publicly assisted, four-year institutions of higher…

  20. Annual State of Public Education Report, SY 2015-2016

    ERIC Educational Resources Information Center

    Guam Department of Education, 2016

    2016-01-01

    This report addresses the reporting requirements of Public Law 26-26 and the provisions of "No Child Left Behind" ("NCLB") as described in the Guam Department of Education Board adopted "District Action Plan" ("DAP"). Public Law 26-26, Section 3106 states that "No later than thirty (30) days following…

  1. Annual State of Public Education Report, SY 2014-2015

    ERIC Educational Resources Information Center

    Guam Department of Education, 2015

    2015-01-01

    This report addresses the reporting requirements of Public Law 26-26 and the provisions of "No Child Left Behind" ("NCLB") as described in the Guam Department of Education Board adopted "District Action Plan" ("DAP"). Public Law 26-26, Section 3106 states that "No later than thirty (30) days following…

  2. Annual State of Public Education Report, SY 2013-2014

    ERIC Educational Resources Information Center

    Guam Department of Education, 2014

    2014-01-01

    This report addresses the reporting requirements of Public Law 26-26 and the provisions of "No Child Left Behind" ("NCLB") as described in the Guam Department of Education Board adopted "District Action Plan" ("DAP"). Public Law 26-26, Section 3106 states that "No later than thirty (30) days following…

  3. Factors influencing publication of abstracts presented at the AAO-HNS Annual Meeting.

    PubMed

    Peng, Phyllis H; Wasserman, Jared M; Rosenfeld, Richard M

    2006-08-01

    To examine abstracts presented at the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS) Annual Meeting and to identify factors associated with publication success. All abstracts published in the August 1999 official program issue of the AAO-HNS Journal were examined. MEDLINE searches were performed to assess publication success. Multivariate analysis was performed to identify factors related to successful publication. We identified 473 abstracts, of which 260 (55%) were poster presentations. Median publication time was 16 months, with a publication rate of 50%. Multivariate analysis revealed oral presentation, statistical analysis, and number of authors to be the most significant predictive factors of publication success (odds ratios of 2.2, 1.9, and 1.2 respectively). Level of evidence did not correlate with publication success, even when case reports (n = 70) were excluded from the analysis. Publication rates in other disciplines ranged from 25% to 68%, with a mean of 47%. The rate of publication from the AAO-HNS Annual Meeting is similar to other disciplines. Oral presentations with inferential statistics in the abstract were most likely to be published. Conversely, level of evidence and direction of study inquiry were not significant predictors, suggesting that research design is a less important determinant of publication success. Our investigation is one of the first to critically analyze the factors in presentations at annual meetings that predict successful publication.

  4. Rethinking Annual Reports: A New Look at the Old Standby of the Campus Publications Office.

    ERIC Educational Resources Information Center

    Phair, Judith T.

    1992-01-01

    The annual report, still vital to most colleges, is a key tool in communicating with the public for fund raising, community and government relations, student recruitment, and public relations. Format and content are more flexible, and institutions are making efforts to be environmentally conscious and save time and money. (MSE)

  5. Statewide Report Card: An Annual Report to the Legislature on Oregon Public Schools, 2013-2014

    ERIC Educational Resources Information Center

    Oregon Department of Education, 2014

    2014-01-01

    The Oregon Statewide Report Card is an annual publication required by law (ORS 329.115), which reports on the state of public schools and their progress towards the goals of the Oregon Educational Act for the 21st Century. The purpose of the Oregon Report Card is to monitor trends among school districts and Oregon's progress toward achieving the…

  6. Statewide Report Card: An Annual Report to the Legislature on Oregon Public Schools, 2011-2012

    ERIC Educational Resources Information Center

    Oregon Department of Education, 2012

    2012-01-01

    The Oregon Statewide Report Card is an annual publication required by law (ORS 329.115), which reports on the state of public schools and their progress towards the goals of the Oregon Educational Act for the 21st Century. The purpose of the Oregon Report Card is to monitor trends among school districts and Oregon's progress toward achieving the…

  7. Alabama Public Library Service, The State Library Agency. 1986 Annual Report.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    Designed to provide an overview of the range and quality of services provided by the Alabama Public Library Service (APLS), this annual report focuses on the 1986 activities of APLS; the state's public library directory and statistical report will be published separately. A discussion of the activities of the Library Development Division includes…

  8. 75 FR 81684 - Order Approving Public Company Accounting Oversight Board Budget and Annual Accounting Support...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-28

    ...; Release No. 34-63596/December 22, 2010] Order Approving Public Company Accounting Oversight Board Budget and Annual Accounting Support Fee for Calendar Year 2011 The Sarbanes-Oxley Act of 2002, as amended (the ``Sarbanes-Oxley Act''), established the Public Company Accounting Oversight Board (``PCAOB'') to...

  9. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Public Participation § 256.61 Requirements for public participation in the annual State work... sufficient interest. (c) The State shall comply with the requirements of Office of Management and...

  10. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Public Participation § 256.61 Requirements for public participation in the annual State work... sufficient interest. (c) The State shall comply with the requirements of Office of Management and...

  11. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Public Participation § 256.61 Requirements for public participation in the annual State work... sufficient interest. (c) The State shall comply with the requirements of Office of Management and...

  12. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Public Participation § 256.61 Requirements for public participation in the annual State work... sufficient interest. (c) The State shall comply with the requirements of Office of Management and...

  13. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Public Participation § 256.61 Requirements for public participation in the annual State work... sufficient interest. (c) The State shall comply with the requirements of Office of Management and...

  14. 76 FR 17657 - Medical Device Epidemiology Network 2011: Second Annual Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-30

    ... HUMAN SERVICES Food and Drug Administration Medical Device Epidemiology Network 2011: Second Annual... and Drug Administration (FDA) is announcing a public workshop entitled ``Medical Device Epidemiology... for studying medical device performance. Date and Time: The public workshop will be held on April...

  15. 5 CFR 630.309 - Time limit for use of restored annual leave-extended exigency of the public business.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... leave-extended exigency of the public business. 630.309 Section 630.309 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ABSENCE AND LEAVE Annual Leave § 630.309 Time limit for use of restored annual leave—extended exigency of the public business. (a) Annual leave restored...

  16. Annual Statistical Report of the Public School of Arkansas and Education Service Cooperatives

    ERIC Educational Resources Information Center

    Arkansas Department of Education, 2016

    2016-01-01

    In compliance with the provisions of A.C.A.§§6-20-2201 et seq., the Annual Statistical Report of the Public Schools of Arkansas, Public Charter Schools, and Education Service Cooperatives, 2014-2015 Actual and 2015-2016 Budgeted, (ASR) is presented here. The Rankings of Selected Items of the Public Schools of Arkansas, 2014-2015 Actual, (Rankings)…

  17. Changing Expectations of College: The 47th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Phi Delta Kappan, 2015

    2015-01-01

    This installment reporting on the 47th Annual PDK/Gallup Poll of American's Attitudes Toward the Public Schools focuses on American's views of the value of a high school and a college education and the affordability of college. It is the first year the poll included enough respondents to be able to break out sentiments of specific demographic…

  18. 75 FR 76018 - Third Annual Sentinel Initiative Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-07

    .... Hosted by the Engelberg Center for Health Care Reform at The Brookings Institution, this 1-day public.... Department of Health and Human Services efforts that use distributed systems of automated health care data... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH...

  19. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    PubMed Central

    2011-01-01

    Background The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin. PMID:21635747

  20. Annual District Reports: New York City Public High Schools, 2000-2001.

    ERIC Educational Resources Information Center

    New York City Board of Education, Brooklyn. Div. of Assessment and Accountability.

    These eight annual district reports present statistical data on New York City public high schools. They include: the Brooklyn Superintendency; the Brooklyn and Staten Island High School (BASIS) Superintendency; the Bronx Superintendency; the Manhattan Superintendency; the Queens Superintendency; the Chancellor's District for High Schools; the…

  1. Annual Progress Report, 1976. Southern Rural Development Center, Mississippi State University. SRDC Series Publication No. 15.

    ERIC Educational Resources Information Center

    Southern Rural Development Center, State College, MS.

    Covering the 1976 activities of the Southern Rural Development Center (SRDC), this third annual report describes SRDC's: history; organization; regional workshops; functional networks; network bibliographies and other publications; Title V reports; grant received for training in rural development; orientation visits; consultants; information…

  2. 76 FR 34091 - Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-10

    ... URBAN DEVELOPMENT Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal, Periodic Updates and Noncompliance Reporting by FHA Approved Lenders AGENCY: Office of...: Reports Liaison Officer, Department of Housing and Urban Development, 451 7th Street, SW., Washington,...

  3. 75 FR 12251 - Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-15

    ... URBAN DEVELOPMENT Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal, Periodic Updates and Noncompliance Reporting by FHA Approved Lenders AGENCY: Office of... Housing and Urban Development, 451 7th Street, SW., Washington, DC 20410; e-mail...

  4. State Governance Action Annual 2004. Balancing Act: Public Higher Education in Transition

    ERIC Educational Resources Information Center

    Johnson, Neal C.; Longanecker, David A.

    2004-01-01

    In this annual report, AGB's Center for Public Trusteeship and Governance provides an up-to-date and insightful description of current state-level policy discussions and actions, many of which could significantly alter the nature of higher education governance in America. Some to the ideas presented in this report may not, on the surface, appear…

  5. 78 FR 13912 - Sunshine Act; Cancellation Notice of Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-01

    ... From the Federal Register Online via the Government Publishing Office OVERSEAS PRIVATE INVESTMENT CORPORATION Sunshine Act; Cancellation Notice of Annual Public Hearing TIME AND DATE: 3:00 p.m., Wednesday, March 13, 2013. PLACE: Offices of the Corporation, Twelfth Floor Board Room, 1100 New York Avenue NW...

  6. 77 FR 63323 - Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-16

    ... URBAN DEVELOPMENT Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal, Periodic Updates and Noncompliance Reporting by FHA Approved Lenders AGENCY: Office of...: Reports Liaison Officer, Department of Housing and Urban Development, 451 7th Street SW., Washington,...

  7. State Governance Action Annual 2004. Balancing Act: Public Higher Education in Transition

    ERIC Educational Resources Information Center

    Johnson, Neal C.; Longanecker, David A.

    2004-01-01

    In this annual report, AGB's Center for Public Trusteeship and Governance provides an up-to-date and insightful description of current state-level policy discussions and actions, many of which could significantly alter the nature of higher education governance in America. Some to the ideas presented in this report may not, on the surface, appear…

  8. 78 FR 59949 - Annual Factors for Determining Public Housing Agency Administrative Fees for the Section 8...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-30

    .... SUMMARY: This notice announces the availability on HUD's Web site of the annual factors for determining... HUD's Web site at http://portal.hud.gov/hudportal/HUD?src=/program_offices/public_indian_housing/programs/hcv . The notice posted on HUD's Web site provides the methodology that HUD used to determine...

  9. 75 FR 23242 - International Whaling Commission; 62nd Annual Meeting; Announcement of Public Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-03

    ... National Oceanic and Atmospheric Administration RIN 0648-XV74 International Whaling Commission; 62nd Annual... International Whaling Commission (IWC) meeting. DATES: The public meetings will be held May 20 and May 26, 2010... the Regulation of Whaling, 1946. The U.S. Commissioner has responsibility for the preparation and...

  10. 76 FR 30921 - International Whaling Commission; 63rd Annual Meeting; Announcement of Public Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-27

    ... National Oceanic and Atmospheric Administration RIN 0648-XA459 International Whaling Commission; 63rd... annual International Whaling Commission (IWC) meeting. DATES: The public meetings will be held June 14... International Convention for the Regulation of Whaling, 1946. The U.S. Commissioner has responsibility for the...

  11. 77 FR 25408 - International Whaling Commission; 64th Annual Meeting; Announcement of Public Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-30

    ... National Oceanic and Atmospheric Administration RIN 0648-XB150 International Whaling Commission; 64th... annual International Whaling Commission (IWC) meeting. DATES: The public meeting will be held June 5... the United States under the International Convention for the Regulation of Whaling, 1946. The U.S. IWC...

  12. Publication bias in papers presented to the Australian Orthopaedic Association Annual Scientific Meeting.

    PubMed

    Harris, Ian A; Mourad, Mohamed S; Kadir, Agus; Solomon, Michael J; Young, Jane M

    2006-06-01

    The selective publication of articles based on factors, such as positive outcome, statistical significance and study size is known as publication bias. If publication bias is present, any clinical decision based on a review of the published work will also be biased. Publication bias has been shown in various specialties, based on review of publication rates for abstracts presented at major scientific meetings. This study was conducted to investigate publication bias in orthopaedics. Abstracts presented at the 1998 Australian Orthopaedic Association Annual Scientific Meeting were reviewed independently by two reviewers. Details of sample size, study setting, country of origin, outcome and study type were recorded for each abstract. Publication within 5 years was ascertained by electronic searching of Medline and Embase databases and direct author contact. Logistic regression analysis was used to identify predictors of publication. The overall publication rate was 31%. Publication was more likely if the study was a laboratory study, rather than a clinical study (odds ratio (OR), 3.45; 95% confidence interval (CI) 1.69-7.01, P < 0.001). Sample size, country of origin, study type, statistical significance and positive outcome were not significantly associated with publication. According to this study, laboratory studies were significantly more likely to be published than clinical studies. In contrast to previous studies, publication bias due to the selective publication of papers with a positive outcome or those reporting statistical significance was not found.

  13. A comprehensive quality control workflow for paired tumor-normal NGS experiments.

    PubMed

    Schroeder, Christopher M; Hilke, Franz J; Löffler, Markus W; Bitzer, Michael; Lenz, Florian; Sturm, Marc

    2017-06-01

    Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS. All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the 'GNU General Public License version 2' as part of the ngs-bits project: https://github.com/imgag/ngs-bits. christopher.schroeder@med.uni-tuebingen.de. Supplementary data are available at Bioinformatics online.

  14. Annual expenditures for nursing home care: private and public payer price growth, 1977 to 2004.

    PubMed

    Stewart, Kate A; Grabowski, David C; Lakdawalla, Darius N

    2009-03-01

    Long-term nursing home care is primarily funded by out-of-pocket payments and public Medicaid programs. Few studies have explored price growth in nursing home care, particularly trends in the real cost of a year spent in a nursing home. To evaluate changes in private and public prices for annual nursing home care from 1977 to 2004, and to compare nursing home price growth to overall price growth and growth in the price of medical care. We estimated annual private prices for nursing home care between 1977 and 2004 using data from the National Nursing Home Survey. We compared private nursing home price growth to public prices obtained from surveys of state Medicaid offices, and evaluated the Bureau of Labor Statistics Consumer Price Indexes to compare prices for nursing homes, medical care, and general goods and services over time. Annual private pay nursing homes prices grew by 7.5% annually from $8645 in 1977 to $60,249 in 2004. Medicaid prices grew by 6.7% annually from $9491 in 1979 to $48,056 in 2004. Annual price growth for private pay nursing home care outpaced medical care and other goods and services (7.5% vs. 6.6% and 4.4%, respectively) between 1977 and 2004. The recent rapid growth in nursing home prices is likely to persist, because of an aging population and greater disability among the near-elderly. The result will place increasing financial pressure on Medicaid programs. Better data on nursing prices are critical for policy-makers and researchers.

  15. Using Annual Data to Estimate the Public Health Impact of Extreme Temperatures.

    PubMed

    Goggins, William B; Yang, Chunyuh; Hokama, Tomiko; Law, Lewis S K; Chan, Emily Y Y

    2015-07-01

    Short-term associations between both hot and cold ambient temperatures and higher mortality have been found worldwide. Few studies have examined these associations on longer time scales. Age-standardized mortality rates (ASMRs) were calculated for 1976-2012 for Hong Kong SAR, People's Republic of China, defining "annual" time periods in 2 ways: from May through April of the following year and from November through October. Annual frequency and severity of extreme temperatures were summarized by using a degree-days approach with extreme heat expressed as annual degree-days >29.3°C and cold as annual degree-days <27.5°C. For example, a day with a mean temperature of 25.0°C contributes 2.5 cold degree-days to the annual total. Generalized additive models were used to estimate the association between annual hot and cold degree-days and the ASMR, with adjustment for long-term trends. Increases of 10 hot or 200 cold degree-days in an annual period, the approximate interquartile ranges for these variables, were significantly (all P's ≤ 0.011) associated with 1.9% or 3.1% increases, respectively, in the annual ASMR for the May-April analyses and with 2.2% or 2.8% increases, respectively, in the November-October analyses. Associations were stronger for noncancer and elderly mortality. Mortality increases associated with extreme temperature are not simply due to short-term forward displacement of deaths that would have occurred anyway within a few weeks. © The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Improving diagnosis for congenital cataract by introducing NGS genetic testing

    PubMed Central

    Musleh, Mohammud; Ashworth, Jane; Black, Graeme; Hall, Georgina

    2016-01-01

    Childhood cataract (CC) has an incidence of 3.5 per 10,000 by age 15 years. Diagnosis of any underlying cause is important to ensure effective and prompt management of multisystem complications, to facilitate accurate genetic counselling and to streamline multidisciplinary care. Next generation sequencing (NGS) has been shown to be effective in providing an underlying diagnosis in 70% of patients with CC in a research setting. This project aimed to integrate NGS testing in CC within six months of presentation and increase the rate of diagnosis. A retrospective case note review was undertaken to define the baseline efficacy of current care in providing a precise diagnosis. Quality improvement methods were used to integrate and optimize NGS testing in clinical care and measure the improvements made. The percentage of children receiving an NGS result within six months increased from 26% to 71% during the project period. The mean time to NGS testing and receiving a report decreased and there was a reduction in variation over the study period. Several patients and families had a change in management or genetic counselling as a direct result of the diagnosis given by the NGS test. The current recommended investigation of patients with bilateral CC is ineffective in identifying a diagnosis. Quality Improvement methods have facilitated successful integration of NGS testing into clinical care, improving time to diagnosis and leading to development of a new care pathway. PMID:27933154

  17. The 16th Annual Gallup Poll of the Public's Attitudes toward the Public Schools.

    ERIC Educational Resources Information Center

    Gallup, George H.

    1984-01-01

    Reports results from the 1984 survey, which found Americans respond more favorably to public schools than at any time in the past decade. Survey results show that they also feel education contributes more to national strength than industrial or military power. (MD)

  18. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    PubMed

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  19. lociNGS: A Lightweight Alternative for Assessing Suitability of Next-Generation Loci for Evolutionary Analysis

    PubMed Central

    Hird, Sarah M.

    2012-01-01

    Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci) they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses – NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads). lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License. PMID:23071651

  20. 78 FR 12290 - Annual List of Newspapers Used for Publication of Legal Notice of Decisions Appealable Under 36...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-22

    ...; ] DEPARTMENT OF AGRICULTURE Forest Service Annual List of Newspapers Used for Publication of Legal Notice of...: Notice. SUMMARY: This notice lists the newspapers that Ranger Districts, Forests, and the Regional Office... the public which newspapers will be used to publish legal notices of actions subject to public comment...

  1. 78 FR 11138 - Annual List of Newspapers Used for Publication of Legal Notice of Decisions for the Rocky...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-15

    ... Forest Service Annual List of Newspapers Used for Publication of Legal Notice of Decisions for the Rocky...: Notice. SUMMARY: This notice lists the newspapers that Ranger Districts, Forests, and the Regional Office... the public which newspapers will be used to publish legal notices of actions subject to public comment...

  2. Publication Rates of Presentations at Annual Scientific Meetings of the Turkish Neurosurgical Society.

    PubMed

    Eksi, Murat Sakir; Kaplan, Sumeyye Coruh; Yilmaz, Baran; Akakin, Akin; Toktas, Zafer Orkun; Konya, Deniz; Kilic, Turker

    2017-01-01

    National and international society meetings are suitable mediums at which diverse research topics from basic, clinical and translational sciences can be presented to an audience of peers. In this study, our purpose was to evaluate publication rates of presentations in the last recent four years" annual scientific meetings of Turkish Neurosurgical Society (TNS). Abstracts of both podium and poster presentations were retrieved from the congress booklets of TNS. Study timeline included TNS annual scientific meetings of 2011, 2012, 2013, and 2014. Abstract titles and author names of the abstracts were searched in Pubmed/MEDLINE and Google Scholar databases. In total, 3105 presentations to an audience took place in the annual scientific meetings of TNS organized between 2011 and 2014. Acceptance rate of these studies by peer-reviewed scientific journals was 326 (10.5%). In sub-analysis, there were 2408 electronic posters (148 accepted, 6.1%), 195 poster presentations with discussion (44 accepted, 22.6%), and 502 podium presentations (134 accepted, 26.7%). Acceptance rate of podium presentations in annual scientific meeting of TNS is at comparable levels with similar organizations on the world. However, the rate is lower for poster presentations.

  3. Subsequent full publication of abstracts presented in the annual meetings of the Spanish Society of Cardiology.

    PubMed

    Alonso-Arroyo, Adolfo; Aleixandre-Benavent, Rafael; Vidal-Infer, Antonio; Anguita-Sánchez, Manuel; Chorro-Gascó, Francisco J; Bolaños-Pizarro, Máxima; Castelló-Cogollos, Lourdes; Navarro-Molina, Carolina; Valderrama-Zurián, Juan C

    2014-01-01

    The Spanish Society of Cardiology holds an annual national meeting with a large number of presentations but the number of full-text publications resulting from these presentations and the journals accepting these manuscripts is unknown. This study aimed to identify the full-text publication rate of accepted abstracts and to analyze the bibliometric features of subsequent publications. We randomly selected a sample of 300 oral presentations at the meetings of the Spanish Society of Cardiology in 2002, 2005 and 2008. Subsequent publications were identified through the Science Citation Index-Expanded, Scopus, Índice Médico Español, and Índice Bibliográfico Español en Ciencias de la Salud. Of 300 abstracts, 115 resulted in 147 full publications, representing a publication rate of 38.33%. The meeting with the highest publication rate (43%) was held in 2005. The subject category with the highest number of publications was Pediatric Cardiology/Congenital Heart Disease (58.8%). Time to full publication was usually 2 years (30.61%). Articles were published in 57 journals. The journals publishing the highest number of articles were Revista Española de Cardiología (n=55; 37.41%) and the European Heart Journal (n=8; 5.44%). The high percentage of articles published in the upper half of journals listed in Journal Citation Reports under the category of cardiac and cardiovascular system (83%) can be taken as an objective quality indicator of the results presented at these meetings. However, more than 60% of the abstracts did not result in full publications, thus depriving the scientific community of potentially interesting results. Copyright © 2013 Sociedad Española de Cardiología. Published by Elsevier Espana. All rights reserved.

  4. CRCDA—Comprehensive resources for cancer NGS data analysis

    PubMed Central

    Thangam, Manonanthini; Gopal, Ramesh Kumar

    2015-01-01

    Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL: http://bioinfo.au-kbc.org.in/ngs

  5. Next generation sequencing (NGS)technologies and applications

    SciTech Connect

    Vuyisich, Momchilo

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  6. NGS-Trex: Next Generation Sequencing Transcriptome profile explorer

    PubMed Central

    2013-01-01

    Background Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure. Results To address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples. By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data. Conclusions NGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies

  7. CRCDA--Comprehensive resources for cancer NGS data analysis.

    PubMed

    Thangam, Manonanthini; Gopal, Ramesh Kumar

    2015-01-01

    Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL: http://bioinfo.au-kbc.org.in/ngs

  8. Factors influencing publication rates of abstracts presented at the ADEA annual session & exhibition.

    PubMed

    Galang, Maria T S; Yuan, Judy Chia-Chun; Lee, Damian J; Barao, Valentim A R; Shyamsunder, Nodesh; Sukotjo, Cortino

    2011-04-01

    Factors related to the path of abstracts from presentation at a conference to publication as a full article have been analyzed in the medical field, but only a few studies have been performed in dentistry. This study investigated the rate of publication of articles based on abstracts presented at the American Dental Education Association (ADEA) Annual Session & Exhibition in 2002 and 2003 and the time lag to publication. This study also aimed to characterize the abstracts and subsequent articles and determine if there were any significant factors related to expansion of an abstract into a full manuscript. A total of 370 abstracts met the inclusion criteria and were examined for this study. Subsequent published articles were located using a standard PubMed search. Descriptive statistics and bivariate analyses were used to analyze the data collected (α=0.05). Results suggest that there was a low (19 percent) publication rate for articles based on abstracts presented at the meetings studied. The median time between abstract presentation and article publication was ten months. Factors that showed significant correlation to likelihood of article publication were multiple affiliations, presence of analytical statistics, and, to a lesser extent, funding. We suggest that presenters at these meetings should expand their abstracts into full manuscripts and seek to publish them in peer-reviewed journals for the benefit of the profession.

  9. The Use of GOCE/GRACE Information in the Latest NGS xGeoid15 Model for the USA

    NASA Astrophysics Data System (ADS)

    Holmes, S. A.; Li, X.; Youngman, M.

    2015-12-01

    The U.S. National Geodetic Survey [NGS], through its Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, is flying airborne gravity surveys over the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Towards this end, all available airborne data has been incorporated into a new NGS experimental geoid model - xGEOID15. The xGEOID15 model is the second in a series of annual experimental geoid models that incorporates NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques, to ultimately compute a geoid model that can support a national physical height system by 2022. Here, we focus on the combination of the latest GOCE/GRACE models with the terrestrial gravimetry (land/airborne) that was applied for xGeoid15. Comparisons against existing combination gravitational solutions, such as EGM2008 and EIGEN6C4, as well as recent geoid models, such as xGeoid14 and CGG2013, are interesting for what they reveal about the respective use of the GOCE/GRACE satgrav information.

  10. Radiolytic Treatment of the Next-Generation Caustic-Side Solvent Extraction (NGS) Solvent and its Effect on the NGS Process

    DOE PAGES

    Roach, Benjamin D.; Williams, Neil J.; Duncan, Nathan C.; ...

    2014-12-01

    We show in this work that the solvent used in the Next Generation Caustic-Side Solvent Extraction (NGS) process can withstand a radiation dose well in excess of the dose it would receive in multiple years of treating legacy salt waste at the US Department of Energy Savannah River Site. The solvent was subjected to a maximum of 50 kGy of gamma radiation while in dynamic contact with each of the aqueous phases of the current NGS process, namely SRS−15 (a highly caustic waste simulant), sodium hydroxide scrub solution (0.025 M), and boric acid strip solution (0.01 M). Bench-top testing ofmore » irradiated solvent confirmed that irradiation has inconsequential impact on the extraction, scrubbing, and stripping performance of the solvent up to 13 times the estimated 0.73 kGy/y annual absorbed dose. Lastly, stripping performance is the most sensitive step to radiation, deteriorating more due to buildup of p-sec-butylphenol (SBP) and possibly other proton-ionizable products than to degradation of the guanidine suppressor, as shown by chemical analyses.« less

  11. Radiolytic Treatment of the Next-Generation Caustic-Side Solvent Extraction (NGS) Solvent and its Effect on the NGS Process

    SciTech Connect

    Roach, Benjamin D.; Williams, Neil J.; Duncan, Nathan C.; Delmau, Lætitia H.; Lee, Denise L.; Birdwell, Joseph F.; Moyer, Bruce A.

    2014-12-01

    We show in this work that the solvent used in the Next Generation Caustic-Side Solvent Extraction (NGS) process can withstand a radiation dose well in excess of the dose it would receive in multiple years of treating legacy salt waste at the US Department of Energy Savannah River Site. The solvent was subjected to a maximum of 50 kGy of gamma radiation while in dynamic contact with each of the aqueous phases of the current NGS process, namely SRS−15 (a highly caustic waste simulant), sodium hydroxide scrub solution (0.025 M), and boric acid strip solution (0.01 M). Bench-top testing of irradiated solvent confirmed that irradiation has inconsequential impact on the extraction, scrubbing, and stripping performance of the solvent up to 13 times the estimated 0.73 kGy/y annual absorbed dose. Lastly, stripping performance is the most sensitive step to radiation, deteriorating more due to buildup of p-sec-butylphenol (SBP) and possibly other proton-ionizable products than to degradation of the guanidine suppressor, as shown by chemical analyses.

  12. Publication Rates of Podium Presentation Abstracts at the Arthroscopy Association of North America Annual Meetings 2004-2012.

    PubMed

    Lehman, Jason D; Nwachukwu, Benedict U; Ferraro, Richard; Rebolledo, Brian J; Makhni, Eric C; Verma, Nikhil N; Gulotta, Lawrence V

    2017-01-24

    To determine the publication rates of podium presentation abstracts at the Arthroscopy Association of North America (AANA) annual scientific meetings from 2004 to 2012. A database of podium presentation abstracts at the annual meetings of the AANA was compiled. Abstract presentations that reached manuscript publication were determined by a PubMed search of the MEDLINE database and Google Scholar. The journal and publication date were then recorded for all identified published abstracts. A total of 658 abstracts were selected for podium presentations at AANA annual meetings from 2004-2012 (range, 53-102 per year). Of these 658 abstracts, 443 (67.3%) went on to eventual publication in peer-reviewed journals. The mean time from the meeting to publication was 20.0 months. Most abstracts were published within 3 years of the meeting (n = 380, 85.8%), with a significant number of published abstracts reaching publication before the time of the meeting (n = 41, 9.3%). Published abstracts were most frequently published in Arthroscopy (n = 186, 42.0%), The American Journal of Sports Medicine (20.3%), and The Journal of Bone and Joint Surgery (6.1%). The overall publication rate of podium presentations at AANA annual meetings (67.3%) was similar to publication rates for other major orthopaedic annual meetings. Most published abstracts (85.8%) were published within 3 years, and the mean time to publication was 20.0 months. The rates of publication of podium presentations at AANA annual meetings show the impact and importance of these meetings in the advancement of orthopaedic research. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  13. Try It Again, Uncle Sam: The 46th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools. [Part I

    ERIC Educational Resources Information Center

    Bushaw, William J.; Calderon, Valerie J.

    2014-01-01

    The 46th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools reveals that Americans say they know a lot more this year about the Common Core State Standards than they indicated a year ago, and they like it a lot less. Americans also say local school boards should have the greatest influence in deciding what is taught in the…

  14. Americans Speak out: Are Educators and Policy Makers Listening?--The 40th Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Bushaw, William J.; Gallup, Alec M.

    2008-01-01

    Parents, educators, political leaders--all Americans need the information contained in this article. But why this poll? First, it's not just a quick snapshot of public perception. Rather, it is a serious research tool, conducted annually, that allows Phi Delta Kappa (PDK) members and other educators and policy makers to track public opinion from…

  15. Audit of the annual reports of directors of public health: production methods.

    PubMed

    Sidhu, K S

    1992-07-01

    An audit of production methods used for the Directors of Public Health (DsPH) Annual Report of the health of their local population. Postal questionnaire survey. 23 Departments of Public Health in the West Midlands Region. Costs and problems relating to different production techniques used. The majority of DsPH favoured reports with figures and graphs. This led to most DsPH using in-house desktop publishing or employing external graphic designers. Those using the former technique had more problems related to computers and felt they spent too much medical time working on the document. However, they also valued the relative low cost, editorial freedom and the ability to correct mistakes easily. Departments which employed external graphic designers generally paid more, but appreciated the extra time made available by delegating the work. They also felt that the expertise was valuable in document design. However, inaccuracies were cited as being more difficult to correct. Perhaps the best way of producing an annual report is to amalgamate the two commonest production techniques (i.e. external graphic design and in-house desktop publishing).

  16. 26 CFR 301.6104(d)-1 - Public inspection and distribution of applications for tax exemption and annual information...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 18 2011-04-01 2011-04-01 false Public inspection and distribution of....6104(d)-1 Public inspection and distribution of applications for tax exemption and annual information... favorable determination letter or a list of questions from the Internal Revenue Service about...

  17. Canadian Association of Radiologists Annual Scientific Meetings: How Many Abstracts Go on to Publication?

    PubMed

    Dressler, Danielle; Leswick, David

    2015-05-01

    To determine the percentage of abstracts presented at the Canadian Association of Radiologists (CAR) annual scientific meetings that go on to publication. Records of previous CAR meetings from the years 2005-2011 were obtained. An Internet search was performed to determine which abstracts went on to publication. Abstracts were assessed according to exhibit category (Resident Award Papers), educational institution, publishing journal, and time to publication. Of the 402 abstracts presented, 112 (28%) were published. Overall, an average of 37% of Radiologists-In-Training Presentations, 34% of Scientific Exhibits, and 20% of Educational Exhibits went on to publication. The University of British Columbia and University of Ottawa published the largest number of abstracts (66 and 62, respectively) from the years 2005-2011. The University of Montreal had the largest percentage of abstracts published (42%). The range of publishing journals was wide, but the top publisher was the Canadian Association of Radiologists Journal (27%). Eighty-three percent of abstracts were published within 3 years of being presented. In total, 28% of all the abstracts presented at the CAR conferences between 2005 and 2011 were published. Further exploration into the reasons and barriers for abstracts not being published may be a next step in future research. Copyright © 2015 Canadian Association of Radiologists. Published by Elsevier Inc. All rights reserved.

  18. Americans Put Teacher Quality on Center Stage: The 46th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools. Part II

    ERIC Educational Resources Information Center

    Bushaw, William J.; Calderon, Valerie J.

    2014-01-01

    In this, the second installment of a two-part report of the 46th annual PDK/Gallup Poll of the Public's Attitudes Toward the Public Schools, the report unveils what Americans are thinking about public schools--in particular their views of teachers and the classrooms where they work. Some findings were surprising, others were not. For example,…

  19. Americans Put Teacher Quality on Center Stage: The 46th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools. Part II

    ERIC Educational Resources Information Center

    Bushaw, William J.; Calderon, Valerie J.

    2014-01-01

    In this, the second installment of a two-part report of the 46th annual PDK/Gallup Poll of the Public's Attitudes Toward the Public Schools, the report unveils what Americans are thinking about public schools--in particular their views of teachers and the classrooms where they work. Some findings were surprising, others were not. For example,…

  20. Annual Statistical Report of the Public Schools of Arkansas, Public Charter Schools, and Education Service Cooperatives, 2013-2014 Actual and 2014-2015 Budgeted, (ASR)

    ERIC Educational Resources Information Center

    Arkansas Department of Education, 2015

    2015-01-01

    In compliance with the provisions of A.C.A.§§6-20-2201 et seq., the Annual Statistical Report of the Public Schools of Arkansas, Public Charter Schools, and Education Service Cooperatives, 2013-2014 Actual and 2014-2015 Budgeted, (ASR) is presented here. The Rankings of Selected Items of the Public Schools of Arkansas, 2013-2014 Actual, (Rankings)…

  1. Informativeness of NGS Analysis for Vaginal Fluid Identification.

    PubMed

    Giampaoli, Saverio; DeVittori, Elisabetta; Valeriani, Federica; Berti, Andrea; Romano Spica, Vincenzo

    2017-01-01

    The identification of vaginal fluids in forensic examinations plays an important role in crime scene reconstruction. Molecular detection of vaginal bacterial communities can lead to the correct discrimination of body fluids. These kinds of studies can be performed through multiplex real-time PCR using primers for a specific selection of bacteria. The availability of next-generation sequencing (NGS) protocols provided for the extension of the analysis to evaluate the prokaryotes present in specimens. In this study, DNA was extracted from 18 samples (vaginal, oral, fecal, yoghurt) and analyzed by real-time PCR and NGS. The comparison between the two approaches has demonstrated that the information developed through NGS can augment the more conventional real-time PCR detection of a few key bacterial species to provide a more probative result and the correct identification of vaginal fluid from samples that are more forensically challenged.

  2. Publication Rate of Abstracts Presented at the Society for Obstetric Anesthesia and Perinatology Annual Meetings 2010-2014.

    PubMed

    Gerlach, Brent; Shah, Anuj M; Lee, Michael T; Wong, Cynthia A; Sullivan, John T; Toledo, Paloma

    2017-03-01

    The Society for Obstetric Anesthesia and Perinatology (SOAP) annual meeting provides a forum to present new scientific work with the goal of broader dissemination of knowledge. The objective of this study was to evaluate the proportion of research abstracts presented at SOAP meetings, from 2010 to 2014, which resulted in peer-reviewed publications. The abstract-to-publication rate was compared with the percent of abstracts presented at biomedical meetings resulting in publication, as estimated by a 2007 Cochrane Review. The SOAP abstract-to-publication rate was lower than that of the Cochrane Review (26.8% vs 44.5%, P < .0001). Future work should identify barriers to publication.

  3. Public Utility Regulatory Policies Act of 1978. Annual report to Congress

    SciTech Connect

    None,

    1980-05-01

    The Public Utility Regulatory Policies Act of 1978 requires State regulatory authorities and nonregulated utilities to consider and make determinations regarding a set of Federal standards that show promise of furthering three statutory purposes: end-use conservation, utility efficiency, and equitable rates. PURPA sections 116 and 309 require the Secretary of Energy to report annually to Congress regarding the progress of these State regulatory authorities and nonregulated utilities in carrying out their PURPA obligations. DOE is also required to report on its own PURPA-related activities and to recommend any further Federal initiatives, including legislation, that may be necessary to carry out the purposes of the Act. In addition, section 206 of the Energy Conservation and Production Act of 1976 requires DOE to report annually regarding its activities under Title II of ECPA. This document fulfills these statutory reporting requirements for 1980, and assesses the progress made by State regulatory authorities and nonregulated utilities prior to June 30, 1979, in carrying out their PURPA duties and responsibilities. The report concludes that while there was more progress made on the regulatory standards than on the ratemaking standards, progress on all standards as of June 30, 1979, was limited. The report also describes DOE's efforts to assist State regulatory authorities and nonregulated utilities in carrying out their PURPA responsibilities.

  4. NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

    PubMed

    Mendoza-Parra, Marco Antonio; Saleem, Mohamed-Ashick M; Blum, Matthias; Cholley, Pierre-Etienne; Gronemeyer, Hinrich

    2016-01-01

    The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.

  5. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

    PubMed Central

    2014-01-01

    Background Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data. PMID:24735413

  6. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

    PubMed

    Shen, Li; Shao, Ningyi; Liu, Xiaochuan; Nestler, Eric

    2014-04-15

    Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot - a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.

  7. Annual public health and economic benefits of seasonal influenza vaccination: a European estimate.

    PubMed

    Preaud, Emmanuelle; Durand, Laure; Macabeo, Bérengère; Farkas, Norbert; Sloesen, Brigitte; Palache, Abraham; Shupo, Francis; Samson, Sandrine I

    2014-08-07

    Vaccination is currently the most effective means of preventing influenza infection. Yet evidence of vaccine performance, and the impact and value of seasonal influenza vaccination across risk groups and between seasons, continue to generate much discussion. Moreover, vaccination coverage is below recommended levels. A model was generated to assess the annual public health benefits and economic importance of influenza vaccination in 5 WHO recommended vaccination target groups (children 6 - 23 months of age; persons with underlying chronic health conditions; pregnant women; health care workers; and, the elderly, 65 years of age) in 27 countries of the European Union. Model estimations were based on standard calculation methods, conservative assumptions, age-based and country-specific data. Out of approximately 180 million Europeans for whom influenza vaccination is recommended, only about 80 million persons are vaccinated. Seasonal influenza vaccination currently prevents an annual average of between 1.6 million and 2.1 million cases of influenza, 45,300 to 65,600 hospitalizations, and 25,200 to 37,200 deaths. To reach the 75% vaccination coverage target set by the EU Council Recommendation in 2009, an additional 57.4 million person would need to be vaccinated in the elderly and other risk groups. By achieving the 75% target rate set in EU-27 countries, average annual influenza- related events averted would increase from current levels to an additional +1.6 to +1.7 million cases, +23,800 to +31,400 hospitalization, +9,800 to +14,300 deaths, +678,500 to +767,800 physician visits, and +883,800 to +1,015,100 lost days of work yearly. Influenza-related costs averted because of vaccination would increase by an additional + €190 to + €226 million yearly, in vaccination target groups. Full implementation of current influenza vaccination recommendations of 75% vaccination coverage rate (VCR) in Europe by the 2014-2015 influenza season could immediately reduce an

  8. Fiscal Year 1980: Annual Program Plan Amendment for Part B Public Law 94-142 and Public Law 89-313.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    The Annual Program Plan for Fiscal Year 1980 presents descriptions of Oregon's efforts to serve handicapped children under Part B P.L. 94-142 (the Education for All Handicapped Children Act) and P.L. 89-313. Addressed are procedures in the following areas: public notice and opportunity for comment, policy on priorities, procedural safeguards,…

  9. Assessing the Eventual Publication of Clinical Trial Abstracts Submitted to a Large Annual Oncology Meeting

    PubMed Central

    Wang, Ruibin; Prasad, Vinay; Bates, Susan E.; Fojo, Tito

    2016-01-01

    . This is the largest reported study examining why oncology trials are not published. The data show that 4−6 years after appearing as abstracts, 39% of oncology clinical trials remain unpublished. Larger sample size and advanced trial phase were associated with eventual publication; among randomized trials, an industry-affiliated author or a cooperative group increased likelihood of publication. Unfortunately, we found that, despite widespread recognition of the problem and the creation of central data repositories, timely publishing of oncology clinical trials results remains unsatisfactory. Implications for Practice: The Declaration of Helsinki Ethical Principles for Medical Research Involving Human Subjects notes the ethical obligation to report clinical trial data, whether positive or negative. This obligation is listed alongside requirements for risk minimization, access, confidentiality, and informed consent, all bedrocks of the clinical trial system, yet clinical trials are often not published, particularly if negative or difficult to complete. This study found that among American Society for Clinical Oncology (ASCO) Annual Meeting abstracts, 2009–2011, only 61% were published 4–6 years later: 75% of randomized trials and 54% of nonrandomized trials. Clinicians need to insist that every study in which they participate is published. PMID:26888691

  10. Analysis of publication status of abstracts presented at the annual meeting of the korean academy of rehabilitation medicine.

    PubMed

    Lim, Jae Kuk; Han, Jun Young; Lee, Hyun Cheol; Lee, Jiwon; Chung, Hong; Kim, Jong Moon; Kim, Shin Kyoung

    2013-06-01

    To analyze publication rate, time to publication and the characteristics of the abstracts presented at the annual Korean Academy of Rehabilitation Medicine (KARM) meetings. A total of 1,027 abstracts presented at the 2008 and 2009 annual KARM meetings were enrolled in the database and searched for their subsequent citation in PubMed, KoreaMed, and Google Scholar. The data analysis revealed that 317 (30.87%) abstracts, were published as full-length journal articles and publication rates by subject were not significantly different. The mean time to publication was 17.17±10.48 months, and the journals written in English (20.39±10.20) required a longer duration than those written in Korean (11.94±8.44) with statistical significance (p<0.001). There was no statistical difference (p=0.284) in the duration between domestic (17.61±10.37) and foreign (16.48±10.51) of the 220 domestic journal articles, 190 (86.76%) were published in the Annals of Rehabilitation Medicine and the 97 articles published in foreign journals were scattered over 60 different journals. The publication rate of abstracts presented at the 2008 and 2009 annual KARM meetings was 30.87% and the mean time to publication was 17.17±10.48 months.

  11. Analysis of Publication Status of Abstracts Presented at the Annual Meeting of the Korean Academy of Rehabilitation Medicine

    PubMed Central

    Lim, Jae Kuk; Han, Jun Young; Lee, Hyun Cheol; Lee, Jiwon; Chung, Hong; Kim, Jong Moon

    2013-01-01

    Objective To analyze publication rate, time to publication and the characteristics of the abstracts presented at the annual Korean Academy of Rehabilitation Medicine (KARM) meetings. Methods A total of 1,027 abstracts presented at the 2008 and 2009 annual KARM meetings were enrolled in the database and searched for their subsequent citation in PubMed, KoreaMed, and Google Scholar. Results The data analysis revealed that 317 (30.87%) abstracts, were published as full-length journal articles and publication rates by subject were not significantly different. The mean time to publication was 17.17±10.48 months, and the journals written in English (20.39±10.20) required a longer duration than those written in Korean (11.94±8.44) with statistical significance (p<0.001). There was no statistical difference (p=0.284) in the duration between domestic (17.61±10.37) and foreign (16.48±10.51) of the 220 domestic journal articles, 190 (86.76%) were published in the Annals of Rehabilitation Medicine and the 97 articles published in foreign journals were scattered over 60 different journals. Conclusion The publication rate of abstracts presented at the 2008 and 2009 annual KARM meetings was 30.87% and the mean time to publication was 17.17±10.48 months. PMID:23869340

  12. A Report to the People. 20 Years of Your National Commitment to Public Broadcasting, 1967-1987. 1986 Annual Report.

    ERIC Educational Resources Information Center

    Corporation for Public Broadcasting, Washington, DC.

    This annual report for the Corporation for Public Broadcasting (CPB) for fiscal year 1986 also summarizes the CPB's activities over the last 20 years. The front inside cover folds out to three pages and provides a chronology of the important events in CPB history from its inception in 1967 to 1987. A narrative report on the CPB's 20 years of…

  13. Tennessee Public Education: Positioned for Progress in the 1990s. Annual Joint Report on Preschool through Graduate Education in Tennessee.

    ERIC Educational Resources Information Center

    Tennessee Higher Education Commission, Nashville.

    Plans for restructuring Tennessee public education have been interrupted by the prolonged national recession and a $276.4 million reduction in the 1991-92 state education budget. The state's 1991 Annual Joint Report identified 26 essential educational objectives. Although progress in some areas has been limited, Tennessee has achieved a 25 percent…

  14. Privacy Act of 1974; annual publication of systems of records--CDC.

    PubMed

    1983-11-29

    The Centers for Disease Control (CDC) is publishing this document to meet the requirement of the Privacy Act, as amended by the Congressional Reports Elimination Act (Pub. L. 97-375), to republish the notices of systems of records which have been revised. This publication provides a table of contents which contains the numerical designations and titles of all systems of records maintained by CDC and its organizational components, including the National Institute for Occupational Safety and Health (NIOSH). In addition, the notices of systems of records which have been revised following a comprehensive review are indicated by an asterisk in the Table of Contents and are published below in their entirety. CDC's system notices were last published in the Federal Register, Vol. 47, No. 198, pp. 45469-45513, October 13, 1982. One additional new system of records: 09-20-0161, "Records of Health Professional in Disease Prevention and Control Training Programs," HHS/CD/CPS, has been published in the Federal Register Vol. 48, No. 127, pp. 30187-30188, June 30, 1983. Twenty-five of the forty-two notices which were published in the 1982 annual compilation have been modified to clarify the descriptions and to ensure that they are complete, accurate, and timely. None of these changes requires a report of altered system to be sent to the Congress and the Office of Management and Budget. The notices are complete and accurate as of August 15, 1983.

  15. CRISPR-DAV: CRISPR NGS Data Analysis and Visualization Pipeline.

    PubMed

    Wang, Xuning; Tilford, Charles; Neuhaus, Isaac; Mintier, Gabe; Guo, Qi; Feder, John N; Kirov, Stefan

    2017-08-14

    The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, BWA and ABRA are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view. CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/ . xuning.wang@bms.com.

  16. Publication rate of abstracts of papers and posters presented at Medical Library Association annual meetings*†

    PubMed Central

    Harvey, Sally A; Wandersee, Janene R

    2010-01-01

    Objectives: This study sought to ascertain the publication rate of abstracts presented at the annual meetings of the Medical Library Association (MLA) for the years of 2002 and 2003. The secondary objectives were to examine possible reasons for non-publication and factors influencing publication. Methods: A total of 442 abstracts from both meeting years, consisting of presented papers and posters, were examined. The 2 methods used to obtain a publication rate were literature searches and an online questionnaire sent to first authors. The questionnaire also asked abstract authors about reasons for non-publication and other factors that might have influenced their decisions about whether or not to submit the project for publication. Results: The overall publication rate from the survey was 26.5%, and the publication rate found via literature searching was 27.6%. The most common reason given for non-publication was time restrictions. Also notable was the large proportion of abstracts written by librarians working at universities and those having 25 or more years in the library profession. Discussion: Publication rates for abstracts presented at the Medical Library Association meetings for the years studied rank at the low end in comparison with other medical professional associations. Further research into factors affecting publication may reveal ways to increase this rate. PMID:20648260

  17. Proceedings from the 9th Annual Meeting of International Society for Medical Publication Professionals Roundtable Session: key insights.

    PubMed

    Simcoe, Donna; Juneja, Renu; Scott, Gayle Nicholas; Sridharan, Kanaka; Williams-Hughes, Celeste

    2014-03-01

    During the 9th Annual Meeting of the International Society for Medical Publication Professionals (ISMPP, April 29-May 1, 2013 in Baltimore, MD), ∼650 participants attended two of 13 available roundtable sessions. Participants included medical publication professionals from industry, communication agencies, and journals. DISCUSSION TOPICS: Roundtable participants discussed how to best interpret and implement various guidances, such as Good Publication Practices 2 (GPP2), the International Committee of Medical Journal Editors (ICMJE) guidelines, and the Physician Payment Sunshine Act. The impact of and compliance with Corporate Integrity agreements (CIAs) on medical publication planning practices was debated. Roundtable participants also discussed ways of advancing both advocacy for the medical publication professional field and internal and external collaborations. The development of review manuscripts, publications from regions newly emerging in publication planning, medical devices publications, and real-world experience publications were discussed. Participants also considered the benefits and uncertainties of new technologies in medical publications such as multimedia and social media. This is the first ever article to be published following the well-attended ISMPP roundtable sessions. The objective of this manuscript is to summarize key learnings that will aid continued discussions about challenges and opportunities facing medical publication professionals.

  18. Make Teaching More Professional: The 47th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Starr, Joshua P.

    2015-01-01

    Americans want higher professional requirements for teachers and believe teacher pay is too low, but they don't like tenure, according to the newest PDK/Gallup Poll of the Public's Attitudes To­ward the Public Schools. Public school parents trust and have confidence in the nation's teachers, and they said communicating with their child's teacher…

  19. The 31st Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools.

    ERIC Educational Resources Information Center

    Rose, Lowell C.; Gallup, Alec M.

    1999-01-01

    Public support for improving public schools over seeking alternatives remains high (70%). Opposition to private contracting is growing. Fully 79% of public-school parents think schools effectively prepare students for the labor market; 72% want higher promotion standards. Inadequate discipline, violence, and scanty funding remain top problems.…

  20. Make Teaching More Professional: The 47th Annual PDK/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Starr, Joshua P.

    2015-01-01

    Americans want higher professional requirements for teachers and believe teacher pay is too low, but they don't like tenure, according to the newest PDK/Gallup Poll of the Public's Attitudes To­ward the Public Schools. Public school parents trust and have confidence in the nation's teachers, and they said communicating with their child's teacher…

  1. 76 FR 9044 - Notice of Extension of Information Collection for Public Comment; Consolidated Plan and Annual...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-16

    ... and Annual Performance Report AGENCY: Office of the Assistant Secretary for Community Planning and... forms of information submission of responses. Title of Proposal: Consolidated Plan & Annual Performance Report. OMB Control Number: OMB 2506-0117. Description of the Need for the Information and Proposed...

  2. 77 FR 4824 - Notice of Revised Information Collection for Public Comment; Consolidated Plan & Annual...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-31

    ... & Annual Performance Report AGENCY: Office of the Assistant Secretary for Community Planning and... reports) or other forms of information submission of responses. Title of Proposal: Consolidated Plan & Annual Performance Report. OMB Control Number: 2506-011. Agency Form Numbers: None. Description of...

  3. Publication Rates of Abstracts Accepted to the 2010-2012 Annual Meetings of the North American Spine Society.

    PubMed

    Narain, Ankur S; Hijji, Fady Y; Kudaravalli, Krishna T; Yom, Kelly H; Singh, Kern

    2017-04-18

    Retrospective review of conference abstracts. To determine the publication rate of podium and poster presentations at the 2010-2012 North American Spine Society (NASS) annual meetings. Presentations at medical conferences are utilized to disseminate new clinical information. The orthopaedic literature estimates the rate of publication for abstracts presented at major meetings to be between 34.0-67.1%. However, few studies have analyzed the publication rate of accepted abstracts to the NASS annual meetings. All abstracts presented at the 2010-2012 NASS annual meetings were reviewed. PubMed and Google Scholar databases were searched to determine if each abstract was published as a full-length manuscript before or up to 3 years after its NASS meeting presentation. Statistical analyses included descriptive statistics, poisson regression with robust error variance, and linear regression. A total of 1045 abstracts were accepted to the 2010-2012 NASS annual meetings. 43.8% were published before or up 3 years after their NASS presentation. Podium presentations were more likely to be published than poster presentations (47.1% vs. 37.7%, p = 0.005). Abstracts with "Best" or "Outstanding" designations were also more likely to be published than abstracts without those designations (54.4% vs. 45.0%, p = 0.034). Presentations designated as "Best" or "Outstanding" papers had shorter time to publication than presentations without those designations (369 vs 486 days, p = 0.002). This study suggests that only 43.8% of abstracts accepted to NASS are published as full-length manuscripts. As such, practitioners should use caution when altering clinical practice based solely on conference presentations. Additionally, podium presentations are more likely to be published than poster presentations. This trend may be reflective of the higher quality of abstracts accepted as podiums, or may be associated with a larger number of lower quality abstracts being accepted due to the

  4. Publication rate of scientific papers presented at the XXVI Annual Convention of National Neonatology Forum (NEOCON 2006).

    PubMed

    Singh, Archana; Solanki, Priyanka; Mishra, Devendra

    2015-01-01

    To document the publication rate of papers presented at the Annual Convention of National Neonatology Forum of India (NNF), and study the factors associated with their subsequent publication. All papers presented at the NEOCON 2006, the XXVI annual convention of NNF at Varanasi, India, were searched for subsequent full publication, by an internet-based search using Pubmed, Google Scholar and Indmed. Publication of the presented paper was looked for in English language, peer-reviewed, indexed journals over the next five years (1st January 2007 to 31st December, 2011). The full published papers were compared with the abstract and differences noted. One hundred and two papers and posters were presented at the conference and 14 (13.7 %) of these were published in the next five years. None was published in any un-indexed journal. The highest percentage of paper publication was from the Award paper category (83.3 %) and least from Innovation category (none). The only factor significantly associated with subsequent publication was presentation as an Award paper (P < 0.001). On comparison of the presented abstracts and the published papers, there was a change in authors in 78.5 %, title in 42.8 %, and the data in 35.7 %. The subsequent publication of conference abstracts as a full-paper is sub-optimal in the field of neonatology. Further research is needed to identify the factors responsible for the poor subsequent publication, and efforts need to be made to address them both at the institutional and the researchers' level.

  5. COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists

    PubMed Central

    Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

    2014-01-01

    Abstract COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/. This website is free and open to users without any login requirement. PMID:24512253

  6. COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

    PubMed

    Monot, Marc; Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

    2014-03-01

    COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

  7. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data.

    PubMed

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-12-15

    Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software. © The Author 2015. Published by Oxford University Press.

  8. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

    PubMed Central

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    Motivation: Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. Results: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. Availability: NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software. Contact: ida@binf.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26323718

  9. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.

    PubMed

    Li, Jian; Batcha, Aarif Mohamed Nazeer; Grüning, Björn; Mansmann, Ulrich R

    2015-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

  10. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

    PubMed Central

    Li, Jian; Batcha, Aarif Mohamed Nazeer; Grüning, Björn; Mansmann, Ulrich R.

    2015-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility. PMID:27081306

  11. NGS WFSs module for MAORY at E-ELT

    NASA Astrophysics Data System (ADS)

    Esposito, S.; Agapito, G.; Antichi, J.; Bonanno, A.; Carbonaro, L.; Giordano, C.; Spanò, P.

    We report on the natural guide star (NGS) wavefront sensors (WFS) module for MAORY, the multi-cojugate adaptive optics (MCAO) system for the ESO E-ELT. Three low-order, near-infrared (H-band), Shack-Hartmann sensors provide fast acquisition of the first 5 modes (tip, tilt, focus, astigmatism) on 3 natural guide stars over a 160 arcsec field of view. Three moderate-order (20x20), visible (600-800 nm), pyramid WFSs provide the slow Truth sensing to correct LGS wavefront estimates of low-order modes. These sensors are mounted onto three R-theta stages to patrol the field of view. The module is also equipped with a retractable, on-axis, high-order (80x80), visible, pyramid WFS for the single-conjugate AO (SCAO) mode of MAORY and MICADO. The visible WFSs share the same 80x80 pyramid WFS design. This choice enables also a MCAO NGS capability. Simulations show that Strehl ratios (SR) over 40% are reached with MCAO and three, 2x2 sub-apertures, NIR low-order WFSs working with H-mag=20 reference stars. In SCAO mode, 90% SR for a 8mag stars with a contrast down to 10-5, and 45% SR for a 16mag star, are achieved.

  12. Center for Collegiate Mental Health (CCMH) 2010 Annual Report. Publication No. STA 11-000

    ERIC Educational Resources Information Center

    Center for Collegiate Mental Health, 2010

    2010-01-01

    With nearly six years of effort, the work of hundreds of institutions, hundreds of counseling center staff members, a dedicated advisory board, and a committed group of students and faculty at Penn State University, CCMH has realized some important goals. The movement towards an "Annual Report" reflects commitment to offering an annual…

  13. 78 FR 11915 - Order Approving Public Company Accounting Oversight Board Budget and Annual Accounting Support...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-20

    ..., accurate and independent audit reports. The PCAOB is to accomplish these goals through registration of... auditors of broker-dealers registered with the Commission. In addition, the PCAOB must allocate the annual..., and a list of definitions that apply to the rule and to general discussions of PCAOB budget matters...

  14. Annual Progress Report, 1978. Southern Rural Development Center, Mississippi State University. SRDC Series Publication No. 28.

    ERIC Educational Resources Information Center

    Southern Rural Development Center, State College, MS.

    Summarizing Southern Rural Development Center (SRDC) activities during the October 1977-September 1978 fiscal year, this fifth annual report indicates that with Title V funding SRDC has continued its efforts to bring research and extension personnel together to work on problems in rural development. Support for programs and research at land grant…

  15. Synthesis--An Annual Publication of The Higher Learning Commission, 2001.

    ERIC Educational Resources Information Center

    North Central Association of Colleges and Schools, Chicago, IL. Higher Learning Commission.

    This report, first of a projected annual series, focuses on the key commitments of the mission statement of the Higher Learning Commission of the North Central Association of Colleges and Schools and highlights new Commission initiatives. The issue opens with two essays related to the Commission's purposes: "Serving the Common Good in a…

  16. Teacher Supply and Demand in Kansas Public Schools. Twentieth Annual Survey.

    ERIC Educational Resources Information Center

    Tompkins, Loren; Mehring, Teresa A.; Hedstrom, Cora Z.; Switzer, Maggie

    This annual report investigates Kansas' current teacher job market. Data came from surveys of superintendents from all 304 unified school districts, special education directors, directors of teacher education programs, and college placement directors. The nine sections are (1) Historical Perspective, (2) Sources of Data, (3) Relevance of Each Data…

  17. Center for Collegiate Mental Health (CCMH) 2012 Annual Report. Publication No. STA 13-68

    ERIC Educational Resources Information Center

    Center for Collegiate Mental Health, 2012

    2012-01-01

    This report is based on the 2011-2012 Center for Collegiate Mental Health (CCMH) data set, which closed on June 30, 2012. Data was contributed by 120 colleges and universities describing 81,000 unique college students seeking treatment, 2,823 clinicians, and over 730,567 appointments. In addition to summarizing data, these annual reports are…

  18. Increasing Understanding of Public Problems and Policies: 1993. [Proceedings of the Annual Conference of the National Public Policy Education Committee (43rd, Clearwater Beach, Florida, September 12-15, 1993).

    ERIC Educational Resources Information Center

    Halbrook, Steve A., Ed.; Grace, Teddee E., Ed.

    The annual conference of the National Public Policy Education Committee (NPPEC) is held to improve the policy education efforts of extension workers responsible for public affairs programs. This publication contains 26 conference papers: "Rural America and the Information Revolution: An Exploration of Possibilities and Potentialities"…

  19. Knowledge Production, Publication Productivity, and Intimate Academic Partnerships. ASHE Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Creamer, Elizabeth G.

    Individual interviews with 27 tenured faculty members who had coauthored one or more scholarly publications with a spouse or partner were conducted to identify patterns of collaboration associated with knowledge production and publication productivity. The study identified three patterns of collaboration: (1) short term usually a one-time effort…

  20. Strategic Plan to Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education, 2011. Annual Report

    ERIC Educational Resources Information Center

    Connecticut Department of Higher Education (NJ1), 2011

    2011-01-01

    Increasing the participation of minority groups at public colleges and universities is a longstanding goal of the Board of Governors for Higher Education, as first outlined in its 1983 "Strategic Plan to Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education." The minority groups defined by the plan are:…

  1. 77 FR 48160 - Division of Cardiovascular Devices 30-Day Notices and Annual Reports; Public Workshop; Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-13

    ... a disability, please contact Joyce Raines, Center for Devices and Radiological Health, Food and Drug....raines@fda.hhs.gov . To register for the public workshop, please visit FDA's Medical Devices News...

  2. Documenting stewardship responsibilities across the annual cycle for birds on U.S. public lands.

    PubMed

    La Sorte, Frank A; Fink, Daniel; Hochachka, Wesley M; Aycrigg, Jocelyn L; Rosenberg, Kenneth V; Rodewald, Amanda D; Bruns, Nicholas E; Farnsworth, Andrew; Sullivan, Brian L; Wood, Chris; Kelling, Steve

    2015-01-01

    In the face of global environmental change, the importance of protected areas in biological management and conservation is expected to grow. Birds have played an important role as biological indicators of the effectiveness of protected areas, but with little consideration given to where species occur outside the breeding season. We estimated weekly probability of occurrence for 308 bird species throughout the year within protected areas in the western contiguous USA using eBird occurrence data for the combined period 2004 to 2011. We classified species based on their annual patterns of occurrence on lands having intermediate conservation mandates (GAP status 2 and 3) administered by the Bureau of Land Management (BLM) and the United States Forest Service (USFS). We identified species having consistent annual association with one agency, and species whose associations across the annual cycle switched between agencies. BLM and USFS GAP status 2 and 3 lands contained low to moderate proportions of species occurrences, with proportions highest for species that occurred year-round or only during the summer. We identified two groups of species whose annual movements resulted in changes in stewardship responsibilities: (1) year-round species that occurred on USFS lands during the breeding season and BLM lands during the nonbreeding season; and (2) summer species that occurred on USFS lands during the breeding season and BLM lands during spring and autumn migration. Species that switched agencies had broad distributions, bred on high-elevation USFS lands, were not more likely to be identified as species of special management concern, and migrated short (year-round species) to long distances (summer species). Our findings suggest cooperative efforts that address the requirements of short-distance migratory species on GAP status 2 lands (n = 20 species) and GAP status 3 lands (n = 24) and long-distance migratory species on GAP status 2 lands (n = 9) would likely benefit

  3. Assessing the Eventual Publication of Clinical Trial Abstracts Submitted to a Large Annual Oncology Meeting.

    PubMed

    Massey, Paul R; Wang, Ruibin; Prasad, Vinay; Bates, Susan E; Fojo, Tito

    2016-03-01

    Despite the ethical imperative to publish clinical trials when human subjects are involved, such data frequently remain unpublished. The objectives were to tabulate the rate and ascertain factors associated with eventual publication of clinical trial results reported as abstracts in the Proceedings of the American Society of Clinical Oncology (American Society of Clinical Oncology). Abstracts describing clinical trials for patients with breast, lung, colorectal, ovarian, and prostate cancer from 2009 to 2011 were identified by using a comprehensive online database (http://meetinglibrary.asco.org/abstracts). Abstracts included reported results of a treatment or intervention assessed in a discrete, prospective clinical trial. Publication status at 4-6 years was determined by using a standardized search of PubMed. Primary outcomes were the rate of publication for abstracts of randomized and nonrandomized clinical trials. Secondary outcomes included factors influencing the publication of results. A total of 1,075 abstracts describing 378 randomized and 697 nonrandomized clinical trials were evaluated. Across all years, 75% of randomized and 54% of nonrandomized trials were published, with an overall publication rate of 61%. Sample size was a statistically significant predictor of publication for both randomized and nonrandomized trials (odds ratio [OR] per increase of 100 participants = 1.23 [1.11-1.36], p < .001; and 1.64 [1.15-2.34], p = .006, respectively). Among randomized studies, an industry coauthor or involvement of a cooperative group increased the likelihood of publication (OR 2.37, p = .013; and 2.21, p = .01, respectively). Among nonrandomized studies, phase II trials were more likely to be published than phase I (p < .001). Use of an experimental agent was not a predictor of publication in randomized (OR 0.76 [0.38-1.52]; p = .441) or nonrandomized trials (OR 0.89 [0.61-1.29]; p = .532). This is the largest reported study examining why oncology trials are

  4. Publication rate of abstracts presented at European Paediatric Orthopaedic Society Annual Meetings, 2006 to 2008.

    PubMed

    Kleine-Konig, Marie-Theres; Schulte, Tobias L; Gosheger, Georg; Rödl, Robert; Schiedel, Frank M

    2014-09-01

    The quality of the abstracts presented at a conference reflects the scientific work and level of activity of the scientific association concerned. The aim of the present study was to determine the rate of publications of podium presentations and posters at the conferences of the European Paediatric Orthopaedic Society (EPOS) from 2006 to 2008 and to identify factors that favor publication in peer-reviewed journals. The results are compared with those of other international societies. All 646 abstracts (including podiums, posters, and e-posters) presented at the EPOS conferences were investigated using the PubMed database to identify any corresponding published articles in the journals listed in the database. A period of 5 years before and after the relevant conference was used for the PubMed search. Factors influencing publication and the quality of the study, such as the type of presentation and the level of evidence, were also investigated. A publication rate of 36.7% was observed, corresponding to 237 publications of 646 abstracts. The period to publication showed a mean of 13.88 ± 1.34 months. It was found that abstracts of podium presentations were published significantly more often than poster abstracts (P<0.001). Experimental studies, with a publication rate of 50.9%, showed better results than clinical studies (36.0%). Overall, the articles were published in 61 different journals, with the largest number (n=50) appearing in the Journal of Pediatric Orthopaedics. In addition, the present study shows that abstracts with a higher level of evidence were associated with a higher publication rate. At 36.7%, the rate of publication of EPOS abstracts is within the range reached by other specialist orthopaedics societies, such as the German Society of Orthopaedics and Trauma Surgery (36%) and the British Orthopaedic Association (36%). However, it is lower than the publication rate of the Pediatric Orthopaedic Society of North America (POSNA), at 50%. The high

  5. Publication fate of abstracts presented at British association of clinical anatomists annual meetings.

    PubMed

    Furness, Hugh N; Miller, George W; Lewis, Thomas L

    2017-03-01

    Dissemination of research is an integral part of the scientific process. Failure to disseminate research limits the scope for critical appraisal and potentially wastes valuable resources. The gold standard for dissemination of research is peer-reviewed publication following presentation at a national meeting. The primary objective of this study was quantitative assessment of the abstracts presented at British Association of Clinical Anatomists (BACA) summer and winter meetings with regards to the rates of subsequent publication and comparison to other medical specialties. Published abstracts from the summer and winter meetings of BACA between the years of 2000 and 2014 were analyzed. MEDLINE was searched to identify peer-reviewed publications arising from each presented abstract. In total, 1,807 abstracts were presented between the years of 2000 and 2014. The mean number of abstracts presented each year was 60.2, (range 26-157). In total, 20.4% of abstracts were subsequently published in MEDLINE-indexed journals with a median publication time of 19 months. The mean number of cadaveric prosections was 45.2 ± 78.8, (range 1-960). Analysis of abstracts focusing on radiographic imaging found the mean number of scans was 224.4 ± 807.1, (range 1-6,439). Biannual meetings of BACA are a forum for the presentation of high-quality anatomical research. BACA meeting abstracts have generally reduced publication rates compared to some surgical specialty meetings; however, there is no analysis available for an equivalent anatomical meeting. Further work should try to identify reasons that may hinder or limit subsequent publication of the anatomy abstracts presented at BACA. Clin. Anat. 30:133-139, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Categories of Electronic Publications in a College Information System. AIR 1992 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Taylor, Allan

    This paper identifies and describes the categories of electronic publications (EPs) in a document-based communication and information system called JIMMY, developed by Queen Margaret College (Edinburgh, Scotland) for use by students and staff in general arts and paramedical courses. The use of computer-mediated communication systems like bulletin…

  7. Strategic Plan To Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education. 2002 Annual Report.

    ERIC Educational Resources Information Center

    Connecticut State Board of Governors for Higher Education, Hartford.

    This report describes progress made on Connecticut's strategic plan to ensure racial and ethnic diversity. Connecticut's public colleges and universities are becoming more diverse every year, and 2001 was no exception. The overall numbers of students, graduates, and professional employees from minority groups are higher than ever, although…

  8. Annual Research Review: Resilience and Child Well-Being--Public Policy Implications

    ERIC Educational Resources Information Center

    Ager, Alastair

    2013-01-01

    Background: There has been an 8-fold increase in use of the term resilience within scientific and scholar literature over the last twenty years. The arena of public policy has also seen increasing use made of the concept, both with respect to child well-being and development and wider issues. Method: A focal sample of literature comprising 108…

  9. Strategic Plan To Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education. 2001 Annual Report.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Higher Education, Hartford.

    This report describes progress made on Connecticut's strategic plan to ensure racial and ethnic diversity in higher education. The public colleges and universities of Connecticut continue to make incremental, year-to-year progress toward achieving the diversity goals established by the state's Board of Governors for Higher Education in its…

  10. Montgomery County Public Schools Annual Report to the Community, 2014 [Summary

    ERIC Educational Resources Information Center

    Montgomery County Public Schools, 2015

    2015-01-01

    Montgomery County Public Schools (MCPS) is more than a school system, it is a community. It's a community of people working together to provide Montgomery County students with an education that prepares them for success today, tomorrow, and in the years to come. That is MCPS' core purpose: to prepare students to thrive in their future. The Annual…

  11. Denver Public Schools, Department of Health Services. Forty-Eighth Annual Report, 1972-1973.

    ERIC Educational Resources Information Center

    Denver Public Schools, CO.

    This report details the programs and activities of the Department of Health Services of the Denver Public Schools, 1972-73. The first section, New Projects and Special Activities of the Department, presents health programs initiated in elementary and secondary schools and among adult employees. The development of a joint plan to give community…

  12. Institute Series for Developing Public Library Services for Disadvantaged Adults. Annual Report, 1974. Volume 2.

    ERIC Educational Resources Information Center

    Eyster, George W.

    Volume 2 presents the background and methodology of four state institute projects (Alabama, Kentucky, South Carolina, West Virginia) designed to expand public library services to disadvantaged adults, and also provides a description of the national, state, and local dissemination activities of the seven library/Adult Basic Education demonstration…

  13. SPIRES (Stanford Public Information Retrieval System) 1970-71 Annual Report.

    ERIC Educational Resources Information Center

    Parker, Edwin B.

    SPIRES (Stanford Public Information REtrieval System) is a computer information storage and retrieval system being developed at Stanford University with funding from the National Science Foundation. SPIRES has two major goals: to provide a user-oriented, interactive, on-line retrieval system for a variety of researchers at Stanford; and to support…

  14. The Study of Public Service in Higher Education. ASHE 1988 Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Crosson, Patricia H.

    Many important institutional policy and practice issues related to public service in universities are discussed, including: (1) mission statements and definitions (formal mission statements and broad and narrow definitions); (2) organizational structures (centralization and decentralization); (3) leadership (line officer, staff officer, and other…

  15. Integrated Library Systems in Canadian Public, Academic and Special Libraries: Fourth Annual Survey.

    ERIC Educational Resources Information Center

    Merilees, Bobbie

    1990-01-01

    Reports the results of a survey of integrated library system vendors that examined installations in Canadian academic, public and special libraries during 1989. Findings discussed include large library system versus PC-based system market shares, an analysis of system selection by type of library, and other factors that affect system selection. A…

  16. Annual Research Review: Resilience and Child Well-Being--Public Policy Implications

    ERIC Educational Resources Information Center

    Ager, Alastair

    2013-01-01

    Background: There has been an 8-fold increase in use of the term resilience within scientific and scholar literature over the last twenty years. The arena of public policy has also seen increasing use made of the concept, both with respect to child well-being and development and wider issues. Method: A focal sample of literature comprising 108…

  17. 77 FR 61748 - Annual Public Meeting of the Interagency Steering Committee on Multimedia Environmental Modeling

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-11

    ...) Development of frameworks and platforms; (2) subsurface biogeochemical studies; (3) cyber-water research... opportunity for the scientific community, ISCMEM members and other Federal and State agencies, and the public... wheel-chair accessible. Please allow time to register with building security and bring two photo ID's...

  18. What's public? What's private? Policy trade-offs and the debate over mandatory annual influenza vaccination for health care workers.

    PubMed

    Mah, Catherine L

    2008-01-01

    Policy decisions about public health services differ from those for personal health services. Both require trade-offs between such policy goals as liberty, security, efficiency, and equity. In public health, however, decisions about who will approve, pay for, and deliver services are often accompanied by decisions on when and how to compel individual behaviour. Policy becomes complex because different stakeholders interpret evidence differently: stakeholders may assign different weights to policy goals and may even define the same goals differently. In the debate over mandatory annual influenza vaccination for health care workers, for example, proponents as well as opponents of mandatory vaccination may convey arguments in security terms. Those in favour of mandatory vaccination emphasize subclinical infections and duty of care (public security) while those opposed emphasize risk of adverse events (personal security). Proponents assert less worker absenteeism (efficiency) while opponents stress coercion and alternate personal infection control measures (liberty and individual rights/responsibilities). Consequently, stakeholders talk past each other. Determining the place of mandatory influenza vaccination for health care workers thus demands reconciling policy trade-offs and clarifying the underlying disputes hidden in the language of the policy debate.

  19. Full publication of papers presented at the 1995 through 1999 European Association of Plastic Surgeons annual scientific meetings: a systemic bibliometric analysis.

    PubMed

    van der Steen, Lydia P E; Hage, J Joris; Loonen, Martijn P J; Kon, Moshe

    2004-07-01

    From the multitude of oral presentations at major medical meetings, the most informative and highest-quality studies make it to full publication in peer-reviewed journals. The rate of publication may be regarded as an indicator of the scientific level of the meeting. Study of the publication rates of consecutive annual meetings allows for the evaluation of the consistency of the scientific level of these meetings and for comparison with publication rates of other meetings in the same field of interest. To grade how useful any publication is to other authors, one can furthermore measure how frequently they cite it in their own publications. Finally, the time lag between oral presentation and full publication is of importance to both its authors and the audience at the meeting. The main objectives of this study were to determine the publication rate of papers of various fields of interest as presented at five consecutive annual meetings of the European Association of Plastic Surgeons (EURAPS) and the time lag between these presentations and their publication. The authors compared their overall findings to those reported for other surgical specialties. Moreover, they identified and classified the journals in which the full publications appeared as an indicator of the scientific value of the meeting. They conclude that a greater than average number of papers presented at the 1995 through 1999 annual EURAPS meetings went on to full publication in peer-reviewed journals. Among these journals, Plastic and Reconstructive Surgery was the best source for information presented at the meetings. Although approximately 90 percent of the publications appeared before 3 years had passed after a meeting, additional publications may be expected to appear even more than 6 years after the meeting. Given the high publication rate and the high average normalized impact factor of the journals in which the presentations appeared, the five studied EURAPS meetings overall had high scientific

  20. Cas-analyzer: an online tool for assessing genome editing results using NGS data.

    PubMed

    Park, Jeongbin; Lim, Kayeong; Kim, Jin-Soo; Bae, Sangsu

    2017-01-15

    Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

  1. Annual variation of the angular distribution of the UV beneath public shade structures.

    PubMed

    Turnbull, D J; Parisi, A V

    2004-10-25

    Local governments provide many shade structures at parks and sporting ovals for public use. However, the question remains of how effective are public shade structures at reducing biologically effective UV radiation throughout the year? Broadband measurements of the angular distribution of scattered UV beneath three specific public shade structures was conducted for relatively clear skies and for a solar zenith angle (SZA) ranging from 13 degrees to 76 degrees. The ultraviolet protection factors (UPF) for the shade structures ranged from 18.3 to 1.5 for an increasing SZA. Measurements showed that the horizontal plane received the highest SUV levels from the SZA of 28 degrees to 75 degrees, 42 degrees to 76 degrees, and 50 degrees to 76 degrees for the small, medium and large structures, respectively. This was due to the angle of the sun causing the shade created by the shade structure to be outside the structure. For the small shade structure, the measurements directed to the west were the highest levels in the shade after approximately 28 degrees. For the medium and large shade structures, the measurements directed to the west and south were the highest levels in the shade after roughly 42 degrees and 50 degrees, respectively.

  2. Using REDItools to Detect RNA Editing Events in NGS Datasets.

    PubMed

    Picardi, Ernesto; D'Erchia, Anna Maria; Montalvo, Antonio; Pesole, Graziano

    2015-03-09

    RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.

  3. Studying binary asteroids with NGS and LGS AO systems

    NASA Astrophysics Data System (ADS)

    Marchis, Franck; Berthier, Jerome; Descamps, Pascal; Hestroffer, Daniel; Vachier, Frederic; Laver, Conor; de Pater, Imke; Gavel, Don T.

    2004-10-01

    Since the discovery of Dactyl orbiting around Ida by the Galileo spacecraft in 1993, over twenty-five binary asteroid systems have been discovered using radar, direct imaging and Adaptive Optics observations. Asteroidal moon discoveries dramatically increased with the advent of this last technique on ground based telescopes. Our group focuses on the search and study of double asteroids in the main-belt, in the Trojan population and beyond Neptune's orbit. We have been using several of the AO systems available (Lick-3m, Palomar-5m, VLT-8m, Keck-10m) and related techniques such as Appulse and Laser Guide Star observations to broaden the sample of asteroids observed from the main-belt out to the Kuiper Belt. We will present a quality comparison between various techniques and different AO systems with NGS and will detail our first successful observations with the Lick LGS system. Precise orbital elements of the secondary can be determined by multiple observations spanning large periods of time (several months). Our group developed a method to predict the ephemeris of a secondary companion. Without any assumptions, this method, tested successfully on 22 Kalliope and 121 Hermione binary systems, leads to the direct determination of important physical parameters of the targets, such as their mass and the interior structure, as well as gives direct insights on their formation processes that may be otherwise only be speculated on from spacecraft mission flybys.

  4. Electric and Magnetic Fields Research and Public Information Dissemination Program annual report for fiscal year 1996

    SciTech Connect

    1997-06-01

    The Electric and Magnetic Fields (EMF) Research and Public Information Dissemination (RAPID) Program was authorized by the Energy Policy Act of 1992 as a near-term effort to expand and accelerate the research needed to address the EMF issue. As required by this legislation, the EMF Interagency Committee, the National EMF Advisory Committee (NEMFAC), and the National Academy of Sciences (NAS) are providing valued input and advice for the direction of this program. With this input and advice, the Department of Energy (DOE) and the National Institute of Environmental Health Sciences (NIEHS) have developed and are implementing five-year program plans. Multi-year health effects research projects and related EMF measurement and exposure assessment projects are underway using funds appropriated in fiscal years 1994, 1995, and 1996 together with voluntary non-Federal contributions. The results of these research projects, along with the results of other EMF research, will be used as input to the hazard evaluation effort, which is the focus of the EMF RAPID Program. A coordinated interagency program is underway to communicate needed information on the EMF issue in a clear manner to the public and other decision makers.

  5. Annual Research Review: Resilience and child well-being--public policy implications.

    PubMed

    Ager, Alastair

    2013-04-01

    There has been an 8-fold increase in use of the term resilience within scientific and scholar literature over the last twenty years. The arena of public policy has also seen increasing use made of the concept, both with respect to child well-being and development and wider issues. A focal sample of literature comprising 108 papers addressing public policy implications of work on child resilience was identified by a structured bibliographic search. This literature suggests that current work: is characterized by a breadth of sectoral engagement across the fields of education, social work, and health; demonstrates diversity with regard to the systemic levels--individual (biological and psychological), communal (including systems of faith and cultural identity), institutional and societal--with which it engages; but is based more upon conceptual rather than empirical analysis. Major themes of policy recommendation target strengthened family dynamics, increased capacity for counseling and mental health services, supportive school environments, development of community programs, promotion of socioeconomic improvement and adoption of a more comprehensive conception of resilience. Evaluations of resiliency-informed policy initiatives are limited in number, with greatest rigor in design associated with more discrete programmatic interventions. A number of strategies to strengthen research-policy linkages are identified. These include greater commitment to operationalize indicators of resilience at all levels of analysis; more coherent engagement with the policy making process through explicit knowledge translation initiatives; and developing complex adaptive systems models amenable to exploring policy scenarios. © 2013 The Author. Journal of Child Psychology and Psychiatry © 2013 Association for Child and Adolescent Mental Health.

  6. Trends and opportunities abroad, 1987: an annual special publication of International Demographics.

    PubMed

    1986-12-01

    rather than to an increase in numbers. 4 demographic factors help identify market potential--the average annual population growth rate, the average number of lifetime births per woman, the status of women, and urbanization. Countries not currently considered good potential markets are growing very rapidly at an average population growth rate of 2.5% or more and will continue to do so. The status of women is low, and the urban population is concentrated in 1 city. countries with good market potential are growing more slowly, at a rate of 1.5-2.5% a year. Fertility is under control, the status of women is improving, and urbanization is spread throughout the country.

  7. Publication rates of manuscript presentations at the American College of Foot and Ankle Surgeons Annual Scientific Conference between 1999 and 2008.

    PubMed

    Roukis, Thomas S

    2011-01-01

    Publication is the ultimate desired end point of scientific research. However, oral manuscript presentations of research studies are often referenced in textbooks, journal articles, and industry white papers, and, as a result, influence treatment care plans. No data exist for the actual publication rate of podiatric foot and ankle surgery oral manuscript presentations. Therefore, the objective of this study was to determine the actual publication rates of oral manuscript presentations at the American College of Foot and Ankle Surgeons (ACFAS) Annual Scientific Conference over 10 years. Print or electronic media for the ACFAS Annual Scientific Conference official program between 1999 and 2008 were obtained. Each year's official program was hand searched for any oral manuscript presentation, and, when identified, the title and authors were individually searched through electronic internet-based search engines to determine whether an oral manuscript presentation had been followed by publication of a full-text article. Additionally, pertinent journals were hand searched for potential articles. A total of 67.5% (139/206) oral manuscript presentations were ultimately published in 1 of 12 medical journals in a mean of 14.5 months. All journals except one (91.7%) represented peer-reviewed journals. The publication rate of oral manuscript presentations at the ACFAS Annual Scientific Conference is similar to or greater than orthopaedic subspecialties, including foot and ankle surgery, publication rates. Based on the above, attendees of the ACFAS Annual Scientific Conference should be aware that the majority of oral manuscript material presented at the ACFAS Annual Scientific Conference can be considered as accurate because they survive the rigors of the peer-review process more than two thirds of the time.

  8. Public Utility Regulatory Policies Act of 1978. Annual report to Congress

    SciTech Connect

    None,

    1980-05-01

    Titles I and III of the Public Utility Regulatory Policies Act of 1978 (PURPA) establish retail regulatory policies for electric and natural gas utilities, respectively, aimed at achieving three purposes: conservation of energy supplied by electric and gas utilities; efficiency in the use of facilities and resources by these utilities; equitable rates to electricity and natural gas consumers. PURPA also continues the pilot utility implementation program, authorized under Title II of the Energy Conservation and Production ACT (ECPA), to encourage adoption of cost-based rates and efficient energy-management practices. The purpose of this report is twofold: (1) to summarize and analyze the progress that state regulatory authorities and certain nonregulated utilities have made in their consideration of the PURPA standards; and (2) to summarize the Department of Energy (DOE) activities relating to PURPA and ECPA. The report provides a broad overview and assessment of the status of electric and gas regulation nationwide, and thus helps provide the basis for congressional and DOE actions targeted on the utility industry to address pressing national energy problems.

  9. Association Between Study Quality and Publication Rates of Medical Education Abstracts Presented at the Society of General Internal Medicine Annual Meeting.

    PubMed

    Sawatsky, Adam P; Beckman, Thomas J; Edakkanambeth Varayil, Jithinraj; Mandrekar, Jayawant N; Reed, Darcy A; Wang, Amy T

    2015-08-01

    Studies reveal that 44.5% of abstracts presented at national meetings are subsequently published in indexed journals, with lower rates for abstracts of medical education scholarship. We sought to determine whether the quality of medical education abstracts is associated with subsequent publication in indexed journals, and to compare the quality of medical education abstracts presented as scientific abstracts versus innovations in medical education (IME). Retrospective cohort study. Medical education abstracts presented at the Society of General Internal Medicine (SGIM) 2009 annual meeting. Publication rates were measured using database searches for full-text publications through December 2013. Quality was assessed using the validated Medical Education Research Study Quality Instrument (MERSQI). Overall, 64 (44%) medical education abstracts presented at the 2009 SGIM annual meeting were subsequently published in indexed medical journals. The MERSQI demonstrated good inter-rater reliability (intraclass correlation range, 0.77-1.00) for grading the quality of medical education abstracts. MERSQI scores were higher for published versus unpublished abstracts (9.59 vs. 8.81, p = 0.03). Abstracts with a MERSQI score of 10 or greater were more likely to be published (OR 3.18, 95% CI 1.47-6.89, p = 0.003). ). MERSQI scores were higher for scientific versus IME abstracts (9.88 vs. 8.31, p < 0.001). Publication rates were higher for scientific abstracts (42 [66%] vs. 37 [46%], p = 0.02) and oral presentations (15 [23%] vs. 6 [8%], p = 0.01). The publication rate of medical education abstracts presented at the 2009 SGIM annual meeting was similar to reported publication rates for biomedical research abstracts, but higher than publication rates reported for medical education abstracts. MERSQI scores were associated with higher abstract publication rates, suggesting that attention to measures of quality--such as sampling, instrument validity, and data analysis

  10. QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.

    PubMed

    Wagle, Prerana; Nikolić, Miloš; Frommolt, Peter

    2015-07-01

    Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive amounts of data remains challenging. Since multiple algorithmic approaches for the basic data analysis have been developed, there is now an increasing need to efficiently use these tools to obtain results in reasonable time. We have developed QuickNGS, a new workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. We demonstrate the efficiency of our new software by a comprehensive analysis of 10 RNA-Seq samples which we can finish in only a few minutes of hands-on time. The approach we have taken is suitable to process even much larger numbers of samples and multiple projects at a time. Our approach considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

  11. NDCEE Annual Technologies Publication

    DTIC Science & Technology

    2004-07-01

    ionization of coating material. The high percentage of coating material ionization, combined with substrate biasing leads to excellent film adhesion and...denser coatings than conventional PVD processes. In general, good quality films are deposited throughout a wide range of deposition conditions...with deformation and poor adhesion). PACVD is used for the application of thin film coatings and particularly for the deposition of diamond films

  12. NDCEE Annual Technologies Publication

    DTIC Science & Technology

    2003-04-01

    Demanufacturing and Recycling and Reuse System ................... 17 ElectroSpark Deposition Micro-Welding Process...environmental solutions 19 Technologies ElectroSpark Deposition Micro-Welding Process The NDCEE has demonstrated and evaluated the feasibility of using the... ElectroSpark Deposition (ESD) process to replace electroplated hard chromium (EHC). The NDCEE has determined that ESD offers life-cycle performance and

  13. NGS-Trex: an automatic analysis workflow for RNA-Seq data.

    PubMed

    Boria, Ilenia; Boatti, Lara; Saggese, Igor; Mignone, Flavio

    2015-01-01

    RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. Here we describe the complete analysis of sample data from raw sequences to data mining of results by using NGS-Trex platform, a low user interaction, fully automatic analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome of the samples identifying expressed genes, transcripts, and new and known splice variants. It also detects differentially expressed genes and transcripts across different experiments.

  14. KNIME4NGS: a comprehensive toolbox for Next Generation Sequencing analysis.

    PubMed

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Werner Mewes, H-; Küffner, Robert

    2017-01-09

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.

  15. RESULTS OF ANALYSIS OF NGS CONCENTRATE DRUM SAMPLES [Next Generation Solvent

    SciTech Connect

    Peters, T.; Williams, M.

    2013-09-13

    Savannah River National Laboratory (SRNL) prepared two drums (50 gallons each in Drum#2 and Drum#4) of NGS-MCU (Next Generation Solvent-Modular CSSX Unit) concentrate for future use at MCU in downblending the BOBCalixC6 based solvent to produce NGS-MCU solvent. Samples of each drum were sent for analysis. The results of all the analyses indicate that the blend concentrate is of the correct composition and should produce a blended solvent at MCU of the desired formulation.

  16. [The impact of the annual scientific meetings of the Israel Society of Rheumatology as measured by publication rates of the abstracts in peer-reviewed journals].

    PubMed

    Perez, Shira; Hashkes, Philip J; Uziel, Yosef

    2004-04-01

    We aimed to examine the impact and quality of the research presented in the Israel Society of Rheumatology (ISR) annual scientific meetings by measuring publication rates of the abstracts in peer-reviewed journals and investigating the factors that influenced publication. We examined the outcome of all 79 abstracts submitted to the ISR for the 1998-2000 annual meetings. A MEDLINE search of all abstracts, by authors, topics and keywords was performed. Senior authors of abstracts not found to be published in this search were interviewed regarding publication and factors influencing submission. We described the effect of variable factors on the rate of publication. As of September 2002, 63 (80%) abstracts were published in peer-reviewed journals or are currently in-press. Most abstracts were published in prominent journals (with a high impact factor). The majority of the abstracts (61%) were published in rheumatologic journals, 65% of the studies originated from tertiary centers and 19% of the studies were multicenter. The most common diseases studied were antiphospholipid syndrome (20%), systemic lupus erythematosus (19%) and inflammatory arthritis (18%). Most of the studies were of disease pathogenesis (35%) and clinical manifestations (33%). The most common study designs were basic science (34%). An overall 57% of the studies reported "positive" results and 9% reported "negative" results. None of the factors studied were associated with publication or non-publication. The main cause cited by authors for not publishing their abstract was lack of time to prepare a full paper or a desire to further expand the study. Within this group of 16 authors of abstracts, 11 authors still plan to submit a paper. The ISR annual meetings have an important clinical scientific impact as measured by the high rate of abstracts published as full length articles in leading peer-reviewed journals.

  17. Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

    PubMed Central

    Weber, Marc; Teeling, Hanno; Huang, Sixing; Waldmann, Jost; Kassabgy, Mariette; Fuchs, Bernhard M; Klindworth, Anna; Klockow, Christine; Wichels, Antje; Gerdts, Gunnar; Amann, Rudolf; Glöckner, Frank Oliver

    2011-01-01

    Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion. PMID:21160538

  18. Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.

    PubMed

    Weber, Marc; Teeling, Hanno; Huang, Sixing; Waldmann, Jost; Kassabgy, Mariette; Fuchs, Bernhard M; Klindworth, Anna; Klockow, Christine; Wichels, Antje; Gerdts, Gunnar; Amann, Rudolf; Glöckner, Frank Oliver

    2011-05-01

    Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.

  19. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    EPA Science Inventory

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  20. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    EPA Science Inventory

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  1. Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.

    PubMed

    Qian, Xiaoqin; Hou, Jiayi; Wang, Zheng; Ye, Yi; Lang, Min; Gao, Tianzhen; Liu, Jing; Hou, Yiping

    2017-09-12

    There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.

  2. From Abstract to Publication in a Peer-Reviewed Journal: Evaluation of the 63rd Annual Meeting of the German Society of Neurosurgery.

    PubMed

    Czorlich, Patrick; Regelsberger, Jan; Meixensberger, Jürgen; Westphal, Manfred; Eicker, Sven Oliver

    2016-01-01

    The presentation and academic discussion of the latest scientific research is the central purpose of meetings like the annual meeting of the German Society of Neurosurgery (DGNC). The aim of this study was to investigate the publication rate of all oral and poster abstracts of the DGNC meeting 2012 held in Leipzig, Germany, in peer-reviewed journals and to identify factors that are associated with a higher publication rate. We reviewed all accepted oral and poster presentations of the meeting. Then a search in PubMed was performed to determine the publication rate within 3 years after the abstract submission deadline. We used the information to identify factors associated with a higher publication rate. The publication rate in a peer-reviewed journal was 40.4% for all presented abstracts. Overall, 41.5% of all poster presentations and 40.1% of all oral presentations were published within 3 years. Abstracts presenting prospective studies or university research had a statistically higher chance of publication. The average journal impact factor for all published abstracts was 2.99, and 81 different journals were chosen for publication. Overall, 40.4% of all presented abstracts at the 2012 DGNC were published in a peer-reviewed journal indexed in PubMed, which reflects the high scientific standard of this meeting. Prospective studies and studies presented by authors from universities had a higher chance of being published. Georg Thieme Verlag KG Stuttgart · New York.

  3. An Assessment of Airborn Gravimetry Collected under the NGS GRAV-D Project

    NASA Astrophysics Data System (ADS)

    Holmes, S. A.

    2009-12-01

    In the United States, the National Geodetic Survey [NGS] holds the official charter to maintain the vertical datum for the USA and its territories. This includes the responsibility to maintain a current geoid model for transforming between orthometric (H) and geodetic (h) heights. The latest (2009) NGS geoid model incorporates the latest GRACE-based satellite-only geopotential solutions, very-high-resolution digital elevation models [DEMs] derived from the Shuttle Radar Topography Mission [SRTM], and other additional data and processing improvements. This recent geoid model also benefited greatly from the prior release of the National Geospatial-Intelligence Agency’s [NGA] Earth Gravitational Model 2008 [EGM2008], which served as a computational reference field for the new geoid, but was also particularly useful for identifying and removing corrupted data from the NGS gravimetry database. Looking forwards, NGS intends to increase its efforts to refine and improve its future national geoid models. To this end, their ambitious "Gravity for the Re-definition of the American Datum” [GRAV-D] project aims to update the NGS gravimetry holdings by flying new airborn gravity surveys over a large fraction of the USA and it territories. Concurrent efforts will focus on developing new processing techniques for optimally incorporating improved gravimetry into the final geoid solution. To this end, the GRAV-D team has already flown several surveys in the Gulf of Mexico, Puerto Rico, US Virgin Islands, and Alaska. Testing and analysis aimed at calibrating and validating the preliminary survey data is already underway. The latest assessment of these recent efforts, including the extent to which this new data can be expected to contribute to an improved gravimetric geoid model, is presented here.

  4. National Academy of Sciences, National Academy of Engineering, Institute of Medicine, National Research Council, Annual Report Fiscal Year 1975-76. Committee on Labor and Public Welfare, 94th Congress, 2nd Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. Senate Committee on Labor and Public Welfare.

    Presented is the annual report for fiscal year 1975-76 of the National Academy of Sciences (NAS), including the annual reports of the National Academy of Engineering and the Institute of Medicine. Contents include: (1) report of the President; (2) reports on completed studies including food and nutrition, public health, natural resources, space…

  5. National Academy of Sciences, National Academy of Engineering, Institute of Medicine, National Research Council, Annual Report Fiscal Year 1975-76. Committee on Labor and Public Welfare, 94th Congress, 2nd Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. Senate Committee on Labor and Public Welfare.

    Presented is the annual report for fiscal year 1975-76 of the National Academy of Sciences (NAS), including the annual reports of the National Academy of Engineering and the Institute of Medicine. Contents include: (1) report of the President; (2) reports on completed studies including food and nutrition, public health, natural resources, space…

  6. Publications

    Cancer.gov

    Information about NCI publications including PDQ cancer information for patients and health professionals, patient-education publications, fact sheets, dictionaries, NCI blogs and newsletters and major reports.

  7. Publication of abstracts submitted to the annual meeting of the Pediatric Orthopaedic Society of North America: is there a difference between accepted versus rejected abstracts?

    PubMed

    Varghese, Ranjit A; Chang, Justin; Miyanji, Firoz; Reilly, Christopher W; Mulpuri, Kishore

    2011-01-01

    The purpose of this study was to determine publication rates of all abstracts submitted for presentation at the annual conference of the Pediatric Orthopaedic Society of North America (POSNA) comparing papers accepted for presentation with those that were not accepted and to determine the median times to publication and the mean impact factor of journals that published papers from the 2 groups. The titles and authors of all abstracts submitted for presentation to the POSNA for the years 2003 to 2005 were identified. To determine publication status, we conducted a computerized Pubmed search using the first author's name. If multiple publications were identified, the Boolean search operator AND was used to combine author names with key words. The title of each located published article was compared with the title of the abstract. If differences were noted, the abstract content was compared with the final publication. The journals, impact factor was determined using the journal citation report. The median time from conference presentation to publication was determined using a Kaplan-Meier survival analysis. Of 1191 abstracts submitted to the annual meetings of POSNA from the years 2003 through 2005, 440 (37%) were accepted for presentation. Acceptance of submitted abstracts increased from 30% in 2003 to 40% in 2005. Of the 1191 abstracts 599 (50%) were subsequently published by August 2009. The mean publication rate for abstracts accepted for presentation was 58.9% (259 of 440) compared with 45% (339 of 751) for rejected abstracts. The median time to publication of accepted abstracts was not significantly different when compared with that of rejected abstracts. The mean journal impact factor for accepted articles was 2.2 compared with 1.5 for rejected abstracts. The publication rates of abstracts submitted to POSNA is high compared with those of other international orthopaedic associations. The mean publication rate for accepted abstracts and rejected abstracts has

  8. Journal Publication of Material Presented at the 1967 Annual Meeting of the Geophysical Union During the Year Following the Meeting.

    ERIC Educational Resources Information Center

    Johns Hopkins Univ., Baltimore, MD. Center for Research in Scientific Communication.

    The April 1967 Annual Meeting of the American Geophysical Union was the subject of an investigation of scientific information exchange among geophysicists. The study focused on meeting presentation papers and drew a sample of 240 of the 800 presentation authors. The results of the meeting study demonstrated the currency of the work reported by…

  9. Environmental Sciences Division annual progress report for period ending September 30, 1982. Environmental Sciences Division Publication No. 2090. [Lead abstract

    SciTech Connect

    Not Available

    1983-04-01

    Separate abstracts were prepared for 12 of the 14 sections of the Environmental Sciences Division annual progress report. The other 2 sections deal with educational activities. The programs discussed deal with advanced fuel energy, toxic substances, environmental impacts of various energy technologies, biomass, low-level radioactive waste management, the global carbon cycle, and aquatic and terrestrial ecology. (KRM)

  10. The Power of Possibility. Defining Moments: How IDRA and Its Partners Are Changing Public Education. IDRA Annual Report 2014

    ERIC Educational Resources Information Center

    Intercultural Development Research Association, 2014

    2014-01-01

    Intercultural Development Research Association's (IDRA) 2014 Annual Report highlights seven defining moments in the work of the previous year: (1) Securing Opportunity; (2) Defending Children's Educational and Civil Rights; (3) Building a National Grassroots Family Model; (4) Putting Quality Early Education at the Forefront; (5) Empowering…

  11. Journal Publication of Material Presented at the 1967 Annual Meeting of the Geophysical Union During the Year Following the Meeting.

    ERIC Educational Resources Information Center

    Johns Hopkins Univ., Baltimore, MD. Center for Research in Scientific Communication.

    The April 1967 Annual Meeting of the American Geophysical Union was the subject of an investigation of scientific information exchange among geophysicists. The study focused on meeting presentation papers and drew a sample of 240 of the 800 presentation authors. The results of the meeting study demonstrated the currency of the work reported by…

  12. The 49th Annual PDK Poll of the Public's Attitudes toward the Public Schools: Academic Achievement Isn't the Only Mission

    ERIC Educational Resources Information Center

    Phi Delta Kappan, 2017

    2017-01-01

    The 2017 PDK Poll of the Public's Attitudes Toward the Public Schools finds that Americans overwhelmingly want schools to do more than educate students in academic subjects. While they value traditional academic preparation, Americans say they want schools to substantially help position students for their working lives after school, which means…

  13. Publication rates of poster presentations at the American College of Foot and Ankle Surgeons annual scientific conference between 1999 and 2008.

    PubMed

    Abicht, Bradley P; Donnenwerth, Michael P; Borkosky, Sara L; Plovanich, Elizabeth J; Roukis, Thomas S

    2012-01-01

    Publication is the desired end point of scientific research. Ultimately, it is desired that research presented in poster format at a scientific conference will be developed into a report and become published in a peer-reviewed scientific journal. Moreover, poster presentations of research studies are often referenced and, as a result, influence treatment care plans. No data exist for the actual publication rate of podiatric foot and ankle surgery poster presentations. Therefore, the objective of the present study was to determine the actual publication rates of poster presentations at the American College of Foot and Ankle Surgeons (ACFAS) annual scientific conference (ASC) during a 10-year period. Print or electronic media for the ACFAS ASC official program from 1999 to 2008 were obtained. Each year's official program was manually searched for any poster presentation and, when identified, the authors and title were individually searched using Internet-based search engines to determine whether a poster presentation had been followed by publication. Of the 825 posters, 198 (24%) poster presentations were ultimately published in 1 of 32 medical journals within a weighted mean of 17.6 months. Of the 32 journals, 25 (78.1%) represented peer-reviewed journals. The publication rate of poster presentations at the ACFAS ASC was less than that of oral manuscripts presented at the same meeting during the same period and was also less than the orthopedic subspecialty poster presentation publication rates. Therefore, attendees of the ACFAS ASC should be aware that only a few of the posters presented at the ACFAS ASC will be valid because they will not survive the rigors of publication 76% of the time. Additionally, more stringent selection criteria should be used so that the selected poster presentations can ultimately withstand the publication process. Copyright © 2012 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  14. Publication rates of abstracts presented at the annual congress of the Turkish Society of Colorectal Surgery (years 2003-2011).

    PubMed

    Meral, Ulvi Mehmet; Urkan, Murat; Alakuş, Ümit; Lapsekili, Emin; İflazoğlu, Nidal; Ünlü, Aytekin; Özmen, Pelin; Demirbaş, Sezai

    2017-01-01

    The aim of our study is to examine the Publication Rate of Congress of Turkish Society of Colorectal Surgery meeting abstracts and determine the factors affecting publication rate. All presentations at Congress of Turkish Society of Colorectal Surgery congresses held in 2003, 2007, 2009, 2011 were retrospectively assessed. Manuscripts indexed in Google-Scholar database were included. The meeting year, study type, presentation type, title and time to publication of studies were assessed. Actual impact factor values were assessed to introduce the scientific power of the journals. Among a total of 614 abstracts presented at these congresses, 139 (22.6%) presentations were published in various medical journals. The publication rate was higher in oral presentations as group compared to poster presentations (29.7% vs. 19.5%) (p<0.001). Mean time to publication period was 20.4 (±21.1) months. 78 (56.1%) of published articles were published in SCI-E journals while 61 (43.9%) were published in non-SCI-E journals. Experimental studies had a higher Publication Rate in analysis of publication rate according to study type (p<0.001). Prospective clinical studies had a higher publication rate than retrospective studies. The journals in which oral presentations had been published had greater impact factor than journals in which poster presentations had been published (p=0.02). If published; prospective clinical studies were published in journals with greater impact factor than retrospective studies (p=0.04). The quality of a meeting is correlated with the publication of abstracts accepted as presentations. Congress of Turkish Society of Colorectal Surgery congress is an efficient meeting for researchers, and have a lower PR as compared to international congresses while having a similar publication rate to equivalent scientific meetings. Being more selective during abstract acceptance should increase the Publication Rate and quality of Congress of Turkish Society of Colorectal

  15. Annual Conference of the Public Service Satellite Consortium (4th, Washington, D.C., October 11-12, 1979).

    ERIC Educational Resources Information Center

    Public Service Satellite Consortium, Washington, DC.

    This collection of papers delivered at the conference provides information on the current state of communications satellite applications and technology, the relationship of cable television and satellites, the role of satellites in public broadcasting, and the future of satellites in serving the needs of the public. Remarks and addresses by the…

  16. Annual Conference of the Public Service Satellite Consortium (4th, Washington, D.C., October 11-12, 1979).

    ERIC Educational Resources Information Center

    Public Service Satellite Consortium, Washington, DC.

    This collection of papers delivered at the conference provides information on the current state of communications satellite applications and technology, the relationship of cable television and satellites, the role of satellites in public broadcasting, and the future of satellites in serving the needs of the public. Remarks and addresses by the…

  17. Public Higher Education and the State: Models for Financing, Budgeting, and Accountability. ASHE 1986 Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Curry, Denis J.; Fischer, Norman M.

    The trend toward greater state regulation of public higher education is discussed, along with alternative structures or models for state financing of public institutions. The situation in Washington State is briefly described as an illustration. It is proposed that interests of the state, college, and student can be enhanced by allowing colleges…

  18. Environmental Performance Report 2013: Annual Site Environmental Report per the U.S. Department of Energy Order 231.1-1B (Management Publication)

    SciTech Connect

    Schlomberg, K.; Eickhoff, J.; Beatty, B.; Braus, G.; Durbin, L.; Fiehweg, R.; Ray, M.; Ryon, T.; Schmitz, E.

    2014-08-01

    The National Renewable Energy Laboratory's (NREL's) Environmental Performance Report provides a description of the laboratory's environmental management activities for 2013, including information on environmental and sustainability performance, environmental compliance activities and status, and environmental protection programs, highlights, and successes. The purpose of this report is to ensure that U.S. Department of Energy (DOE) and the public receive timely, accurate information about events that have affected or could adversely affect the health, safety, and security of the public or workers; the environment; or the operations of DOE facilities. This report meets the requirements of the Annual Site Environmental Report and is prepared in accordance with the DOE Order 231.1B, Environment, Safety and Health Reporting.

  19. Peer review in publication: factors associated with the full-length publication of studies presented in abstract form at the annual meeting of the Society for Medical Decision Making.

    PubMed

    Greenberg, Dan; Wacht, Oren; Pliskin, Joseph S

    2008-01-01

    : Many studies are presented at scientific meetings and are summarized in abstract form prior to their full-length publication. Publication rates of these studies may be an indicator in judging their quality. To determine the rate at which studies reported in an abstract form are subsequently published in full length and identify factors associated with publication success. : All abstracts presented at the 25th Annual Meeting of SMDM in October 2003 were reviewed and assessed for subsequent publication in peer-reviewed journals through December 31, 2007. For each abstract we recorded the presenting author's affiliation, presentation mode, and country of origin. For published articles, we recorded the publication date, type of journal, and the journal's impact factor. We calculated the mean and median time from conference presentation to publication using a Kaplan-Meier survival analysis. : Of 239 presented abstracts, 64 (27%) were subsequently published in full-length, including 39% of podium, and 20% of poster presentations (P = 0.002). Mean and median times from presentation to publication were 20.5 and 19.0 months, respectively. There was no significant difference in mean publication lag for podium and poster presentations. : A significant proportion of studies presented at the SMDM meeting are not published in full length. This failure to publish is substantially higher as compared with findings from other medical and biomedical meetings. A further study is needed to explore the reasons for this low publication rate and to compare the fate of SMDM meeting abstracts to those of similar conferences.

  20. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.

    PubMed

    Patel, Ravi K; Jain, Mukesh

    2012-01-01

    Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

  1. NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

    PubMed Central

    Patel, Ravi K.; Jain, Mukesh

    2012-01-01

    Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis. PMID:22312429

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

    PubMed

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

    2017-08-01

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

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

    PubMed Central

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

    2017-01-01

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

  4. The variation game: Cracking complex genetic disorders with NGS and omics data.

    PubMed

    Cui, Hongzhu; Dhroso, Andi; Johnson, Nathan; Korkin, Dmitry

    2015-06-01

    Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.

  5. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    PubMed Central

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  6. BAL31-NGS approach for identification of telomeres de novo in large genomes.

    PubMed

    Peška, Vratislav; Sitová, Zdeňka; Fajkus, Petr; Fajkus, Jiří

    2017-02-01

    This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n=14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples.

  7. Refining Our Mission: Continuing Education's Role in Engagement, Outreach and Public Service. Proceedings of the Annual Meeting of the Association for Continuing Higher Education (69th, Roanoke, VA, October 27-30, 2007)

    ERIC Educational Resources Information Center

    Barrineau, Irene T., Ed.

    2007-01-01

    The 2007 Annual Meeting of the Association for Continuing Higher Education was themed "Refining Our Mission: Continuing Education's Role in Engagement, Outreach and Public Service." Opportunities were available to participate in sessions relating to outreach, partnerships and public service and perspectives on this theme were presented…

  8. The Tsimane’ Amazonian Panel Study (TAPS): Nine years (2002-2010) of annual data available to the public

    PubMed Central

    Leonard, William R.; Reyes-García, Victoria; Tanner, Susan; Rosinger, Asher; Schultz, Alan; Vadez, Vincent; Zhang, Rebecca; Godoy, Ricardo

    2016-01-01

    This brief communication contains a description of the 2002-2010 annual panel collected by the Tsimane’ Amazonian Panel Study team. The study took place among the Tsimane’, a native Amazonian society of forager-horticulturalists. The team tracked a wide range of socio-economic and anthropometric variables from all residents (633 adults ≥16 years; 820 children) in 13 villages along the Maniqui River, department of Beni. The panel is ideally suited to examine how market exposure and modernization affect the well-being of a highly autarkic population and to examine human growth in a non-Western rural setting. PMID:26280812

  9. The Tsimane' Amazonian Panel Study (TAPS): Nine years (2002-2010) of annual data available to the public.

    PubMed

    Leonard, William R; Reyes-García, Victoria; Tanner, Susan; Rosinger, Asher; Schultz, Alan; Vadez, Vincent; Zhang, Rebecca; Godoy, Ricardo

    2015-12-01

    This brief communication contains a description of the 2002-2010 annual panel collected by the Tsimane' Amazonian Panel Study team. The study took place among the Tsimane', a native Amazonian society of forager-horticulturalists. The team tracked a wide range of socio-economic and anthropometric variables from all residents (633 adults ≥16 years; 820 children) in 13 villages along the Maniqui River, Department of Beni. The panel is ideally suited to examine how market exposure and modernization affect the well-being of a highly autarkic population and to examine human growth in a non-Western rural setting.

  10. Publication bias in pediatric hematology and oncology: analysis of abstracts presented at the annual meeting of the American Society of Pediatric Hematology and Oncology.

    PubMed

    Salami, Khadra; Alkayed, Khaldoun

    2013-04-01

    Publication bias (PB) is a threat to the validity of medical literature, and has not been studied in the field of pediatric hematology/oncology. We analyzed the abstracts presented at the 2005 American Society of Pediatric Hematology/Oncology annual meeting to assess for PB. Abstracts were categorized by type of research, number of centers, funding status, presentation format, sample size, statistical significance, and the direction of results. Publication status was determined by searching PubMed. Thirty nine abstracts (51%) were categorized as clinical studies, 67 (36%) as basic research, and 24 (13%) as others. One hundred and twenty three abstracts (67%) were considered to have positive results, 14 (8%) negative results, and 47 (25%) with neutral or not stated results. About 62% of the abstracts were published in peer-reviewed journals at a median time to publication of 19 months (IQR = 11-29 months). Abstracts with positive results were more likely to get published than others (combined negative and neutral results) (P = .002). Factors like sample size, number of centers, or statistical significance reporting did not affect the publication rate. Our data suggests the existence of PB in the field of pediatric hematology/oncology. Still, further analysis of other international meetings is needed to validate our findings.

  11. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

    PubMed

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y-H; Thompson, Janelle R

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  12. Brazilian abstracts presented at the American Urological Association annual meetings: contribution, publication rates, and comparison with oncology abstracts.

    PubMed

    Arap, Marco A; Reis, Rodolfo Borges dos; Torricelli, Fábio César Miranda; Masson, André L S; Saad, Everardo D

    2014-01-01

    Scientific research originating from Brazil appears to be rising in several medical fields. Research results are often presented at scientific meetings before publication in peer-reviewed journals. We investigated the publication rate of Brazilian studies presented in American Urological Association (AUA) meetings and compared with the rate of publication of Brazilian oncological studies presented at the American Society of Clinical Oncology (ASCO) meetings. a hand search of 12,454 abstracts presented at aua meetings 2001-2007 was conducted. abstracts for which at least two-thirds of institutions were from brazil were considered as brazilian. final publication was searched in pubmed and lilacs databases. oncological abstracts were also hand searched in the asco meetings proceedings in the same years. There was no significant temporal trend in the proportion of AUA studies originating from Brazil along those 7 years. A total of 195 abstracts (1.57%) were from Brazil. One hundred (51.3%) abstracts were published in full, and the estimated 5-year publication rate was 48.2%. There was a progressive increase in publication rates for studies categorized as video, poster, and podium presentations. Considering abstracts presented in years 2001-2005, urologic publication rate was significantly higher than for abstracts presented at the ASCO meeting. Our results suggest that the Brazilian contribution to AUA meetings is at a plateau and that the Brazilian literature contribution is greater in urology than in oncology. Efforts must be invested towards raising this plateau and understanding qualitative aspects of the urology scientific output from Brazil.

  13. Betting on Teachers: The 43rd Annual Phi Delta Kappa/Gallup Poll of the Public's Attitudes toward the Public Schools

    ERIC Educational Resources Information Center

    Bushaw, William J.; Lopez, Shane J.

    2011-01-01

    This is the latest in a series of polls sponsored by Phi Delta Kappa International with the Gallup organization. Some important findings of this year's poll include: About half of us believe teacher unions are hurting public education, but we're more likely to support teacher union leaders than governors in disputes over teacher collective…

  14. 78 FR 46695 - Secretarial Review and Publication of the Annual Report to Congress Submitted by the Contracted...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-01

    ...This notice acknowledges the Secretary of the Department of Health and Human Services' (HHS) receipt and review of the Annual Report submitted to the Secretary and Congress by the contracted consensus-based entity (CBE) as mandated by section 1890(b)(5) of the Social Security Act, as created by section 183 of the Medicare Improvements for Patients and Providers Act of 2008 (MIPPA) and amended by section 3014 of the Affordable Care Act of 2010. The statute requires the Secretary to review and publish the report in the Federal Register together with any comments of the Secretary on the report not later than six months after receiving the report. This notice fulfills those requirements.

  15. ADMINISTRATION OF PUBLIC LAWS 874 AND 815. ANNUAL REPORT (16TH) OF THE COMMISSIONER OF EDUCATION, JUNE 30, 1966.

    ERIC Educational Resources Information Center

    HOWE, HAROLD, II

    SIGNIFICANT PROGRAM OPERATIONS DATA ARE SUMMARIZED FOR PUBLIC LAWS 874 AND 815, AUTHORIZING RESPECTIVELY, FEDERAL PAYMENTS TO LOCAL EDUCATIONAL AGENCIES IN FEDERALLY AFFECTED AREAS FOR CURRENT OPERATING EXPENSES OF SCHOOLS AND FOR CONSTRUCTION OF SCHOOL FACILITIES. BRIEF REVIEWS GIVE PROVISIONS OF THE AUTHORIZING LEGISLATION, ADMINISTRATIVE…

  16. Michigan Council on Physical Fitness and Health Annual Report to the Michigan Department of Public Health, December 29, 1978.

    ERIC Educational Resources Information Center

    Michigan State Dept. of Public Health, Lansing. Council on Physical Fitness & Health.

    The projects which the Michigan Council on Physical Fitness and Health undertook in 1978 are reported and described here. The projects and activities include: a school physical fitness program that provided assistance to public, private, and parochial schools in monitoring the physical fitness levels of all students in grades kindergarten through…

  17. Michigan Council on Physical Fitness and Health Annual Report to the Michigan Department of Public Health, December 29, 1978.

    ERIC Educational Resources Information Center

    Michigan State Dept. of Public Health, Lansing. Council on Physical Fitness & Health.

    The projects which the Michigan Council on Physical Fitness and Health undertook in 1978 are reported and described here. The projects and activities include: a school physical fitness program that provided assistance to public, private, and parochial schools in monitoring the physical fitness levels of all students in grades kindergarten through…

  18. Strategic Plan To Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education. Annual Report: December, 1994.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Higher Education, Hartford.

    This report describes the activities and results of three programs instituted under Connecticut's Minority Advancement Program (MAP) to promote racial and ethnic diversity in Connecticut public higher education. The Connecticut Collegiate Awareness and Preparation Program (ConnCAP), which enrolled 1,585 students in 1993-94, is designed to give…

  19. Publication patterns of oral and poster presentations at the annual meetings of the Congress of Neurological Surgeons and the American Association of Neurological Surgeons.

    PubMed

    Patel, Akash J; Cherian, Jacob; Fox, Benjamin D; Whitehead, William E; Curry, Daniel J; Luerssen, Thomas G; Jea, Andrew

    2011-12-01

    National and international meetings, such as the Congress of Neurological Surgeons (CNS) and the American Association of Neurological Surgeons (AANS) meetings, provide a central location for the gathering and dissemination of research. The purpose of this study was to determine the publication rates of both oral and poster presentations at CNS and AANS meetings in peer-reviewed journals. The authors reviewed all accepted abstracts, presented as either oral or poster presentations, at the CNS and AANS meetings from 2003 to 2005. This information was then used to search PubMed to determine the rate of publication of the abstracts presented at the meetings. Abstracts were considered published if the data presented at the meeting was identical to that in the publication. The overall publication rate was 32.48% (1243 of 3827 abstracts). On average, 41.28% of oral presentations and 29.03% of poster presentations were eventually published. Of those studies eventually published, 98.71% were published within 5 years of presentation at the meeting. Published abstracts were published most frequently in the Journal of Neurosurgery and Neurosurgery. Approximately one-third of all presentations at the annual CNS and AANS meetings will be published in peer-reviewed, MEDLINE-indexed journals. These meetings are excellent forums for neurosurgical practitioners to be exposed to current research. Oral presentations have a significantly higher rate of eventual publication compared with poster presentations, reflecting their higher quality. The Journal of Neurosurgery and Neurosurgery have been the main outlets of neurosurgical research from these meetings.

  20. Publication Rate of Abstracts Presented at the Annual Congress of the European Society for Surgical Research during 2008-2011.

    PubMed

    Meral, Ulvi Mehmet; Alakus, Umit; Urkan, Murat; Ureyen, Orhan; Oren, Nisa Cem; Ozturk Meral, Aylin; Çağıltay, Eylem; Can, Mehmet Fatih

    2016-01-01

    The presentation of scientific studies at major meetings serves to rapidly share study results with the scientific community. On the other hand, full-text publication of abstracts in peer-reviewed journals ensures the dissemination of science. This study examines the publication rate (PR) of meeting abstracts presented at the European Society for Surgical Research (ESSR) congresses and determines/compares the factors affecting the PRs. All presentations at the ESSR congresses held during 2008-2011 were retrospectively assessed. Manuscripts indexed in PubMed were included. The meeting year, journal impact factor (IF) in the publication year, study type, presentation type, time to publication and geographic origin of studies were assessed. Among a total of 1,368 oral and poster abstracts, 48.7% (n = 391) of the oral presentations (OPs) and 29.7% (n = 168) of the poster presentations (PPs) were published in medical journals indexed in PubMed. The mean IF of the journals was 2.696 (0.17-14.95). The journals that published OPs had a higher IF than the journals in which PPs were published (2.944 vs. 2.118; p < 0.001). The PR was also higher in the OP group than in the PP group of journals (p < 0.001). The time to publication was 17.5 months (-166 to 82) and was shorter for PPs than for OPs (14.02 vs. 19.09 months; p = 0.01). According to the study type, experimental studies had a significantly higher PR (53.7%; p < 0.001); however, there was no significant difference in PR in terms of the prospective or retrospective nature of clinical studies. The clinical studies were also compared according to the IF values of the journals in terms of the prospective or retrospective nature of the study, and no significant difference was found (p = 0.62). The ESSR congress is an efficient meeting for researchers from varied surgical disciplines and has a PR equivalent to that of similar scientific meetings. The congress has achieved a PR of 40.9% over 4 years with an average IF of 2

  1. Annual committee reports on significant legislative, judicial, and administrative developments in 1982: Public Lands and Land-Use Committee

    SciTech Connect

    Not Available

    1983-01-01

    Public lands legislative developments reported include: (1) the Small Tracts Act; (2) additions to the National Wilderness Program; (3) oil and gas leasing in wilderness areas; and (4) a brief summary of amendments to the Endangered Species Act. Judicial developments involving public lands include brief summaries of about 15 specific court cases. Administrative developments include brief statements regarding the Asset Management Program, Forest Service RPA planning program, contingent rights stipulations, national forest timber sale procedures, and national wild and scenic rivers regulations. Land use legislative developments are reported briefly for California, Oregon, Washington, and Utah. Judicial developments include court cases regarding (1) tidelands ownership involving the City of Los Angeles; (2) City of Denver depositing hazardous waste and sewage sludge at Lowry Landfill; (3) and the Oregon Court of Appeals deciding whether a school-closure decision is a land-use decision.

  2. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money.

    PubMed

    Vincent, Antony T; Derome, Nicolas; Boyle, Brian; Culley, Alexander I; Charette, Steve J

    2016-03-16

    The Sanger sequencing method produces relatively long DNA sequences of unmatched quality and has been considered for long time as the gold standard for sequencing DNA. Many improvements of the Sanger method that culminated with fluorescent dyes coupled with automated capillary electrophoresis enabled the sequencing of the first genomes. Nevertheless, using this technology to sequence whole genomes was costly, laborious and time consuming even for genomes that are relatively small in size. A major technological advance was the introduction of next-generation sequencing (NGS) pioneered by 454 Life Sciences in the early part of the 21th century. NGS allowed scientists to sequence thousands to millions of DNA molecules in a single machine run. Since then, new NGS technologies have emerged and existing NGS platforms have been improved, enabling the production of genome sequences at an unprecedented rate as well as broadening the spectrum of NGS applications. The current affordability of generating genomic information, especially with microbial samples, has resulted in a false sense of simplicity that belies the fact that many researchers still consider these technologies a black box. In this review, our objective is to identify and discuss four steps that we consider crucial to the success of any NGS-related project. These steps are: (1) the definition of the research objectives beyond sequencing and appropriate experimental planning, (2) library preparation, (3) sequencing and (4) data analysis. The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research. Regardless of the evolution and improvement of the sequencing technologies, these four steps will remain relevant.

  3. The Implications for Higher-Accuracy Absolute Measurements for NGS and its GRAV-D Project

    NASA Astrophysics Data System (ADS)

    Childers, V. A.; Winester, D.; Roman, D. R.; Eckl, M. C.; Smith, D. A.

    2013-12-01

    Absolute and relative gravity measurements play an important role in the work of NOAA's National Geodetic Survey (NGS). When NGS decided to replace the US national vertical datum, the Gravity for the Redefinition of the American Vertical Datum (GRAV-D) project added a new dimension to the NGS gravity program. Airborne gravity collection would complement existing satellite and surface gravity data to allow the creation of a gravimetric geoid sufficiently accurate to form the basis of the new reference surface. To provide absolute gravity ties for the airborne surveys, initially new FG5 absolute measurements were made at existing absolute stations and relative measurements were used to transfer those measurements to excenters near the absolute mark and to the aircraft sensor height at the parking space. In 2011, NGS obtained a field-capable A10 absolute gravimeter from Micro-g LaCoste which became the basis of the support of the airborne surveys. Now A10 measurements are made at the aircraft location and transferred to sensor height. Absolute and relative gravity play other roles in GRAV-D. Comparison of surface data with new airborne collection will highlight surface surveys with bias or tilt errors and can provide enough information to repair or discard the data. We expect that areas of problem surface data may be re-measured. The GRAV-D project also plans to monitor the geoid in regions of rapid change and update the vertical datum when appropriate. Geoid change can result from glacial isostatic adjustment (GIA), tectonic change, and the massive drawdown of large scale aquifers. The NGS plan for monitoring these changes over time is still in its preliminary stages and is expected to rely primarily on the GRACE and GRACE Follow On satellite data in conjunction with models of GIA and tectonic change. We expect to make absolute measurements in areas of rapid change in order to verify model predictions. With the opportunities presented by rapid, highly accurate

  4. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

    PubMed

    Lai, Binbin; Wang, Fumeng; Wang, Xiaoqi; Duan, Liping; Zhu, Huaiqiu

    2015-08-07

    Next-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads generated by sequencers such as Illumina. To date, how to generate a high-quality draft assembly for metagenomic sequencing projects has not been fully addressed. We conducted a comprehensive assessment on state-of-the-art de novo assemblers and revealed that the performance of each assembler depends critically on the sequencing depth. To address this problem, we developed a pipeline named InteMAP to integrate three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision of which assembling approaches to use according to the sequencing coverage estimation algorithm for each short read, the pipeline presents an automatic platform suitable to assemble real metagenomic NGS data with uneven coverage distribution of sequencing depth. By comparing the performance of InteMAP with current assemblers on both synthetic and real NGS metagenomic data, we demonstrated that InteMAP achieves better performance with a longer total contig length and higher contiguity, and contains more genes than others. We developed a de novo pipeline, named InteMAP, that integrates existing tools for metagenomics assembly. The pipeline outperforms previous assembly methods on metagenomic assembly by providing a longer total contig length, a higher contiguity and covering more genes. InteMAP, therefore, could potentially be a useful tool for the research community of metagenomics.

  5. SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

    PubMed

    Hatakeyama, Masaomi; Opitz, Lennart; Russo, Giancarlo; Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert

    2016-06-02

    Next generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools, where each application performs a single step towards the final result. This situation leaves the bioinformaticians with the tasks to combine the tools, manage the data files and meta-information, document the analysis, and ensure reproducibility. We present SUSHI, an agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts. As distinguishing features, SUSHI provides an expert command line interface as well as a convenient web interface to run bioinformatics tools. SUSHI datasets are self-contained and self-documented on the file system. This makes them fully reproducible and ready to be shared. With the associated meta-information being formatted as plain text tables, the datasets can be readily further analyzed and interpreted outside SUSHI. SUSHI provides an exquisite recipe for analysing NGS data. By following the SUSHI recipe, SUSHI makes data analysis straightforward and takes care of documentation and administration tasks. Thus, the user can fully dedicate his time to the analysis itself. SUSHI is suitable for use by bioinformaticians as well as life science researchers. It is targeted for, but by no means constrained to, NGS data analysis. Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available.

  6. Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

    SciTech Connect

    Washington, A. L. II; Peters, T. B.

    2014-03-03

    This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or DCs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction DCs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.

  7. Precise GPS ephemerides from DMA and NGS tested by time transfer

    NASA Technical Reports Server (NTRS)

    Lewandowski, Wlodzimierz W.; Petit, Gerard; Thomas, Claudine

    1992-01-01

    It was shown that the use of the Defense Mapping Agency's (DMA) precise ephemerides brings a significant improvement to the accuracy of GPS time transfer. At present a new set of precise ephemerides produced by the National Geodetic Survey (NGS) has been made available to the timing community. This study demonstrates that both types of precise ephemerides improve long-distance GPS time transfer and remove the effects of Selective Availability (SA) degradation of broadcast ephemerides. The issue of overcoming SA is also discussed in terms of the routine availability of precise ephemerides.

  8. The environmental biological signature: NGS profiling for forensic comparison of soils.

    PubMed

    Giampaoli, S; Berti, A; Di Maggio, R M; Pilli, E; Valentini, A; Valeriani, F; Gianfranceschi, G; Barni, F; Ripani, L; Romano Spica, V

    2014-07-01

    The identification of the source of a specific soil sample is a crucial step in forensic investigations. Rapid advances in next generation sequencing (NGS) technology and the strong reduction of the cost of sequencing have recently opened new perspectives. In the present work a metabarcoding approach has been successfully applied to forensic and environmental soil samples, allowing the accurate and sensitive analysis of microflora (mfDNA), plants, metazoa, and protozoa DNA. The identification of the biological component by DNA metabarcoding is a strong element for the discrimination of samples geologically very similar but coming for distinct environments.

  9. A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform.

    PubMed

    Lee, Howon; Kim, Hyoki; Kim, Sungsik; Ryu, Taehoon; Kim, Hwangbeom; Bang, Duhee; Kwon, Sunghoon

    2015-02-02

    Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.

  10. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses

    PubMed Central

    Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Oler, Andrew J.; Quiñones, Mariam; Hurt, Darrell; Fursov, Mikhail; Huyen, Yentram

    2014-01-01

    The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines “Variant Calling with SAMtools”, “Tuxedo Pipeline for RNA-seq Data Analysis” and “Cistrome Pipeline for ChIP-seq Data Analysis” integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows. PMID:25392756

  11. NGS and blood group systems: State of the art and perspectives.

    PubMed

    Fichou, Y; Férec, C

    2017-09-01

    Molecular analysis, or genotyping, of genes involved in the expression of blood group antigens has been a standard strategy used in immunohaematology laboratories routinely. For the past ten years, next-generation sequencing (NGS), or second-generation sequencing, has become the reference method in genetics. Extensive study of distinct targets, large genomic regions, and even whole genome is henceforth possible by this approach at minimal cost. Blood group genotyping has thus taken advantage of this technological advent. A few preliminary studies have open the way to NGS in this field by studying one or several genes, in a wide range of samples (donors and patients) by using several different platforms. These works have helped in the identification of both the benefits and limitations of the technology. Other recently published studies have benefited from these preliminary data to improve the methodology, specificity and accuracy of output data. In parallel novel strategies, i.e. third-generation sequencing, which can sequence long DNA regions at the single-molecule level, have emerged and shown promise for the potential resolution of complex rearrangements involving genes of the Rh and MNS blood group systems respectively. As technological and methodological hurdles have been overcome, these approaches may be used in a clinical situation in a near future. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  12. Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

    PubMed Central

    Cheng, Yinhe; Tzeng, Tzy-Hwa Kathy

    2016-01-01

    This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156–186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory. PMID:27861637

  13. Assessment of the latest NGS enrichment capture methods in clinical context.

    PubMed

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  14. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS).

    PubMed

    El-Husny, Antonette; Raiol-Moraes, Milene; Amador, Marcos; Ribeiro-Dos-Santos, André M; Montagnini, André; Barbosa, Silvanira; Silva, Artur; Assumpção, Paulo; Ishak, Geraldo; Santos, Sidney; Pinto, Pablo; Cruz, Aline; Ribeiro-Dos-Santos, Ândrea

    2016-05-13

    Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform.

  15. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS)

    PubMed Central

    El-Husny, Antonette; Raiol-Moraes, Milene; Amador, Marcos; Ribeiro-dos-Santos, André M.; Montagnini, André; Barbosa, Silvanira; Silva, Artur; Assumpção, Paulo; Ishak, Geraldo; Santos, Sidney; Pinto, Pablo; Cruz, Aline; Ribeiro-dos-Santos, Ândrea

    2016-01-01

    Abstract Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform. PMID:27192129

  16. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

    PubMed Central

    Bianchi, Valerio; Ceol, Arnaud; Ogier, Alessandro G. E.; de Pretis, Stefano; Galeota, Eugenia; Kishore, Kamal; Bora, Pranami; Croci, Ottavio; Campaner, Stefano; Amati, Bruno; Morelli, Marco J.; Pelizzola, Mattia

    2016-01-01

    Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: (1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; (2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; (3) ensuring complete traceability of the analysis performed; (4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; (5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts. PMID:27200084

  17. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

    PubMed

    Bianchi, Valerio; Ceol, Arnaud; Ogier, Alessandro G E; de Pretis, Stefano; Galeota, Eugenia; Kishore, Kamal; Bora, Pranami; Croci, Ottavio; Campaner, Stefano; Amati, Bruno; Morelli, Marco J; Pelizzola, Mattia

    2016-01-01

    Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: (1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; (2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; (3) ensuring complete traceability of the analysis performed; (4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; (5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  18. NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa.

    PubMed

    Ge, Zhongqi; Bowles, Kristen; Goetz, Kerry; Scholl, Hendrik P N; Wang, Feng; Wang, Xinjing; Xu, Shan; Wang, Keqing; Wang, Hui; Chen, Rui

    2015-12-15

    The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE(®)) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE(®)'s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE(®).

  19. Assessment of the latest NGS enrichment capture methods in clinical context

    PubMed Central

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-01-01

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelectQXT, against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelectQXT showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach. PMID:26864517

  20. Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools.

    PubMed

    Ogasawara, Takeshi; Cheng, Yinhe; Tzeng, Tzy-Hwa Kathy

    2016-01-01

    This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory.

  1. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    SciTech Connect

    Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

    2015-01-01

    Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-end NGS analysis requirements. The Globus Genomics system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  2. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    DOE PAGES

    Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; ...

    2015-01-01

    Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-end NGS analysis requirements. The Globus Genomicsmore » system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.« less

  3. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    PubMed Central

    Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

    2014-01-01

    Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research. PMID:26925205

  4. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    PubMed Central

    Someswara Rao, Chinta; Raju, S. Viswanadha

    2016-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  5. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

    PubMed Central

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

  6. Commissioner's Annual Report to the Education Committees of the Senate and General Assembly on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, July 1, 2006 to June 30, 2007

    ERIC Educational Resources Information Center

    New Jersey Department of Education, 2008

    2008-01-01

    The "Commissioner of Education's Report on Violence, Vandalism and Substance Abuse in New Jersey Public Schools", submitted annually to the education committees of the Senate and Assembly, provides the Legislature with data in four broad incident categories: violence, vandalism, weapons, and substance abuse. This year's report highlights…

  7. Commissioner's Annual Report to the Education Committees of the Senate and General Assembly on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, July 1, 2005 to June 30, 2006

    ERIC Educational Resources Information Center

    New Jersey Department of Education, 2007

    2007-01-01

    The Commissioner of Education's Report on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, submitted annually to the education committees of the Senate and Assembly, provides the Legislature with data in four broad incident categories: violence, vandalism, weapons, and substance abuse. The report also summarizes initiatives…

  8. Commissioner's Annual Report to the Education Committees of the Senate and General Assembly on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, July 1, 2004 to June 30, 2005

    ERIC Educational Resources Information Center

    New Jersey Department of Education, 2006

    2006-01-01

    The Commissioner of Education's Report on Violence, Vandalism and Substance Abuse in New Jersey Public Schools is submitted annually to the education committees of the Senate and Assembly of the New Jersey State Legislature. It provides the Legislature with data in four broad categories of incidents: violence, vandalism, weapons, and substance…

  9. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

    PubMed Central

    2015-01-01

    Background The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). Moreover, the huge volume of data generated by NGS platforms introduces unprecedented computational and technological challenges to efficiently analyze and store sequence data and results. Methods In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Results Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy

  10. Use of Sequence-independent, single-primer amplification (SISPA) with NGS platform for detection of RNA viruses in clinical samples

    USDA-ARS?s Scientific Manuscript database

    Current technologies for next generation sequencing (NGS) have revolutionized metagenomics analysis of clinical samples. One advantage of the NGS platform is the possibility to sequence the genetic material in samples without any prior knowledge of the sequence contained within. Sequence-Independent...

  11. [Molecular-genetic analysis of DNA pol and TK of HSV-1 population using NGS technology].

    PubMed

    Gus'kova, A A; Skoblov, M Iu; Lavrov, A V; Zubtsov, D A; Andronova, V L; Gol'dshteĭn, D V; Galegov, G A; Skoblov, Iu S

    2013-01-01

    It was determined the ratio of viral DNA and DNA from Vero cells using the polymerase chain reaction in real time in Vero cell lysate, infected with L2 strain of the herpes simplex virus type 1. Copy number of the virus reached a maximum after 24 hours of incubation of infection. Total DNA was isolated and sequenced using NGS technology by Ion Torrent device. Nucleotide sequences of the thymidine kinase gene (UL23) and DNA polymerase (UL30) were determined for a population of HSV-1 strain L2. Comparison of the primary structure of these genes with the corresponding nucleotide sequences of known strains of HSV-1 KOS and 17 was conducted. Differences in the structure of genes UL23 and UL30 between strain L2 and reference strains KOS and 17 are not important, because changes are found in non-conservative regions.

  12. ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.

    PubMed

    Raine, Keiran M; Van Loo, Peter; Wedge, David C; Jones, David; Menzies, Andrew; Butler, Adam P; Teague, Jon W; Tarpey, Patrick; Nik-Zainal, Serena; Campbell, Peter J

    2016-12-08

    We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.

  13. Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case.

    PubMed

    Marsh, Adam G; Cottrell, Matthew T; Goldman, Morton F

    2016-01-01

    Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE). An integrated pipeline efficiently incorporates raw NGS metrics into a statistical discrimination platform to identify functional linkages between shifts in epigenetic DNA methylation and disease phenotypes in samples being analyzed. In this pilot proof-of-concept study we quantify and compare DNA methylation in blood serum of individuals with Parkinson's Disease relative to matched healthy blood profiles. Even with a small study of only six samples, a high degree of statistical discrimination was achieved based on CpG methylation profiles between groups, with 1008 statistically different CpG sites (p < 0.0025, after false discovery rate correction). A methylation load calculation was used to assess higher order impacts of methylation shifts on genes and pathways and most notably identified FGF3, FGF8, HTT, KMTA5, MIR8073, and YWHAG as differentially methylated genes with high relevance to Parkinson's Disease and neurodegeneration (based on PubMed literature citations). Of these, KMTA5 is a histone methyl-transferase gene and HTT is Huntington Disease Protein or Huntingtin, for which there are well established neurodegenerative impacts. The future need for precision diagnostics now requires more tools for exploring epigenetic processes that may be linked to cellular dysfunction and subsequent disease progression.

  14. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

    PubMed

    D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

    2015-01-01

    The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

  15. DEVELOPMENT OF ANALYTICAL METHODS FOR DETERMINING SUPPRESSOR CONCENTRATION IN THE MCU NEXT GENERATION SOLVENT (NGS)

    SciTech Connect

    Taylor-Pashow, K.; Fondeur, F.; White, T.; Diprete, D.; Milliken, C.

    2013-07-31

    Savannah River National Laboratory (SRNL) was tasked with identifying and developing at least one, but preferably two methods for quantifying the suppressor in the Next Generation Solvent (NGS) system. The suppressor is a guanidine derivative, N,N',N"-tris(3,7-dimethyloctyl)guanidine (TiDG). A list of 10 possible methods was generated, and screening experiments were performed for 8 of the 10 methods. After completion of the screening experiments, the non-aqueous acid-base titration was determined to be the most promising, and was selected for further development as the primary method. {sup 1}H NMR also showed promising results from the screening experiments, and this method was selected for further development as the secondary method. Other methods, including {sup 36}Cl radiocounting and ion chromatography, also showed promise; however, due to the similarity to the primary method (titration) and the inability to differentiate between TiDG and TOA (tri-n-ocytlamine) in the blended solvent, {sup 1}H NMR was selected over these methods. Analysis of radioactive samples obtained from real waste ESS (extraction, scrub, strip) testing using the titration method showed good results. Based on these results, the titration method was selected as the method of choice for TiDG measurement. {sup 1}H NMR has been selected as the secondary (back-up) method, and additional work is planned to further develop this method and to verify the method using radioactive samples. Procedures for analyzing radioactive samples of both pure NGS and blended solvent were developed and issued for the both methods.

  16. Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS

    PubMed Central

    Tian, Xia; Liang, Wen-Chen; Feng, Yanming; Wang, Jing; Zhang, Victor Wei; Chou, Chih-Hung; Huang, Hsien-Da; Lam, Ching Wan; Hsu, Ya-Yun; Lin, Thy-Sheng; Chen, Wan-Tzu

    2015-01-01

    Objective: To establish and evaluate the effectiveness of a comprehensive next-generation sequencing (NGS) approach to simultaneously analyze all genes known to be responsible for the most clinically and genetically heterogeneous neuromuscular diseases (NMDs) involving spinal motoneurons, neuromuscular junctions, nerves, and muscles. Methods: All coding exons and at least 20 bp of flanking intronic sequences of 236 genes causing NMDs were enriched by using SeqCap EZ solution-based capture and enrichment method followed by massively parallel sequencing on Illumina HiSeq2000. Results: The target gene capture/deep sequencing provides an average coverage of ∼1,000× per nucleotide. Thirty-five unrelated NMD families (38 patients) with clinical and/or muscle pathologic diagnoses but without identified causative genetic defects were analyzed. Deleterious mutations were found in 29 families (83%). Definitive causative mutations were identified in 21 families (60%) and likely diagnoses were established in 8 families (23%). Six families were left without diagnosis due to uncertainty in phenotype/genotype correlation and/or unidentified causative genes. Using this comprehensive panel, we not only identified mutations in expected genes but also expanded phenotype/genotype among different subcategories of NMDs. Conclusions: Target gene capture/deep sequencing approach can greatly improve the genetic diagnosis of NMDs. This study demonstrated the power of NGS in confirming and expanding clinical phenotypes/genotypes of the extremely heterogeneous NMDs. Confirmed molecular diagnoses of NMDs can assist in genetic counseling and carrier detection as well as guide therapeutic options for treatable disorders. PMID:27066551

  17. Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case

    PubMed Central

    Marsh, Adam G.; Cottrell, Matthew T.; Goldman, Morton F.

    2016-01-01

    Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE). An integrated pipeline efficiently incorporates raw NGS metrics into a statistical discrimination platform to identify functional linkages between shifts in epigenetic DNA methylation and disease phenotypes in samples being analyzed. In this pilot proof-of-concept study we quantify and compare DNA methylation in blood serum of individuals with Parkinson's Disease relative to matched healthy blood profiles. Even with a small study of only six samples, a high degree of statistical discrimination was achieved based on CpG methylation profiles between groups, with 1008 statistically different CpG sites (p < 0.0025, after false discovery rate correction). A methylation load calculation was used to assess higher order impacts of methylation shifts on genes and pathways and most notably identified FGF3, FGF8, HTT, KMTA5, MIR8073, and YWHAG as differentially methylated genes with high relevance to Parkinson's Disease and neurodegeneration (based on PubMed literature citations). Of these, KMTA5 is a histone methyl-transferase gene and HTT is Huntington Disease Protein or Huntingtin, for which there are well established neurodegenerative impacts. The future need for precision diagnostics now requires more tools for exploring epigenetic processes that may be linked to cellular dysfunction and subsequent disease progression. PMID:27853465

  18. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling.

    PubMed

    Rovigatti, Ugo

    2015-11-01

    It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Determining performance characteristics of an NGS-based HLA typing method for clinical applications.

    PubMed

    Duke, J L; Lind, C; Mackiewicz, K; Ferriola, D; Papazoglou, A; Gasiewski, A; Heron, S; Huynh, A; McLaughlin, L; Rogers, M; Slavich, L; Walker, R; Monos, D S

    2016-03-01

    This study presents performance specifications of an in-house developed human leukocyte antigen (HLA) typing assay using next-generation sequencing (NGS) on the Illumina MiSeq platform. A total of 253 samples, previously characterized for HLA-A, -B, -C, -DRB1 and -DQB1 were included in this study, which were typed at high-resolution using a combination of Sanger sequencing, sequence-specific primer (SSP) and sequence-specific oligonucleotide probe (SSOP) technologies and recorded at the two-field level. Samples were selected with alleles that cover a high percentage of HLA specificities in each of five different race/ethnic groups: European, African-American, Asian Pacific Islander, Hispanic and Native American. Sequencing data were analyzed by two software programs, Omixon's target and GenDx's NGSengine. A number of metrics including allele balance, sensitivity, specificity, precision, accuracy and remaining ambiguity were assessed. Data analyzed by the two software systems are shown independently. The majority of alleles were identical in the exonic sequences (third field) with both programs for HLA-A, -B, -C and -DQB1 in 97.7% of allele determinations. Among the remaining discrepant genotype calls at least one of the analysis programs agreed with the reference typing. Upon additional manual analysis 100% of the 2530 alleles were concordant with the reference HLA genotypes; the remaining ambiguities did not exceed 0.8%. The results demonstrate the feasibility and significant benefit of HLA typing by NGS as this technology is highly accurate, eliminates virtually all ambiguities, provides complete sequencing information for the length of the HLA gene and forms the basis for utilizing a single methodology for HLA typing in the immunogenetics labs. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets.

    PubMed

    Shcherbina, Anna

    2014-08-15

    High-throughput next generation sequencing technologies have enabled rapid characterization of clinical and environmental samples. Consequently, the largest bottleneck to actionable data has become sample processing and bioinformatics analysis, creating a need for accurate and rapid algorithms to process genetic data. Perfectly characterized in silico datasets are a useful tool for evaluating the performance of such algorithms. Background contaminating organisms are observed in sequenced mixtures of organisms. In silico samples provide exact truth. To create the best value for evaluating algorithms, in silico data should mimic actual sequencer data as closely as possible. FASTQSim is a tool that provides the dual functionality of NGS dataset characterization and metagenomic data generation. FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with specific error profiles obtained in the characterization step. FASTQSim enables users to assess the quality of NGS datasets. The tool provides information about read length, read quality, repetitive and non-repetitive indel profiles, and single base pair substitutions. FASTQSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate. Such datasets are valuable in a number of applications, including the training of assemblers for multiple platforms, benchmarking bioinformatics algorithm performance, and creating challenge

  1. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    PubMed Central

    Philippe, Julien; Derhourhi, Mehdi; Durand, Emmanuelle; Vaillant, Emmanuel; Dechaume, Aurélie; Rabearivelo, Iandry; Dhennin, Véronique; Vaxillaire, Martine; De Graeve, Franck; Sand, Olivier; Froguel, Philippe; Bonnefond, Amélie

    2015-01-01

    Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing. PMID:26599467

  2. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    PubMed

    Philippe, Julien; Derhourhi, Mehdi; Durand, Emmanuelle; Vaillant, Emmanuel; Dechaume, Aurélie; Rabearivelo, Iandry; Dhennin, Véronique; Vaxillaire, Martine; De Graeve, Franck; Sand, Olivier; Froguel, Philippe; Bonnefond, Amélie

    2015-01-01

    Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing.

  3. MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

    PubMed

    Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2016-01-01

    Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

  4. NGS panel analysis in 24 ectopia lentis patients; a clinically relevant test with a high diagnostic yield.

    PubMed

    Overwater, E; Floor, K; van Beek, D; de Boer, K; van Dijk, T; Hilhorst-Hofstee, Y; Hoogeboom, A J M; van Kaam, K J; van de Kamp, J M; Kempers, M; Krapels, I P C; Kroes, H Y; Loeys, B; Salemink, S; Stumpel, C T R M; Verhoeven, V J M; Wijnands-van den Berg, E; Cobben, J M; van Tintelen, J P; Weiss, M M; Houweling, A C; Maugeri, A

    2017-09-01

    Several genetic causes of ectopia lentis (EL), with or without systemic features, are known. The differentiation between syndromic and isolated EL is crucial for further treatment, surveillance and counseling of patients and their relatives. Next generation sequencing (NGS) is a powerful tool enabling the simultaneous, highly-sensitive analysis of multiple target genes. The aim of this study was to evaluate the diagnostic yield of our NGS panel in EL patients. Furthermore, we provide an overview of currently described mutations in ADAMTSL4, the main gene involved in isolated EL. A NGS gene panel was analysed in 24 patients with EL. A genetic diagnosis was confirmed in 16 patients (67%). Of these, four (25%) had a heterozygous FBN1 mutation, 12 (75%) were homozygous or compound heterozygous for ADAMTSL4 mutations. The known European ADAMTSL4 founder mutation c.767_786del was most frequently detected. The diagnostic yield of our NGS panel was high. Causative mutations were exclusively identified in ADAMTSL4 and FBN1. With this approach the risk of misdiagnosis or delayed diagnosis can be reduced. The value and clinical implications of establishing a genetic diagnosis in patients with EL is corroborated by the description of two patients with an unexpected underlying genetic condition. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  5. Genotype-phenotype correlation in a cohort of Portuguese patients comprising the entire spectrum of VWD types: impact of NGS.

    PubMed

    Fidalgo, Teresa; Salvado, Ramon; Corrales, Irene; Pinto, Silva Catarina; Borràs, Nina; Oliveira, Ana; Martinho, Patricia; Ferreira, Gisela; Almeida, Helena; Oliveira, Cristina; Marques, Dalila; Gonçalves, Elsa; Diniz, MJoão; Antunes, Margarida; Tavares, Alice; Caetano, Gonçalo; Kjöllerström, Paula; Maia, Raquel; Sevivas, Teresa S; Vidal, Francisco; Ribeiro, Leticia

    2016-07-04

    The diagnosis of von Willebrand disease (VWD), the most common inherited bleeding disorder, is characterised by a variable bleeding tendency and heterogeneous laboratory phenotype. The sequencing of the entire VWF coding region has not yet become a routine practice in diagnostic laboratories owing to its high costs. Nevertheless, next-generation sequencing (NGS) has emerged as an alternative to overcome this limitation. We aimed to determine the correlation of genotype and phenotype in 92 Portuguese individuals from 60 unrelated families with VWD; therefore, we directly sequenced VWF. We compared the classical Sanger sequencing approach and NGS to assess the value-added effect on the analysis of the mutation distribution in different types of VWD. Sixty-two different VWF mutations were identified, 27 of which had not been previously described. NGS detected 26 additional mutations, contributing to a broad overview of the mutant alleles present in each VWD type. Twenty-nine probands (48.3 %) had two or more mutations; in addition, mutations with pleiotropic effects were detected, and NGS allowed an appropriate classification for seven of them. Furthermore, the differential diagnosis between VWD 2B and platelet type VWD (n = 1), Bernard-Soulier syndrome and VWD 2B (n = 1), and mild haemophilia A and VWD 2N (n = 2) was possible. NGS provided an efficient laboratory workflow for analysing VWF. These findings in our cohort of Portuguese patients support the proposal that improving VWD diagnosis strategies will enhance clinical and laboratory approaches, allowing to establish the most appropriate treatment for each patient.

  6. 42 CFR 457.750 - Annual report.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Annual report. 457.750 Section 457.750 Public..., Reporting, and Evaluation § 457.750 Annual report. (a) Report required for each Federal fiscal year. A State... State's assessment of the operation of the State plan. (b) Contents of annual report. In the...

  7. 42 CFR 1007.17 - Annual report.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 5 2010-10-01 2010-10-01 false Annual report. 1007.17 Section 1007.17 Public... STATE MEDICAID FRAUD CONTROL UNITS § 1007.17 Annual report. At least 60 days prior to the expiration of... (the first 9 months of the certification period for the first annual report), and containing...

  8. 45 CFR 2400.2 - Annual competition.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Annual competition. 2400.2 Section 2400.2 Public... FELLOWSHIP PROGRAM REQUIREMENTS General § 2400.2 Annual competition. To achieve its principal purposes, the Foundation holds an annual national competition to select teachers in grades 7-12, college seniors,...

  9. 45 CFR 2400.2 - Annual competition.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Annual competition. 2400.2 Section 2400.2 Public... FELLOWSHIP PROGRAM REQUIREMENTS General § 2400.2 Annual competition. To achieve its principal purposes, the Foundation holds an annual national competition to select teachers in grades 7-12, college seniors,...

  10. 45 CFR 2400.2 - Annual competition.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Annual competition. 2400.2 Section 2400.2 Public... FELLOWSHIP PROGRAM REQUIREMENTS General § 2400.2 Annual competition. To achieve its principal purposes, the Foundation holds an annual national competition to select teachers in grades 7-12, college seniors,...

  11. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (86th, Kansas City, Missouri, July 30-August 2, 2003). Public Relations Division.

    ERIC Educational Resources Information Center

    2003

    The Public Relations Division of the proceedings contains the following 20 papers: "Communicating for Technical Change: Business-to-Business Communication with Small Manufacturing Firms" (Danielle Pontiff); "Integrating Editorial Presentation and Public Relations Publications: New Frontiers for Convergence and Collaborative…

  12. Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine

    PubMed Central

    Paleeva, Anna; Kremenetskaya, Olga; Vinogradov, Dmitriy

    2016-01-01

    Nowadays, the personalized approach to health care and cancer care in particular is becoming more and more popular and is taking an important place in the translational medicine paradigm. In some cases, detection of the patient-specific individual mutations that point to a targeted therapy has already become a routine practice for clinical oncologists. Wider panels of genetic markers are also on the market which cover a greater number of possible oncogenes including those with lower reliability of resulting medical conclusions. In light of the large availability of high-throughput technologies, it is very tempting to use complete patient-specific New Generation Sequencing (NGS) or other “omics” data for cancer treatment guidance. However, there are still no gold standard methods and protocols to evaluate them. Here we will discuss the clinical utility of each of the data types and describe a systems biology approach adapted for single patient measurements. We will try to summarize the current state of the field focusing on the clinically relevant case-studies and practical aspects of data processing. PMID:27191992

  13. A kinetic model-based algorithm to classify NGS short reads by their allele origin.

    PubMed

    Marinoni, Andrea; Rizzo, Ettore; Limongelli, Ivan; Gamba, Paolo; Bellazzi, Riccardo

    2015-02-01

    Genotyping Next Generation Sequencing (NGS) data of a diploid genome aims to assign the zygosity of identified variants through comparison with a reference genome. Current methods typically employ probabilistic models that rely on the pileup of bases at each locus and on a priori knowledge. We present a new algorithm, called Kimimila (KInetic Modeling based on InforMation theory to Infer Labels of Alleles), which is able to assign reads to alleles by using a distance geometry approach and to infer the variant genotypes accurately, without any kind of assumption. The performance of the model has been assessed on simulated and real data of the 1000 Genomes Project and the results have been compared with several commonly used genotyping methods, i.e., GATK, Samtools, VarScan, FreeBayes and Atlas2. Despite our algorithm does not make use of a priori knowledge, the percentage of correctly genotyped variants is comparable to these algorithms. Furthermore, our method allows the user to split the reads pool depending on the inferred allele origin.

  14. Profiling of the dynamically alteredgene expression in peripheral nerve injury using NGS RNA sequencing technique

    PubMed Central

    Han, Duanyang; Chen, Yixun; Kou, Yuhui; Weng, Jian; Chen, Bo; Yu, Youlai; Zhang, Peixun; Jiang, Baoguo

    2016-01-01

    Functional recovery of peripheral nerve injuries is of major demand in clinical practice worldwide. Although, to some extent, peripheral nervous system can spontaneously regenerate, post-injury recovery is often associated with poor functional outcome. The molecular mechanism controlling the peripheral nerve repair process is still majorly unclear. In this study, by utilizing the Next Generation Sequencing (NGS) RNA sequencing technique, we aim to profile the gene expression spectrum of the peripheral nerve repair. In total, we detected 2847 were differentially expressed at day 7 post crush nerve injury. The GO, Panther, IPA and GSEA analysis was performed to decipher the biological processes involving the differentially expressed genes. Collectively, our results highlighted the inflammatory response and related signaling pathway (NFkB and TNFa signaling) play key role in peripheral nerve repair regulation. Furthermore, Network analysis illustrated that the IL10, IL18, IFN-γ and PDCD1 were four key regulators with multiple participations in peripheral nerve repair and potentially exert influence to the repair process. The expression changes of IL10, IL18, IFN-γ, PDCD1 and TNFSF14 (LIGHT) were further validated by western blot analysis. Hopefully, the present study may provide useful platform to further reveal the molecular mechanism of peripheral nerve repair and discover promising treatment target to enhance peripheral nerve regeneration. PMID:27158375

  15. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. II - Surface photometry

    NASA Technical Reports Server (NTRS)

    Cutri, Roc M.; Low, Frank J.; Guhathakurta, Puragra

    1993-01-01

    In this paper we present a method to calibrate surface photometry of faint sources measured from direct photographic plates, such as those of the NGS/POSS and ESO/SRC Sky Survey. This calibration procedure does not require scanning sensitometer spots on the plates, but instead uses measurements of the brightness profiles of many faint stars of known brightness to fit a linearized approximation to the characteristic curve. The approximation is valid for only low- to medium-density emulsions, so this technique is appropriate only for relatively faint emission. Comparison between measurements of representative extended sources on the NGS/POSS and CCD images indicates that surface photometry can be obtained from the Sky Survey plates accurate to 0.1-0.3 mag in the range mu(B) between 23 and 27 and mu(R) between 22 and 26 mag/sq arcsec.

  16. RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.

    PubMed

    Yuan, Cheng; Sun, Yanni

    2013-01-01

    The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs) are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS) data, especially for very short reads. In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE) for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity with other tools. The source codes of RNA-CODE can be downloaded at http://www.cse.msu.edu/~chengy/RNA_CODE.

  17. A new method to prevent carry-over contaminations in two-step PCR NGS library preparations.

    PubMed

    Seitz, Volkhard; Schaper, Sigrid; Dröge, Anja; Lenze, Dido; Hummel, Michael; Hennig, Steffen

    2015-11-16

    Two-step PCR procedures are an efficient and well established way to generate amplicon libraries for NGS sequencing. However, there is a high risk of cross-contamination by carry-over of amplicons from first to second amplification rounds, potentially leading to severe misinterpretation of results. Here we describe a new method able to prevent and/or to identify carry-over contaminations by introducing the K-box, a series of three synergistically acting short sequence elements. Our K-boxes are composed of (i) K1 sequences for suppression of contaminations, (ii) K2 sequences for detection of possible residual contaminations and (iii) S sequences acting as separators to avoid amplification bias. In order to demonstrate the effectiveness of our method we analyzed two-step PCR NGS libraries derived from a multiplex PCR system for detection of T-cell receptor beta gene rearrangements. We used this system since it is of high clinical relevance and may be affected by very low amounts of contaminations. Spike-in contaminations are effectively blocked by the K-box even at high rates as demonstrated by ultra-deep sequencing of the amplicons. Thus, we recommend implementation of the K-box in two-step PCR-based NGS systems for research and diagnostic applications demanding high sensitivity and accuracy.

  18. A new method to prevent carry-over contaminations in two-step PCR NGS library preparations

    PubMed Central

    Seitz, Volkhard; Schaper, Sigrid; Dröge, Anja; Lenze, Dido; Hummel, Michael; Hennig, Steffen

    2015-01-01

    Two-step PCR procedures are an efficient and well established way to generate amplicon libraries for NGS sequencing. However, there is a high risk of cross-contamination by carry-over of amplicons from first to second amplification rounds, potentially leading to severe misinterpretation of results. Here we describe a new method able to prevent and/or to identify carry-over contaminations by introducing the K-box, a series of three synergistically acting short sequence elements. Our K-boxes are composed of (i) K1 sequences for suppression of contaminations, (ii) K2 sequences for detection of possible residual contaminations and (iii) S sequences acting as separators to avoid amplification bias. In order to demonstrate the effectiveness of our method we analyzed two-step PCR NGS libraries derived from a multiplex PCR system for detection of T-cell receptor beta gene rearrangements. We used this system since it is of high clinical relevance and may be affected by very low amounts of contaminations. Spike-in contaminations are effectively blocked by the K-box even at high rates as demonstrated by ultra-deep sequencing of the amplicons. Thus, we recommend implementation of the K-box in two-step PCR-based NGS systems for research and diagnostic applications demanding high sensitivity and accuracy. PMID:26152304

  19. Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

    PubMed

    Scarcelli, N; Mariac, C; Couvreur, T L P; Faye, A; Richard, D; Sabot, F; Berthouly-Salazar, C; Vigouroux, Y

    2016-03-01

    Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  20. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Li, Weizhong [San Diego Supercomputer Center

    2016-07-12

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  1. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Li, Weizhong

    2011-10-12

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  2. 42 CFR 51.8 - Annual reports.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 1 2011-10-01 2011-10-01 false Annual reports. 51.8 Section 51.8 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES GRANTS REQUIREMENTS APPLICABLE TO THE PROTECTION AND ADVOCACY FOR INDIVIDUALS WITH MENTAL ILLNESS PROGRAM Basic Requirements § 51.8 Annual reports...

  3. 42 CFR 51.8 - Annual reports.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 1 2014-10-01 2014-10-01 false Annual reports. 51.8 Section 51.8 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES GRANTS REQUIREMENTS APPLICABLE TO THE PROTECTION AND ADVOCACY FOR INDIVIDUALS WITH MENTAL ILLNESS PROGRAM Basic Requirements § 51.8 Annual reports...

  4. 42 CFR 51.8 - Annual reports.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 1 2013-10-01 2013-10-01 false Annual reports. 51.8 Section 51.8 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES GRANTS REQUIREMENTS APPLICABLE TO THE PROTECTION AND ADVOCACY FOR INDIVIDUALS WITH MENTAL ILLNESS PROGRAM Basic Requirements § 51.8 Annual reports...

  5. 42 CFR 51.8 - Annual reports.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 1 2012-10-01 2012-10-01 false Annual reports. 51.8 Section 51.8 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES GRANTS REQUIREMENTS APPLICABLE TO THE PROTECTION AND ADVOCACY FOR INDIVIDUALS WITH MENTAL ILLNESS PROGRAM Basic Requirements § 51.8 Annual reports...

  6. 42 CFR 51.8 - Annual reports.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Annual reports. 51.8 Section 51.8 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES GRANTS REQUIREMENTS APPLICABLE TO THE PROTECTION AND ADVOCACY FOR INDIVIDUALS WITH MENTAL ILLNESS PROGRAM Basic Requirements § 51.8 Annual reports...

  7. 45 CFR 1176.5 - Annual plan.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 3 2012-10-01 2012-10-01 false Annual plan. 1176.5 Section 1176.5 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for...

  8. 45 CFR 1176.5 - Annual plan.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 3 2013-10-01 2013-10-01 false Annual plan. 1176.5 Section 1176.5 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for...

  9. 45 CFR 1176.5 - Annual plan.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Annual plan. 1176.5 Section 1176.5 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for...

  10. 45 CFR 1176.5 - Annual plan.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 3 2011-10-01 2011-10-01 false Annual plan. 1176.5 Section 1176.5 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for...

  11. 45 CFR 1176.5 - Annual plan.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 3 2014-10-01 2014-10-01 false Annual plan. 1176.5 Section 1176.5 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for...

  12. 45 CFR 1801.11 - Annual nomination.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Annual nomination. 1801.11 Section 1801.11 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.11 Annual nomination. (a) Except as provided in §§ 1801.11...

  13. 45 CFR 1801.11 - Annual nomination.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Annual nomination. 1801.11 Section 1801.11 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.11 Annual nomination. (a) Except as provided in §§ 1801.11...

  14. 45 CFR 1801.11 - Annual nomination.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Annual nomination. 1801.11 Section 1801.11 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.11 Annual nomination. (a) Except as provided in §§ 1801.11...

  15. 45 CFR 1801.11 - Annual nomination.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Annual nomination. 1801.11 Section 1801.11 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.11 Annual nomination. (a) Except as provided in §§ 1801.11...

  16. 45 CFR 1801.11 - Annual nomination.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Annual nomination. 1801.11 Section 1801.11 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.11 Annual nomination. (a) Except as provided in §§ 1801.11...

  17. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients.

    PubMed

    Pulsipher, Michael A; Carlson, Chris; Langholz, Bryan; Wall, Donna A; Schultz, Kirk R; Bunin, Nancy; Kirsch, Ilan; Gastier-Foster, Julie M; Borowitz, Michael; Desmarais, Cindy; Williamson, David; Kalos, Michael; Grupp, Stephan A

    2015-05-28

    Positive detection of minimal residual disease (MRD) by multichannel flow cytometry (MFC) prior to hematopoietic cell transplantation (HCT) of patients with acute lymphoblastic leukemia (ALL) identifies patients at high risk for relapse, but many pre-HCT MFC-MRD negative patients also relapse, and the predictive power MFC-MRD early post-HCT is poor. To test whether the increased sensitivity of next-generation sequencing (NGS)-MRD better identifies pre- and post-HCT relapse risk, we performed immunoglobulin heavy chain (IgH) variable, diversity, and joining (V[D]J) DNA sequences J NGS-MRD on 56 patients with B-cell ALL enrolled in Children's Oncology Group trial ASCT0431. NGS-MRD predicted relapse and survival more accurately than MFC-MRD (P < .0001), especially in the MRD negative cohort (relapse, 0% vs 16%; P = .02; 2-year overall survival, 96% vs 77%; P = .003). Post-HCT NGS-MRD detection was better at predicting relapse than MFC-MRD (P < .0001), especially early after HCT (day 30 MFC-MRD positive relapse rate, 35%; NGS-MRD positive relapse rate, 67%; P = .004). Any post-HCT NGS positivity resulted in an increase in relapse risk by multivariate analysis (hazard ratio, 7.7; P = .05). Absence of detectable IgH-V(D)J NGS-MRD pre-HCT defines good-risk patients potentially eligible for less intense treatment approaches. Post-HCT NGS-MRD is highly predictive of relapse and survival, suggesting a role for this technique in defining patients early who would be eligible for post-HCT interventions. The trial was registered at www.clinicaltrials.gov as #NCT00382109.

  18. Folklife Annual, 1987.

    ERIC Educational Resources Information Center

    Jabbour, Alan, Ed.; Hardin, James, Ed.

    This annual publication is intended to promote the documentation and study of the folklife of the United States, to share the traditions, values, and activities of U.S. folk culture, and to serve as a national forum for the discussion of ideas and issues in folklore and folklife. The articles in this collection are: (1) "Eating in the Belly…

  19. UNICEF Annual Report 1983.

    ERIC Educational Resources Information Center

    United Nations Children's Fund, New York, NY.

    In introducing this annual report, the executive director of UNICEF delineates the four techniques for primary health care and basic services reported in the publication "State of the World's Children, 1982-1983." The ensuing review of UNICEF's activities illustrates highlights of the year's program cooperation, including trends and key…

  20. UNICEF Annual Report 1983.

    ERIC Educational Resources Information Center

    United Nations Children's Fund, New York, NY.

    In introducing this annual report, the executive director of UNICEF delineates the four techniques for primary health care and basic services reported in the publication "State of the World's Children, 1982-1983." The ensuing review of UNICEF's activities illustrates highlights of the year's program cooperation, including trends and key…

  1. Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect.

    PubMed

    Rappaport, Noa; Fishilevich, Simon; Nudel, Ron; Twik, Michal; Belinky, Frida; Plaschkes, Inbar; Stein, Tsippi Iny; Cohen, Dana; Oz-Levi, Danit; Safran, Marilyn; Lancet, Doron

    2017-08-18

    A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses. VarElect, our NGS interpretation tool, leverages the broad information in the GeneCards suite databases. MalaCards algorithms unify disease-related terms and annotations from 69 sources. Further, MalaCards defines hierarchical relatedness-aliases, disease families, a related diseases network, categories and ontological classifications. GeneCards and MalaCards delineate and share a multi-tiered, scored gene-disease network, with stringency levels, including the definition of elite status-high quality gene-disease pairs, coming from manually curated trustworthy sources, that includes 4500 genes for 8000 diseases. This unique resource is key to NGS interpretation by VarElect. VarElect, a comprehensive search tool that helps infer both direct and indirect links between genes and user-supplied disease/phenotype terms, is robustly strengthened by the information found in MalaCards. The indirect mode benefits from GeneCards' diverse gene-to-gene relationships, including SuperPaths-integrated biological pathways from 12 information sources. We are currently adding an important information layer in the form of "disease SuperPaths", generated from the gene-disease matrix by an algorithm similar to that previously employed for biological pathway unification. This allows the discovery of novel gene-disease and disease-disease relationships. The advent of whole genome sequencing necessitates capacities to go beyond

  2. AG-NGS: a powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms.

    PubMed

    Callejas, Sergio; Álvarez, Rebeca; Benguria, Alberto; Dopazo, Ana

    2014-01-01

    Next-generation sequencing (NGS) is becoming one of the most widely used technologies in the field of genomics. Library preparation is one of the most critical, hands-on, and time-consuming steps in the NGS workflow. Each library must be prepared in an independent well, increasing the number of hours required for a sequencing run and the risk of human-introduced error. Automation of library preparation is the best option to avoid these problems. With this in mind, we have developed automatic genomics NGS (AG-NGS), a computing application that allows an open liquid handling platform to be transformed into a library preparation station without losing the potential of an open platform. Implementation of AG-NGS does not require programming experience, and the application has also been designed to minimize implementation costs. Automated library preparation with AG-NGS generated high-quality libraries from different samples, demonstrating its efficiency, and all quality control parameters fell within the range of optimal values.

  3. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads.

    PubMed

    Suez, Marie; Behdenna, Abdelkader; Brouillet, Sophie; Graça, Paula; Higuet, Dominique; Achaz, Guillaume

    2016-03-01

    Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods. © 2015 John Wiley & Sons Ltd.

  4. NGS Transcriptomes and Enzyme Inhibitors Unravel Complexity of Picrosides Biosynthesis in Picrorhiza kurroa Royle ex. Benth.

    PubMed

    Shitiz, Kirti; Sharma, Neha; Pal, Tarun; Sood, Hemant; Chauhan, Rajinder S

    2015-01-01

    Picrorhiza kurroa is an important medicinal herb valued for iridoid glycosides, Picroside-I (P-I) and Picroside-II (P-II), which have several pharmacological activities. Genetic interventions for developing a picroside production platform would require knowledge on biosynthetic pathway and key control points, which does not exist as of today. The current study reports that geranyl pyrophosphate (GPP) moiety is mainly contributed by the non-mevalonate (MEP) route, which is further modified to P-I and P-II through phenylpropanoid and iridoid pathways, in total consisting of 41 and 35 enzymatic steps, respectively. The role of the MEP pathway was ascertained through enzyme inhibitors fosmidomycin and mevinolin along with importance of other integrating pathways using glyphosate, aminooxy acetic acid (AOA) and actinomycin D, which overall resulted in 17%-92% inhibition of P-I accumulation. Retrieval of gene sequences for enzymatic steps from NGS transcriptomes and their expression analysis vis-à-vis picrosides content in different tissues/organs showed elevated transcripts for twenty genes, which were further shortlisted to seven key genes, ISPD, DXPS, ISPE, PMK, 2HFD, EPSPS and SK, on the basis of expression analysis between high versus low picrosides content strains of P. kurroa so as to eliminate tissue type/ developmental variations in picrosides contents. The higher expression of the majority of the MEP pathway genes (ISPD, DXPS and ISPE), coupled with higher inhibition of DXPR enzyme by fosmidomycin, suggested that the MEP route contributed to the biosynthesis of P-I in P. kurroa. The outcome of the study is expected to be useful in designing a suitable genetic intervention strategy towards enhanced production of picrosides. Possible key genes contributing to picroside biosynthesis have been identified with potential implications in molecular breeding and metabolic engineering of P. kurroa.

  5. NGS Transcriptomes and Enzyme Inhibitors Unravel Complexity of Picrosides Biosynthesis in Picrorhiza kurroa Royle ex. Benth

    PubMed Central

    Shitiz, Kirti; Sharma, Neha; Pal, Tarun; Sood, Hemant; Chauhan, Rajinder S.

    2015-01-01

    Picrorhiza kurroa is an important medicinal herb valued for iridoid glycosides, Picroside-I (P-I) and Picroside-II (P-II), which have several pharmacological activities. Genetic interventions for developing a picroside production platform would require knowledge on biosynthetic pathway and key control points, which does not exist as of today. The current study reports that geranyl pyrophosphate (GPP) moiety is mainly contributed by the non-mevalonate (MEP) route, which is further modified to P-I and P-II through phenylpropanoid and iridoid pathways, in total consisting of 41 and 35 enzymatic steps, respectively. The role of the MEP pathway was ascertained through enzyme inhibitors fosmidomycin and mevinolin along with importance of other integrating pathways using glyphosate, aminooxy acetic acid (AOA) and actinomycin D, which overall resulted in 17%-92% inhibition of P-I accumulation. Retrieval of gene sequences for enzymatic steps from NGS transcriptomes and their expression analysis vis-à-vis picrosides content in different tissues/organs showed elevated transcripts for twenty genes, which were further shortlisted to seven key genes, ISPD, DXPS, ISPE, PMK, 2HFD, EPSPS and SK, on the basis of expression analysis between high versus low picrosides content strains of P. kurroa so as to eliminate tissue type/ developmental variations in picrosides contents. The higher expression of the majority of the MEP pathway genes (ISPD, DXPS and ISPE), coupled with higher inhibition of DXPR enzyme by fosmidomycin, suggested that the MEP route contributed to the biosynthesis of P-I in P. kurroa. The outcome of the study is expected to be useful in designing a suitable genetic intervention strategy towards enhanced production of picrosides. Possible key genes contributing to picroside biosynthesis have been identified with potential implications in molecular breeding and metabolic engineering of P. kurroa. PMID:26658062

  6. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

    PubMed Central

    Charlier, Carole; Li, Wanbo; Harland, Chad; Littlejohn, Mathew; Coppieters, Wouter; Creagh, Frances; Davis, Steve; Druet, Tom; Faux, Pierre; Guillaume, François; Karim, Latifa; Keehan, Mike; Kadri, Naveen Kumar; Tamma, Nico; Spelman, Richard; Georges, Michel

    2016-01-01

    We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility. PMID:27646536

  7. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

    PubMed

    Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

    2017-05-15

    Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

  8. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    SciTech Connect

    Moyer, Bruce A.; Birdwell, Jr, Joseph F.; Bonnesen, Peter V.; Bruffey, Stephanie H.; Delmau, Laetitia Helene; Duncan, Nathan C.; Ensor, Dale; Hill, Talon G.; Lee, Denise L.; Rajbanshi, Arbin; Roach, Benjamin D.; Szczygiel, Patricia L.; Frederick V. Sloop, Jr.; Stoner, Erica L.; Williams, Neil J.

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  9. Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly

    PubMed Central

    Liu, Tsunglin; Tsai, Cheng-Hung; Lee, Wen-Bin; Chiang, Jung-Hsien

    2013-01-01

    Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/. PMID:23922726

  10. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (74th, Boston, Massachusetts, August 7-10, 1991). Part XV: Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of the proceedings contains the following 14 papers: "Telling the Truth in Public Relations: An Application of the Narrative Paradigm" (Stephen P. Banks); "Teaching Fund Raising in Public Relations Programs: A National Study of the Attitudes and Behaviors of Educators" (Kathleen S. Kelly); "The…

  11. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (85th, Miami, Florida, August 5-8, 2002). Public Relations Division.

    ERIC Educational Resources Information Center

    2002

    The Public Relations Division of the proceedings contains the following 15 papers: "Virtual Issues in Traditional Texts: How Introductory Public Relations Textbooks Address Internet Technology Issues" (Lois A. Boynton and Cassandra Imfeld Gajkowski); "Crisis Public Relations: A Study of Leadership, Culture, Demand and Delivery"…

  12. Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS.

    PubMed

    Tuononen, Katja; Mäki-Nevala, Satu; Sarhadi, Virinder Kaur; Wirtanen, Aino; Rönty, Mikko; Salmenkivi, Kaisa; Andrews, Jenny M; Telaranta-Keerie, Aino I; Hannula, Sari; Lagström, Sonja; Ellonen, Pekka; Knuuttila, Aija; Knuutila, Sakari

    2013-05-01

    The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next-generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real-time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens from 81 non-small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real-time PCR. Moreover, targeted NGS revealed seven nonsynonymous single-nucleotide variations and one insertion-deletion variation in EGFR not detectable by the real-time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material.

  13. Making a Difference Early On: The Infant/Toddler Program in Michigan. 1990-91 Annual Report. Public Law 99-457, Part H.

    ERIC Educational Resources Information Center

    Michigan State Board of Education, Lansing.

    This annual report examines the implications, for the state of Michigan, of Part H of the 1986 Amendments to the U.S. Individuals with Disabilities Education Act and discusses the planning, development, and demonstration activities related to the implementation of the required components of the law. This legislation provides states with funding to…

  14. Petroleum marketing annual 1994

    SciTech Connect

    1995-08-24

    The Petroleum Marketing Annual (PMA) provides information and statistical data on a variety of crude oils and refined petroleum products. The publication presents statistics on crude oil costs and refined petroleum products sales for use by industry, government, private sector analysis, educational institutions, and consumers. Data on crude oil include the domestic first purchase price, the fob and landed cost of imported crude oil, and the refiners` acquisition cost of crude oil. Refined petroleum product sales data include motor gasoline, distillates, residuals, aviation fuels, kerosene, and propane. The Petroleum Marketing Division, Office of Oil and Gas, Energy Information Administration ensures the accuracy, quality, and confidentiality of the published data in the Petroleum Marketing Annual. For this production, all estimates have been recalculated since their earlier publication in the Petroleum Marketing Monthly (PMM). These calculations made use of additional data and corrections that were received after the PMM publication date.

  15. Does the Level of Evidence of Paper Presentations at the Arthroscopy Association of North America Annual Meetings From 2006-2010 Correlate With the 5-Year Publication Rate or the Impact Factor of the Publishing Journal?

    PubMed

    Kay, Jeffrey; Memon, Muzammil; de Sa, Darren; Duong, Andrew; Simunovic, Nicole; Ayeni, Olufemi R

    2017-01-01

    The purpose of this study was to determine the proportion of paper (podium) presentations at the 2006-2010 Arthroscopy Association of North America (AANA) annual scientific meetings that were ultimately published in a peer-reviewed journal. Furthermore, we aimed to evaluate whether the level of evidence correlated with the publication rate of these presentations or the impact factor (IF) of the publishing journal. Paper presentations from the 2006-2010 AANA annual meetings were included for evaluation. Clinical studies were graded for quality using the level of evidence by 2 independent reviewers. A comprehensive strategy was used to search the databases PubMed, Medline, and Embase for publications in scientific journals that corresponded to the presentations and were published within 5 years of the presentation date. Three hundred twenty-eight presentations were evaluated. Overall, 179 peer-reviewed publications corresponding to particular meeting presentations were identified, for a 5-year publication rate of 55%. There was no correlation between the publication rate and the level of evidence (P = .836), the type of study (P = .628), or the joint of focus (P = .07) of the presentations. The mean IF of journals that published Level I studies (4.8 [standard error, 2.3]) was significantly higher than the mean IF of journals that published Level II, III, or IV studies (2.58 [standard error, 0.10]) (P = .017). Between 2006 and 2010, presentations of the highest level of evidence at AANA meetings were subsequently published at a similar rate to presentations of lower levels of evidence, albeit in journals with higher IFs. This study is an important initial evaluation of the ultimate clinical impact of AANA meeting presentations. The study type, joint of focus, and level of evidence of the presentations all had no correlation with the rate at which these presentations were ultimately published. Copyright © 2016 Arthroscopy Association of North America. Published

  16. 28 CFR 16.208 - Annual report.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 28 Judicial Administration 1 2012-07-01 2012-07-01 false Annual report. 16.208 Section 16.208 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission Meetings § 16.208 Annual report. The Commission shall report annually...

  17. 28 CFR 16.208 - Annual report.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 1 2011-07-01 2011-07-01 false Annual report. 16.208 Section 16.208 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission Meetings § 16.208 Annual report. The Commission shall report annually...

  18. 28 CFR 16.208 - Annual report.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 28 Judicial Administration 1 2014-07-01 2014-07-01 false Annual report. 16.208 Section 16.208 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission Meetings § 16.208 Annual report. The Commission shall report annually...

  19. 28 CFR 16.208 - Annual report.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 28 Judicial Administration 1 2013-07-01 2013-07-01 false Annual report. 16.208 Section 16.208 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission Meetings § 16.208 Annual report. The Commission shall report annually...

  20. 28 CFR 16.208 - Annual report.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Annual report. 16.208 Section 16.208 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission Meetings § 16.208 Annual report. The Commission shall report annually to...

  1. 22 CFR 62.15 - Annual reports.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Annual reports. 62.15 Section 62.15 Foreign Relations DEPARTMENT OF STATE PUBLIC DIPLOMACY AND EXCHANGES EXCHANGE VISITOR PROGRAM General Provisions § 62.15 Annual reports. Sponsors shall submit an annual report to the Department of State....

  2. 36 CFR 901.5 - Annual report.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Annual report. 901.5 Section... CORPORATION § 901.5 Annual report. The Executive Director shall prepare annually a comprehensive and detailed report of the Corporation's operations, activities, and accomplishments for the review of the Board...

  3. Title II Elementary and Secondary Education Act (Public Law 89-10) as Amended. Annual Report, Fiscal Year 1972, School Library Resources, Textbooks, and Other Instructional Materials.

    ERIC Educational Resources Information Center

    Office of Education (DHEW), Washington, DC.

    Title II of the Elementary and Secondary Education Act (ESEA) of 1965 (Public Law 89-10) as amended, provides direct Federal assistance for the acquisition of school library resources, textbooks, and other instructional materials for the use of children and teachers in public and private elementary and secondary schools. Its purpose is to improve…

  4. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (80th, Chicago, Illinois, July 30-August 2, 1997): Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of the Proceedings contains the following 13 papers: "Pluralistic Ignorance and Educators in Public Relations: Underestimating Professionalism of Our Educator Peers and of Practitioners in the Field" (Lynne M. Sallot; Glen T. Cameron; Ruth Ann Weaver-Lariscy); "Critical Conflict Issues in Public…

  5. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (82nd, New Orleans, Louisiana, August 3-8, 1999). Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of the Proceedings contains the following 8 papers: "The Cultural Competence Spiral: An Assessment and Profile of U.S. Public Relations Practitioners' Preparation for International Assignments" (Alan R. Freitag); "Trust, Communication, and Quality Relationships in the Workplace: Comparing Views of CEOs…

  6. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (81st, Baltimore, Maryland, August 5-8, 1988). Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of the Proceedings contains the following 15 papers: "The World Wide Web as a Public Relations Medium: The Use of Research, Planning, and Evaluation by Web Site Decision-Makers" (Candace White and Niranjan Raman); "Enlightened Self Interest--An Ethical Baseline for Teaching Corporate Public…

  7. Using GC-FID to Quantify the Removal of 4-sec-Butylphenol from NGS Solvent by NaOH

    SciTech Connect

    Sloop, Jr., Frederick V.; Moyer, Bruce A.

    2014-12-01

    A caustic wash of the solvent used in the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process was found to remove the modifier breakdown product 4-sec-butylphenol (SBP) with varying efficiency depending on the aqueous NaOH concentration. Recent efforts at ORNL have aimed at characterizing the flowsheet chemistry and reducing the technical uncertainties of the NG-CSSX process. One technical uncertainty has been the efficacy of caustic washing of the solvent for the removal of lipophilic anions, in particular, the efficient removal of SBP, an important degradation product of the solvent modifier, Cs-7SB. In order to make this determination, it was necessary to develop a sensitive and reliable analytical technique for the detection and quantitation of SBP. This report recounts the development of a GC-FID-based (Gas Chromatography Flame Ionization Detection) technique for analyzing SBP and the utilization of the technique to subsequently confirm the ability of the caustic wash to efficiently remove SBP from the Next Generation Solvent (NGS) used in NG-CSSX. In particular, the developed technique was used to monitor the amount of SBP removed from a simple solvent and the full NGS by contact with sodium hydroxide wash solutions over a range of concentrations. The results show that caustic washing removes SBP with effectively the same efficiency as it did in the original Caustic-Side Solvent Extraction (CSSX) process.

  8. Annual Energy Review 2007

    SciTech Connect

    Seiferlein, Katherine E.

    2008-06-01

    The Annual Energy Review (AER) is the Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are data on total energy production, consumption, and trade; overviews of petroleum, natural gas, coal, electricity, nuclear energy, renewable energy, international energy, as well as financial and environment indicators; and data unit conversion tables. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....”

  9. International energy annual 1997

    SciTech Connect

    1999-04-01

    The International Energy Annual presents an overview of key international energy trends for production, consumption, imports, and exports of primary energy commodities in over 220 countries, dependencies, and areas of special sovereignty. Also included are population and gross domestic product data, as well as prices for crude oil and petroleum products in selected countries. Renewable energy reported in the International Energy Annual includes hydroelectric power and geothermal, solar, and wind electric power. Also included are biomass electric power for Brazil and the US, and biomass, geothermal, and solar energy produced in the US and not used for electricity generation. This report is published to keep the public and other interested parties fully informed of primary energy supplies on a global basis. The data presented have been largely derived from published sources. The data have been converted to units of measurement and thermal values (Appendices E and F) familiar to the American public. 93 tabs.

  10. Preparing Our Young People for a Changing World: Policymakers, Business Leaders and the Public Speak out on the Role of Education Technology in America's Classrooms. The Second Annual Milken Exchange on Education Technology Public Opinion Survey.

    ERIC Educational Resources Information Center

    Milken Exchange on Education Technology, Santa Monica, CA.

    This research, based on nationwide telephone surveys of voters, state legislators and legislative staff, and high-level business executives, addressed the priority that respondents place on computers/technology in public education, the perceived benefits--and drawbacks--of computers in public education, and the expectations that respondents have…

  11. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

    PubMed

    Katta, Mohan A V S K; Khan, Aamir W; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

  12. Petroleum marketing annual 1993

    SciTech Connect

    Not Available

    1995-01-01

    The Petroleum Marketing Annual (PMA) contains statistical data on a variety of crude oils and refined petroleum products. The publication provides statistics on crude oil costs and refined petroleum products sales for use by industry, government, private sector analysts, educational institutions, and consumers. Data on crude oil include the domestic first purchase price, the free-on-board (f.o.b.) and landed cost of imported crude oil, and the refiners acquisition cost of crude oil. Sales data for motor gasoline, distillates, residuals, aviation fuels, kerosene, and propane are presented. For this publication, all estimates have been recalculated since their earlier publication in the Petroleum Marketing Monthly (PMM). These calculations made use of additional data and corrections that were received after the PMM publication dates.

  13. Changes in the Demand for Public Land-Grant Universities in New England, 1976-1999. AIR 2000 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Toutkoushian, Robert K.

    This study focuses on initial student interest in or demand for public, land-grant universities (PLGUs) within the six New England states for the years 1976-99. The study has three distinguishing features. First, time-series data for the six New England states are combined into a panel data set, and fixed effects and random effects models are used…

  14. Fiscal Year 1978 Annual Program Plan Amendment for Part B of the Education of the Handicapped Act as Amended by Public Law 94-142.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    This document has been published to fulfill the U. S. Bureau for the Education of the Handicapped's requirements to receive funds under Public Law 94-142. Local education and state agencies involved in the education of handicapped children will refer to this plan for policies and procedures the state will use to implement the requirements of…

  15. Analysis and Interpretation of ABE Experience in the Inner City: Toward a Theory of Practice in the Public Schools. Annual Report, May 1969 - June 1970.

    ERIC Educational Resources Information Center

    Columbia Univ., New York, NY. Center for Adult Education.

    The project here reported was conceived as a two-year effort involving analysis, interpretation, and dissemination. Its first year was funded to permit comprehensive, in-depth, comparative study of selected public school Adult Basic Education (ABE) programs in six metropolitan areas. The purpose was to utilize field research methods to construct a…

  16. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (84th, Washington, DC, August 5-8, 2001). Public Relations Division.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of the proceedings contains the following 11 selected papers: "If We Build It, Will They Come? Testing the Theory of Planned Behavior as a Predictive Model for Use in Determining How Career Counseling Centers Can Better Promote Their Facilities and Services" (Carolyn Ringer Lepre); "Student Preferences…

  17. The Career Education Policy Project (CEPP): Connecting Educators, Policymakers, and the Public. Annual Evaluation Report. Final Report, July 1, 1975-June 30, 1976.

    ERIC Educational Resources Information Center

    Siegal, Jane

    To inform and interconnect educational practitioners, knowledge-makers, policymakers, and the consuming public around the issues and potential of career education, the Career Education Policy Project (CEEP) collaborated with several existing programs to expose out-of-town leaders of the career education movement to the federal policymaking…

  18. 45 CFR 96.17 - Annual reporting requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Annual reporting requirements. 96.17 Section 96.17... Procedures § 96.17 Annual reporting requirements. (a) Except for the low-income home energy assistance program activity reports, a state must make public and submit to the Department each annual...

  19. Alberta Advanced Education Annual Report 2005-06

    ERIC Educational Resources Information Center

    Alberta Advanced Education, 2006

    2006-01-01

    The Public Accounts of Alberta are prepared in accordance with the Financial Administration Act and the "Government Accountability Act." The Public Accounts consist of the annual report of the Government of Alberta and the annual reports of each of the 24 ministries. The annual report of the Government of Alberta released June 26, 2006…

  20. Thirteenth Annual Brown Lecture in Education Research: Public Education and the Social Contract: Restoring the Promise in an Age of Diversity and Division.

    PubMed

    Tienda, Marta

    2017-01-01

    Building on the premise that closing achievement gaps is an economic imperative both to regain international educational supremacy and to maintain global economic competitiveness, I ask whether it is possible to rewrite the social contract so that education is a fundamental right-a statutory guarantee-that is both uniform across states and federally enforceable. I argue that the federal government was complicit in aggravating educational inequality by not guaranteeing free, public education as a basic right during propitious political moments; by enabling the creation of a segregated public higher education system; by relegating the Department of Education and its predecessors to a secondary status in the federal administration, thereby compromising its enforcement capability; and by proliferating incremental reforms while ignoring the unequal institutional arrangements that undermine equal opportunity to learn. History shows that a strong federal role can potentially strengthen the educational social contract.

  1. Annual Energy Review 2004

    SciTech Connect

    Seiferlein, Katherine E.

    2005-08-01

    The Annual Energy Review (AER) is the Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are data on total energy production, consumption, and trade; overviews of petroleum, natural gas, coal, electricity, nuclear energy, renewable energy, international energy, as well as financial and environment indicators; and data unit conversion tables. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications.

  2. Annual Energy Review 2011

    SciTech Connect

    Fichman, Barbara T.

    2012-09-01

    The Annual Energy Review (AER) is the U.S. Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are statistics on total energy production, consumption, trade, and energy prices; overviews of petroleum, natural gas, coal, electricity, nuclear energy, and renewable energy; financial and environment indicators; and data unit conversions. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding the content of the AER and other EIA publications.

  3. Annual Energy Review 2006

    SciTech Connect

    Seiferlein, Katherine E.

    2007-06-01

    The Annual Energy Review (AER) is the Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are data on total energy production, consumption, and trade; overviews of petroleum, natural gas, coal, electricity, nuclear energy, renewable energy, international energy, as well as financial and environment indicators; and data unit conversion tables. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications.

  4. Annual Energy Review 2005

    SciTech Connect

    Seiferlein, Katherine E.

    2006-07-01

    The Annual Energy Review (AER) is the Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are data on total energy production, consumption, and trade; overviews of petroleum, natural gas, coal, electricity, nuclear energy, renewable energy, international energy, as well as financial and environment indicators; and data unit conversion tables. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications.

  5. Annual Energy Review 2009

    SciTech Connect

    Fichman, Barbara T.

    2010-08-01

    The Annual Energy Review (AER) is the U.S. Energy Information Administration's (EIA) primary report of annual historical energy statistics. For many series, data begin with the year 1949. Included are statistics on total energy production, consumption, trade, and energy prices; overviews of petroleum, natural gas, coal, electricity, nuclear energy, renewable energy, and international energy; financial and environment indicators; and data unit conversions. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the EIA under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding the content of the AER and other EIA publications.

  6. Electric power annual 1992

    SciTech Connect

    Not Available

    1994-01-06

    The Electric Power Annual presents a summary of electric utility statistics at national, regional and State levels. The objective of the publication is to provide industry decisionmakers, government policymakers, analysts and the general public with historical data that may be used in understanding US electricity markets. The Electric Power Annual is prepared by the Survey Management Division; Office of Coal, Nuclear, Electric and Alternate Fuels; Energy Information Administration (EIA); US Department of Energy. ``The US Electric Power Industry at a Glance`` section presents a profile of the electric power industry ownership and performance, and a review of key statistics for the year. Subsequent sections present data on generating capability, including proposed capability additions; net generation; fossil-fuel statistics; retail sales; revenue; financial statistics; environmental statistics; electric power transactions; demand-side management; and nonutility power producers. In addition, the appendices provide supplemental data on major disturbances and unusual occurrences in US electricity power systems. Each section contains related text and tables and refers the reader to the appropriate publication that contains more detailed data on the subject matter. Monetary values in this publication are expressed in nominal terms.

  7. Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches.

    PubMed

    Billoud, Bernard; Jouanno, Émilie; Nehr, Zofia; Carton, Baptiste; Rolland, Élodie; Chenivesse, Sabine; Charrier, Bénédicte

    2015-01-01

    Mutagenesis is the only process by which unpredicted biological gene function can be identified. Despite that several macroalgal developmental mutants have been generated, their causal mutation was never identified, because experimental conditions were not gathered at that time. Today, progresses in macroalgal genomics and judicious choices of suitable genetic models make mutated gene identification possible. This article presents a comparative study of two methods aiming at identifying a genetic locus in the brown alga Ectocarpus siliculosus: positional cloning and Next-Generation Sequencing (NGS)-based mapping. Once necessary preliminary experimental tools were gathered, we tested both analyses on an Ectocarpus morphogenetic mutant. We show how a narrower localization results from the combination of the two methods. Advantages and drawbacks of these two approaches as well as potential transfer to other macroalgae are discussed.

  8. Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches

    PubMed Central

    Billoud, Bernard; Jouanno, Émilie; Nehr, Zofia; Carton, Baptiste; Rolland, Élodie; Chenivesse, Sabine; Charrier, Bénédicte

    2015-01-01

    Mutagenesis is the only process by which unpredicted biological gene function can be identified. Despite that several macroalgal developmental mutants have been generated, their causal mutation was never identified, because experimental conditions were not gathered at that time. Today, progresses in macroalgal genomics and judicious choices of suitable genetic models make mutated gene identification possible. This article presents a comparative study of two methods aiming at identifying a genetic locus in the brown alga Ectocarpus siliculosus: positional cloning and Next-Generation Sequencing (NGS)-based mapping. Once necessary preliminary experimental tools were gathered, we tested both analyses on an Ectocarpus morphogenetic mutant. We show how a narrower localization results from the combination of the two methods. Advantages and drawbacks of these two approaches as well as potential transfer to other macroalgae are discussed. PMID:25745426

  9. NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds.

    PubMed

    Diaz-Real, J; Serrano, D; Piriz, A; Jovani, R

    2015-10-01

    Understanding the ecological function of species and the structure of communities is crucial in the study of ecological interactions among species. For this purpose, not only the occurrence of particular species but also their abundance in ecological communities is required. However, abundance quantification of species through morphological characters is often difficult or time/money consuming when dealing with elusive or small taxa. Here we tested the use of next-generation sequencing (NGS) for abundance estimation of two species of feather mites (Proctophyllodes stylifer and Pteronyssoides parinus) under five proportions (16:1, 16:4, 16:16, 16:64, and 16:256 mites) against a mock community composed by Proctophyllodes clavatus and Proctophyllodes sylviae. In all mixtures, we retrieved sequence reads from all species. We found a strong linear relationship between 454 reads and the real proportion of individuals in the mixture for both focal species. The slope for Pr. stylifer was close to one (0.904), and the intercept close to zero (-0.007), thus showing an almost perfect correspondence between real and estimated proportions. The slope for Pt. parinus was 0.351 and the intercept 0.307, showing that while the estimated proportion increased linearly relative to real proportions of individuals in the samples, proportions were overestimated at low real proportions and underestimated at larger ones. Additionally, pyrosequencing replicates from each DNA extraction were highly repeatable (R = 0.920 and 0.972, respectively), showing that the quantification method is highly consistent given a DNA extract. Our study suggests that NGS is a promising tool for abundance estimation of feather mites' communities in birds.

  10. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species.

    PubMed

    Wang, Yi; Leung, Henry C M; Yiu, S M; Chin, Francis Y L

    2012-02-01

    Next-generation sequencing (NGS) technologies allow the sequencing of microbial communities directly from the environment without prior culturing. The output of environmental DNA sequencing consists of many reads from genomes of different unknown species, making the clustering together reads from the same (or similar) species (also known as binning) a crucial step. The difficulties of the binning problem are due to the following four factors: (1) the lack of reference genomes; (2) uneven abundance ratio of species; (3) short NGS reads; and (4) a large number of species (can be more than a hundred). None of the existing binning tools can handle all four factors. No tools, including both AbundanceBin and MetaCluster 3.0, have demonstrated reasonable performance on a sample with more than 20 species. In this article, we introduce MetaCluster 4.0, an unsupervised binning algorithm that can accurately (with about 80% precision and sensitivity in all cases and at least 90% in some cases) and efficiently bin short reads with varying abundance ratios and is able to handle datasets with 100 species. The novelty of MetaCluster 4.0 stems from solving a few important problems: how to divide reads into groups by a probabilistic approach, how to estimate the 4-mer distribution of each group, how to estimate the number of species, and how to modify MetaCluster 3.0 to handle a large number of species. We show that Meta Cluster 4.0 is effective for both simulated and real datasets. Supplementary Material is available at www.liebertonline.com/cmb.

  11. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

    PubMed

    Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

    2014-03-01

    Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

  12. LLNL NESHAP's 1999 Annual Report

    SciTech Connect

    Gallegos, G.; Biermann, A.H.; Harrach, R.J.; Bertoldo, N.A.; Berger, R.L.; Surano,K.A.

    2000-06-01

    This annual report is prepared pursuant to the National Emissions Standards for Hazardous Air Pollutants (NESHAPs) 40 CFR Part 61, Subpart H; Subpart H governs radionuclide emissions to air from Department of Energy (DOE) facilities. NESHAPs limits the emission of radionuclides to the ambient air from DOE facilities to levels resulting in an annual effective dose equivalent (EDE) of 10 mrem (100 {micro}Sv) to any member of the public. The EDEs for the Lawrence Livermore National Laboratory (LLNL) site-wide maximally exposed members of the public from 1999 operations are summarized.

  13. Coal industry annual 1997

    SciTech Connect

    1998-12-01

    Coal Industry Annual 1997 provides comprehensive information about US coal production, number of mines, prices, productivity, employment, productive capacity, and recoverable reserves. US Coal production for 1997 and previous years is based on the annual survey EIA-7A, Coal Production Report. This report presents data on coal consumption, coal distribution, coal stocks, coal prices, and coal quality for Congress, Federal and State agencies, the coal industry, and the general public. Appendix A contains a compilation of coal statistics for the major coal-producing States. This report includes a national total coal consumption for nonutility power producers that are not in the manufacturing, agriculture, mining, construction, or commercial sectors. 14 figs., 145 tabs.

  14. AAPCC Annual Reports

    MedlinePlus

    ... Annual Report 2000 Annual Report 1999 Annual Report Poison Data National Poison Data System Uses for NPDS ... Elements NPDS FAQs Annual Reports Find Your Local Poison Center Poison centers offer free, private, confidential medical ...

  15. 45 CFR 1620.5 - Annual review.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Annual review. 1620.5 Section 1620.5 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION PRIORITIES IN USE OF... recipient; (3) Changes in the size, distribution, or needs of the eligible client population; and (4) The...

  16. 45 CFR 1620.5 - Annual review.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Annual review. 1620.5 Section 1620.5 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION PRIORITIES IN USE OF... recipient; (3) Changes in the size, distribution, or needs of the eligible client population; and (4) The...

  17. 45 CFR 1620.5 - Annual review.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Annual review. 1620.5 Section 1620.5 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION PRIORITIES IN USE OF... recipient; (3) Changes in the size, distribution, or needs of the eligible client population; and (4) The...

  18. 45 CFR 2400.2 - Annual competition.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Annual competition. 2400.2 Section 2400.2 Public Welfare Regulations Relating to Public Welfare (Continued) JAMES MADISON MEMORIAL FELLOWSHIP FOUNDATION... college graduates to be James Madison Fellows. ...

  19. 45 CFR 2400.2 - Annual competition.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Annual competition. 2400.2 Section 2400.2 Public Welfare Regulations Relating to Public Welfare (Continued) JAMES MADISON MEMORIAL FELLOWSHIP FOUNDATION... college graduates to be James Madison Fellows. ...

  20. 45 CFR 671.14 - Annual review.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 3 2014-10-01 2014-10-01 false Annual review. 671.14 Section 671.14 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION WASTE REGULATION... to health or the environment if improperly treated or processed, stored, transported, or disposed...

  1. 43 CFR 2524.2 - Annual proof.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Annual proof. 2524.2 Section 2524.2 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Desert-Land Entries Within...

  2. 43 CFR 2524.2 - Annual proof.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Annual proof. 2524.2 Section 2524.2 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Desert-Land Entries Within...

  3. 43 CFR 2524.2 - Annual proof.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Annual proof. 2524.2 Section 2524.2 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Desert-Land Entries Within...

  4. 43 CFR 2524.2 - Annual proof.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Annual proof. 2524.2 Section 2524.2 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR LAND RESOURCE MANAGEMENT (2000) DESERT-LAND ENTRIES Desert-Land Entries Within...

  5. Annual report to Congress

    SciTech Connect

    1992-03-01

    This is the eighth annual report submitted by the Office of Civilian Radioactive Waste Management (OCRWM) to Congress. It covers activities and expenditures during Fiscal Year 1991, which ended September 30, 1991. Chapter 1 of this report describes OCRWM`s mission and objectives. Chapters 2 through 8 cover the following topics: earning public trust and confidence; geological disposal; monitored retrieval storage; transportation; systems integration and regulatory compliance; international programs; and program management. Financial statements for the Nuclear Waste Fund are presented in Chapter 9.

  6. Annual Progress Report.

    DTIC Science & Technology

    1981-10-20

    AD-AIO6 983 ILLINOIS UNIV AT URBANA COORDINATEO SCIENCE LAB F/0 12/1 ANNUAL PROGRESS REPOMT ,(U1 OCT 81 H V POOR NOOOII-81-K-O014 UNCLASSIFIED T-111...34 University of Illinois at Urbana -Chaimpaign Urbana , Illinois 61801 I ~~ ~ ~ ~ I I7 CONROLINOFIC______NDADDES Office of Naval Research - Octe--mm...Unclassified Approved for public release; dis tribu tion ’anlimi ted. 17. DISTRIBUTION STATEMENT (of the aboeet onfored a Weak 20. 1# Offrmoaw Repeol

  7. 43 CFR 3835.30 - Annual FLPMA documents.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Annual FLPMA documents. 3835.30 Section 3835.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) WAIVERS FROM ANNUAL MAINTENANCE FEES...

  8. 43 CFR 3835.30 - Annual FLPMA documents.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Annual FLPMA documents. 3835.30 Section 3835.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) WAIVERS FROM ANNUAL MAINTENANCE FEES...

  9. Strategic petroleum reserve annual report

    SciTech Connect

    1996-02-15

    Section 165 of the Energy Policy and Conservation Act (Public Law 94- 163), as amended, requires the Secretary of Energy to submit annual reports to the President and the Congress on activities of the Strategic Petroleum Reserve (SPR). This report describes activities for the year ending December 31, 1995.

  10. Annual Energy Review 2002

    SciTech Connect

    Seiferlein, Katherine E.

    2003-10-01

    The Annual Energy Review (AER) presents the Energy Information Administration’s historical energy statistics. For many series, statistics are given for every year from 1949 through 2002. The statistics, expressed in either physical units or British thermal units, cover all major energy activities, including consumption, production, trade, stocks, and prices, for all major energy commodities, including fossil fuels, electricity, and renewable energy sources. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the Energy Information Administration (EIA) under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications. Related Publication: Readers of the AER may also be interested in EIA’s Monthly Energy Review, which presents monthly updates of many of the data in the AER. Contact our National Energy Information Center for more information.

  11. 45 CFR 1801.54 - Annual report.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Payment Conditions and Procedures § 1801.54 Annual report. (a) Scholars with remaining eligibility for scholarship stipends must submit no later than July 15 an annual report to the...

  12. 45 CFR 1801.54 - Annual report.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Payment Conditions and Procedures § 1801.54 Annual report. (a) Scholars with remaining eligibility for scholarship stipends must submit no later than July 15 an annual report to the...

  13. 45 CFR 1801.54 - Annual report.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Payment Conditions and Procedures § 1801.54 Annual report. (a) Scholars with remaining eligibility for scholarship stipends must submit no later than July 15 an annual report to the...

  14. 45 CFR 1801.54 - Annual report.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Payment Conditions and Procedures § 1801.54 Annual report. (a) Scholars with remaining eligibility for scholarship stipends must submit no later than July 15 an annual report to the...

  15. Orione, a web-based framework for NGS analysis in microbiology

    PubMed Central

    Cuccuru, Gianmauro; Orsini, Massimiliano; Pinna, Andrea; Sbardellati, Andrea; Soranzo, Nicola; Travaglione, Antonella; Uva, Paolo; Zanetti, Gianluigi; Fotia, Giorgio

    2014-01-01

    Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics. Availability and implementation: Orione is available online at http://orione.crs4.it. Contact: gianmauro.cuccuru@crs4.it Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24618473

  16. Uranium industry annual 1994

    SciTech Connect

    1995-07-05

    The Uranium Industry Annual 1994 (UIA 1994) provides current statistical data on the US uranium industry`s activities relating to uranium raw materials and uranium marketing during that survey year. The UIA 1994 is prepared for use by the Congress, Federal and State agencies, the uranium and nuclear electric utility industries, and the public. It contains data for the 10-year period 1985 through 1994 as collected on the Form EIA-858, ``Uranium Industry Annual Survey.`` Data collected on the ``Uranium Industry Annual Survey`` (UIAS) provide a comprehensive statistical characterization of the industry`s activities for the survey year and also include some information about industry`s plans and commitments for the near-term future. Where aggregate data are presented in the UIA 1994, care has been taken to protect the confidentiality of company-specific information while still conveying accurate and complete statistical data. A feature article, ``Comparison of Uranium Mill Tailings Reclamation in the United States and Canada,`` is included in the UIA 1994. Data on uranium raw materials activities including exploration activities and expenditures, EIA-estimated resources and reserves, mine production of uranium, production of uranium concentrate, and industry employment are presented in Chapter 1. Data on uranium marketing activities, including purchases of uranium and enrichment services, and uranium inventories, enrichment feed deliveries (actual and projected), and unfilled market requirements are shown in Chapter 2.

  17. EPA Announces 2015 Annual Environmental Enforcement Results

    EPA Pesticide Factsheets

    WASHINGTON - The U.S. Environmental Protection Agency (EPA) today released its annual enforcement and compliance results highlighted by large cases that reduce pollution, level the playing field for responsible companies, and protect public health i

  18. Coal industry annual 1993

    SciTech Connect

    Not Available

    1994-12-06

    Coal Industry Annual 1993 replaces the publication Coal Production (DOE/FIA-0125). This report presents additional tables and expanded versions of tables previously presented in Coal Production, including production, number of mines, Productivity, employment, productive capacity, and recoverable reserves. This report also presents data on coal consumption, coal distribution, coal stocks, coal prices, coal quality, and emissions for a wide audience including the Congress, Federal and State agencies, the coal industry, and the general public. In addition, Appendix A contains a compilation of coal statistics for the major coal-producing States. This report does not include coal consumption data for nonutility Power Producers who are not in the manufacturing, agriculture, mining, construction, or commercial sectors. This consumption is estimated to be 5 million short tons in 1993.

  19. Annual Report.

    ERIC Educational Resources Information Center

    Tellstrom, A. Theodore

    1978-01-01

    This Music Educators National Conference (MENC) 1977-78 report covers the following areas: audit, the government relations program, committees and commissions, the Music Industry Council, publications, student chapters, Music in Our Schools Week 1978, Presidential Scholars Program, MENC Historical Center, the National Inservice Conference, and the…

  20. Uranium industry annual 1995

    SciTech Connect

    1996-05-01

    The Uranium Industry Annual 1995 (UIA 1995) provides current statistical data on the U.S. uranium industry`s activities relating to uranium raw materials and uranium marketing. The UIA 1995 is prepared for use by the Congress, Federal and State agencies, the uranium and nuclear electric utility industries, and the public. It contains data for the period 1986 through 2005 as collected on the Form EIA-858, ``Uranium Industry Annual Survey``. Data collected on the ``Uranium Industry Annual Survey`` provide a comprehensive statistical characterization of the industry`s plans and commitments for the near-term future. Where aggregate data are presented in the UIA 1995, care has been taken to protect the confidentiality of company-specific information while still conveying accurate and complete statistical data. Data on uranium raw materials activities for 1986 through 1995 including exploration activities and expenditures, EIA-estimated reserves, mine production of uranium, production of uranium concentrate, and industry employment are presented in Chapter 1. Data on uranium marketing activities for 1994 through 2005, including purchases of uranium and enrichment services, enrichment feed deliveries, uranium fuel assemblies, filled and unfilled market requirements, uranium imports and exports, and uranium inventories are shown in Chapter 2. The methodology used in the 1995 survey, including data edit and analysis, is described in Appendix A. The methodologies for estimation of resources and reserves are described in Appendix B. A list of respondents to the ``Uranium Industry Annual Survey`` is provided in Appendix C. For the reader`s convenience, metric versions of selected tables from Chapters 1 and 2 are presented in Appendix D along with the standard conversion factors used. A glossary of technical terms is at the end of the report. 14 figs., 56 tabs.

  1. Annual Energy Review 1993

    SciTech Connect

    Not Available

    1994-07-14

    This twelfth edition of the Annual Energy Review (AER) presents the Energy Information Administration`s historical energy statistics. For most series, statistics are given for every year from 1949 through 1993. Because coverage spans four and a half decades, the statistics in this report are well-suited to long-term trend analyses. The AER is comprehensive. It covers all major energy activities, including consumption, production, trade, stocks, and prices, for all major energy commodities, including fossil fuels and electricity. The AER also presents Energy Information Administration (EIA) statistics on some renewable energy sources. EIA estimates that its consumption series include about half of the renewable energy used in the United States. For a more complete discussion of EIA`s renewables data, see p. xix, ``Introducing Expanded Coverage of Renewable Energy Data Into the Historical Consumption Series.`` Copies of the 1993 edition of the Annual Energy Review may be obtained by using the order form in the back of this publication. Most of the data in the 1993 edition also are available on personal computer diskette. For more information about the diskettes, see the back of this publication. In addition, the data are available as part of the National Economic, Social, and Environmental Data Bank on a CD-ROM. For more information about the data bank, contact the US Department of Commerce Economics and Statistics Administration, on 202-482-1986.

  2. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. I - Stellar photometry

    NASA Technical Reports Server (NTRS)

    Cutri, Roc M.; Low, Frank J.; Marvel, Kevin B.

    1992-01-01

    The PDS/Monet measuring engine at the National Optical Astronomy Observatory was used to obtain photometry of nearly 10,000 stars on the NGS/POSS and 2000 stars on the ESO/SRC Survey glass plates. These measurements have been used to show that global transformation functions exist that allow calibration of stellar photometry from any blue or red plate to equivalent Johnson B and Cousins R photoelectric magnitudes. The four transformation functions appropriate for the POSS O and E and ESO/SRC J and R plates were characterized, and it was found that, within the measurement uncertainties, they vary from plate to plate only by photometric zero-point offsets. A method is described to correct for the zero-point shifts and to obtain calibrated B and R photometry of stellar sources to an average accuracy of 0.3-0.4 mag within the range R between values of 8 and 19.5 for red plates in both surveys, B between values of 9 and 20.5 on POSS blue plates, and B between values of 10 and 20.5 on ESO/SRC blue plates. This calibration procedure makes it possible to obtain rapid photometry of very large numbers of stellar sources.

  3. Species identification and comparative population genetics of four coastal houndsharks based on novel NGS-mined microsatellites.

    PubMed

    Maduna, Simo N; Rossouw, Charné; da Silva, Charlene; Soekoe, Michelle; Bester-van der Merwe, Aletta E

    2017-03-01

    The common smooth-hound (Mustelus mustelus) is the topmost bio-economically and recreationally important shark species in southern Africa, western Africa, and Mediterranean Sea. Here, we used the Illumina HiSeq™ 2000 next-generation sequencing (NGS) technology to develop novel microsatellite markers for Mustelus mustelus. Two microsatellite multiplex panels were constructed from 11 polymorphic loci and characterized in two populations of Mustelus mustelus representative of its South African distribution. The markers were then tested for cross-species utility in Galeorhinus galeus, Mustelus palumbes, and Triakis megalopterus, three other demersal coastal sharks also subjected to recreational and/or commercial fishery pressures in South Africa. We assessed genetic diversity (NA, AR, HO, HE, and PIC) and differentiation (FST and Dest) for each species and also examined the potential use of these markers in species assignment. In each of the four species, all 11 microsatellites were variable with up to a mean NA of 8, AR up to 7.5, HE and PIC as high as 0.842. We were able to reject genetic homogeneity for all species investigated here except for T. megalopterus. We found that the panel of the microsatellite markers developed in this study could discriminate between the study species, particularly for those that are morphologically very similar. Our study provides molecular tools to address ecological and evolutionary questions vital to the conservation and management of these locally and globally exploited shark species.

  4. Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions.

    PubMed

    Keravnou, Anna; Ioannides, Marios; Tsangaras, Kyriakos; Loizides, Charalambos; Hadjidaniel, Michael D; Papageorgiou, Elisavet A; Kyriakou, Skevi; Antoniou, Pavlos; Mina, Petros; Achilleos, Achilleas; Neofytou, Maria; Kypri, Elena; Sismani, Carolina; Koumbaris, George; Patsalis, Philippos C

    2016-11-11

    DNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples. Next, using specific criteria, 331 fetal-specific DMRs were selected and confirmed in eight CVS, eight WBF and eight PL samples by combining MeDIP and in-solution targeted enrichment followed by NGS. Results showed higher enrichment in CVS samples as compared to both WBF and PL samples, confirming the distinct methylation levels between fetal and maternal DNA for the selected DMRs. We have successfully implemented a novel approach for the discovery and confirmation of a significant number of fetal-specific DMRs by combining for the first time MeDIP and in-solution targeted enrichment followed by NGS. The implementation of this double-enrichment approach is highly efficient and enables the detailed analysis of multiple DMRs by targeted NGS. Also, this is, to our knowledge, the first reported application of MeDIP on plasma samples, which leverages the implementation of our enrichment methodology in the detection of fetal abnormalities in maternal plasma.

  5. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

    PubMed Central

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses. PMID:27667992

  6. Annual Energy Review 2000

    SciTech Connect

    Seiferlein, Katherine E.

    2001-08-01

    The Annual Energy Review (AER) presents the Energy Information Administration’s historical energy statistics. For many series, statistics are given for every year from 1949 through 2000. The statistics, expressed in either physical units or British thermal units, cover all major energy activities, including consumption, production, trade, stocks, and prices, for all major energy commodities, including fossil fuels, electricity, and renewable energy sources. Publication of this report is required under Public Law 95–91 (Department of Energy Organization Act), Section 205(c), and is in keeping with responsibilities given to the Energy Information Administration under Section 205(a)(2), which states: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications.

  7. Annual Energy Review 1997

    SciTech Connect

    Seiferlein, Katherine E.

    1998-07-01

    The Annual Energy Review (AER) presents the Energy Information Administration’s historical energy statistics. For many series, statistics are given for every year from 1949 through 1997. The statistics, expressed in either physical units or British thermal units, cover all major energy activities, including consumption, production, trade, stocks, and prices, for all major energy commodities, including fossil fuels, electricity, and renewable energy sources. Publication of this report is in keeping with responsibilities given to the Energy Information Administration (EIA) in Public Law 95–91 (Department of Energy Organization Act), which states, in part, in Section 205(a)(2) that: “The Administrator shall be responsible for carrying out a central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information....” The AER is intended for use by Members of Congress, Federal and State agencies, energy analysts, and the general public. EIA welcomes suggestions from readers regarding data series in the AER and in other EIA publications.

  8. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    PubMed Central

    Pasmant, Eric; Parfait, Béatrice; Luscan, Armelle; Goussard, Philippe; Briand-Suleau, Audrey; Laurendeau, Ingrid; Fouveaut, Corinne; Leroy, Chrystel; Montadert, Annelore; Wolkenstein, Pierre; Vidaud, Michel; Vidaud, Dominique

    2015-01-01

    Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of ∼150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with ∼90€ for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours. PMID:25074460

  9. FGFR2 mutation in a patient without typical features of Pfeiffer syndrome--The emerging role of combined NGS and phenotype based strategies.

    PubMed

    Flöttmann, Ricarda; Knaus, Alexej; Zemojtel, Tomasz; Robinson, Peter N; Mundlos, Stefan; Horn, Denise; Spielmann, Malte

    2015-08-01

    Pfeiffer syndrome (MIM: #101600) is a rare autosomal dominant disorder classically characterized by limb and craniofacial anomalies. It is caused by heterozygous mutations in the fibroblast growth factor receptors types 1 and 2 (FGFR1 and FGFR2). We applied a next generation sequencing (NGS) panel approach comprising all 2877 genes currently known to be causative for one or more Mendelian diseases combined with the phenotype based computational tool PhenIX (Phenotypic Interpretation of eXomes). We report on a patient presenting with multiple anomalies of hands and feet including brachydactyly and symphalangism. No clinical diagnosis could be established based on the clinical findings and testing of several genes associated with brachydactyly and symphalangism failed to identify mutations. Via next generation sequencing (NGS) panel approach we then identified a novel de novo missense FGFR2 mutation affecting an amino acid reported to be mutated in Pfeiffer syndrome. Since our patient shows typical radiological findings of Pfeiffer syndrome in hands and feet but at the same time lacks several characteristic features such as clinical signs of craniosynostosis and prominent eyes we suggest introducing the term "FGFR2 associated phenotypes" for similar cases. Our results highlight the emerging role of combined NGS and phenotype based bioinformatics strategies to establish clinical diagnoses.

  10. USGS Annual Water Data Reports

    SciTech Connect

    2012-04-01

    Water resources data are published annually for use by engineers, scientists, managers, educators, and the general public. These archival products supplement direct access to current and historical water data provided by the National Water Information System (NWIS). Beginning with Water Year 2006, annual water data reports are available as individual electronic Site Data Sheets for the entire Nation for retrieval, download, and localized printing on demand. National distribution includes tabular and map interfaces for search, query, display and download of data. Data provided include extreme and mean discharge rates.

  11. 14 CFR 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Requirements for annual report. 1206.900... AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On or before February 1 of each year, NASA shall submit a report covering the preceding fiscal year to...

  12. 47 CFR 0.417 - The Annual Reports.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false The Annual Reports. 0.417 Section 0.417... Publications § 0.417 The Annual Reports. At the end of each fiscal year, the Commission publishes an Annual Report containing general information concerning the Commission and the history of regulation, a...

  13. 47 CFR 0.417 - The Annual Reports.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false The Annual Reports. 0.417 Section 0.417... Publications § 0.417 The Annual Reports. At the end of each fiscal year, the Commission publishes an Annual Report containing general information concerning the Commission and the history of regulation, a summary...

  14. 14 CFR § 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On or before February 1 of each year, NASA shall submit a report covering the preceding fiscal year to the... 14 Aeronautics and Space 5 2014-01-01 2014-01-01 false Requirements for annual report. § 1206.900...

  15. 14 CFR 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On or before February 1 of each year, NASA shall submit a report covering the preceding fiscal year to the... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Requirements for annual report. 1206.900...

  16. 14 CFR 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On or before February 1 of each year, NASA shall submit a report covering the preceding fiscal year to the... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Requirements for annual report. 1206.900...

  17. 14 CFR 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On or before February 1 of each year, NASA shall submit a report covering the preceding fiscal year to the... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Requirements for annual report. 1206.900...

  18. 76 FR 1471 - FY 2010 Annual Compliance Report; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-10

    ... FY 2010 Annual Compliance Report; Comment Request AGENCY: Postal Regulatory Commission. ACTION: Notice. SUMMARY: The Postal Service has filed an Annual Compliance Report on the costs, revenues, rates... Commission seeks public comments on the Postal Service's Annual Compliance Report. DATES: Comments are...

  19. High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma

    PubMed Central

    Yoshikawa, Yoshie; Emi, Mitsuru; Hashimoto-Tamaoki, Tomoko; Ohmuraya, Masaki; Sato, Ayuko; Tsujimura, Tohru; Hasegawa, Seiki; Nakano, Takashi; Nasu, Masaki; Pastorino, Sandra; Szymiczek, Agata; Bononi, Angela; Tanji, Mika; Pagano, Ian; Gaudino, Giovanni; Napolitano, Andrea; Goparaju, Chandra; Pass, Harvey I.; Yang, Haining; Carbone, Michele

    2016-01-01

    We used a custom-made comparative genomic hybridization array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1 (breast cancer 1)-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (<3 kb) in 46 of 251 genes: four were cancer-associated genes: SETD2 (SET domain-containing protein 2) (7 of 33), BAP1 (8 of 33), PBRM1 (polybromo 1) (3 of 33), and SMARCC1 (switch/sucrose nonfermentable- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily c, member 1) (2 of 33). These four genes were further investigated by targeted next-generation sequencing (tNGS), which revealed sequence-level mutations causing biallelic inactivation. Combined high-density aCGH and tNGS revealed biallelic gene inactivation in SETD2 (9 of 33, 27%), BAP1 (16 of 33, 48%), PBRM1 (5 of 33, 15%), and SMARCC1 (2 of 33, 6%). The incidence of genetic alterations detected is much higher than reported in the literature because minute deletions are not detected by NGS or commercial aCGH. Many of these minute deletions were not contiguous, but rather alternated with segments showing oscillating copy number changes along the 3p21 region. In summary, we found that in MM: (i) multiple minute simultaneous biallelic deletions are frequent in chromosome 3p21, where they occur as distinct events involving multiple genes; (ii) in addition to BAP1, mutations of SETD2, PBRM1, and SMARCC1 are frequent in MM; and (iii) our results suggest that high-density aCGH combined with tNGS provides a more precise estimate of the frequency and types of genes inactivated in human cancer than approaches based exclusively on NGS strategy. PMID:27834213

  20. Assessment of the Impact of a New Guanidine Suppressor In NGS on F/H Laboratory Analyses For DWPF and Saltstone MCU Transfers

    SciTech Connect

    Bannochie, C. J.

    2013-04-29

    Implementation of the Next Generation Solvent (NGS) in the Modular Caustic-Side Solvent Extraction Unit (MCU) will now proceed with a new suppressor compound, 1,2,3-tris(3,7-dimethyloctyl)guanidine (TiDG), replacing the originally planned suppressor for NGS, 1,3-dicyclohexyl-2-(11-methyldodecyl) guanidine (DCiTG). The Savannah River National Laboratory (SRNL) was tasked with evaluating the potential impact to F/H Laboratory analyses supporting the Defense Waste Processing Facility (DWPF) Waste Acceptance Criteria (WAC) used to qualify transfers of MCU Strip Effluent (SE) into the facility and the Saltstone WAC used to qualify transfers of Tank 50 containing Decontaminated Salt Solution (DSS) from MCU into Saltstone. This assigned scope is covered by a Task Technical and Quality Assurance Plan (TTQAP). Previous impact evaluations were conducted when the DCiTG suppressor was planned for NGS and concluded that there was no impact to either the determination of MCU SE pH nor the analysis of Isopar® L carryover in the MCU SE and DSS streams. SRNL reported on this series of cross-check studies between the SRNL and F/H Laboratories. The change in suppressor from DCiTG to TiDG in the NGS should not impact the measurement of Isopar® L or pH in SE or DSS necessary to satisfy DWPF and Saltstone WAC (Tank 50) criteria, respectively. A statistical study of the low bias observed in Isopar® L measurements in both SRNL and F/H Laboratories may be necessary now that the final NGS composition is fixed in order to quantify the low bias so that a proper correction can be applied to measurements critical to the DWPF and Saltstone WACs. Depending upon the final DWPF WAC requirement put in place for SE pH, it could become necessary to implement an alternative ICP-AES measurement of boron. The current blended solvent system testing in SRNL should address any impacts to Isopar® L carryover into either the DSS or the SE. It is recommended that SRNL monitor the current blended solvent

  1. FY04 NDCEE Annual Technologies Publications

    DTIC Science & Technology

    2006-03-14

    42 Field-Based Perchlorate Measurement ............................................................................ 44 Halogenated Volatile Organic... measure of success for the NDCEE. Since its inception, the NDCEE has provided technology demonstration, validation, implementation and other technical...implementing technologies. Key activities include determining the nature and extent of the issue, engaging stakeholders early in the process, conducting

  2. FY04 NDCEE Annual Technologies Publication

    DTIC Science & Technology

    2006-03-14

    42 Field-Based Perchlorate Measurement ............................................................................ 44 Halogenated Volatile Organic... measure of success for the NDCEE. Since its inception, the NDCEE has provided technology demonstration, validation, implementation and other technical...implementing technologies. Key activities include determining the nature and extent of the issue, engaging stakeholders early in the process, conducting

  3. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

    PubMed Central

    Bastías, Adriana; Correa, Francisco; Rojas, Pamela; Almada, Rubén; Muñoz, Carlos; Sagredo, Boris

    2016-01-01

    Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species. PMID:27459734

  4. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS).

    PubMed

    Bastías, Adriana; Correa, Francisco; Rojas, Pamela; Almada, Rubén; Muñoz, Carlos; Sagredo, Boris

    2016-01-01

    Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

  5. Petroleum supply annual 1993. Volume 2

    SciTech Connect

    Not Available

    1994-06-01

    This publication contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1993 through annual and monthly surveys. This second volume contains final statistics for each month of 1993.

  6. 77 FR 3408 - Annual Stress Test

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-24

    ... enter all comments received into the docket and publish them on the Regulations.gov Web site without... readily accessible to the public, for example, by publication on a covered institution's Web site. In... institution shall publish a summary of the results of its annual stress tests on its Web site or in any...

  7. Uranium industry annual 1996

    SciTech Connect

    1997-04-01

    The Uranium Industry Annual 1996 (UIA 1996) provides current statistical data on the US uranium industry`s activities relating to uranium raw materials and uranium marketing. The UIA 1996 is prepared for use by the Congress, Federal and State agencies, the uranium and nuclear electric utility industries, and the public. Data on uranium raw materials activities for 1987 through 1996 including exploration activities and expenditures, EIA-estimated reserves, mine production of uranium, production of uranium concentrate, and industry employment are presented in Chapter 1. Data on uranium marketing activities for 1994 through 2006, including purchases of uranium and enrichment services, enrichment feed deliveries, uranium fuel assemblies, filled and unfilled market requirements, uranium imports and exports, and uranium inventories are shown in Chapter 2. A feature article, The Role of Thorium in Nuclear Energy, is included. 24 figs., 56 tabs.

  8. Uranium Industry Annual, 1992

    SciTech Connect

    Not Available

    1993-10-28

    The Uranium Industry Annual provides current statistical data on the US uranium industry for the Congress, Federal and State agencies, the uranium and electric utility industries, and the public. The feature article, ``Decommissioning of US Conventional Uranium Production Centers,`` is included. Data on uranium raw materials activities including exploration activities and expenditures, resources and reserves, mine production of uranium, production of uranium concentrate, and industry employment are presented in Chapter 1. Data on uranium marketing activities including domestic uranium purchases, commitments by utilities, procurement arrangements, uranium imports under purchase contracts and exports, deliveries to enrichment suppliers, inventories, secondary market activities, utility market requirements, and uranium for sale by domestic suppliers are presented in Chapter 2.

  9. 75 FR 12584 - Sunshine Act; Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-16

    ... CORPORATION Sunshine Act; Public Hearing March 17, 2010. OPIC's Sunshine Act notice of its Annual Public Hearing meeting was published in the Federal Register (Volume 75, Number 38, Pages 9004 and 9005) on... record; therefore, OPIC's annual public hearing scheduled for 2 p.m. on March 17, 2010 has been cancelled...

  10. American Psychological Association annual report.

    PubMed

    2010-01-01

    Presents the 2009 American Psychological Association annual report. It highlights a very important year for APA and psychology by summarizing activities within each directorate. It describes strides made toward the goal of infusing psychology into the health care marketplace and of bringing psychology-and the unique skills of psychologists-to the attention of the public. This report aims to give insight into the contributions psychologists make to our communities and our country.

  11. LLNL NESHAPs 1995 annual report

    SciTech Connect

    Gallegos, G.M.; Harrach, R.J.; Biermann, A.H.; Tate, P.J.

    1996-06-01

    This annual report is prepared pursuant to the National Emissions Standards for Hazardous Air Pollutants (NESHAPs) 40 CFR Part 61, Subpart H; Subpart H governs radionuclide emissions to air from Department of Energy (DOE) facilities. NESHAPs limits the emission of radionuclides to the ambient air from DOE facilities to levels resulting in an effective dose equivalent (EDE) of 10 mrem to any member of the public. This document contains the EDEs for the Lawrence Livermore National Laboratory (LLNL) site-wide maximally exposed members of the public from 1995 operations.

  12. Unusual multisystemic involvement and a novel BAG3 mutation revealed by NGS screening in a large cohort of myofibrillar myopathies

    PubMed Central

    2014-01-01

    Background Myofibrillar myopathies (MFM) are a group of phenotypically and genetically heterogeneous neuromuscular disorders, which are characterized by protein aggregations in muscle fibres and can be associated with multisystemic involvement. Methods We screened a large cohort of 38 index patients with MFM for mutations in the nine thus far known causative genes using Sanger and next generation sequencing (NGS). We studied the clinical and histopathological characteristics in 38 index patients and five additional relatives (n = 43) and particularly focused on the associated multisystemic symptoms. Results We identified 14 heterozygous mutations (diagnostic yield of 37%), among them the novel p.Pro209Gln mutation in the BAG3 gene, which was associated with onset in adulthood, a mild phenotype and an axonal sensorimotor polyneuropathy, in the absence of giant axons at the nerve biopsy. We revealed several novel clinical phenotypes and unusual multisystemic presentations with previously described mutations: hearing impairment with a FLNC mutation, dysphonia with a mutation in DES and the first patient with a FLNC mutation presenting respiratory insufficiency as the initial symptom. Moreover, we described for the first time respiratory insufficiency occurring in a patient with the p.Gly154Ser mutation in CRYAB. Interestingly, we detected a polyneuropathy in 28% of the MFM patients, including a BAG3 and a MYOT case, and hearing impairment in 13%, including one patient with a FLNC mutation and two with mutations in the DES gene. In four index patients with a mutation in one of the MFM genes, typical histological findings were only identified at the ultrastructural level (29%). Conclusions We conclude that extraskeletal symptoms frequently occur in MFM, particularly cardiac and respiratory involvement, polyneuropathy and/or deafness. BAG3 mutations should be considered even in cases with a mild phenotype or an adult onset. We identified a genetic defect in one of

  13. Unusual multisystemic involvement and a novel BAG3 mutation revealed by NGS screening in a large cohort of myofibrillar myopathies.

    PubMed

    Semmler, Anna-Lena; Sacconi, Sabrina; Bach, J Elisa; Liebe, Claus; Bürmann, Jan; Kley, Rudolf A; Ferbert, Andreas; Anderheiden, Roland; Van den Bergh, Peter; Martin, Jean-Jacques; De Jonghe, Peter; Neuen-Jacob, Eva; Müller, Oliver; Deschauer, Marcus; Bergmann, Markus; Schröder, J Michael; Vorgerd, Matthias; Schulz, Jörg B; Weis, Joachim; Kress, Wolfram; Claeys, Kristl G

    2014-08-01

    Myofibrillar myopathies (MFM) are a group of phenotypically and genetically heterogeneous neuromuscular disorders, which are characterized by protein aggregations in muscle fibres and can be associated with multisystemic involvement. We screened a large cohort of 38 index patients with MFM for mutations in the nine thus far known causative genes using Sanger and next generation sequencing (NGS). We studied the clinical and histopathological characteristics in 38 index patients and five additional relatives (n = 43) and particularly focused on the associated multisystemic symptoms. We identified 14 heterozygous mutations (diagnostic yield of 37%), among them the novel p.Pro209Gln mutation in the BAG3 gene, which was associated with onset in adulthood, a mild phenotype and an axonal sensorimotor polyneuropathy, in the absence of giant axons at the nerve biopsy. We revealed several novel clinical phenotypes and unusual multisystemic presentations with previously described mutations: hearing impairment with a FLNC mutation, dysphonia with a mutation in DES and the first patient with a FLNC mutation presenting respiratory insufficiency as the initial symptom. Moreover, we described for the first time respiratory insufficiency occurring in a patient with the p.Gly154Ser mutation in CRYAB. Interestingly, we detected a polyneuropathy in 28% of the MFM patients, including a BAG3 and a MYOT case, and hearing impairment in 13%, including one patient with a FLNC mutation and two with mutations in the DES gene. In four index patients with a mutation in one of the MFM genes, typical histological findings were only identified at the ultrastructural level (29%). We conclude that extraskeletal symptoms frequently occur in MFM, particularly cardiac and respiratory involvement, polyneuropathy and/or deafness. BAG3 mutations should be considered even in cases with a mild phenotype or an adult onset. We identified a genetic defect in one of the known genes in less than half of the

  14. Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly.

    PubMed

    Debat, Humberto J; Grabiele, Mauro; Aguilera, Patricia M; Bubillo, Rosana E; Otegui, Mónica B; Ducasse, Daniel A; Zapata, Pedro D; Marti, Dardo A

    2014-01-01

    Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes

  15. Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly

    PubMed Central

    Aguilera, Patricia M.; Bubillo, Rosana E.; Otegui, Mónica B.; Ducasse, Daniel A.; Zapata, Pedro D.; Marti, Dardo A.

    2014-01-01

    Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes

  16. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 3 2011-10-01 2011-10-01 false Semi-annual compilation. 604.600 Section 604.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW..., shall be available for public inspection 30 days after receipt of the report by the Secretary and...

  17. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 3 2014-10-01 2014-10-01 false Semi-annual compilation. 604.600 Section 604.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW..., shall be available for public inspection 30 days after receipt of the report by the Secretary and...

  18. A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism.

    PubMed

    Goodrich, David; Tao, Xin; Bohrer, Chelsea; Lonczak, Agnieszka; Xing, Tongji; Zimmerman, Rebekah; Zhan, Yiping; Scott, Richard T; Treff, Nathan R

    2016-11-01

    A subset of preimplantation stage embryos may possess mosaicism of chromosomal constitution, representing a possible limitation to the clinical predictive value of comprehensive chromosome screening (CCS) from a single biopsy. However, contemporary methods of CCS may be capable of predicting mosaicism in the blastocyst by detecting intermediate levels of aneuploidy within a trophectoderm biopsy. This study evaluates the sensitivity and specificity of aneuploidy detection by two CCS platforms using a cell line mixture model of a mosaic trophectoderm biopsy. Four cell lines with known karyotypes were obtained and mixed together at specific ratios of six total cells (0:6, 1:5, 2:4, 3:3, 4:2, 5:1, and 6:0). A female euploid and a male trisomy 18 cell line were used for one set, and a male trisomy 13 and a male trisomy 15 cell line were used for another. Replicates of each mixture were prepared, randomized, and blinded for analysis by one of two CCS platforms (quantitative polymerase chain reaction (qPCR) or VeriSeq next-generation sequencing (NGS)). Sensitivity and specificity of aneuploidy detection at each level of mosaicism was determined and compared between platforms. With the default settings for each platform, the sensitivity of qPCR and NGS were not statistically different, and 100 % specificity was observed (no false positives) at all levels of mosaicism. However, the use of previously published custom criteria for NGS increased sensitivity but also significantly decreased specificity (33 % false-positive prediction of aneuploidy). By demonstrating increased false-positive diagnoses when reducing the stringency of predicting an abnormality, these data illustrate the importance of preclinical evaluation of new testing paradigms before clinical implementation.

  19. Development and application of a next-generation-sequencing (NGS) approach to detect known and novel gene defects underlying retinal diseases

    PubMed Central

    2012-01-01

    Background Inherited retinal disorders are clinically and genetically heterogeneous with more than 150 gene defects accounting for the diversity of disease phenotypes. So far, mutation detection was mainly performed by APEX technology and direct Sanger sequencing of known genes. However, these methods are time consuming, expensive and unable to provide a result if the patient carries a new gene mutation. In addition, multiplicity of phenotypes associated with the same gene defect may be overlooked. Methods To overcome these challenges, we designed an exon sequencing array to target 254 known and candidate genes using Agilent capture. Subsequently, 20 DNA samples from 17 different families, including four patients with known mutations were sequenced using Illumina Genome Analyzer IIx next-generation-sequencing (NGS) platform. Different filtering approaches were applied to identify the genetic defect. The most likely disease causing variants were analyzed by Sanger sequencing. Co-segregation and sequencing analysis of control samples validated the pathogenicity of the observed variants. Results The phenotype of the patients included retinitis pigmentosa, congenital stationary night blindness, Best disease, early-onset cone dystrophy and Stargardt disease. In three of four control samples with known genotypes NGS detected the expected mutations. Three known and five novel mutations were identified in NR2E3, PRPF3, EYS, PRPF8, CRB1, TRPM1 and CACNA1F. One of the control samples with a known genotype belongs to a family with two clinical phenotypes (Best and CSNB), where a novel mutation was identified for CSNB. In six families the disease associated mutations were not found, indicating that novel gene defects remain to be identified. Conclusions In summary, this unbiased and time-efficient NGS approach allowed mutation detection in 75% of control cases and in 57% of test cases. Furthermore, it has the possibility of associating known gene defects with novel phenotypes

  20. NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.

    PubMed

    Endris, Volker; Stenzinger, Albrecht; Pfarr, Nicole; Penzel, Roland; Möbs, Markus; Lenze, Dido; Darb-Esfahani, Silvia; Hummel, Michael; Sabine-Merkelbach-Bruse; Jung, Andreas; Lehmann, Ulrich; Kreipe, Hans; Kirchner, Thomas; Büttner, Reinhard; Jochum, Wolfram; Höfler, Gerald; Dietel, Manfred; Weichert, Wilko; Schirmacher, Peter

    2016-06-01

    With the approval of olaparib as monotherapy treatment in platinum-sensitive, relapsed high-grade serous ovarian cancer by the European Medical Agency (EMA), comprehensive genotyping of BRCA1 and BRCA2 in tumor tissue has become a mandatory pre-therapeutic test. This requires significant advances in routine tumor test methodologies due to the large size of both genes and the lack of mutational hot spots. Classical focused screening approaches, like Sanger sequencing, do not allow for a sensitive, rapid, and economic analysis of tumor tissue. Next-generation sequencing (NGS) approaches employing targeted panels for BRCA1/2 to interrogate formalin-fixed and paraffin-embedded tumor samples from either surgical resection or biopsy specimens can overcome these limitations. Although focused NGS methods have been implemented by few centers in routine molecular diagnostics for the analysis of some druggable oncogenic mutations, the reliable diagnostic testing of the entire coding regions of BRCA1 and BRCA2 was a new challenge requiring extensive technological improvement and quality management. Here, we describe the implementation and results of the first round robin trial for BRCA1/2 mutation testing in tumor tissue that was conducted in central Europe on May 2015, shortly after the approval and prior to the official release of olaparib. The high success rate of 81 % (21/26 test centers) demonstrates that BRCA1/2 multicenter mutation testing is well feasible in FFPE tumor tissue, extending to other tumor entities beyond ovarian cancer. The high number of test centers passing the trial demonstrates the success of the concerted efforts by German, Swiss, and Austrian pathology centers to ensure quality-controlled NGS-based testing and proves the potential of this technology in routine molecular pathology. On the basis of our results, we provide recommendations for predictive testing of tumor tissue for BRCA1/2 to clinical decision making in ovarian cancer patients.

  1. Proceedings of the 1990 Annual Meeting of the Association for Education in Journalism and Mass Communication (73rd, Minneapolis, Minnesota, August 1-4, 1990). Part IV: Public Relations Studies.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The public relations studies section of the proceedings includes the following seven papers: "Ethical Inclinations of Public Relations Practitioners" (Cornelius B. Pratt); "Losing Control: An Examination of the Management Function in Public Relations" (Martha M. Lauzen); "Shifting the Public Relations Paradigm: A Theory of…

  2. Proceedings of the 1990 Annual Meeting of the Association for Education in Journalism and Mass Communication (73rd, Minneapolis, Minnesota, August 1-4, 1990). Part IV: Public Relations Studies.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The public relations studies section of the proceedings includes the following seven papers: "Ethical Inclinations of Public Relations Practitioners" (Cornelius B. Pratt); "Losing Control: An Examination of the Management Function in Public Relations" (Martha M. Lauzen); "Shifting the Public Relations Paradigm: A Theory of…

  3. 43 CFR 2.34 - Where can I get a copy of DOI's FOIA annual report?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... annual report? 2.34 Section 2.34 Public Lands: Interior Office of the Secretary of the Interior RECORDS AND TESTIMONY; FREEDOM OF INFORMATION ACT FOIA Annual Report § 2.34 Where can I get a copy of DOI's FOIA annual report? Under 5 U.S.C. 552(e), DOI is required to prepare an annual report regarding...

  4. Petroleum supply annual 1993. Volume 1

    SciTech Connect

    Not Available

    1994-06-01

    The Petroleum Supply Annual (PSA) contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1993 through annual and monthly surveys. The PSA is divided into two volumes. This first volume contains four sections: Summary Statistics, Detailed Statistics, Refinery Capacity, and Oxygenate Capacity each with final annual data. The second volume contains final statistics for each month of 1993, and replaces data previously published in the Petroleum Supply Monthly (PSM). The tables in Volumes 1 and 2 are similarly numbered to facilitate comparison between them. Below is a description of each section in Volume 1 of the PSA.

  5. Petroleum supply annual 1994. Volume 1

    SciTech Connect

    1995-05-22

    The Petroleum Supply Annual (PSA) contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1994 through annual and monthly surveys. The PSA is divided into two volumes. This first volume contains four sections: Summary Statistics, Detailed Statistics, Refinery Capacity, and Oxygenate Capacity each with final annual data. The second volume contains final statistics for each month of 1994, and replaces data previously published in the Petroleum Supply Monthly (PSM). The tables in Volumes 1 and 2 are similarly numbered to facilitate comparison between them. Below is a description of each section in Volume 1 of the PSA.

  6. Petroleum supply annual 1998: Volume 1

    SciTech Connect

    1999-06-01

    The ``Petroleum Supply Annual`` (PSA) contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1998 through annual and monthly surveys. The PSA is divided into two volumes. This first volume contains three sections: Summary Statistics, Detailed Statistics, and Refinery Statistics; each with final annual data. The second volume contains final statistics for each month of 1998, and replaces data previously published in the PSA. The tables in Volumes 1 and 2 are similarly numbered to facilitate comparison between them. 16 figs., 59 tabs.

  7. Petroleum supply annual, 1997. Volume 1

    SciTech Connect

    1998-06-01

    The Petroleum Supply Annual (PSA) contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1997 through annual and monthly surveys. The PSA is divided into two volumes. This first volume contains three sections: Summary Statistics, Detailed Statistics, and Refinery Statistics; each with final annual data. The second volume contains final statistics for each month of 1997, and replaces data previously published in the Petroleum Supply Monthly (PSM). The tables in Volumes 1 and 2 are similarly numbered to facilitate comparison between them. 16 figs., 48 tabs.

  8. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    PubMed Central

    de Brevern, Alexandre G.; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries. PMID:26125026

  9. Application of an NGS-based 28-gene panel in myeloproliferative neoplasms reveals distinct mutation patterns in essential thrombocythaemia, primary myelofibrosis and polycythaemia vera.

    PubMed

    Delic, Sabit; Rose, Dominic; Kern, Wolfgang; Nadarajah, Niroshan; Haferlach, Claudia; Haferlach, Torsten; Meggendorfer, Manja

    2016-11-01

    Molecular routine diagnostics for BCR-ABL1-negative myeloproliferative neoplasms (MPN) currently focusses on mutations in JAK2, CALR and MPL. In recent years, recurrent mutations in MPNs have been identified in several other genes. We here present the validation of a next generation sequencing (NGS)-based 28-gene panel and its use in MPN. We analysed the mutation status of 28 genes in 100 MPN patients [40 essential thrombocythaemia (ET), 30 primary myelofibrosis (PMF), 30 polycythaemia vera (PV)] and found two or more mutated genes in 53 patients. Moreover, significantly more mutated splicing genes (SF3B1, SRSF2 and U2AF1) were present in PMF (0·60 mutated genes/patient) compared to ET (0·15) while no mutations in splicing genes were found in PV. Additionally, chromatin modification genes (ASXL1 and EZH2) were frequently mutated in PMF patients (0·50) and, to a significantly lesser extent, in ET (0·13) and PV (0·07). Contrarily, DNA methylation genes (DNMT3A, IDH1, IDH2 and TET2) were mutated most often in PV (0·5) and less frequently in ET (0·23) and PMF (0·20), but without reaching statistical significance. Our results demonstrate the feasibility and utility of NGS-based panel diagnostics for MPN. With 53% of the patients bearing two or more mutated genes, their prognostic relevance needs further studies.

  10. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    PubMed Central

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-01-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes. PMID:24764758

  11. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.

    PubMed

    de Brevern, Alexandre G; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  12. [Identification of key markers of normal and pathogenic microbiota determining health of periodontium by NGS-sequencing 16S-rDNA libraries of periodontal swabs].

    PubMed

    Zorina, O A; Petrukhina, N B; Basova, A A; Shibaeva, A V; Trubnikova, E V; Shevelev, A B

    2014-01-01

    By using NGS-sequencing libraries of DNA from periodontal swabs with primers specific to V6 region of 16S rDNA prevalence of bacterial genera and species in periodontal microbiota of patients with aggressive periodontitis and healthy donors was analyzed. Six genera of putative periodontal protectors and eight periodontal pathogens were identified with respect to aggressive (but not chronic) periodontitis. Statistically relevant over-colonization by general Porphyromonas, Treponema, Synergistes, Tannerella, Filifactor, Ruminococcus, Parvimonas and Mycoplasma was found to be associated with the condition. From these, only three genera Porphyromonas, Treponema and Tannerella are traditionally considered as periodontal pathogens. Statistically confidential over-colonization by genus Veillonella was found in healthy patients. This genus should be considered as a relevant marker of a healthy periodontium. Genera Streptococcus, Bergeyella, Granulicatella, Kingella and Corynebacterium may be considered as putative periodontal protectors. Comparison of data of NGS-sequencing and real-time PCR demonstrated a good agreement if different PCR efficiency using independent primer pairs is taken into account.

  13. Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens.

    PubMed

    Perlejewski, Karol; Popiel, Marta; Laskus, Tomasz; Nakamura, Shota; Motooka, Daisuke; Stokowy, Tomasz; Lipowski, Dariusz; Pollak, Agnieszka; Lechowicz, Urszula; Caraballo Cortés, Kamila; Stępień, Adam; Radkowski, Marek; Bukowska-Ośko, Iwona

    2015-12-15

    Encephalitis is a severe neurological syndrome usually caused by viruses. Despite significant progress in diagnostic techniques, the causative agent remains unidentified in the majority of cases. The aim of the present study was to test an alternative approach for the detection of putative pathogens in encephalitis using next-generation sequencing (NGS). RNA was extracted from cerebrospinal fluid (CSF) from a 60-year-old male patient with encephalitis and subjected to isothermal linear nucleic acid amplification (Ribo-SPIA, NuGen) followed by next-generation sequencing using MiSeq (Illumina) system and metagenomics data analysis. The sequencing run yielded 1,578,856 reads overall and 2579 reads matched human herpesvirus I (HHV-1) genome; the presence of this pathogen in CSF was confirmed by specific PCR. In subsequent experiments we found that the DNAse I treatment, while lowering the background of host-derived sequences, lowered the number of detectable HHV-1 sequences by a factor of 4. Furthermore, we found that the routine extraction of total RNA by the Chomczynski method could be used for identification of both DNA and RNA pathogens in typical clinical settings, as it results in retention of a significant amount of DNA. In summary, it seems that NGS preceded by nucleic acid amplification could supplement currently used diagnostic methods in encephalitis. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Next-generation sequencing (NGS) as a fast molecular diagnosis tool for left ventricular noncompaction in an infant with compound mutations in the MYBPC3 gene.

    PubMed

    Schaefer, Elise; Helms, Pauline; Marcellin, Luc; Desprez, Philippe; Billaud, Philippe; Chanavat, Valérie; Rousson, Robert; Millat, Gilles

    2014-03-01

    Left ventricular noncompaction (LVNC) is a clinically heterogeneous disorder characterized by a trabecular meshwork and deep intertrabecular myocardial recesses that communicate with the left ventricular cavity. LVNC is classified as a rare genetic cardiomyopathy. Molecular diagnosis is a challenge for the medical community as the condition shares morphologic features of hypertrophic and dilated cardiomyopathies. Several genetic causes of LVNC have been reported, with variable modes of inheritance, including autosomal dominant and X-linked inheritance, but relatively few responsible genes have been identified. In this report, we describe a case of a severe form of LVNC leading to death at 6 months of life. NGS sequencing using a custom design for hypertrophic cardiomyopathy panel allowed us to identify compound heterozygosity in the MYBPC3 gene (p.Lys505del, p.Pro955fs) in 3 days, confirming NGS sequencing as a fast molecular diagnosis tool. Other studies have reported neonatal presentation of cardiomyopathies associated with compound heterozygous or homozygous MYBPC3 mutations. In this family and in families in which parental truncating MYBPC3 mutations are identified, preimplantation or prenatal genetic screening should be considered as these genotypes leads to neonatal mortality and morbidity.

  15. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies.

    PubMed

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-03-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes.

  16. Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler™ NGS STR Panel and the Ion PGM™ System.

    PubMed

    Wang, Zheng; Zhou, Di; Wang, Hui; Jia, Zhenjun; Liu, Jing; Qian, Xiaoqin; Li, Chengtao; Hou, Yiping

    2017-09-08

    Massively parallel sequencing (MPS) technologies have proved capable of sequencing the majority of the key forensic STR markers. By MPS, not only the repeat-length size but also sequence variations could be detected. Recently, Thermo Fisher Scientific has designed an advanced MPS 32-plex panel, named the Precision ID GlobalFiler™ NGS STR Panel, where the primer set has been designed specifically for the purpose of MPS technologies and the data analysis are supported by a new version HID STR Genotyper Plugin (V4.0). In this study, a series of experiments that evaluated concordance, reliability, sensitivity of detection, mixture analysis, and the ability to analyze case-type and challenged samples were conducted. In addition, 106 unrelated Han individuals were sequenced to perform genetic analyses of allelic diversity. As expected, MPS detected broader allele variations and gained higher power of discrimination and exclusion rate. MPS results were found to be concordant with current capillary electrophoresis methods, and single source complete profiles could be obtained stably using as little as 100pg of input DNA. Moreover, this MPS panel could be adapted to case-type samples and partial STR genotypes of the minor contributor could be detected up to 19:1 mixture. Aforementioned results indicate that the Precision ID GlobalFiler™ NGS STR Panel is reliable, robust and reproducible and have the potential to be used as a tool for human forensics. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Publicity and public relations

    NASA Technical Reports Server (NTRS)

    Fosha, Charles E.

    1990-01-01

    This paper addresses approaches to using publicity and public relations to meet the goals of the NASA Space Grant College. Methods universities and colleges can use to publicize space activities are presented.

  18. Ames research center publications, 1975

    NASA Technical Reports Server (NTRS)

    Sherwood, B. R. (Compiler)

    1977-01-01

    This bibliography cites 851 documents by Ames Research Center personnel and contractors which appeared in formal NASA publications, journals, books, patents, and contractor reports in 1975, or not included in previous annual bibliographies. An author index is provided.

  19. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (76th, Kansas City, Missouri, August 11-14, l993). Part VIII: Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Public Relations section of this collection of conference papers contains the following six papers: "Spanning the Boundaries: Support for First Amendment Rights among Public Relations Practitioners, Journalists and the Public" (Robert O. Wyatt and Sharon S. Smith); "Organizational Factors That Contribute to Practicing…

  20. Commissioner's Annual Report to the Education Committees of the Senate and General Assembly on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, July 1, 2008 to June 30, 2009

    ERIC Educational Resources Information Center

    New Jersey Department of Education, 2010

    2010-01-01

    The Commissioner's annual report provides the Legislature with information reported by school districts concerning incidents of serious student misconduct grouped into the following four major reporting categories: violence, vandalism, weapons, and substance abuse. An analysis of trends yields indications of progress and of ongoing concern, and…

  1. Commissioner's Annual Report to the Education Committees of the Senate and General Assembly on Violence, Vandalism and Substance Abuse in New Jersey Public Schools, July 1, 2007 to June 30, 2008

    ERIC Educational Resources Information Center

    New Jersey Department of Education, 2009

    2009-01-01

    The Commissioner's annual report provides the Legislature with information reported by school districts concerning incidents of serious student misconduct grouped into the following four major reporting categories: violence, vandalism, weapons, and substance abuse. An analysis of trends yields indications of progress and of ongoing concern, and…

  2. Science, Technology, and American Diplomacy 1985. Sixth Annual Report Submitted to the Congress by the President Pursuant to Section 503(b) of Title V of Public Law 95-426. Serial E.

    ERIC Educational Resources Information Center

    Department of State, Washington, DC.

    The Reagan administration's annual report to the Congress on international activities in the fields of science and technology (S&T) for fiscal year 1984 consists of three parts. The two chapters in part I (S&T in American diplomacy) examine S&T in American foreign policy and resources necessary for successful diplomacy. The two chapters in part II…

  3. Threshold Concepts: From Personal Practice to Communities of Practice. Proceedings of the National Academy's Sixth Annual Conference and the Fourth Biennial Threshold Concepts Conference [E-publication] (Dublin, Ireland, June 27-29, 2012)

    ERIC Educational Resources Information Center

    O'Mahony, Catherine, Ed.; Buchanan, Avril, Ed.; O'Rourke, Mary, Ed.; Higgs, Bettie, Ed.

    2014-01-01

    The 6th Annual Conference of the National Academy for the Integration of Research, Teaching and Learning (NAIRTL) and the 4th Biennial Threshold Concepts Conference was held at Trinity College Dublin, Ireland, on June 27-29, 2012. The NAIRTL is a collaborative initiative between University College Cork, Cork Institute of Technology, National…

  4. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS).

    PubMed

    Barbosa, Amanda D; Gofton, Alexander W; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%), T. gilletti (25%, 95% CI: 18.7-32.3%), T. copemani (27.4%, 95% CI: 20.8-34.8%) and T. vegrandis (10.1%, 95% CI: 6.0-15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21-35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the

  5. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS)

    PubMed Central

    Gofton, Alexander W.; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2–39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2–39.8%), T. gilletti (25%, 95% CI: 18.7–32.3%), T. copemani (27.4%, 95% CI: 20.8–34.8%) and T. vegrandis (10.1%, 95% CI: 6.0–15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0–3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1–9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21–35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2–9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides

  6. 45 CFR 1603.9 - Annual report of council.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Annual report of council. 1603.9 Section 1603.9 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION STATE... do with provision of legal services to eligible clients in the State as the council may...

  7. 45 CFR 1603.9 - Annual report of council.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Annual report of council. 1603.9 Section 1603.9 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION STATE... do with provision of legal services to eligible clients in the State as the council may...

  8. 45 CFR 1603.9 - Annual report of council.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Annual report of council. 1603.9 Section 1603.9 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION STATE... do with provision of legal services to eligible clients in the State as the council may...

  9. 45 CFR 1603.9 - Annual report of council.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Annual report of council. 1603.9 Section 1603.9 Public Welfare Regulations Relating to Public Welfare (Continued) LEGAL SERVICES CORPORATION STATE... do with provision of legal services to eligible clients in the State as the council may...

  10. 45 CFR 1168.600 - Semi-annual compilation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 3 2011-10-01 2011-10-01 false Semi-annual compilation. 1168.600 Section 1168.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES NEW RESTRICTIONS ON LOBBYING Agency Reports § 1168.600 Semi...

  11. 45 CFR 1168.600 - Semi-annual compilation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 3 2014-10-01 2014-10-01 false Semi-annual compilation. 1168.600 Section 1168.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES NEW RESTRICTIONS ON LOBBYING Agency Reports § 1168.600 Semi...

  12. 45 CFR 1168.600 - Semi-annual compilation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 3 2012-10-01 2012-10-01 false Semi-annual compilation. 1168.600 Section 1168.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES NEW RESTRICTIONS ON LOBBYING Agency Reports § 1168.600 Semi...

  13. 45 CFR 1168.600 - Semi-annual compilation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 3 2013-10-01 2013-10-01 false Semi-annual compilation. 1168.600 Section 1168.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES NEW RESTRICTIONS ON LOBBYING Agency Reports § 1168.600 Semi...

  14. 45 CFR 1168.600 - Semi-annual compilation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Semi-annual compilation. 1168.600 Section 1168.600 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES NEW RESTRICTIONS ON LOBBYING Agency Reports § 1168.600 Semi...

  15. Apprentices and Trainees: Annual, 2009. Terms and Definitions. Support Document

    ERIC Educational Resources Information Center

    National Centre for Vocational Education Research (NCVER), 2010

    2010-01-01

    This document covers the data terms used in the "Apprentices and trainees: Annual 2009" publication and its associated data tables. The primary purpose of this document is to assist users of the publication to understand the specific data terms used within it. Terms that appear in the publication are listed in alphabetical order with the…

  16. 45 CFR 2540.300 - What must be included in annual State reports to the Corporation?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false What must be included in annual State reports to the Corporation? 2540.300 Section 2540.300 Public Welfare Regulations Relating to Public Welfare... Requirements for Recipients of Corporation Assistance § 2540.300 What must be included in annual State...

  17. 45 CFR 2540.300 - What must be included in annual State reports to the Corporation?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false What must be included in annual State reports to the Corporation? 2540.300 Section 2540.300 Public Welfare Regulations Relating to Public Welfare... Requirements for Recipients of Corporation Assistance § 2540.300 What must be included in annual State...

  18. Petroleum supply annual 1994, Volume 2

    SciTech Connect

    1995-06-01

    The Petroleum Supply Annual (PSA) contains information on the supply and disposition of crude oil and petroleum products. The publication reflects data that were collected from the petroleum industry during 1994 through annual and monthly surveys. The PSA is divided into two volumes. This first volume contains four sections: Summary Statistics, Detailed Statistics, Refinery Capacity, and Oxygenate Capacity each with final annual data. The second volume contains final statistics for each month of 1994, and replaces data previously published in the Petroleum Supply Monthly (PSM). The tables in Volumes 1 and 2 are similarly numbered to facilitate comparison between them. Explanatory Notes, located at the end of this publication, present information describing data collection, sources, estimation methodology, data quality control procedures, modifications to reporting requirements and interpretation of tables. Industry terminology and product definitions are listed alphabetically in the Glossary.

  19. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies.

    PubMed

    Massart, Sebastien; Candresse, Thierry; Gil, José; Lacomme, Christophe; Predajna, Lukas; Ravnikar, Maja; Reynard, Jean-Sébastien; Rumbou, Artemis; Saldarelli, Pasquale; Škorić, Dijana; Vainio, Eeva J; Valkonen, Jari P T; Vanderschuren, Hervé; Varveri, Christina; Wetzel, Thierry

    2017-01-01

    Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.

  20. DUSTiNGS. III. Distribution of Intermediate-age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    McQuinn, Kristen B.; Boyer, Martha; DUSTiNGS Team

    2017-06-01

    As part of the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey, we have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group. We find intermediate age stars are well mixed with the older populations and extend to large radii, indicating that chemical enrichment from these dust-producing stars may occur in the outer regions of galaxies with some frequency. Theories of structure formation in dwarf galaxies must account for the lack of radial gradients in intermediate-age populations and the presence of these stars in the outer extremities of dwarfs. We also identify the tip of the red giant branch (TRGB) in Spitzer IRAC 3.6 μm photometry. Unlike the constant TRGB in the I band, at 3.6 μm, the TRGB magnitude varies by ˜0.7 mag and is not a metallicity independent distance indicator.

  1. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

    PubMed Central

    Massart, Sebastien; Candresse, Thierry; Gil, José; Lacomme, Christophe; Predajna, Lukas; Ravnikar, Maja; Reynard, Jean-Sébastien; Rumbou, Artemis; Saldarelli, Pasquale; Škorić, Dijana; Vainio, Eeva J.; Valkonen, Jari P. T.; Vanderschuren, Hervé; Varveri, Christina; Wetzel, Thierry

    2017-01-01

    Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios. PMID:28174561

  2. Annual Report to the President 1985.

    ERIC Educational Resources Information Center

    Administration on Aging (DHHS), Washington, DC. Federal Council on the Aging.

    This document is the annual report of the Federal Council on Aging whose purpose is to review and evaluate federal policies and programs affecting older Americans, serve as a spokesperson for older Americans, and inform the public about needs of this group. The first section discusses affiliations and committees of the Council. The second section…

  3. American Psychological Association: Annual Report, 2008

    ERIC Educational Resources Information Center

    American Psychologist, 2009

    2009-01-01

    This article presents the 2008 annual reports from the various directorates and offices of the American Psychological Association (APA). In 2008, APA continued to work on initiatives, programs, and products that lend value to the member's psychology career, support the future of their discipline, and serve the public. APA's goal is to strengthen…

  4. Scientific Directory 1977 and Annual Bibliography 1976.

    ERIC Educational Resources Information Center

    National Institutes of Health, (DHEW), Bethesda, MD. Div. of Scientific Reports.

    The Scientific Directory and Annual Bibliography of the National Institutes of Health (NIH) is intended for reference use by research workers in the biomedical sciences. It presents a broad outline of NIH organizational structure, the professional staff, and their scientific and technical publications covering work done at NIH. The volume also…

  5. Electric power annual 1995. Volume I

    SciTech Connect

    1996-07-01

    The Electric Power Annual presents a summary of electric power industry statistics at national, regional, and State levels. The objective of the publication is to provide industry decisionmakers, government policymakers, analysts, and the general public with data that may be used in understanding U.S. electricity markets. The Electric Power Annual is prepared by the Coal and Electric Data and Renewables Division; Office of Coal, Nuclear, Electric and Alternate Fuels; Energy Information Administration (EIA); U.S. Department of Energy. In the private sector, the majority of the users of the Electric Power Annual are researchers and analysts and, ultimately, individuals with policy- and decisionmaking responsibilities in electric utility companies. Financial and investment institutions, economic development organizations interested in new power plant construction, special interest groups, lobbyists, electric power associations, and the news media will find data in the Electric Power Annual useful. In the public sector, users include analysts, researchers, statisticians, and other professionals with regulatory, policy, and program responsibilities for Federal, State, and local governments. The Congress and other legislative bodies may also be interested in general trends related to electricity at State and national levels. Much of the data in these reports can be used in analytic studies to evaluate new legislation. Public service commissions and other special government groups share an interest in State-level statistics. These groups can also compare the statistics for their States with those of other jurisdictions.

  6. New Mexico Charter Schools Annual Report

    ERIC Educational Resources Information Center

    New Mexico Public Education Department, 2013

    2013-01-01

    In 2011, the New Mexico legislature passed changes to the Charter School Act that provided more accountability for both charters and authorizers in New Mexico. As part of that law, the Public Education Department (PED) is asked to submit an annual report on the status of charter schools in New Mexico. This is the first report submitted under that…

  7. Making Schools Work. 2010 Annual Report

    ERIC Educational Resources Information Center

    New Mexico Public Education Department, 2010

    2010-01-01

    The New Mexico Public Education Department 2010 Annual Report was created as a way to reflect on the accomplishments in education that occurred under Governor Bill Richardson's administration from 2002-2010. In 2003, the Governor outlined a reform agenda and pledged his commitment to improve education in New Mexico. In the fall of 2003, Governor…

  8. Basic Communication Course Annual. Volume 9.

    ERIC Educational Resources Information Center

    Hugenberg, Lawrence W., Ed.

    This volume of an annual collection presents nine essays relating to instruction in the basic communication course. The essays are: "Three Metaphors for the Competencies Acquired in the Public Speaking Class" (Michael Osborn); "Perceptions of Basic Communication Texts: Factors in Student Learning and Textbook Adoption…

  9. American Psychological Association: Annual Report, 2008

    ERIC Educational Resources Information Center

    American Psychologist, 2009

    2009-01-01

    This article presents the 2008 annual reports from the various directorates and offices of the American Psychological Association (APA). In 2008, APA continued to work on initiatives, programs, and products that lend value to the member's psychology career, support the future of their discipline, and serve the public. APA's goal is to strengthen…

  10. Helping Students Succeed. Annual Report, 2009

    ERIC Educational Resources Information Center

    Mulry, Laura J., Ed.; Weldon, Tyler, Ed.

    2009-01-01

    This annual report shows the breadth and scope of the work achieved on behalf of the students across New Mexico. This document is a reflection of the commitment from the higher education and public education communities as well as that of the New Mexico Higher Education Department to further educational and professional opportunities for every…

  11. American Reference Books Annual 1974. Fifth Edition.

    ERIC Educational Resources Information Center

    Wynar, Bohdan S., Ed.; And Others

    The fifth edition of American Reference Books Annual (ARBA 74) provides a comprehensive listing of reference books published or distributed in the United States with 1973 imprints, plus those published too late in 1972 to be included in the fourth edition. Like other editions of ARBA, ARBA 74 reviews library science publications, reprints, and…

  12. The Carolinas Speech Communication Annual, 1997.

    ERIC Educational Resources Information Center

    McKinney, Bruce C.

    1997-01-01

    This 1997 issue of "The Carolinas Speech Communication Annual" contains the following articles: "'Bridges of Understanding': UNESCO's Creation of a Fantasy for the American Public" (Michael H. Eaves and Charles F. Beadle, Jr.); "Developing a Communication Cooperative: A Student, Faculty, and Organizational Learning…

  13. Perceptions and Experiences of Annual Report Preparers.

    ERIC Educational Resources Information Center

    Dixon, Keith; And Others

    1995-01-01

    A study investigated the attitudes of 48 researchers who prepare annual reports for New Zealand's public colleges and universities during a period of substantial change in the reporting process. The analysts felt the reporting changes were driven externally by legislation and internally by institutional administrators and accountants. Responses to…

  14. Basic Communication Course Annual. Volume 6.

    ERIC Educational Resources Information Center

    Newburger, Craig, Ed.

    This volume of an annual collection presents 14 essays relating to instruction in the basic communication course. Essays in the collection are "Using Interactive Video Instruction to Enhance Public Speaking Instruction" (Michael W. Cronin and William R. Kennan); "Interactive Video Instruction for Teaching Organizational Techniques…

  15. Basic Communication Course Annual. Volume 8.

    ERIC Educational Resources Information Center

    Newburger, Craig, Ed.

    This volume of an annual collection presents 13 essays relating to instruction in the basic communication course. Six of the essays are on the theme of cultural diversity in the basic course. The essays are: "The Differential Impact of a Basic Public Speaking Course on Perceived Communication Competencies in Class, Work, and Social…

  16. Basic Communication Course Annual. Volume 12.

    ERIC Educational Resources Information Center

    Hugenberg, Lawrence W., Ed.

    This volume of an annual collection presents seven essays relating to instruction in the basic communication course. The essays are: "The Effects of Praise on Student Motivation in the Basic Communication Course" (B. Scott Titsworth); "The Relationship between a Required Self-Disclosure Speech and Public Speaking Anxiety: Considering Gender…

  17. Student Aid Annual 1975/1976.

    ERIC Educational Resources Information Center

    1975

    The Student Aid Annual contains information on financial aid programs offered nationally or regionally, primarily by noncollegiate organizations, public and private. The scope of these financial assistance programs extends from the incoming freshman through baccalaureate, graduate, and postdoctoral students. Program range from essay awards, loans,…

  18. Health, United States, 1981. [Sixth Annual Report].

    ERIC Educational Resources Information Center

    National Center for Health Services Research (DHHS/PHS), Hyattsville, MD.

    This document provides the sixth annual report on the health status of the citizens of the United States. Submitted by the Secretary of Health and Human Services to the President and Congress in compliance with Section 308 of the Public Health Services Act, the report presents statistics concerning recent trends in the health care sector along…

  19. Why Public Workers Stay

    ERIC Educational Resources Information Center

    Dodson, Charles; Haskew, Barbara

    1976-01-01

    This study of state employees pursues the hypothesis that inertia accounts for most workers' continuing employment. (Available from Public Personnel Management, Room 240, 1313 East 60th Street, Chicago, IL 60637; $15.00 annually, $3.00 single copy.) (Author/IRT)

  20. The Annual Report of the ACTFL Executive Director.

    ERIC Educational Resources Information Center

    Scebold, C. Edward

    1979-01-01

    Presents an overview of the President's Commission on Foreign Language and International Studies and the MLA/ACLS Task Force reports. The annual report of the American Council on the Teaching of Foreign Language includes: its organization, publications; annual meeting and preconference workshops, and projects. (EJS)

  1. 45 CFR 1603.9 - Annual report of council.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Annual report of council. 1603.9 Section 1603.9... ADVISORY COUNCILS § 1603.9 Annual report of council. On or before March 31, 1977, and on or before March 31 of each succeeding year, a council shall submit to the Corporation a report of the activities of...

  2. 40 CFR 35.673 - Annual amount reserved by EPA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Annual amount reserved by EPA. 35.673... ASSISTANCE STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Public Water System Supervision (section 1443(a) and Section 1451) § 35.673 Annual amount reserved by EPA. Each year, EPA shall reserve...

  3. 40 CFR 35.673 - Annual amount reserved by EPA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Annual amount reserved by EPA. 35.673... ASSISTANCE STATE AND LOCAL ASSISTANCE Environmental Program Grants for Tribes Public Water System Supervision (section 1443(a) and Section 1451) § 35.673 Annual amount reserved by EPA. Each year, EPA shall reserve...

  4. 45 CFR 96.74 - Annual reporting requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION BLOCK GRANTS Social Services Block Grants § 96.74 Annual reporting requirements. (a) Annual report. In accordance with 42 U.S.C... individuals who receive services paid for in whole or in part with federal funds under the Social Services...

  5. 78 FR 10180 - Annual Computational Science Symposium; Conference

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-13

    ... HUMAN SERVICES Food and Drug Administration Annual Computational Science Symposium; Conference AGENCY... public conference entitled ``The FDA/PhUSE Annual Computational Science Symposium.'' The purpose of the conference is to help the broader community align and share experiences to advance computational science. At...

  6. The Annual Report of the ACTFL Executive Director.

    ERIC Educational Resources Information Center

    Scebold, C. Edward

    1979-01-01

    Presents an overview of the President's Commission on Foreign Language and International Studies and the MLA/ACLS Task Force reports. The annual report of the American Council on the Teaching of Foreign Language includes: its organization, publications; annual meeting and preconference workshops, and projects. (EJS)

  7. 45 CFR 1801.1 - Annual Truman Scholarship competition.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Annual Truman Scholarship competition. 1801.1... SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM General § 1801.1 Annual Truman Scholarship competition. Each year, the Harry S. Truman Scholarship Foundation carries out a nationwide competition to...

  8. 45 CFR 1801.1 - Annual Truman Scholarship competition.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Annual Truman Scholarship competition. 1801.1... SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM General § 1801.1 Annual Truman Scholarship competition. Each year, the Harry S. Truman Scholarship Foundation carries out a nationwide competition to...

  9. 45 CFR 1801.1 - Annual Truman Scholarship competition.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Annual Truman Scholarship competition. 1801.1... SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM General § 1801.1 Annual Truman Scholarship competition. Each year, the Harry S. Truman Scholarship Foundation carries out a nationwide competition to...

  10. 45 CFR 1801.1 - Annual Truman Scholarship competition.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Annual Truman Scholarship competition. 1801.1... SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM General § 1801.1 Annual Truman Scholarship competition. Each year, the Harry S. Truman Scholarship Foundation carries out a nationwide competition to...

  11. 45 CFR 1801.1 - Annual Truman Scholarship competition.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 4 2014-10-01 2014-10-01 false Annual Truman Scholarship competition. 1801.1... SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM General § 1801.1 Annual Truman Scholarship competition. Each year, the Harry S. Truman Scholarship Foundation carries out a nationwide competition to...

  12. Diagnosis for choroideremia in a large Chinese pedigree by next-generation sequencing (NGS) and non-invasive prenatal testing (NIPT)

    PubMed Central

    Zhu, Li; Cheng, Jingliang; Zhou, Boxu; Wei, Chunli; Yang, Weichan; Jiang, Dong; Ijaz, Iqra; Tan, Xiaojun; Chen, Rui; Fu, Junjiang

    2017-01-01

    To develop an effective strategy to isolate and use cell-free fetal DNA (cffDNA) for the combined use of next-generation sequencing (NGS) for diagnosing choroideremia and non-invasive prenatal testing (NIPT) for Y chromosome determination, a large Chinese family with an X-linked recessive disease, choroideremia, was recruited. Cell-free DNA was extracted from maternal plasma, and SRY polymerase chain reaction amplification was performed using NIPT. Sanger sequencing was subsequently used for fetal amniotic fluid DNA verification. A nonsense mutation (c.C799T:p.R267X) of the CHM gene on the X chromosome of the proband (IV:7) and another 5 males with choroideremia were detected, while 3 female carriers with no symptoms were also identified. The fetus (VI:7) was identified as female from the cffDNA, and the same heterozygous nonsense mutation present in her mother was also confirmed. At one and a half years of age, the female baby did not present with any associated symptoms of choroideremia. Therefore, cffDNA was successfully used for the combined use of NGS for diagnosing choroideremia in a large Chinese pedigree, and NIPT for Y chromosome determination. This approach should result in a markedly increased use of prenatal diagnosis and improvement, and more sophisticated clinical management of diseases in China and other developing countries. The establishment of a highly accurate method for prenatal gene diagnosis will allow for more reliable gene diagnosis, improved genetic counseling, and personalized clinical management of our patients. PMID:28098911

  13. Applicability and Efficiency of NGS in Routine Diagnosis: In-Depth Performance Analysis of a Complete Workflow for CFTR Mutation Analysis

    PubMed Central

    Pagin, Adrien; Devos, Aurore; Figeac, Martin; Truant, Maryse; Willoquaux, Christelle; Broly, Franck; Lalau, Guy

    2016-01-01

    Background Actually, about 2000 sequence variations have been documented in the CFTR gene requiring extensive and multi-step genetic testing in the diagnosis of cystic fibrosis and CFTR-related disorders. We present a two phases study, with validation and performance monitoring, of a single experiment methodology based on multiplex PCR and high throughput sequencing that allows detection of all variants, including large rearrangements, affecting the coding regions plus three deep intronic loci. Methods A total of 340 samples, including 257 patients and 83 previously characterized control samples, were sequenced in 17 MiSeq runs and analyzed with two bioinformatic pipelines in routine diagnostic conditions. We obtained 100% coverage for all the target regions in every tested sample. Results We correctly identified all the 87 known variants in the control samples and successfully confirmed the 62 variants identified among the patients without observing false positive results. Large rearrangements were identified in 18/18 control samples. Only 17 patient samples showed false positive signals (6.6%), 12 of which showed a borderline result for a single amplicon. We also demonstrated the ability of the assay to detect allele specific dropout of amplicons when a sequence variation occurs at a primer binding site thus limiting the risk for false negative results. Conclusions We described here the first NGS workflow for CFTR routine analysis that demonstrated equivalent diagnostic performances compared to Sanger sequencing and multiplex ligation-dependent probe amplification. This study illustrates the advantages of NGS in term of scalability, workload reduction and cost-effectiveness in combination with an improvement of the overall data quality due to the simultaneous detection of SNVs and large rearrangements. PMID:26900683

  14. Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.

    PubMed

    Fehlmann, Tobias; Backes, Christina; Kahraman, Mustafa; Haas, Jan; Ludwig, Nicole; Posch, Andreas E; Würstle, Maximilian L; Hübenthal, Matthias; Franke, Andre; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2017-09-06

    The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. ISS Update: 1st Annual ISS R&D Conference

    NASA Image and Video Library

    NASA Public Affairs Officer Kelly Humphries talks by phone on Wednesday with Julie Robinson, ISS Program Scientist, about the 1st Annual International Space Station Research and Development Confere...

  16. The 47th annual Florida pesticide residue workshop

    USDA-ARS?s Scientific Manuscript database

    This is an introductory article to a special section of the Journal of Agricultural and Food Chemistry consisting of publications from the 47th Annual Florida Pesticide Residue Workshop held in St. Pete Beach, FL in July of 2010....

  17. LLNL NESHAPs 2014 Annual Report

    SciTech Connect

    Wilson, K.; Bertoldo, N.; Gallegos, G.; MacQueen, D.; Wegrecki, A.

    2015-07-01

    Lawrence Livermore National Security, LLC operates facilities at Lawrence Livermore National Laboratory (LLNL) where radionuclides are handled and stored. These facilities are subject to the U.S. Environmental Protection Agency (EPA) National Emission Standards for Hazardous Air Pollutants (NESHAPs) in Code of Federal Regulations (CFR) Title 40, Part 61, Subpart H, which regulates radionuclide emissions to air from Department of Energy (DOE) facilities. Specifically, NESHAPs limits the emission of radionuclides to the ambient air to levels resulting in an annual effective dose equivalent of 10 mrem (100 μSv) to any member of the public. Using measured and calculated emissions, and building-specific and common parameters, LLNL personnel applied the EPA-approved computer code, CAP88-PC, Version 4.0.1.17, to calculate the dose to the maximally exposed individual member of the public for the Livermore Site and Site 300.

  18. Keeping Public Information Public.

    ERIC Educational Resources Information Center

    Kelley, Wayne P.

    1998-01-01

    Discusses the trend toward the transfer of federal government information from the public domain to the private sector. Topics include free access, privatization, information-policy revision, accountability, copyright issues, costs, pricing, and market needs versus public needs. (LRW)

  19. LLNL NESHAPs 1996 Annual Report

    SciTech Connect

    Gallegos, G.M.

    1997-01-06

    This annual report is prepared pursuant to the National Emissions Standards for Hazardous Air Pollutants (NESHAPs) 40 CFR Part 61, Subpart H; Subpart H governs radionuclide emissions to air from Department of Energy (DOE) facilities. NESHAPs limits the emission of radionuclides to the ambient air from DOE facilities to levels resulting in an annual effective dose equivalent (EDE) of 10 mrem (10 microsieverts) to any member of the public. The EDEs for the Lawrence Livermore National Laboratory (LLNL) site-wide maximally exposed members of the public from 1996 operations were (1) Livermore site: 0. 093 mrem (0.93 microsievert) (52% from point-source emissions, 48% from diffuse-source emissions); (2) Site 300: 0.033 mrem (0.33 microsievert) (99% from point-source, 1% from diffuse-source emissions). The EDEs were generally calculated using the EPA-approved CAP88-PC air-dispersion/dose-assessment model. Site-specific meteorological data, stack flow data, and emissions estimates based on radionuclide inventory data or continuous-monitoring systems data were the specific input to CAP88-PC for each modeled source. 5 figs., 8 tabs.

  20. LLNL NESHAPs 2002 Annual Report

    SciTech Connect

    Harrach, R J; Gallegos, G M; Peterson, S-R; Tate, P J; Bertoldo, N A; Wilson, K R; Althouse, P E; Larson, J M

    2003-06-01

    This annual report is prepared pursuant to the National Emission Standards for Hazardous Air Pollutants (NESHAPs; Title 40 Code of Federal Regulations [CFR] Part 61, Subpart H). Subpart H governs radionuclide emissions to air from Department of Energy (DOE) facilities. NESHAPs limits the emission of radionuclides to the ambient air from DOE facilities to levels resulting in an annual effective dose equivalent (EDE) of 10 mrem (100 {micro}Sv) to any member of the public. The EDEs for the Lawrence Livermore National Laboratory (LLNL) site-wide maximally exposed members of the public from operations in 2002 are summarized here: (1) Livermore site: 0.023 mrem (0.23 {micro}Sv) (43% from point-source emissions, 57% from diffuse-source emissions). The point-source emissions include gaseous tritium modeled as tritiated water vapor as directed by EPA Region IX; the resulting dose is used for compliance purposes; and (2) Site 300: 0.021 mrem (0.21 {micro}Sv) (85% from point-source emissions, 15% from diffuse-source emissions). The EDEs were calculated using the EPA-approved CAP88-PC air dispersion/dose-assessment model, except for doses for three diffuse sources, which were calculated from measured concentrations and dose coefficients. Site specific meteorological data, stack flow data, and emissions estimates based on radionuclide usage inventory data or continuous stack monitoring data were the specific inputs to CAP88-PC for each modeled source.